Daily Papers

After a runtime or API migration, an LLM-repaired procedure can run cleanly yet return wrong results, and a release check on typical test inputs ships it. We report a preregistered study of 73 tasks covering 60 documented changes in CPython, Node.js and SQLite. Every candidate is executed on the real runtimes against withheld contracts. Over the complete repair space, the all-assertions gate on typical inputs released 0.410 of wrong repairs. One edge input written from the release note cut this to 0.065, and to 0.061 on 15 unseen clusters. Three inputs from a blind GPT-5.6-luna writer that never saw the program reached 0.070. Two further frozen stages enlarged the menu to 1491 fragments and then added 233 hard distractors that match the legacy output on typical inputs. The edge input (0.058) and the frontier-model writer (0.058) passed their preregistered tests. Yet 0.168 and 0.153 of the hard wrong programs still passed. Two local-model writers failed their preregistered tests. Across four model families, the edge input cut wrong releases per attempt in all three open-weight families on all three menus, for example from 0.233 to 0.057, without lowering correct completion. Self-tests helped less. A blind AI audit flagged 34 contracts as stricter than their requirements. Dropping the disputed checks changed 0 verdicts, but class-label disputes remain open. No model-written code was executed. Artifacts are available from the authors on request.

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.

Program repair techniques offer cost-saving benefits for debugging within software development and programming education scenarios. With the proven effectiveness of Large Language Models (LLMs) in code-related tasks, researchers have explored their potential for program repair. However, it is crucial to recognize that existing repair benchmarks may have influenced LLM training data, potentially causing data leakage. To evaluate LLMs' realistic repair capabilities, (1) we introduce an extensive, non-crawled benchmark, referred to as TutorCode, comprising 1,239 C++ defect codes and associated information such as tutor guidance, solution description, failing test cases, and the corrected code. Our work assesses the repair performance of 12 LLMs on TutorCode, measuring repair correctness (TOP-5 and AVG-5) and patch precision (RPSR). (2) We then provide a comprehensive investigation into which types of extra information can help LLMs improve their performance in repairing defects. Among these types, tutor guidance was found to be the most effective information in enhancing LLM repair capabilities. To fully harness LLMs' conversational capabilities and the benefits of augmented information, (3) we introduce a novel conversational semi-automatic repair framework CREF assisting human tutor. It demonstrates a remarkable AVG-5 improvement of 17.2%-24.6% compared to the baseline, achieving an impressive AVG-5 of 76.6% when utilizing GPT-4. These results highlight the potential for enhancing LLMs' repair capabilities through interactions with tutors and historical conversations involving incorrect responses. The successful application of CREF in a real-world educational setting demonstrates its effectiveness in reducing tutors' workload and improving students' learning experience, while also showcasing its promise for facilitating other software engineering tasks, such as code review.

Large language models (LLMs) have revolutionized various domains, yet their utility comes with significant challenges related to outdated or problematic knowledge embedded during pretraining. This paper addresses the challenge of modifying LLMs to unlearn problematic and outdated information while efficiently integrating new knowledge without retraining from scratch. Here, we propose LLM Surgery, a framework to efficiently modify LLM behaviour by optimizing a three component objective function that: (1) Performs reverse gradient on unlearning dataset (problematic and outdated information), (2) Performs gradient descent on the update dataset (new and updated information), and (3) Minimizes the KL divergence on the retain dataset (small subset of unchanged text), ensuring alignment between pretrained and modified model outputs. Due to the lack of publicly available datasets specifically tailored for our novel task, we compiled a new dataset and an evaluation benchmark. Using Llama2-7B, we demonstrate that LLM Surgery can achieve significant forgetting on the unlearn set, a 20\% increase in accuracy on the update set, and maintain performance on the retain set.

APR (Automated Program Repair) aims to automatically locate program defects, generate patches and validate the repairs. Existing techniques for APR are often combined with LLMs (Large Language Models), which leverages the code-related knowledge of LLMs to improve repair effectiveness. Current LLM-based APR methods typically utilize test cases only during the inference stage, adopting an iterative approach that performs repair first and validates it through test execution afterward. This conventional paradigm neglects two important aspects: the potential contribution of test cases in the training phase, and the possibility of leveraging testing prior to repair. To address this, we propose Repair-R1, which introduces test cases into the model's training phase and shifts test generation to precede repair. The model is required to first generate discriminative test cases that can distinguish defective behaviors, and then perform repair based on these tests. This enables the model to better locate defects and understand the underlying causes of defects, thereby improving repair effectiveness. We implement Repair-R1 with three different backbone models, using RL (reinforcement learning) to co-optimize test generation and bug repair. Experimental results on four widely adopted benchmarks demonstrate the superiority of Repair-R1. Specially, compared to vanilla models, Repair-R1 improves repair success rate by 2.68\% to 48.29\%, test generation success rate by 16.38\% to 53.28\%, and test coverage by 0.78\% to 53.96\%. We publish the code and weights at https://github.com/Tomsawyerhu/APR-RL and https://huggingface.co/tomhu/Qwen3-4B-RL-5000-step.

Automated Program Repair (APR) has evolved significantly with the advent of Large Language Models (LLMs). Fine-tuning LLMs for program repair is a recent avenue of research, with many dimensions which have not been explored. Existing work mostly fine-tunes LLMs with naive code representations and is fundamentally limited in its ability to fine-tune larger LLMs. To address this problem, we propose RepairLLaMA, a novel program repair approach that combines 1) code representations for APR and 2) the state-of-the-art parameter-efficient LLM fine-tuning technique called LoRA. This results in RepairLLaMA producing a highly effective `program repair adapter' for fixing bugs with language models. Our experiments demonstrate the validity of both concepts. First, fine-tuning adapters with program repair specific code representations enables the model to use meaningful repair signals. Second, parameter-efficient fine-tuning helps fine-tuning to converge and contributes to the effectiveness of the repair adapter to fix data-points outside the fine-tuning data distribution. Overall, RepairLLaMA correctly fixes 125 Defects4J v2 and 82 HumanEval-Java bugs, outperforming all baselines.

Large language model (LLM) agents are increasingly used for multi-step, stateful tool-use tasks, yet production reliability remains limited. Unlike static software repair, agent repair must recover dynamic trajectories whose early decisions can propagate into later errors and external state changes. Existing automatic remedies address only part of this problem: blind retry adds no diagnosis, outcome feedback says whether a run failed but not where or why, and self-reflection often lacks grounded evidence to prevent the same failure from recurring. We present AgentTether, a run-time repair framework that automates post-run diagnosis and guided recovery without modifying the underlying agent or environment. AgentTether abstracts each run into Transition Units, links them through a dependency-aware Critical Transition Graph, and localizes failure-critical subtrajectories by combining an offline normal-behavior model with a run-local graph detector. It then converts the localized cause into behavior-scoped guidance backed by cross-iteration Repair Memory, and can optionally apply guarded run-time intervention to keep the correction active during re-execution. The same design can be deployed as an offline diagnostic-and-guidance tool or as an online repair layer. We evaluate AgentTether on 261 tau-bench tasks across three domains with Qwen3.7-max, and test cross-model transfer on Banking with GPT-5.4. On the hardest Banking domain, AgentTether repairs 59.04% (49/83) of initially failed Qwen3.7-max tasks and 65.12% (56/86) of initially failed GPT-5.4 tasks. Overall, AgentTether improves repair effectiveness while reducing agent turns and end-to-end approach tokens, suggesting a practical reliability layer that can wrap existing agent deployments, reduce wasted re-execution, and improve recovery without retraining the agent.

With the recent advancement of Large Language Models (LLMs), generating functionally correct code has become less complicated for a wide array of developers. While using LLMs has sped up the functional development process, it poses a heavy risk to code security. Code generation with proper security measures using LLM is a significantly more challenging task than functional code generation. Security measures may include adding a pair of lines of code with the original code, consisting of null pointer checking or prepared statements for SQL injection prevention. Currently, available code repair LLMs generate code repair by supervised fine-tuning, where the model looks at cross-entropy loss. However, the original and repaired codes are mostly similar in functionality and syntactically, except for a few (1-2) lines, which act as security measures. This imbalance between the lines needed for security measures and the functional code enforces the supervised fine-tuned model to prioritize generating functional code without adding proper security measures, which also benefits the model by resulting in minimal loss. Therefore, in this work, for security hardening and strengthening of generated code from LLMs, we propose a reinforcement learning-based method for program-specific repair with the combination of semantic and syntactic reward mechanisms that focus heavily on adding security and functional measures in the code, respectively.

Recently, multiple Automated Program Repair (APR) techniques based on Large Language Models (LLMs) have been proposed to enhance the repair performance. While these techniques mainly focus on the single-line or hunk-level repair, they face significant challenges in real-world application due to the limited repair task scope and costly statement-level fault localization. However, the more practical function-level APR, which broadens the scope of APR task to fix entire buggy functions and requires only cost-efficient function-level fault localization, remains underexplored. In this paper, we conduct the first comprehensive study of LLM-based function-level APR including investigating the effect of the few-shot learning mechanism and the auxiliary repair-relevant information. Specifically, we adopt six widely-studied LLMs and construct a benchmark in both the Defects4J 1.2 and 2.0 datasets. Our study demonstrates that LLMs with zero-shot learning are already powerful function-level APR techniques, while applying the few-shot learning mechanism leads to disparate repair performance. Moreover, we find that directly applying the auxiliary repair-relevant information to LLMs significantly increases function-level repair performance. Inspired by our findings, we propose an LLM-based function-level APR technique, namely SRepair, which adopts a dual-LLM framework to leverage the power of the auxiliary repair-relevant information for advancing the repair performance. The evaluation results demonstrate that SRepair can correctly fix 300 single-function bugs in the Defects4J dataset, largely surpassing all previous APR techniques by at least 85%, without the need for the costly statement-level fault location information. Furthermore, SRepair successfully fixes 32 multi-function bugs in the Defects4J dataset, which is the first time achieved by any APR technique ever to our best knowledge.

Large Language Models (LLMs) have shown tremendous promise in automated software engineering. In this paper, we investigate the opportunities of LLMs for automatic regression test generation for programs that take highly structured, human-readable inputs, such as XML parsers or JavaScript interpreters. Concretely, we explore the following regression test generation scenarios for such programs that have so far been difficult to test automatically in the absence of corresponding input grammars: bullet Bug finding. Given a code change (e.g., a commit or pull request), our LLM-based approach generates a test case with the objective of revealing any bugs that might be introduced if that change is applied. bullet Patch testing. Given a patch, our LLM-based approach generates a test case that fails before but passes after the patch. This test can be added to the regression test suite to catch similar bugs in the future. We implement Cleverest, a feedback-directed, zero-shot LLM-based regression test generation technique, and evaluate its effectiveness on 22 commits to three subject programs: Mujs, Libxml2, and Poppler. For programs using more human-readable file formats, like XML or JavaScript, we found Cleverest performed very well. It generated easy-to-understand bug-revealing or bug-reproduction test cases for the majority of commits in just under three minutes -- even when only the code diff or commit message (unless it was too vague) was given. For programs with more compact file formats, like PDF, as expected, it struggled to generate effective test cases. However, the LLM-supplied test cases are not very far from becoming effective (e.g., when used as a seed by a greybox fuzzer or as a starting point by the developer).

Large Language Models (LLMs) have demonstrated remarkable proficiency across a variety of complex tasks. One significant application of LLMs is in tackling software engineering challenges, particularly in resolving real-world tasks on GitHub by fixing code based on the issues reported by the users. However, many current approaches rely on proprietary LLMs, which limits reproducibility, accessibility, and transparency. The critical components of LLMs for addressing software engineering issues and how their capabilities can be effectively enhanced remain unclear. To address these challenges, we introduce SWE-Fixer, a novel open-source LLM designed to effectively and efficiently resolve GitHub issues. SWE-Fixer comprises two essential modules: a code file retrieval module and a code editing module. The retrieval module employs BM25 along with a lightweight LLM model to achieve coarse-to-fine file retrieval. Subsequently, the code editing module utilizes the other LLM model to generate patches for the identified files. Then, to mitigate the lack of publicly available datasets, we compile an extensive dataset that includes 110K GitHub issues along with their corresponding patches, and train the two modules of SWE-Fixer separately. We assess our approach on the SWE-Bench Lite and Verified benchmarks, achieving state-of-the-art performance among open-source models with scores of 23.3% and 30.2%, respectively. These outcomes highlight the efficacy of our approach. We will make our model, dataset, and code publicly available at https://github.com/InternLM/SWE-Fixer.

We propose patching for large language models (LLMs) like software versions, a lightweight and modular approach for addressing safety vulnerabilities. While vendors release improved LLM versions, major releases are costly, infrequent, and difficult to tailor to customer needs, leaving released models with known safety gaps. Unlike full-model fine-tuning or major version updates, our method enables rapid remediation by prepending a compact, learnable prefix to an existing model. This "patch" introduces only 0.003% additional parameters, yet reliably steers model behavior toward that of a safer reference model. Across three critical domains (toxicity mitigation, bias reduction, and harmfulness refusal) policy patches achieve safety improvements comparable to next-generation safety-aligned models while preserving fluency. Our results demonstrate that LLMs can be "patched" much like software, offering vendors and practitioners a practical mechanism for distributing scalable, efficient, and composable safety updates between major model releases.

Large language models (LLMs) have advanced automatic program repair (APR) to the point where agentic systems routinely resolve real-world, repository-level issues. Yet the generated patch has received little scrutiny beyond whether it passes tests. In this paper, we identify patch verbosity as a major yet overlooked concern in LLM-based APR. Characterizing 28 state-of-the-art approaches on SWE-bench Verified, we find that even successful patches are consistently larger and more complex than developer patches, with the median approach producing 121.78% more total changes, 80.91% more net changes, and 43.99% higher cyclomatic complexity. We further show that this verbosity is rooted in capability-oriented design choices such as iterative refinement and broad context, and can hardly be reduced by surface-level controls such as output format or minimality prompts. Motivated by these findings, we formulate post-generation patch refinement and propose RECAP, a lightweight, plug-and-play adapter that attaches to existing repair frameworks after generation. RECAP's refiner is trained via supervised fine-tuning and direct preference optimization with distilled reasoning traces, on a dataset of patch pairs we construct from multiple sources. Across four host systems, prompting, commit-untangling, and minimality-aware baselines reduce patch size only by sacrificing 49 to 217 resolved instances. In contrast, RECAP achieves a substantially better size-correctness tradeoff, cutting average total changes from +242.14% to +4.24% and net changes from +348.24% to -39.75% relative to developer patches while preserving or improving resolution by up to 42 instances. Our results indicate that minimality cannot be simply reduced to syntactic compression, and that decoupling minimization from generation offers a practical path to more reviewable repairs.

Iterative repair loops have become a core design pattern in LLM-based software engineering systems. These workflows repeatedly generate, validate, and repair artifacts using feedback such as compiler errors or test failures. Despite their widespread use, the impact of repair-loop iteration limits remains poorly understood, as most prior work adopts fixed, often arbitrary, repair budgets. We study repair-loop effectiveness across multiple software engineering tasks, including code generation, test generation, and code translation. Across several representative workflows, datasets, and contemporary low-cost LLMs, we observe a consistent pattern of diminishing returns: the first three to four repair iterations account for most achievable gains, while later iterations contribute only marginal improvements. We further find that repair behavior is influenced more strongly by workflow orchestration and feedback design than by the underlying model itself. These results suggest that repair budgets should be treated as an explicit experimental variable, as they directly affect evaluation outcomes, computational cost, runtime, and reproducibility in LLM-based software engineering research.

Resolving a real software issue with a large language model (LLM) agent is a long repair episode, often tens to hundreds of steps spanning exploration, hypothesis, implementation, and verification. Success depends on both the base model's local reasoning and the agent's ability to maintain an evolving plan and remember observations across phases. Existing repository-level agents typically strengthen planning or memory in isolation, leaving long trajectories vulnerable to stale evidence, repeated failed edits, and verification inferred from the agent's own claims instead of execution evidence. We present PMCoder, an issue-resolution agent that couples a hierarchical phase planner with episodic memory. The coupling is bidirectional: the current plan phase conditions memory retrieval, while memory-derived trajectory statistics inform stuck detection and replanning. When available, issue-reproduction verdicts ground verification progress in execution evidence rather than self-reported completion. On SWE-bench Verified, PMCoder resolves an average of 25 more cases (+5.0pp) than a harness-matched baseline, with gains persisting even where the reproduction gate never fires. Further Verified-500 evaluations show the same positive direction across Claude Haiku 4.5, DeepSeek-V4-Flash, and an OpenHands port, with at least 14 additional resolved cases (+2.8pp). Separately, evaluation on TerminalWorld's official sample suggests that the plan-memory substrate transfers beyond issue reports. Ablation and trajectory analyses show where the gains come from: coupling planning and memory outperforms either component alone and reduces repeated failed actions, empty-patch exits, and context-window exhaustion.

Automated Program Repair (APR) can help developers automatically generate patches for bugs. Due to the impressive performance obtained using Large Pre-Trained Language Models (LLMs) on many code related tasks, researchers have started to directly use LLMs for APR. However, prior approaches simply repeatedly sample the LLM given the same constructed input/prompt created from the original buggy code, which not only leads to generating the same incorrect patches repeatedly but also miss the critical information in testcases. To address these limitations, we propose conversational APR, a new paradigm for program repair that alternates between patch generation and validation in a conversational manner. In conversational APR, we iteratively build the input to the model by combining previously generated patches with validation feedback. As such, we leverage the long-term context window of LLMs to not only avoid generating previously incorrect patches but also incorporate validation feedback to help the model understand the semantic meaning of the program under test. We evaluate 10 different LLM including the newly developed ChatGPT model to demonstrate the improvement of conversational APR over the prior LLM for APR approach.

Sequence-to-sequence models have been used to transform erroneous programs into correct ones when trained with a large enough dataset. Some recent studies also demonstrated strong empirical evidence that code review could improve the program repair further. Large language models, trained with Natural Language (NL) and Programming Language (PL), can contain inherent knowledge of both. In this study, we investigate if this inherent knowledge of PL and NL can be utilized to improve automated program repair. We applied PLBART and CodeT5, two state-of-the-art language models that are pre-trained with both PL and NL, on two such natural language-based program repair datasets and found that the pre-trained language models fine-tuned with datasets containing both code review and subsequent code changes notably outperformed each of the previous models. With the advent of code generative models like Codex and GPT-3.5-Turbo, we also performed zero-shot and few-shots learning-based prompt engineering to assess their performance on these datasets. However, the practical application of using LLMs in the context of automated program repair is still a long way off based on our manual analysis of the generated repaired codes by the learning models.

Large language models (LLMs) have shown impressive effectiveness in various software engineering tasks, including automated program repair (APR). In this study, we take a deep dive into automated bug fixing utilizing LLMs. In contrast to many deep learning-based APR methods that assume known bug locations, rely on line-level localization tools, or address bug prediction and fixing in one step, our approach uniquely employs LLMs to predict bug location at the token level and subsequently utilizes them for bug fixing. This methodological separation of bug localization and fixing using different LLMs enables effective integration of diverse contextual information and improved incorporation of inductive biases. We introduce Toggle: Token-Granulated Bug Localization and Repair, a comprehensive program repair framework that integrates a bug localization model, an adjustment unit, and a bug-fixing model. Toggle takes a buggy function as input and generates a complete corrected function. We investigate various styles of prompting to the bug fixing model to identify the most effective prompts that better utilize the inductive bias and significantly outperform others. Toggle achieves the new state-of-the-art (SOTA) performance on the CodeXGLUE code refinement benchmark, and exhibits better and comparable performance on several other widely-used APR datasets, including Defects4J.

LLM-based Lean proving systems increasingly organize a proof as a blueprint: a dependency graph of formal statements. We introduce BlueprintRepair, a repair interface that lets a model change this graph through ten schema-checked local operations. An operation names the node it edits, so the target theorem cannot be changed. Lean checks every applied change, and an accepted repair must declare every blueprint lemma its proof uses. We also construct BlueprintTrace, a benchmark of 142 controlled failures with complete accepted and rejected repair trajectories. We compare typed edits, exact source patches, and complete module rewrites under matched source, feedback, model, and budget, one episode per state and interface. With DeepSeek-V4-Flash, the three interfaces solve almost the same number of the benchmark's localized failures. Typed repair is the cheapest per solved state (patching is 1.30x as expensive, rewriting 2.06x), and within 10,000 completion tokens per task it reaches almost all of its final coverage, while both free-form interfaces are well behind. A second model, Qwen3.6-Flash, solves fewer states but keeps typed repair cheapest, puts it ahead on the proof-authoring states, and repeats the localized pattern.

Tool-using LLM agents face a reliability-cost tradeoff: routing every decision through the LLM improves correctness but incurs high latency and inference cost, while pre-coded workflow graphs reduce cost but become brittle under unanticipated compound tool failures. We present Self-Healing Router, a fault-tolerant orchestration architecture that treats most agent control-flow decisions as routing rather than reasoning. The system combines (i) parallel health monitors that assign priority scores to runtime conditions such as tool outages and risk signals, and (ii) a cost-weighted tool graph where Dijkstra's algorithm performs deterministic shortest-path routing. When a tool fails mid-execution, its edges are reweighted to infinity and the path is recomputed -- yielding automatic recovery without invoking the LLM. The LLM is reserved exclusively for cases where no feasible path exists, enabling goal demotion or escalation. Prior graph-based tool-use systems (ControlLLM, ToolNet, NaviAgent) focus on tool selection and planning; our contribution is runtime fault tolerance with deterministic recovery and binary observability -- every failure is either a logged reroute or an explicit escalation, never a silent skip. Across 19 scenarios spanning three graph topologies (linear pipeline, dependency DAG, parallel fan-out), Self-Healing Router matches ReAct's correctness while reducing control-plane LLM calls by 93% (9 vs 123 aggregate) and eliminating the silent-failure cases observed in a well-engineered static workflow baseline under compound failures.

Automated Program Repair (APR) attempts to fix software bugs without human intervention, which plays a crucial role in software development and maintenance. Recently, with the advances in Large Language Models (LLMs), a rapidly increasing number of APR techniques have been proposed with remarkable performance. However, existing LLM-based APR techniques typically adopt trial-and-error strategies, which suffer from two major drawbacks: (1) inherently limited patch effectiveness due to local exploration, and (2) low search efficiency due to redundant exploration. In this paper, we propose APRMCTS, which uses iterative tree search to improve LLM-based APR. APRMCTS incorporates Monte Carlo Tree Search (MCTS) into patch searching by performing a global evaluation of the explored patches and selecting the most promising one for subsequent refinement and generation. APRMCTS effectively resolves the problems of falling into local optima and thus helps improve the efficiency of patch searching. Our experiments on 835 bugs from Defects4J demonstrate that, when integrated with GPT-3.5, APRMCTS can fix a total of 201 bugs, which outperforms all state-of-the-art baselines. Besides, APRMCTS helps GPT-4o-mini, GPT-3.5, Yi-Coder-9B, and Qwen2.5-Coder-7B to fix 30, 27, 37, and 28 more bugs, respectively. More importantly, APRMCTS boasts a significant performance advantage while employing small patch size (16 and 32), notably fewer than the 500 and 10,000 patches adopted in previous studies. In terms of cost, compared to existing state-of-the-art LLM-based APR methods, APRMCTS has time and monetary costs of less than 20% and 50%, respectively. Our extensive study demonstrates that APRMCTS exhibits good effectiveness and efficiency, with particular advantages in addressing complex bugs.

Large language models (LLMs) have demonstrated remarkable capabilities on a broad spectrum of downstream tasks. Within the realm of software engineering, specialized tasks on code, such as program repair, present unique challenges, necessitating fine-tuning to unlock state-of-the-art performance. Fine-tuning approaches proposed in the literature for LLMs on program repair tasks are however generally overlooking the need to reason about the logic behind code changes, beyond syntactic patterns in the data. High-performing fine-tuning experiments also usually come at very high computational costs. With MORepair, we propose a novel perspective on the learning focus of LLM fine-tuning for program repair: we not only adapt the LLM parameters to the syntactic nuances of the task of code transformation (objective 1), but we also specifically fine-tune the LLM with respect to the logical reason behind the code change in the training data (objective 2). Such a multi-objective fine-tuning will instruct LLMs to generate high-quality patches. We apply MORepair to fine-tune four open-source LLMs with different sizes and architectures. Experimental results on C++ and Java repair benchmarks show that the implemented fine-tuning effectively boosts LLM repair performance by 7.6% to 10% in Top-10 repair suggestions. We further show that our fine-tuning strategy yields superior performance compared to the incumbent state-of-the-art in fine-tuned models for program repair, Fine-tune-CoT and RepairLLaMA.

Premature closure, or committing to a conclusion before sufficient information is available, is a recognized contributor to diagnostic error but remains underexamined in large language models (LLMs). We define LLM premature closure as inappropriate commitment under uncertainty: providing an answer, recommendation, or clinical guidance when the safer response would be clarification, abstention, escalation, or refusal. We evaluated five frontier LLMs across structured and open-ended medical tasks. In MedQA (n = 500) and AfriMed-QA (n = 490) questions where the correct choice had been removed, models still selected an answer at high rates, with baseline false-action rates of 55-81% and 53-82%, respectively. In open-ended evaluation, models gave inappropriate answers on an average of 30% of 861 HealthBench questions and 78% of 191 physician-authored adversarial queries. Safety-oriented prompting reduced premature closure across models, but residual failure persisted, highlighting the need to evaluate whether medical LLMs know when not to answer.

Large language models (LLMs) and vision-language models (VLMs) are usually frozen after deployment, so they do not learn from the cases they solve. This is especially concerning in medicine, where new clinical evidence, updated guidelines, and new therapies can change established practice. Fine-tuning can update the model, but it requires access to model weights and additional training. Parameter-free methods avoid training, but they may overfit a fixed validation set, lack reliable domain knowledge, or lose visual details by saving experience only as text. To address these limitations, we present a model-agnostic framework that allows frozen LLMs and VLMs to learn from deployment experience through three forms of external expertise: a Skill that guides reasoning and tool use, a Knowledge Memory that stores reliable facts supported by earlier cases or trusted external evidence, and a Multimodal Knowledge Base that keeps visual examples and guides the model to relate each retrieved case to the current image. Instead of relying on a fixed validation set, a validation strategy keeps an update only if it helps on new cases without degrading performance on earlier ones. Across six benchmarks covering clinical diagnosis, clinical workflows, medical reasoning, and medical and non-medical visual reasoning, and with four open-weight and closed-source base models, our framework improves performance during online deployment by up to 34.2% over the base model on medical tasks, generalizes to unseen cases, transfers to other models without further optimization, and works in non-medical domains.

Large Language Models (LLMs) often generate code with subtle but critical bugs, especially for complex tasks. Existing automated repair methods typically rely on superficial pass/fail signals, offering limited visibility into program behavior and hindering precise error localization. In addition, without a way to learn from prior failures, repair processes often fall into repetitive and inefficient cycles. To overcome these challenges, we present TraceCoder, a collaborative multi-agent framework that emulates the observe-analyze-repair process of human experts. The framework first instruments the code with diagnostic probes to capture fine-grained runtime traces, enabling deep insight into its internal execution. It then conducts causal analysis on these traces to accurately identify the root cause of the failure. This process is further enhanced by a novel Historical Lesson Learning Mechanism (HLLM), which distills insights from prior failed repair attempts to inform subsequent correction strategies and prevent recurrence of similar mistakes. To ensure stable convergence, a Rollback Mechanism enforces that each repair iteration constitutes a strict improvement toward the correct solution. Comprehensive experiments across multiple benchmarks show that TraceCoder achieves up to a 34.43\% relative improvement in Pass@1 accuracy over existing advanced baselines. Ablation studies verify the significance of each system component, with the iterative repair process alone contributing a 65.61\% relative gain in accuracy. Furthermore, TraceCoder significantly outperforms leading iterative methods in terms of both accuracy and cost-efficiency.

Security vulnerability repair is a difficult task that is in dire need of automation. Two groups of techniques have shown promise: (1) large code language models (LLMs) that have been pre-trained on source code for tasks such as code completion, and (2) automated program repair (APR) techniques that use deep learning (DL) models to automatically fix software bugs. This paper is the first to study and compare Java vulnerability repair capabilities of LLMs and DL-based APR models. The contributions include that we (1) apply and evaluate five LLMs (Codex, CodeGen, CodeT5, PLBART and InCoder), four fine-tuned LLMs, and four DL-based APR techniques on two real-world Java vulnerability benchmarks (Vul4J and VJBench), (2) design code transformations to address the training and test data overlapping threat to Codex, (3) create a new Java vulnerability repair benchmark VJBench, and its transformed version VJBench-trans and (4) evaluate LLMs and APR techniques on the transformed vulnerabilities in VJBench-trans. Our findings include that (1) existing LLMs and APR models fix very few Java vulnerabilities. Codex fixes 10.2 (20.4%), the most number of vulnerabilities. (2) Fine-tuning with general APR data improves LLMs' vulnerability-fixing capabilities. (3) Our new VJBench reveals that LLMs and APR models fail to fix many Common Weakness Enumeration (CWE) types, such as CWE-325 Missing cryptographic step and CWE-444 HTTP request smuggling. (4) Codex still fixes 8.3 transformed vulnerabilities, outperforming all the other LLMs and APR models on transformed vulnerabilities. The results call for innovations to enhance automated Java vulnerability repair such as creating larger vulnerability repair training data, tuning LLMs with such data, and applying code simplification transformation to facilitate vulnerability repair.

Software vulnerabilities are increasing at an alarming rate. However, manual patching is both time-consuming and resource-intensive, while existing automated vulnerability repair (AVR) techniques remain limited in effectiveness. Recent advances in large language models (LLMs) have opened a new paradigm for AVR, demonstrating remarkable progress. To examine the capability of LLMs in AVR, several vulnerability benchmarks have been proposed recently. However, they still suffer from key limitations of outdated vulnerabilities, limited language coverage, unreliable patch validation, and insufficient reproducibility. To overcome these challenges, we introduce PATCHEVAL, a multilingual benchmark for Go, JavaScript, and Python, languages for which existing benchmarks remain unexplored. PATCHEVAL curates a dataset of 1,000 vulnerabilities drawn from CVEs reported between 2015 and 2025, covering 65 distinct CWEs. A subset of 230 CVEs is further equipped with runtime sandbox environments, enabling patch verification through both security tests and functionality tests. To provide a systematic comparison of LLM-based vulnerability repair, we evaluate a series of state-of-the-art LLMs and agents, presenting an in-depth analysis that empirically yields key insights to guide future research in AVR.

Ensuring faithful interpretability in large language models is imperative for trustworthy and reliable AI. A key obstacle is self-repair, a phenomenon where networks compensate for reduced signal in one component by amplifying others, masking the true importance of the ablated component. While prior work attributes self-repair to layer normalization and back-up components that compensate for ablated components, we identify a novel form occurring within the attention mechanism, where softmax redistribution conceals the influence of important attention scores. This leads traditional ablation and gradient-based methods to underestimate the significance of all components contributing to these attention scores. We introduce Gradient Interaction Modifications (GIM), a technique that accounts for self-repair during backpropagation. Extensive experiments across multiple large language models (Gemma 2B/9B, LLAMA 1B/3B/8B, Qwen 1.5B/3B) and diverse tasks demonstrate that GIM significantly improves faithfulness over existing circuit identification and feature attribution methods. Our work is a significant step toward better understanding the inner mechanisms of LLMs, which is crucial for improving them and ensuring their safety. Our code is available at https://github.com/JoakimEdin/gim.

We present SQL Query Engine, an open-source, self-hosted service that translates natural language questions into validated PostgreSQL queries through a two-stage LLM pipeline. The first stage performs automatic schema introspection and SQL generation; a multi-strategy response parser extracts SQL from any LLM output format (JSON, code blocks, or raw text) without requiring structured output APIs. The second stage executes the query against PostgreSQL and, upon failure or empty results, enters an iterative self-healing loop in which the LLM diagnoses the error using full SQLSTATE codes and PostgreSQL diagnostic messages. Two mechanisms prevent regressions: early-accept returns successful queries immediately without LLM re-evaluation, and best-result tracking preserves the best partial result across retries. Schema context is cached per session in Redis, progress events stream via Redis Pub/Sub and SSE, and an OpenAI-compatible /v1/chat/completions endpoint lets existing tools work without modification. All database connections are read-only at the driver level. We evaluate across five LLM backends on a synthetic benchmark (75 questions, three databases) where the self-healing loop yields up to +9.3pp accuracy gains with zero regressions on the best model (Llama 4 Scout 17B, 57.3%), and on BIRD (437 questions, 11 databases migrated from SQLite to PostgreSQL) where the full pipeline reaches 49.0% execution accuracy (GPT-OSS-120B, +4.6pp). Source code: https://github.com/codeadeel/sqlqueryengine.

AI assistants store values that a language model derived from a person's records under the person's own definitions, such as their important contacts. Keeping such a value correct takes two steps: detection, noticing that an input changed, and repair, producing the correct new value. Benchmarks that score only the final answer cannot tell which step failed, and they state every change as new text. Seeing this limitation, we present MemShift, a benchmark of five shifts: source revision, deletion, redefinition, writer switch, and export. The first three fork a synthetic world into branches that differ only in the shift. Gold values and dependencies are fixed before any text, and a deterministic scorer replaces an LLM judge. For a memory that reports its invalidations, MemShift shows for each changed item whether the memory noticed the change and whether its repair was right. Moreover, we build a reference memory with known detection and repair to validate the measure. By evaluating four open-weight LLMs, we find that detection helps only as much as repair allows: the LLMs re-derive few values computed by the person's definitions correctly, and programs that the LLM writes over typed records close most of the gap to exact recomputation. Code and data are available at https://github.com/zichuanxu/memshift.

LLM agents fail mid-episode -- they loop, cascade tool errors, drift off goal, fabricate results, or silently absorb corrupted content -- and the standard remedy, judging every step with a second LLM, costs more than the agent itself. We ask how much detection is achievable from observable step telemetry alone, using monitors costing microseconds per step and trained only on healthy runs. On 2,823 committed agent episodes across three frameworks, three local models (qwen2.5 7b/3b, llama3.1 8b) and a commercial API (gemini-2.5-flash), a one-class echo-state-network ensemble with CUSUM alarms detects 0.71 of failures at a 5% false-alarm budget (AUROC 0.872). Its advantage over a memoryless baseline is a monotone function of post-onset horizon (+0.09 at <=3 steps, +0.40 at >=9), predicting its own failure region out of sample on AFTraj-2K. Ranking transfers with no retraining to two corpora from other groups (AFTraj-2K 0.745, ATBench 0.779). Monitors carry two burdens: a per-deployment healthy null (they do not transfer -- AUROC 0.527 cold against 0.885 recalibrated) and a residual false-alarm rate. We add a layer carrying neither: deterministic verification, which recomputes a run's stated total from the tool results it actually received and confirms every required call was made. Head-to-head it catches 60% of failures (96% with the coverage check) at 0 of 63 false positives against the monitor's 54% at 17%, transfers unchanged to llama3.1:8b (110 of 110 at 0 of 10), and trips on 0 of 1825 healthy episodes. Detection is then closed into repair: each flagged run is rolled back and re-run live, recovering 45% of failures against a 16% resampling control (p=0.0005) and lifting task success from 52% to 73% for about one extra model call per run. The system runs at ~200 microseconds per step, three orders of magnitude below a judge call. Code, traces and results are released.

Large language models (LLMs) and LLM-based Agents have been applied to fix bugs automatically, demonstrating the capability in addressing software defects by engaging in development environment interaction, iterative validation and code modification. However, systematic analysis of these agent and non-agent systems remain limited, particularly regarding performance variations among top-performing ones. In this paper, we examine seven proprietary and open-source systems on the SWE-bench Lite benchmark for automated bug fixing. We first assess each system's overall performance, noting instances solvable by all or none of these sytems, and explore why some instances are uniquely solved by specific system types. We also compare fault localization accuracy at file and line levels and evaluate bug reproduction capabilities, identifying instances solvable only through dynamic reproduction. Through analysis, we concluded that further optimization is needed in both the LLM itself and the design of Agentic flow to improve the effectiveness of the Agent in bug fixing.

Before invoking external tools, an agentic LLM must select among a K-way action space: executing a call, seeking clarification, answering directly, or declining. While internal activation steering can alter these pre-execution decisions, conventional aggregate metrics obscure where altered states land and what collateral damage they inflict. We present SAKIKO, an auditing framework that formalizes representation repair via directional error discovery, router-conditioned intervention, destination-resolved verification, and prospectively frozen statistical licensing. Across seven LLMs on When2Call and MetaTool, channel-keyed interventions induce direction-specific net gains in five models; across three sealed evaluations, none of 59 budget-matched random directions matches calibrated target gain. Crucially, destination auditing shows that behavioral movement does not equal repair: an intervention achieving +55 net gain corrupts over half of the baseline-correct decisions it touches, and promising point estimates on Qwen3-4B and Gemma-2-9B are formally declined due to finite-sample uncertainty. SAKIKO establishes the necessity of outcome-resolved adjudication before claiming internal repair. Code: https://github.com/ruizheliUOA/mechanistic-tool-use-llm.

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the increasing attention in this field, a holistic view is still lacking. Many critical aspects remain unclear, such as the diseases and clinical data to which LLMs have been applied, the LLM techniques employed, and the evaluation methods used. In this article, we perform a comprehensive review of LLM-based methods for disease diagnosis. Our review examines the existing literature across various dimensions, including disease types and associated clinical specialties, clinical data, LLM techniques, and evaluation methods. Additionally, we offer recommendations for applying and evaluating LLMs for diagnostic tasks. Furthermore, we assess the limitations of current research and discuss future directions. To our knowledge, this is the first comprehensive review for LLM-based disease diagnosis.

Post-training for large language models (LLMs) is constrained by the high cost of acquiring new knowledge or correcting errors and by the unintended side effects that frequently arise from retraining. To address these issues, we introduce REPAIR (Robust Editing via Progressive Adaptive Intervention and Reintegration), a lifelong editing framework designed to support precise and low-cost model updates while preserving non-target knowledge. REPAIR mitigates the instability and conflicts of large-scale sequential edits through a closed-loop feedback mechanism coupled with dynamic memory management. Furthermore, by incorporating frequent knowledge fusion and enforcing strong locality guards, REPAIR effectively addresses the shortcomings of traditional distribution-agnostic approaches that often overlook unintended ripple effects. Our experiments demonstrate that REPAIR boosts editing accuracy by 10%-30% across multiple model families and significantly reduces knowledge forgetting. This work introduces a robust framework for developing reliable, scalable, and continually evolving LLMs.

Research shows that grammatical mistakes in a sentence can be corrected by translating it to another language and back using neural machine translation with language models. We investigate whether this correction capability of Large Language Models (LLMs) extends to Automatic Program Repair (APR). Current generative models for APR are pre-trained on source code and fine-tuned for repair. This paper proposes bypassing the fine-tuning step and using Round-Trip Translation (RTT): translation of code from one programming language to another programming or natural language, and back. We hypothesize that RTT with LLMs restores the most commonly seen patterns in code during pre-training, i.e., performs a regression toward the mean, which removes bugs as they are a form of noise w.r.t. the more frequent, natural, bug-free code in the training data. To test this hypothesis, we employ eight recent LLMs pre-trained on code, including the latest GPT versions, and four common program repair benchmarks in Java. We find that RTT with English as an intermediate language repaired 101 of 164 bugs with GPT-4 on the HumanEval-Java dataset. Moreover, 46 of these are unique bugs that are not repaired by other LLMs fine-tuned for APR. Our findings highlight the viability of round-trip translation with LLMs as a technique for automated program repair and its potential for research in software engineering. Keywords: automated program repair, large language model, machine translation

Current approaches to program synthesis with Large Language Models (LLMs) exhibit a "near miss syndrome": they tend to generate programs that semantically resemble the correct answer (as measured by text similarity metrics or human evaluation), but achieve a low or even zero accuracy as measured by unit tests due to small imperfections, such as the wrong input or output format. This calls for an approach known as Synthesize, Execute, Debug (SED), whereby a draft of the solution is generated first, followed by a program repair phase addressing the failed tests. To effectively apply this approach to instruction-driven LLMs, one needs to determine which prompts perform best as instructions for LLMs, as well as strike a balance between repairing unsuccessful programs and replacing them with newly generated ones. We explore these trade-offs empirically, comparing replace-focused, repair-focused, and hybrid debug strategies, as well as different template-based and model-based prompt-generation techniques. We use OpenAI Codex as the LLM and Program Synthesis Benchmark 2 as a database of problem descriptions and tests for evaluation. The resulting framework outperforms both conventional usage of Codex without the repair phase and traditional genetic programming approaches.

Operations Research practitioners debug infeasible models through an iterative process: inspecting Irreducible Infeasible Subsystems ( IIS), identifying constraint conflicts, and repairing formulations until feasibility is restored. Existing LLM benchmarks mostly treat OR as one-shot translation from problem descriptions to solver code, omitting this diagnostic loop. We formalize infeasible-model repair as a solver-in-the-loop Markov Decision Process in which each action triggers solver re-execution and IIS recomputation, yielding deterministic, verifiable feedback. We introduce ORLoopBench, a benchmark suite with two components: OR-Debug-Bench releases 5,362 LP/MILP repair instances, while OR-Bias-Bench evaluates closed-form operational decision rationality across inventory settings. Solver-verified RLVR training enables an 8B model to surpass frontier APIs on LP repair (95.3% vs 92.4% RR @5), improves diagnostic behavior, and transfers to MILP repair. The same evaluation exposes semantic drift in whole-model code regeneration: feasible regenerated MILPs can solve the wrong problem. Process-level evaluation with solver oracles enables targeted training for reliable OR self-correction.

LLM-based agents for program repair are increasingly built on a "generate-run-revise" paradigm, iteratively executing tests to evaluate and refine patches. This execution-based approach has become standard practice in state-of-the-art systems. However, executions can be time-consuming and expensive, yet their impact on these agents remains underexplored. In this paper, we conduct a two-stage empirical study over execution behavior in LLM-based program repair. To characterize execution behavior at scale, we first analyze 7,745 agent traces from SWE-bench leaderboard submissions. Second, we evaluate 3,000 end-to-end repair attempts across 200 SWE-bench instances and three agents (Claude Code, Codex, and the open-source OpenCode) under four execution paradigms, which allows for a fine-grained comparison of performance and cost. Our analysis reveals three key observations: (1) Code execution is used across all agents and models analyzed, with an average of 8.8 test runs per task. Execution behavior varies substantially across agents and models, with frequency ranging from 2 to 19 per task, and late-stage executions consistently achieve higher success rates than early-stage ones. (2) Execution restrictions have little effect on repair success: on commercial agents with SOTA models the resolve-rate gap between Prohibited and Unrestricted is only 1.25 percentage points and not statistically significant, while Prohibited saves substantial token and wall-clock cost. (3) Execution benefit is concentrated rather than uniform. These patterns suggest that current agents apply execution indiscriminately, paying its cost on instances where it provides little benefit. Execution, therefore, should be treated as a resource with an explicit cost-benefit tradeoff, not a default capability.

Industry 4.0 has revolutionized manufacturing by driving digitalization and shifting the paradigm toward additive manufacturing (AM). Fused Deposition Modeling (FDM), a key AM technology, enables the creation of highly customized, cost-effective products with minimal material waste through layer-by-layer extrusion, posing a significant challenge to traditional subtractive methods. However, the susceptibility of material extrusion techniques to errors often requires expert intervention to detect and mitigate defects that can severely compromise product quality. While automated error detection and machine learning models exist, their generalizability across diverse 3D printer setups, firmware, and sensors is limited, and deep learning methods require extensive labeled datasets, hindering scalability and adaptability. To address these challenges, we present a process monitoring and control framework that leverages pre-trained Large Language Models (LLMs) alongside 3D printers to detect and address printing defects. The LLM evaluates print quality by analyzing images captured after each layer or print segment, identifying failure modes and querying the printer for relevant parameters. It then generates and executes a corrective action plan. We validated the effectiveness of the proposed framework in identifying defects by comparing it against a control group of engineers with diverse AM expertise. Our evaluation demonstrated that LLM-based agents not only accurately identify common 3D printing errors, such as inconsistent extrusion, stringing, warping, and layer adhesion, but also effectively determine the parameters causing these failures and autonomously correct them without any need for human intervention.

Automatic Speech Recognition (ASR) error correction aims to correct recognition errors while preserving accurate text. Although traditional approaches demonstrate moderate effectiveness, LLMs offer a paradigm that eliminates the need for training and labeled data. However, directly using LLMs will encounter hallucinations problem, which may lead to the modification of the correct text. To address this problem, we propose the Reliable LLM Correction Framework (RLLM-CF), which consists of three stages: (1) error pre-detection, (2) chain-of-thought sub-tasks iterative correction, and (3) reasoning process verification. The advantage of our method is that it does not require additional information or fine-tuning of the model, and ensures the correctness of the LLM correction under multi-pass programming. Experiments on AISHELL-1, AISHELL-2, and Librispeech show that the GPT-4o model enhanced by our framework achieves 21%, 11%, 9%, and 11.4% relative reductions in CER/WER.

Continuous fuzzing platforms such as OSS-Fuzz uncover large numbers of vulnerabilities, yet the subsequent repair process remains largely manual. Unfortunately, existing Automated Vulnerability Repair (AVR) techniques -- including recent LLM-based systems -- are not directly applicable to continuous fuzzing. This is because these systems are designed and evaluated on a static, single-run benchmark setting, making them ill-suited for the diverse, noisy, and failure-prone environments in continuous fuzzing. To address these issues, we introduce PatchIsland, a system for Continuous Vulnerability Repair (CVR) that tightly integrates with continuous fuzzing pipelines. PatchIsland employs an ensemble of diverse LLM agents. By leveraging multiple LLM agents, PatchIsland can cover a wider range of settings (e.g., different projects, bug types, and programming languages) and also improve operational robustness. In addition, PatchIsland utilizes a two-phase patch-based deduplication to mitigate duplicate crashes and patches, which can be problematic in continuous fuzzing. In our internal evaluation, PatchIsland repaired 84 of 92 vulnerabilities, demonstrating strong repair capability. In the official AIxCC competition, the system operated with no human intervention in a fully autonomous environment and successfully patched 31 out of 43 vulnerabilities, achieving a repair rate of 72.1\%.

LLM-based agents are increasingly deployed for software maintenance tasks such as automated program repair (APR). APR agents automatically fetch GitHub issues and use backend LLMs to generate patches that fix the reported bugs. However, existing work primarily focuses on the functional correctness of APR-generated patches, whether they pass hidden or regression tests, while largely ignoring potential security risks. Given the openness of platforms like GitHub, where any user can raise issues and participate in discussions, an important question arises: Can an adversarial user submit a valid issue on GitHub that misleads an LLM-based agent into generating a functionally correct but vulnerable patch? To answer this question, we propose SWExploit, which generates adversarial issue statements designed to make APR agents produce patches that are functionally correct yet vulnerable. SWExploit operates in three main steps: (1) program analysis to identify potential injection points for vulnerable payloads; (2) adversarial issue generation to provide misleading reproduction and error information while preserving the original issue semantics; and (3) iterative refinement of the adversarial issue statements based on the outputs of the APR agents. Empirical evaluation on three agent pipelines and five backend LLMs shows that SWExploit can produce patches that are both functionally correct and vulnerable (the attack success rate on the correct patch could reach 0.91, whereas the baseline ASRs are all below 0.20). Based on our evaluation, we are the first to challenge the traditional assumption that a patch passing all tests is inherently reliable and secure, highlighting critical limitations in the current evaluation paradigm for APR agents.

Large language models frequently fail to produce correct code on their first attempt, yet most benchmarks evaluate them in a single-shot setting. We investigate iterative self-repair (feeding execution errors back to the model for correction) across seven models spanning three families and both open-weight and proprietary providers: Llama 3.1 8B, Llama 3.3 70B, Llama 4 Scout (MoE, 16 experts), Llama 4 Maverick (MoE, 128 experts), Qwen3 32B, Gemini 2.5 Flash, and Gemini 2.5 Pro. On HumanEval (164 problems) and MBPP Sanitized (257 problems) with up to five attempts, self-repair universally improves pass rates: +4.9 to +17.1 pp on HumanEval and +16.0 to +30.0 pp on MBPP. Gemini 2.5 Flash achieves the highest final pass rates (96.3% HumanEval, 93.8% MBPP). Most gains concentrate in the first two rounds.Error-type analysis shows assertion errors (logical mistakes) are the hardest to repair at ~45%, while syntax and name errors are repaired at substantially higher rates, connecting to broader findings on the limits of LLM self-correction. Prior work found that weaker models fail at self-repair or require fine-tuning; we show that modern instruction-tuned models succeed with prompting alone, even at 8B scale. We also provide the first comparison of dense and MoE architectures for self-repair, and extend the repair-vs-resampling tradeoff analysis to modern models. A prompt ablation reveals chain-of-thought repair yields up to +5.5 pp additional self-repair gain (measured as improvement in repair delta) over minimal prompting for capable models.

We aim to present a comprehensive overview of the latest advancements in utilizing Large Language Models (LLMs) within the healthcare sector, emphasizing their transformative impact across various medical domains. LLMs have become pivotal in supporting healthcare, including physicians, healthcare providers, and patients. Our review provides insight into the applications of Large Language Models (LLMs) in healthcare, specifically focusing on diagnostic and treatment-related functionalities. We shed light on how LLMs are applied in cancer care, dermatology, dental care, neurodegenerative disorders, and mental health, highlighting their innovative contributions to medical diagnostics and patient care. Throughout our analysis, we explore the challenges and opportunities associated with integrating LLMs in healthcare, recognizing their potential across various medical specialties despite existing limitations. Additionally, we offer an overview of handling diverse data types within the medical field.

Global healthcare providers are exploring use of large language models (LLMs) to provide medical advice to the public. LLMs now achieve nearly perfect scores on medical licensing exams, but this does not necessarily translate to accurate performance in real-world settings. We tested if LLMs can assist members of the public in identifying underlying conditions and choosing a course of action (disposition) in ten medical scenarios in a controlled study with 1,298 participants. Participants were randomly assigned to receive assistance from an LLM (GPT-4o, Llama 3, Command R+) or a source of their choice (control). Tested alone, LLMs complete the scenarios accurately, correctly identifying conditions in 94.9% of cases and disposition in 56.3% on average. However, participants using the same LLMs identified relevant conditions in less than 34.5% of cases and disposition in less than 44.2%, both no better than the control group. We identify user interactions as a challenge to the deployment of LLMs for medical advice. Standard benchmarks for medical knowledge and simulated patient interactions do not predict the failures we find with human participants. Moving forward, we recommend systematic human user testing to evaluate interactive capabilities prior to public deployments in healthcare.

Large language models (LLMs) are transforming automated program repair (APR) through agent-based approaches that localize bugs, generate patches, and verify fixes. However, the lack of high-quality, scalable training datasets, especially those with verifiable outputs and intermediate reasoning traces-limits progress, particularly for open-source models. In this work, we present SWE-Synth, a framework for synthesizing realistic, verifiable, and process-aware bug-fix datasets at the repository level. SWE-Synth leverages LLM agents to simulate debugging workflows, producing not only bug-fix pairs but also test cases and structured repair trajectories. Compared to manually curated datasets, our method scales with minimal human effort while preserving contextual richness and correctness. Experiments show that models trained on SWE-Synth outperform those trained on real-world datasets by 2.3% on SWE-Bench Lite. Our results highlight the potential of synthetic, agent-generated data to advance the state of the art in APR and software engineering automation.

Large language model (LLM) agents may recover from a failure within an episode or after a retry, yet the same execution failure can recur in later tasks because post-episode feedback rarely revises the persistent harness that guides future interactions. Static harnesses improve reliability through fixed tools, context, memory, and workflow structures, but remain unchanged after deployment. We propose Living-Harness, a self-evolving agent harness that converts each completed trajectory and its evaluator signals into posterior evidence for bounded harness updates. Guided by a domain-level Evolution-SOP (Standard Operating Procedure), Living-Harness extracts an episode abstraction and structured update evidence, and writes two complementary forms of procedural knowledge: episodic memory that records trigger conditions, failure patterns, and recovery actions, and a state graph that records state nodes, repair edges, and transition rules. The updated harness state is retrieved to guide future interactions, while tools and base context remain frozen, allowing procedural repairs to accumulate across evolution cycles. On eight interactive environments derived from τ^2-Bench and MultiWOZ-2.4, Living-Harness improves average Pass@1 over the strongest interactive baseline by 10.07 and 9.91 percentage points, respectively, and supports retrieval-only reuse of the evolved harness state across model backbones.

Tremendous efforts have been devoted to automating software debugging, a time-consuming process involving fault localization and repair generation. Recently, Large Language Models (LLMs) have shown great potential in automated debugging. However, we identified three challenges posed to traditional and LLM-based debugging tools: 1) the upstream imperfection of fault localization affects the downstream repair, 2) the deficiency in handling complex logic errors, and 3) the ignorance of program contexts. In this context, we propose the first automated, unified debugging framework, FixAgent, via LLM agent synergy. FixAgent can perform end-to-end localization, repair, and analysis of bugs. Our insight is that LLMs can benefit from general software engineering principles recognized by human developers in debugging, such as rubber duck debugging, enabling a better understanding of program functionality and logic bugs. Hence, we create three designs inspired by rubber ducking to address these challenges. They are agent specialization and synergy, key variable tracking, and program context comprehension, which request LLMs to provide explicit explanations and force them to focus on crucial program logic information. Experiments on the widely used dataset QuixBugs show that FixAgent correctly fixes 79 out of 80 bugs, 9 of which have never been fixed. It also plausibly patches 1.9X more defects than the best-performing repair tool on CodeFlaws, even with no bug location information and fewer than 0.6% sampling times. On average, FixAgent increases about 20% plausible and correct fixes compared to its base model using different LLMs, showing the effectiveness of our designs. Moreover, the correctness rate of FixAgent reaches remarkably 97.26%, indicating that FixAgent can potentially overcome the overfitting issue of the existing approaches.

In recent years, end-to-end Large Language Model (LLM) technology has shown substantial advantages across various domains. As critical system software and infrastructure, compilers are responsible for transforming source code into target code. While LLMs have been leveraged to assist in compiler development and maintenance, their potential as an end-to-end compiler remains largely unexplored. This paper explores the feasibility of LLM as a Compiler (LaaC) and its future directions. We designed the CompilerEval dataset and framework specifically to evaluate the capabilities of mainstream LLMs in source code comprehension and assembly code generation. In the evaluation, we analyzed various errors, explored multiple methods to improve LLM-generated code, and evaluated cross-platform compilation capabilities. Experimental results demonstrate that LLMs exhibit basic capabilities as compilers but currently achieve low compilation success rates. By optimizing prompts, scaling up the model, and incorporating reasoning methods, the quality of assembly code generated by LLMs can be significantly enhanced. Based on these findings, we maintain an optimistic outlook for LaaC and propose practical architectural designs and future research directions. We believe that with targeted training, knowledge-rich prompts, and specialized infrastructure, LaaC has the potential to generate high-quality assembly code and drive a paradigm shift in the field of compilation.

Application Programming Interfaces (APIs) facilitate the integration of third-party dependencies within the code of client applications. However, changes to an API, such as deprecation, modification of parameter names or types, or complete replacement with a new API, can break existing client code. These changes are called breaking dependency updates; It is often tedious for API users to identify the cause of these breaks and update their code accordingly. In this paper, we explore the use of Large Language Models (LLMs) to automate client code updates in response to breaking dependency updates. We evaluate our approach on the BUMP dataset, a benchmark for breaking dependency updates in Java projects. Our approach leverages LLMs with advanced prompts, including information from the build process and from the breaking dependency analysis. We assess effectiveness at three granularity levels: at the build level, the file level, and the individual compilation error level. We experiment with five LLMs: Google Gemini-2.0 Flash, OpenAI GPT4o-mini, OpenAI o3-mini, Alibaba Qwen2.5-32b-instruct, and DeepSeek V3. Our results show that LLMs can automatically repair breaking updates. Among the considered models, OpenAI's o3-mini is the best, able to completely fix 27% of the builds when using prompts that include contextual information such as the buggy line, API differences, error messages, and step-by-step reasoning instructions. Also, it fixes 78% of the individual compilation errors. Overall, our findings demonstrate the potential for LLMs to fix compilation errors due to breaking dependency updates, supporting developers in their efforts to stay up-to-date with changes in their dependencies.

Software issue resolution aims to address real-world issues in software repositories (e.g., bug fixing and efficiency optimization) based on natural language descriptions provided by users, representing a key aspect of software maintenance. With the rapid development of large language models (LLMs) in reasoning and generative capabilities, LLM-based approaches have made significant progress in automated software issue resolution. However, real-world software issue resolution is inherently complex and requires long-horizon reasoning, iterative exploration, and feedback-driven decision making, which demand agentic capabilities beyond conventional single-step approaches. Recently, LLM-based agentic systems have become mainstream for software issue resolution. Advancements in agentic software issue resolution not only greatly enhance software maintenance efficiency and quality but also provide a realistic environment for validating agentic systems' reasoning, planning, and execution capabilities, bridging artificial intelligence and software engineering. This work presents a systematic survey of 126 recent studies at the forefront of LLM-based agentic software issue resolution research. It outlines the general workflow of the task and establishes a taxonomy across three dimensions: benchmarks, techniques, and empirical studies. Furthermore, it highlights how the emergence of agentic reinforcement learning has brought a paradigm shift in the design and training of agentic systems for software engineering. Finally, it summarizes key challenges and outlines promising directions for future research.

Large language models (LLMs) show promise in medical diagnosis, but real-world deployment remains challenging due to high-stakes clinical decisions and imperfect reasoning reliability. As a result, careful inspection of model behavior is essential for assessing whether diagnostic reasoning is reliable and clinically grounded. However, debugging medical LLMs remains difficult. First, developers often lack sufficient medical domain expertise to interpret model errors in clinically meaningful terms. Second, models can fail across a large and diverse set of instances involving different input types, tasks, and reasoning steps, making it challenging for developers to prioritize which errors deserve focused inspection. Third, developers struggle to identify recurring error patterns across cases, as existing debugging practices are largely instance-centric and rely on manual inspection of isolated failures. To address these challenges, we present VeriLLMed, a visual analytics system that integrates external biomedical knowledge to audit and debug medical LLM diagnostic reasoning. VeriLLMed transforms model outputs into comparable reasoning paths, constructs knowledge graph-grounded reference paths, and identifies three recurring classes of diagnosis errors: relation errors, branch errors, and missing errors. Case studies and expert evaluation demonstrate that VeriLLMed helps developers identify clinically implausible reasoning and generate actionable insights that can inform the improvement of medical LLMs.

Access control policies are vital for securing modern cloud computing, where organizations must manage access to sensitive data across thousands of users in distributed system settings. Cloud administrators typically write and update policies manually, which can be an error-prone and time-consuming process and can potentially lead to security vulnerabilities. Existing approaches based on symbolic analysis have demon- strated success in automated debugging and repairing access control policies; however, their generalizability is limited in the context of cloud-based access control. Conversely, Large Language Models (LLMs) have been utilized for automated program repair; however, their applicability to repairing cloud access control policies remains unexplored. In this work, we introduce CloudFix, the first automated policy repair framework for cloud access control that combines formal methods with LLMs. Given an access control policy and a specification of allowed and denied access requests, CloudFix employs Formal Methods-based Fault Localization to identify faulty statements in the policy and leverages LLMs to generate potential repairs, which are then verified using SMT solvers. To evaluate CloudFix, we curated a dataset of 282 real-world AWS access control policies extracted from forum posts and augmented them with synthetically generated request sets based on real scenarios. Our experimental results show that CloudFix improves repair accuracy over a Baseline implementation across varying request sizes. Our work is the first to leverage LLMs for policy repair, showcasing the effectiveness of LLMs for access control and enabling efficient and automated repair of cloud access control policies. We make our tool Cloudfix and AWS dataset publicly available.

Compilers are critical to modern computing, yet fixing compiler bugs is difficult. While recent large language model (LLM) advancements enable automated bug repair, compiler bugs pose unique challenges due to their complexity, deep cross-domain expertise requirements, and sparse, non-descriptive bug reports, necessitating compiler-specific harnesses. To bridge the gap, we introduce llvm-harness, the first harness designed to assist LLM agents in understanding and fixing compiler bugs. Our current focus is on the middle end of LLVM, one of the most widely used compiler infrastructures. Central to llvm-harness are agent-friendly LLVM tools, a benchmark llvm-bench of 334 reproducible LLVM middle-end bugs, and a tailored mini agent llvm-autofix-mini for fixing LLVM middle-end bugs automatically. We evaluate five frontier models and find that they exhibit a performance decline when tackling compiler bugs with the state-of-the-art agent. With llvm-harness' enhancement, their performance improves by 62%. Our specialized mini agent llvm-autofix-mini further outperforms the llvm-harness-enhanced state-of-the-art by 22%. This emphasizes the necessity for specialized harnesses like ours to assist LLMs in compiler engineering tasks. Despite promising results, our expert review also reveals several open challenges that remain when applying LLMs for compiler engineering tasks. GitHub: https://github.com/dtcxzyw/llvm-harness

Software specifications are essential for ensuring the reliability of software systems. Existing specification extraction approaches, however, suffer from limited generalizability and require manual efforts. The recent emergence of Large Language Models (LLMs), which have been successfully applied to numerous software engineering tasks, offers a promising avenue for automating this process. In this paper, we conduct the first empirical study to evaluate the capabilities of LLMs for generating software specifications from software comments or documentation. We evaluate LLMs' performance with Few Shot Learning (FSL), enabling LLMs to generalize from a small number of examples, as well as different prompt construction strategies, and compare the performance of LLMs with traditional approaches. Additionally, we conduct a comparative diagnosis of the failure cases from both LLMs and traditional methods, identifying their unique strengths and weaknesses. Lastly, we conduct extensive experiments on 15 state of the art LLMs, evaluating their performance and cost effectiveness for generating software specifications. Our results show that with FSL, LLMs outperform traditional methods (by 5.6%), and more sophisticated prompt construction strategies can further enlarge this performance gap (up to 5.1 to 10.0%). Yet, LLMs suffer from their unique challenges, such as ineffective prompts and the lack of domain knowledge, which together account for 53 to 60% of LLM unique failures. The strong performance of open source models (e.g., StarCoder) makes closed source models (e.g., GPT 3 Davinci) less desirable due to size and cost. Our study offers valuable insights for future research to improve specification generation.

Language Models (LMs) have become widely used in software engineering, especially for tasks such as code generation, where they are referred to as code LMs. These models have proven effective in generating code, making it easier for developers to automate coding activities. However, research has highlighted a significant limitation: despite their effectiveness, LMs often produce code that is incorrect, buggy, or not fully functional. Updating these models with limited data can be prohibitively challenging, yet it is essential to maximize their utility. This may require hot-fix techniques (updating models with limited data) to resolve. In this paper, we propose Model Improvement via Neuron Targeting (MINT), a novel approach for repairing code LMs. MINT leverages the semantic property of language models to perform neuron-level repairs in a novel way. Further, by analyzing the relationships between the model's latent representations, the incorrect outputs, and the desired outputs, MINT determines which neurons are worth updating. This approach ensures that only the neurons crucial to the model's failure are targeted, avoiding unnecessary changes and allowing for a more efficient and precise repair process. MINT is effective, efficient, and reliable, capable of correcting a neural model by patching a minimum number of neurons (usually one or two neurons). Our approach is evaluated on three coding tasks: line-level code generation, shellcode generation, and intent-to-bash translation. The experimental results demonstrate that the proposed approach significantly outperforms the state-of-the-art in both effectiveness and efficiency measures. In addition, we analyze and discuss the side effects of model repair techniques, including the balance between generalization and specificity, and the performance after multiple repairs in succession.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

An LLM safety patch can pass a benchmark while still being a poor repair. This risk is especially acute for jailbreak repairs, where the goal is to correct a specific unsafe behaviour without changing unrelated behaviours. A patch may block exact evaluation prompts yet fail on close harmful variants, or suppress harmful behaviour by over-refusing benign prompts that share its wording or structure. Existing protocols primarily test whether models can be broken, while aggregate metrics (attack success, refusal rates, global capability) cannot distinguish selective repairs from broader local suppression. To address this gap, we introduce PatchBench, a benchmark of empirically observed model-specific jailbreak failures inducing actionable harmful answers. Starting from 27,870 prompts from 37 public datasets, we curate 15,314 English prompts and query 8 open-source instruction-tuned models. Combining WildGuard filtering, pairwise Elo ranking, and manual verification, we retain a curated bank of 400 high-confidence jailbreak failures. We further introduce PatchBench-Local, an evaluation protocol testing whether a patch is behaviourally precise. For each harmful source prompt, PatchBench-Local generates three families of local neighbours: harmful variants preserving malicious intent, benign prompts with matched structure, and benign prompts reusing key harmful terms. It evaluates harmful-neighbour correction and benign-neighbour preservation, distinguishing selective repair from broader local suppression. Evaluating four activation steering methods with PatchBench-Local and MMLU shows that global capability can remain nearly unchanged while local benign regressions are severe, confirming aggregate metrics miss important collateral damage. PatchBench-Local provides a more precise basis for developing and comparing jailbreak repair methods.

Large Language models (LLMs) can generate complicated source code from natural language prompts. However, LLMs can generate output that deviates from what the user wants, requiring supervision and editing. To support this process, we offer techniques to localize where generations might be misaligned from user intent. We first create a dataset of "Minimal Intent Aligning Patches" of repaired LLM generated programs. Each program uses test cases to verify correctness. After creating a dataset of programs, we measure how well various techniques can assign a well-calibrated probability to indicate which parts of code will be edited in a minimal patch (i.e., give a probability that corresponds with empirical odds it is edited). We compare white-box probing (where we propose a technique for efficient arbitrary-span querying), against black-box reflective and self-consistency based approaches. We find probes with a small supervisor model can achieve low calibration error and Brier Skill Score of approx 0.2 estimating edited lines on code generated by models many orders of magnitude larger. We discuss the generalizability of the techniques, and the connections to AI oversight and control, finding a probe trained only on code shows some signs of generalizing to natural language errors if new probability scaling is allowed.

Formal reasoning and automated theorem proving constitute a challenging subfield of machine learning, in which machines are tasked with proving mathematical theorems using formal languages like Lean. A formal verification system can check whether a formal proof is correct or not almost instantaneously, but generating a completely correct formal proof with large language models (LLMs) remains a formidable task. The usual approach in the literature is to prompt the LLM many times (up to several thousands) until one of the generated proofs passes the verification system. In this work, we present APOLLO (Automated PrOof repair via LLM and Lean cOllaboration), a modular, model-agnostic pipeline that combines the strengths of the Lean compiler with an LLM's reasoning abilities to achieve better proof-generation results at a low sampling budget. Apollo directs a fully automated process in which the LLM generates proofs for theorems, a set of agents analyze the proofs, fix the syntax errors, identify the mistakes in the proofs using Lean, isolate failing sub-lemmas, utilize automated solvers, and invoke an LLM on each remaining goal with a low top-K budget. The repaired sub-proofs are recombined and reverified, iterating up to a user-controlled maximum number of attempts. On the miniF2F benchmark, we establish a new state-of-the-art accuracy of 75.0% among 7B-parameter models while keeping the sampling budget below one thousand. Moreover, Apollo raises the state-of-the-art accuracy for Goedel-Prover-SFT to 65.6% while cutting sample complexity from 25,600 to a few hundred. General-purpose models (o3-mini, o4-mini) jump from 3-7% to over 40% accuracy. Our results demonstrate that targeted, compiler-guided repair of LLM outputs yields dramatic gains in both efficiency and correctness, suggesting a general paradigm for scalable automated theorem proving.

Large language models (LLMs) have shown promise for automated patching, but their effectiveness depends strongly on how they are integrated into patching systems. While prior work explores prompting strategies and individual agent designs, the field lacks a systematic comparison of patching architectures. In this paper, we present a controlled evaluation of four LLM-based patching paradigms -- fixed workflow, single-agent system, multi-agent system, and general-purpose code agents -- using a unified benchmark and evaluation framework. We analyze patch correctness, failure modes, token usage, and execution time across real-world vulnerability tasks. Our results reveal clear architectural trade-offs: fixed workflows are efficient but brittle, single-agent systems balance flexibility and cost, and multi-agent designs improve generalization at the expense of substantially higher overhead and increased risk of reasoning drift on complex tasks. Surprisingly, general-purpose code agents achieve the strongest overall patching performance, benefiting from general-purpose tool interfaces that support effective adaptation across vulnerability types. Overall, we show that architectural design and iteration depth, rather than model capability alone, dominate the reliability and cost of LLM-based automated patching.

In this study, we evaluate a locally-deployed large-language model (LLM) to convert unstructured endometriosis transvaginal ultrasound (eTVUS) scan reports into structured data for imaging informatics workflows. Across 49 eTVUS reports, we compared three LLMs (7B/8B and a 20B-parameter model) against expert human extraction. The 20B model achieved a mean accuracy of 86.02%, substantially outperforming smaller models and confirming the importance of scale in handling complex clinical text. Crucially, we identified a highly complementary error profile: the LLM excelled at syntactic consistency (e.g., date/numeric formatting) where humans faltered, while human experts provided superior semantic and contextual interpretation. We also found that the LLM's semantic errors were fundamental limitations that could not be mitigated by simple prompt engineering. These findings strongly support a human-in-the-loop (HITL) workflow in which the on-premise LLM serves as a collaborative tool, not a full replacement. It automates routine structuring and flags potential human errors, enabling imaging specialists to focus on high-level semantic validation. We discuss implications for structured reporting and interactive AI systems in clinical practice.

Executable Agent Skills combine natural-language instructions and scripts into reusable packages for LLM agents, and revising them requires fixing errors without breaking correct behavior. Existing benchmarks do not systematically distinguish documentation repair, script repair, and preservation when evaluating skill self-evolution. We introduce SkillScriptBench, a 350-task benchmark designed to evaluate these capabilities separately. From a survey of over 35,000 GitHub-hosted Skill roots, we select 100 packages and construct 150 repair tasks. Each task pairs a package containing injected script faults with a maintenance request and executable checks of the required behavior. A complementary controlled track contains 200 tasks from 50 packages, each evaluated under the same maintenance request in four states: clean, documentation faults, script faults, and faults in both. Across four LLMs, methods that edit both documentation and scripts can repair script faults but do not consistently outperform Markdown-only revision on documentation repair or preservation. We therefore introduce AST-Guided Skill Revision, which uses abstract syntax trees and calling relationships to link maintenance requirements to relevant code locations. It restricts script edits to these locations and updates the documentation to match the revised scripts. Averaged across models, this revision stage yields absolute gains in repair success of 21.9% for Raw Package and 27.7% for CoEvoSkills on faulty packages. Absolute gains in the proportion of tasks solved in all three runs reach 20.8% and 31.5%, respectively, indicating more consistent repair success across repeated runs.

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

As software systems grow increasingly intricate, Artificial Intelligence for IT Operations (AIOps) methods have been widely used in software system failure management to ensure the high availability and reliability of large-scale distributed software systems. However, these methods still face several challenges, such as lack of cross-platform generality and cross-task flexibility. Fortunately, recent advancements in large language models (LLMs) can significantly address these challenges, and many approaches have already been proposed to explore this field. However, there is currently no comprehensive survey that discusses the differences between LLM-based AIOps and traditional AIOps methods. Therefore, this paper presents a comprehensive survey of AIOps technology for failure management in the LLM era. It includes a detailed definition of AIOps tasks for failure management, the data sources for AIOps, and the LLM-based approaches adopted for AIOps. Additionally, this survey explores the AIOps subtasks, the specific LLM-based approaches suitable for different AIOps subtasks, and the challenges and future directions of the domain, aiming to further its development and application.

Surgical scene understanding is critical for surgical training and robotic decision-making in robot-assisted surgery. Recent advances in Multimodal Large Language Models (MLLMs) have demonstrated great potential for advancing scene perception in the medical domain, facilitating surgeons to understand surgical scenes and procedures. However, these methods are primarily oriented towards image-based analysis or global video understanding, overlooking the fine-grained video reasoning that is crucial for analyzing specific processes and capturing detailed task execution within a surgical procedure. To bridge this gap, we propose SurgVidLM, the first video language model designed to address both full and fine-grained surgical video comprehension. To train our SurgVidLM, we construct the SVU-31K that is a large-scale dataset with over 31K video-instruction pairs, enabling both holistic understanding and detailed analysis of surgical procedures. Building on this resource, SurgVidLM incorporates a two-stage StageFocus mechanism: the first stage extracts global procedural context, while the second stage performs high-frequency local analysis guided by temporal cues. We also develop the Multi-frequency Fusion Attention to effectively integrate low- and high-frequency visual tokens, ensuring the preservation of critical task-specific details. Experimental results demonstrate that SurgVidLM significantly outperforms state-of-the-art Vid-LLMs of comparable parameter scale in both full and fine-grained video understanding tasks, showcasing its superior capability in capturing the context of complex robot-assisted surgeries. Our code and dataset will be publicly accessible soon.

Proactive interventions by LLM critic models are often assumed to improve reliability, yet their effects at deployment time are poorly understood. We show that a binary LLM critic with strong offline accuracy (AUROC 0.94) can nevertheless cause severe performance degradation, inducing a 26 percentage point (pp) collapse on one model while affecting another by near zero pp. This variability demonstrates that LLM critic accuracy alone is insufficient to determine whether intervention is safe. We identify a disruption-recovery tradeoff: interventions may recover failing trajectories but also disrupt trajectories that would have succeeded. Based on this insight, we propose a pre-deployment test that uses a small pilot of 50 tasks to estimate whether intervention is likely to help or harm, without requiring full deployment. Across benchmarks, the test correctly anticipates outcomes: intervention degrades performance on high-success tasks (0 to -26 pp), while yielding a modest improvement on the high-failure ALFWorld benchmark (+2.8 pp, p=0.014). The primary value of our framework is therefore identifying when not to intervene, preventing severe regressions before deployment.

Evaluating the output of Large Language Models (LLMs) is one of the most critical aspects of building a performant compound AI system. Since the output from LLMs propagate to downstream steps, identifying LLM errors is crucial to system performance. A common task for LLMs in AI systems is tool use. While there are several benchmark environments for evaluating LLMs on this task, they typically only give a success rate without any explanation of the failure cases. To solve this problem, we introduce SpecTool, a new benchmark to identify error patterns in LLM output on tool-use tasks. Our benchmark data set comprises of queries from diverse environments that can be used to test for the presence of seven newly characterized error patterns. Using SPECTOOL , we show that even the most prominent LLMs exhibit these error patterns in their outputs. Researchers can use the analysis and insights from SPECTOOL to guide their error mitigation strategies.

This study presents a quantitative evaluation of the code quality and security of five prominent Large Language Models (LLMs): Claude Sonnet 4, Claude 3.7 Sonnet, GPT-4o, Llama 3.2 90B, and OpenCoder 8B. While prior research has assessed the functional performance of LLM-generated code, this research tested LLM output from 4,442 Java coding assignments through comprehensive static analysis using SonarQube. The findings suggest that although LLMs can generate functional code, they also introduce a range of software defects, including bugs, security vulnerabilities, and code smells. These defects do not appear to be isolated; rather, they may represent shared weaknesses stemming from systemic limitations within current LLM code generation methods. In particular, critically severe issues, such as hard-coded passwords and path traversal vulnerabilities, were observed across multiple models. These results indicate that LLM-generated code requires verification in order to be considered production-ready. This study found no direct correlation between a model's functional performance (measured by Pass@1 rate of unit tests) and the overall quality and security of its generated code, measured by the number of SonarQube issues in benchmark solutions that passed the functional tests. This suggests that functional benchmark performance score is not a good indicator of overall code quality and security. The goal of this study is not to rank LLM performance but to highlight that all evaluated models appear to share certain weaknesses. Consequently, these findings support the view that static analysis can be a valuable instrument for detecting latent defects and an important safeguard for organizations that deploy AI in software development.

LLM agents interact with Web services to perform tasks on users' behalf. Errors during these interactions can disrupt execution and prevent task completion, motivating external intervention. However, agents may self-recover through continued execution, raising the question of when to intervene and when to wait for self-recovery. We present an empirical study of errors and self-recovery in LLM agents. We construct ReInBench, a dataset containing 1,259 agent traces and 1,403 error events across computer-use and Web tasks. Our study examines how often and how quickly agents self-recover, how self-recovery relates to subsequent execution and task completion, and whether self-recovery can be predicted when an error occurs. We find that 725 error events self-recover, often within a few steps, with self-recovery performance differing across Execution LLMs. Self-recovery can also help agents recover from subsequent errors of the same type and support overall task completion. Intervention should therefore prioritize errors unlikely to self-recover, while allowing agents to continue when self-recovery is likely. Building on these empirical findings, we propose ReCoF, a method that predicts whether an error will self-recover to inform whether additional intervention is needed. ReCoF achieves an average relative improvement of 9.02% in Macro-F1 over the strongest baseline on ReInBench. Our code and data can be found at https://method-notes.github.io/ReCoF/.

In industrial procurement, an LLM answer is useful only if it survives a standards check: recommended material must match operating condition, every parameter must respect a regulated threshold, and no procedure may contradict a safety clause. Partial correctness can mask safety-critical contradictions that aggregate LLM benchmarks rarely capture. We introduce IndustryBench, a 2,049-item benchmark for industrial procurement QA in Chinese, grounded in Chinese national standards (GB/T) and structured industrial product records, organized by seven capability dimensions, ten industry categories, and panel-derived difficulty tiers, with item-aligned English, Russian, and Vietnamese renderings. Our construction pipeline rejects 70.3% of LLM-generated candidates at a search-based external-verification stage, calibrating how unreliable industrial QA remains after LLM-only filtering.Our evaluation decouples raw correctness, scored by a Qwen3-Max judge validated at κ_w = 0.798 against a domain expert, from a separate safety-violation (SV) check against source texts. Across 17 models in Chinese and an 8-model intersection over four languages, we find: (i) the best system reaches only 2.083 on the 0--3 rubric, leaving substantial headroom; (ii) Standards & Terminology is the most persistent capability weakness and survives item-aligned translation; (iii) extended reasoning lowers safety-adjusted scores for 12 of 13 models, primarily by introducing unsupported safety-critical details into longer final answers; and (iv) safety-violation rates reshuffle the leaderboard -- GPT-5.4 climbs from rank 6 to rank 3 after SV adjustment, while Kimi-k2.5-1T-A32B drops seven positions.Industrial LLM evaluation therefore requires source-grounded, safety-aware diagnosis rather than aggregate accuracy. We release IndustryBench with all prompts, scoring scripts, and dataset documentation.

Although LLMs have shown promising potential in vulnerability detection, this study reveals their limitations in distinguishing between vulnerable and similar-but-benign patched code (only 0.06 - 0.14 accuracy). It shows that LLMs struggle to capture the root causes of vulnerabilities during vulnerability detection. To address this challenge, we propose enhancing LLMs with multi-dimensional vulnerability knowledge distilled from historical vulnerabilities and fixes. We design a novel knowledge-level Retrieval-Augmented Generation framework Vul-RAG, which improves LLMs with an accuracy increase of 16% - 24% in identifying vulnerable and patched code. Additionally, vulnerability knowledge generated by Vul-RAG can further (1) serve as high-quality explanations to improve manual detection accuracy (from 60% to 77%), and (2) detect 10 previously-unknown bugs in the recent Linux kernel release with 6 assigned CVEs.

Large language models (LLMs) have been applied to tasks in healthcare, ranging from medical exam questions to responding to patient questions. With increasing institutional partnerships between companies producing LLMs and healthcare systems, real world clinical application is coming closer to reality. As these models gain traction, it is essential for healthcare practitioners to understand what LLMs are, their development, their current and potential applications, and the associated pitfalls when utilized in medicine. This review and accompanying tutorial aim to give an overview of these topics to aid healthcare practitioners in understanding the rapidly changing landscape of LLMs as applied to medicine.

As software projects progress, quality of code assumes paramount importance as it affects reliability, maintainability and security of software. For this reason, static analysis tools are used in developer workflows to flag code quality issues. However, developers need to spend extra efforts to revise their code to improve code quality based on the tool findings. In this work, we investigate the use of (instruction-following) large language models (LLMs) to assist developers in revising code to resolve code quality issues. We present a tool, CORE (short for COde REvisions), architected using a pair of LLMs organized as a duo comprised of a proposer and a ranker. Providers of static analysis tools recommend ways to mitigate the tool warnings and developers follow them to revise their code. The proposer LLM of CORE takes the same set of recommendations and applies them to generate candidate code revisions. The candidates which pass the static quality checks are retained. However, the LLM may introduce subtle, unintended functionality changes which may go un-detected by the static analysis. The ranker LLM evaluates the changes made by the proposer using a rubric that closely follows the acceptance criteria that a developer would enforce. CORE uses the scores assigned by the ranker LLM to rank the candidate revisions before presenting them to the developer. CORE could revise 59.2% Python files (across 52 quality checks) so that they pass scrutiny by both a tool and a human reviewer. The ranker LLM is able to reduce false positives by 25.8% in these cases. CORE produced revisions that passed the static analysis tool in 76.8% Java files (across 10 quality checks) comparable to 78.3% of a specialized program repair tool, with significantly much less engineering efforts.

Unit tests play a key role in ensuring the correctness of software. However, manually creating unit tests is a laborious task, motivating the need for automation. Large Language Models (LLMs) have recently been applied to this problem, utilizing additional training or few-shot learning on examples of existing tests. This paper presents a large-scale empirical evaluation on the effectiveness of LLMs for automated unit test generation without additional training or manual effort, providing the LLM with the signature and implementation of the function under test, along with usage examples extracted from documentation. We also attempt to repair failed generated tests by re-prompting the model with the failing test and error message. We implement our approach in TestPilot, a test generation tool for JavaScript that automatically generates unit tests for all API functions in an npm package. We evaluate TestPilot using OpenAI's gpt3.5-turbo LLM on 25 npm packages with a total of 1,684 API functions. The generated tests achieve a median statement coverage of 70.2% and branch coverage of 52.8%, significantly improving on Nessie, a recent feedback-directed JavaScript test generation technique, which achieves only 51.3% statement coverage and 25.6% branch coverage. We also find that 92.8% of TestPilot's generated tests have no more than 50% similarity with existing tests (as measured by normalized edit distance), with none of them being exact copies. Finally, we run TestPilot with two additional LLMs, OpenAI's older code-cushman-002 LLM and the open LLM StarCoder. Overall, we observed similar results with the former (68.2% median statement coverage), and somewhat worse results with the latter (54.0% median statement coverage), suggesting that the effectiveness of the approach is influenced by the size and training set of the LLM, but does not fundamentally depend on the specific model.

The ability to detect and analyze failed executions automatically is crucial for an explainable and robust robotic system. Recently, Large Language Models (LLMs) have demonstrated strong common sense reasoning skills on textual inputs. To leverage the power of LLM for robot failure explanation, we propose a framework REFLECT, which converts multi-sensory data into a hierarchical summary of robot past experiences and queries LLM with a progressive failure explanation algorithm. Conditioned on the explanation, a failure correction planner generates an executable plan for the robot to correct the failure and complete the task. To systematically evaluate the framework, we create the RoboFail dataset and show that our LLM-based framework is able to generate informative failure explanations that assist successful correction planning. Project website: https://roboreflect.github.io/

Large language models (LLMs) have recently shown strong potential for Automated Program Repair (APR), yet most existing approaches remain unimodal and fail to leverage the rich diagnostic signals contained in visual artifacts such as screenshots and control-flow graphs. In practice, many bug reports convey critical information visually (e.g., layout breakage or missing widgets), but directly using such dense visual inputs often causes context loss and noise, making it difficult for MLLMs to ground visual observations into precise fault localization and executable patches. To bridge this semantic gap, we propose SVRepair, a multimodal APR framework with structured visual representation. SVRepair first fine-tunes a vision-language model, Structured Visual Representation (SVR), to uniformly transform heterogeneous visual artifacts into a semantic scene graph that captures GUI elements and their structural relations (e.g., hierarchy), providing normalized, code-relevant context for downstream repair. Building on the graph, SVRepair drives a coding agent to localize faults and synthesize patches, and further introduces an iterative visual-artifact segmentation strategy that progressively narrows the input to bug-centered regions to suppress irrelevant context and reduce hallucinations. Extensive experiments across multiple benchmarks demonstrate state-of-the-art performance: SVRepair achieves 36.47\% accuracy on SWE-Bench M, 38.02\% on MMCode, and 95.12\% on CodeVision, validating the effectiveness of SVRepair for multimodal program repair.

Pre-trained large language models (LLMs) have recently emerged as a breakthrough technology in natural language processing and artificial intelligence, with the ability to handle large-scale datasets and exhibit remarkable performance across a wide range of tasks. Meanwhile, software testing is a crucial undertaking that serves as a cornerstone for ensuring the quality and reliability of software products. As the scope and complexity of software systems continue to grow, the need for more effective software testing techniques becomes increasingly urgent, and making it an area ripe for innovative approaches such as the use of LLMs. This paper provides a comprehensive review of the utilization of LLMs in software testing. It analyzes 52 relevant studies that have used LLMs for software testing, from both the software testing and LLMs perspectives. The paper presents a detailed discussion of the software testing tasks for which LLMs are commonly used, among which test case preparation and program repair are the most representative ones. It also analyzes the commonly used LLMs, the types of prompt engineering that are employed, as well as the accompanied techniques with these LLMs. It also summarizes the key challenges and potential opportunities in this direction. This work can serve as a roadmap for future research in this area, highlighting potential avenues for exploration, and identifying gaps in our current understanding of the use of LLMs in software testing.

Large language models (LLMs) achieve remarkable performance across a wide range of tasks, but their deployment is constrained by substantial memory and compute requirements. Low-rank compression via singular value decomposition (SVD) is an effective remedy, but existing methods focus on how to factorize and which components to keep. We introduce SVD-Surgeon, a training-free method that brings the Optimal Brain Surgeon (OBS) framework to the singular-value basis. Treating each singular value as a parameter, it computes a closed-form update of the retained singular values that compensates, to second order in the model loss, for those removed by truncation. The same analysis yields a saliency for choosing which values to prune. As it operates directly on the singular-value factorization, SVD-Surgeon can be layered on top of existing SVD compressors. Applied to SVD-LLM, a leading SVD-based method, it improves the perplexity-compression trade-off on the OPT family and LLaMA 2-7B without any retraining.

Medical image analysis is a fundamental component. As deep learning progresses, the focus has shifted from single-task applications, such as classification and segmentation, to more complex multimodal tasks, including medical visual question answering and report generation. Traditional shallow and task-specific models are increasingly limited in addressing the complexity and scalability required in clinical practice. The emergence of large language models (LLMs) has driven the development of medical Large Vision-Language Models (LVLMs), offering a unified solution for diverse vision-language tasks. In this study, we investigate various architectural designs for medical LVLMs based on the widely adopted LLaVA framework, which follows an encoder-connector-LLM paradigm. We construct two distinct models targeting 2D and 3D modalities, respectively. These models are designed to support both general-purpose medical tasks and domain-specific fine-tuning, thereby serving as effective foundation models. To facilitate reproducibility and further research, we develop a modular and extensible codebase, MedM-VL, and release two LVLM variants: MedM-VL-2D for 2D medical image analysis and MedM-VL-CT-Chest for 3D CT-based applications. The code and models are available at: https://github.com/MSIIP/MedM-VL

The SZZ algorithm is the dominant technique for identifying bug-inducing commits and serves as a foundation for many software engineering studies, such as bug prediction and static code analysis. Researchers have proposed many variants to enhance the SZZ algorithm's performance since its introduction. The majority of them rely on static techniques or heuristic assumptions, making them easy to implement, but their performance improvements are often limited. Recently, a deep learning-based SZZ algorithm has been introduced to enhance the original SZZ algorithm. However, it requires complex preprocessing and is restricted to a single programming language. Additionally, while it enhances precision, it sacrifices recall. Furthermore, most of variants overlook crucial information, such as commit messages and patch context, and are limited to bug-fixing commits involving deleted lines. The emergence of large language models (LLMs) offers an opportunity to address these drawbacks. In this study, we investigate the strengths and limitations of LLMs and propose LLM4SZZ, which employs two approaches (i.e., rank-based identification and context-enhanced identification) to handle different types of bug-fixing commits. We determine which approach to adopt based on the LLM's ability to comprehend the bug and identify whether the bug is present in a commit. The context-enhanced identification provides the LLM with more context and requires it to find the bug-inducing commit among a set of candidate commits. In rank-based identification, we ask the LLM to select buggy statements from the bug-fixing commit and rank them based on their relevance to the root cause. Experimental results show that LLM4SZZ outperforms all baselines across three datasets, improving F1-score by 6.9% to 16.0% without significantly sacrificing recall.

Conversation agents powered by large language models are revolutionizing the way we interact with visual data. Recently, large vision-language models (LVLMs) have been extensively studied for both images and videos. However, these studies typically focus on common scenarios. In this work, we introduce an LVLM specifically designed for surgical scenarios. We integrate visual representations of surgical images and videos into the language feature space. Consequently, we establish a LVLM model, Surgical-LLaVA, fine-tuned on instruction following data of surgical scenarios. Our experiments demonstrate that Surgical-LLaVA exhibits impressive multi-modal chat abilities in surgical contexts, occasionally displaying multi-modal behaviors on unseen instructions. We conduct a quantitative evaluation of visual question-answering datasets for surgical scenarios. The results show superior performance compared to previous works, indicating the potential of our model to tackle more complex surgery scenarios.

Large Language Models (LLMs), known for their versatility in textual data, are increasingly being explored for their potential to enhance medical image segmentation, a crucial task for accurate diagnostic imaging. This study explores enhancing Vision Transformers (ViTs) for medical image segmentation by integrating pre-trained LLM transformer blocks. Our approach, which incorporates a frozen LLM transformer block into the encoder of a ViT-based model, leads to substantial improvements in segmentation performance across various medical imaging modalities. We propose a Hybrid Attention Mechanism that combines global and local feature learning with a Multi-Scale Fusion Block for aggregating features across different scales. The enhanced model shows significant performance gains, including an average Dice score increase from 0.74 to 0.79 and improvements in accuracy, precision, and the Jaccard Index. These results demonstrate the effectiveness of LLM-based transformers in refining medical image segmentation, highlighting their potential to significantly boost model accuracy and robustness. The source code and our implementation are available at: https://bit.ly/3zf2CVs

An LLM agent's real-task performance is shaped as much by the harness around its model as by the frozen model itself: its prompts, injected knowledge, runtime control, and configuration. In deployment the harness is often the only lever available, so improving it automatically is the natural way to raise performance without touching the weights. The hard part is not generating changes but knowing which one truly helped. Self-generated feedback is noisy, and an apparent gain can be a measurement artifact or an edit that merely overfits the tasks it was tuned on. We present a self-evolving agent-harness framework that separates proposing changes from crediting them: a language model diagnoses failures and proposes patches, while all sampling, measurement, and significance testing are owned by deterministic code, so every credited improvement is trustworthy by construction. Patches populate a gated, categorical quality-diversity archive (GSME) keyed on the (WHERE x WHY) pathology an edit addresses rather than the tasks it fixes, an anti-overfitting inductive bias; generalization is measured on a sealed test scored only after evolution. Across seven domains with a frozen open-weight model, the harness is train-selected and scored once on a sealed test; its credited gains there are +9 to +15.5pp and retain 86-147% of the training gain, evidence they generalize rather than overfit. The winning patch tracks the model's dominant pathology, not its size or family: changing the model can change the pathology and the patch, while the same pathology-to-patch match recurs across two model families. What transfers is the diagnose-and-credit loop, not any specific harness.

Where an LLM sits in an agent memory pipeline -- between the recall plane that retrieves stored facts (extensively benchmarked) and the control plane that mutates them via supersede, release, purge (largely untested) -- shapes which forgetting failure modes the system recovers. Comparing thirteen system configurations on a 385-case adversarial surface, we observe three placement regimes with partly complementary coverage: deterministic primitives suffice for lexical/temporal categories but fail canonicalization (5% on identifier-obfuscation, 0% on cross-lingual); inscribe-time LLM recovers canonicalization (100%) but cannot help intent-aware deletion (0% on prefix-collision and compound-fact); a mutation-time hook recovers intent-aware deletion (78-85%) and brightens nearly all categories simultaneously (91.7-93.2% overall, $0.17 per 385-case run, 2.3s/case mutation latency vs. 64-191ms/case deterministic, recall path unchanged). We expose the trade-off via ForgetEval, a 1000-case templated suite plus a 385-case adversarial layer (132 hand-crafted + 253 LLM-drafted oracle-validated) scored by deterministic substring match, paired with a six-method Adapter Protocol with honest N/A scoring that lets heterogeneous memory stores enter in 130 lines. Admission is corroborated by 10-annotator IAA (Fleiss' kappa = 0.958) and a 77-case external-authored subset (four blind contributors) that replicates the canonicalization asymmetry and amplifies the joint-placement lift (+27.8 pt). Production failures are predominantly forgetting failures rather than recall failures, yet existing benchmarks measure only recall. ForgetEval and all adapters are released under MIT.

During Automated Program Repair (APR), it can be challenging to synthesize correct patches for real-world systems in general-purpose programming languages. Recent Large Language Models (LLMs) have been shown to be helpful "copilots" in assisting developers with various coding tasks, and have also been directly applied for patch synthesis. However, most LLMs treat programs as sequences of tokens, meaning that they are ignorant of the underlying semantics constraints of the target programming language. This results in plenty of statically invalid generated patches, impeding the practicality of the technique. Therefore, we propose Repilot, a framework to further copilot the AI "copilots" (i.e., LLMs) by synthesizing more valid patches during the repair process. Our key insight is that many LLMs produce outputs autoregressively (i.e., token by token), resembling human writing programs, which can be significantly boosted and guided through a Completion Engine. Repilot synergistically synthesizes a candidate patch through the interaction between an LLM and a Completion Engine, which 1) prunes away infeasible tokens suggested by the LLM and 2) proactively completes the token based on the suggestions provided by the Completion Engine. Our evaluation on a subset of the widely-used Defects4j 1.2 and 2.0 datasets shows that Repilot fixes 66 and 50 bugs, respectively, surpassing the best-performing baseline by 14 and 16 bugs fixed. More importantly, Repilot is capable of producing more valid and correct patches than the base LLM when given the same generation budget.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

The increasing use of generative Artificial Intelligence (AI) in modern software engineering, particularly Large Language Models (LLMs) for code generation, has transformed professional software development by boosting productivity and automating development processes. This adoption, however, has highlighted a significant issue: the introduction of security vulnerabilities into the code. These vulnerabilities result, e.g., from flaws in the training data that propagate into the generated code, creating challenges in disclosing them. Traditional vulnerability handling processes often involve extensive manual review. Applying such traditional processes to AI-generated code is challenging. AI-generated code may include several vulnerabilities, possibly in slightly different forms as developers might not build on already implemented code but prompt similar tasks. In this work, we explore the current state of LLM-based approaches for vulnerability handling, focusing on approaches for vulnerability detection, localization, and repair. We provide an overview of recent progress in this area and highlight open challenges that must be addressed in order to establish a reliable and scalable vulnerability handling process of AI-generated code.

Large Language Models (LLMs) are one of the most promising developments in the field of artificial intelligence, and the software engineering community has readily noticed their potential role in the software development life-cycle. Developers routinely ask LLMs to generate code snippets, increasing productivity but also potentially introducing ownership, privacy, correctness, and security issues. Previous work highlighted how code generated by mainstream commercial LLMs is often not safe, containing vulnerabilities, bugs, and code smells. In this paper, we present a framework that leverages testing and static analysis to assess the quality, and guide the self-improvement, of code generated by general-purpose, open-source LLMs. First, we ask LLMs to generate C code to solve a number of programming tasks. Then we employ ground-truth tests to assess the (in)correctness of the generated code, and a static analysis tool to detect potential safety vulnerabilities. Next, we assess the models ability to evaluate the generated code, by asking them to detect errors and vulnerabilities. Finally, we test the models ability to fix the generated code, providing the reports produced during the static analysis and incorrectness evaluation phases as feedback. Our results show that models often produce incorrect code, and that the generated code can include safety issues. Moreover, they perform very poorly at detecting either issue. On the positive side, we observe a substantial ability to fix flawed code when provided with information about failed tests or potential vulnerabilities, indicating a promising avenue for improving the safety of LLM-based code generation tools.

Recent advances in multimodal large language models (LLMs) have highlighted their potential for medical and surgical applications. However, existing surgical datasets predominantly adopt a Visual Question Answering (VQA) format with heterogeneous taxonomies and lack support for pixel-level segmentation, limiting consistent evaluation and applicability. We present SurgMLLMBench, a unified multimodal benchmark explicitly designed for developing and evaluating interactive multimodal LLMs for surgical scene understanding, including the newly collected Micro-surgical Artificial Vascular anastomosIS (MAVIS) dataset. It integrates pixel-level instrument segmentation masks and structured VQA annotations across laparoscopic, robot-assisted, and micro-surgical domains under a unified taxonomy, enabling comprehensive evaluation beyond traditional VQA tasks and richer visual-conversational interactions. Extensive baseline experiments show that a single model trained on SurgMLLMBench achieves consistent performance across domains and generalizes effectively to unseen datasets. SurgMLLMBench will be publicly released as a robust resource to advance multimodal surgical AI research, supporting reproducible evaluation and development of interactive surgical reasoning models.

Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance in summarizing medical evidence. Utilizing a benchmark dataset, MedReview, consisting of 8,161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the fine-tuned LLMs obtained an increase of 9.89 in ROUGE-L (95% confidence interval: 8.94-10.81), 13.21 in METEOR score (95% confidence interval: 12.05-14.37), and 15.82 in CHRF score (95% confidence interval: 13.89-16.44). The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were also manifested in both human and GPT4-simulated evaluations. Our results can be applied to guide model selection for tasks demanding particular domain knowledge, such as medical evidence summarization.

Agent skills are procedural artifacts that enable LLM agents to execute workflows, verify constraints, and recover from failures. Existing self-evolving methods refine skills using accumulated trajectories. However, they struggle in cold-start settings, where only an initial, imperfect skill is available. Consequently, skill construction defaults to expert authoring or one-shot LLM generation. Expert-authored skills are costly and may not align with how LLM agents actually execute tasks, while one-shot generated skills can be syntactically well formed yet behaviorally weak. To bridge this gap, we propose SkillRevise, an execution-grounded framework designed to iteratively refine these initial skills. SkillRevise diagnoses skill defects from execution evidence, retrieves relevant repair principles from a general memory, and applies execution-anchored edits. By re-executing candidates and measuring empirical utility, it systematically retains the optimal skill version. Evaluated across three benchmarks and five LLMs, SkillRevise substantially outperforms one-shot baselines, improving the base agent's success rate on SkillsBench from 36.05% to 61.63%. Furthermore, the revised skills exhibit strong cross-model transferability, capturing generalized procedural knowledge over model-specific artifacts.

Multimodal Large Language Models (MLLMs) have shown significant potential in medical image analysis. However, their capabilities in interpreting fundus images, a critical skill for ophthalmology, remain under-evaluated. Existing benchmarks lack fine-grained task divisions and fail to provide modular analysis of its two key modules, i.e., large language model (LLM) and vision encoder (VE). This paper introduces FunBench, a novel visual question answering (VQA) benchmark designed to comprehensively evaluate MLLMs' fundus reading skills. FunBench features a hierarchical task organization across four levels (modality perception, anatomy perception, lesion analysis, and disease diagnosis). It also offers three targeted evaluation modes: linear-probe based VE evaluation, knowledge-prompted LLM evaluation, and holistic evaluation. Experiments on nine open-source MLLMs plus GPT-4o reveal significant deficiencies in fundus reading skills, particularly in basic tasks such as laterality recognition. The results highlight the limitations of current MLLMs and emphasize the need for domain-specific training and improved LLMs and VEs.

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to enhance various aspects of healthcare, ranging from medical education to clinical decision support. However, medicine involves multifaceted data modalities and nuanced reasoning skills, presenting challenges for integrating LLMs. This paper provides a comprehensive review on the applications and implications of LLMs in medicine. It begins by examining the fundamental applications of general-purpose and specialized LLMs, demonstrating their utilities in knowledge retrieval, research support, clinical workflow automation, and diagnostic assistance. Recognizing the inherent multimodality of medicine, the review then focuses on multimodal LLMs, investigating their ability to process diverse data types like medical imaging and EHRs to augment diagnostic accuracy. To address LLMs' limitations regarding personalization and complex clinical reasoning, the paper explores the emerging development of LLM-powered autonomous agents for healthcare. Furthermore, it summarizes the evaluation methodologies for assessing LLMs' reliability and safety in medical contexts. Overall, this review offers an extensive analysis on the transformative potential of LLMs in modern medicine. It also highlights the pivotal need for continuous optimizations and ethical oversight before these models can be effectively integrated into clinical practice. Visit https://github.com/mingze-yuan/Awesome-LLM-Healthcare for an accompanying GitHub repository containing latest papers.

Large Language Models (LLMs) have gained significant attention in the medical domain for their human-level capabilities, leading to increased efforts to explore their potential in various healthcare applications. However, despite such a promising future, there are multiple challenges and obstacles that remain for their real-world uses in practical settings. This work discusses key challenges for LLMs in medical applications from four unique aspects: operational vulnerabilities, ethical and social considerations, performance and assessment difficulties, and legal and regulatory compliance. Addressing these challenges is crucial for leveraging LLMs to their full potential and ensuring their responsible integration into healthcare.

Researchers have made significant progress in automating the software development process in the past decades. Recent progress in Large Language Models (LLMs) has significantly impacted the development process, where developers can use LLM-based programming assistants to achieve automated coding. Nevertheless, software engineering involves the process of program improvement apart from coding, specifically to enable software maintenance (e.g. bug fixing) and software evolution (e.g. feature additions). In this paper, we propose an automated approach for solving GitHub issues to autonomously achieve program improvement. In our approach called AutoCodeRover, LLMs are combined with sophisticated code search capabilities, ultimately leading to a program modification or patch. In contrast to recent LLM agent approaches from AI researchers and practitioners, our outlook is more software engineering oriented. We work on a program representation (abstract syntax tree) as opposed to viewing a software project as a mere collection of files. Our code search exploits the program structure in the form of classes/methods to enhance LLM's understanding of the issue's root cause, and effectively retrieve a context via iterative search. The use of spectrum-based fault localization using tests, further sharpens the context, as long as a test-suite is available. Experiments on SWE-bench-lite (300 real-life GitHub issues) show increased efficacy in solving GitHub issues (19% on SWE-bench-lite), which is higher than the efficacy of the recently reported SWE-agent. In addition, AutoCodeRover achieved this efficacy with significantly lower cost (on average, $0.43 USD), compared to other baselines. We posit that our workflow enables autonomous software engineering, where, in future, auto-generated code from LLMs can be autonomously improved.

Recent advances such as LLaVA and Mini-GPT4 have successfully integrated visual information into LLMs, yielding inspiring outcomes and giving rise to a new generation of multi-modal LLMs, or MLLMs. Nevertheless, these methods struggle with hallucinations and the mutual interference between tasks. To tackle these problems, we propose an efficient and accurate approach to adapt to downstream tasks by utilizing LLM as a bridge to connect multiple expert models, namely u-LLaVA. Firstly, we incorporate the modality alignment module and multi-task modules into LLM. Then, we reorganize or rebuild multi-type public datasets to enable efficient modality alignment and instruction following. Finally, task-specific information is extracted from the trained LLM and provided to different modules for solving downstream tasks. The overall framework is simple, effective, and achieves state-of-the-art performance across multiple benchmarks. We also release our model, the generated data, and the code base publicly available.

Verifier-based selection improves LLM performance by generating multiple candidate solutions and using a verifier to select the most promising one. However, existing methods typically treat verification only as a ranking step and discard its feedback once a fixed candidate pool has been evaluated. In this paper, we ask whether verification can also improve the candidate set itself. To this end, we introduce LLM-as-an-Improver and propose Verify--Repair--Reselect (VRR), which uses verification feedback to generate and reselect improved candidates. VRR retains the initial winner while conditionally generating three complementary alternatives: repaired versions of the winner and runner-up, and a solution based on a new approach. It filters invalid and duplicate candidates using only inference-time information and then reselects the final answer under the original evaluation criteria. Across diverse models and code-generation and reasoning benchmarks, VRR improves over fixed-pool verifier-based selection in many settings and can recover correct solutions even when all candidates in the initial pool are incorrect. These results highlight a broader role for LLMs as improvers: verification feedback can not only select among existing solutions but also construct stronger candidates beyond the initial pool.

Large Language Models (LLMs) have shown impressive capabilities in downstream software engineering tasks such as Automated Program Repair (APR). In particular, there has been a lot of research on repository-level issue-resolution benchmarks such as SWE-Bench. Although there has been significant progress on this topic, we notice that in the process of solving such issues, existing agentic systems tend to hyper-localize on immediately suspicious lines of code and fix them in isolation, without a deeper understanding of the issue semantics, code semantics, or execution semantics. Consequently, many existing systems generate patches that overfit to the user issue, even when a more general fix is preferable. To address this limitation, we introduce SemAgent, a novel workflow-based procedure that leverages issue, code, and execution semantics to generate patches that are complete - identifying and fixing all lines relevant to the issue. We achieve this through a novel pipeline that (a) leverages execution semantics to retrieve relevant context, (b) comprehends issue-semantics via generalized abstraction, (c) isolates code-semantics within the context of this abstraction, and (d) leverages this understanding in a two-stage architecture: a repair stage that proposes fine-grained fixes, followed by a reviewer stage that filters relevant fixes based on the inferred issue-semantics. Our evaluations show that our methodology achieves a solve rate of 44.66% on the SWEBench-Lite benchmark beating all other workflow-based approaches, and an absolute improvement of 7.66% compared to our baseline, which lacks such deep semantic understanding. We note that our approach performs particularly well on issues requiring multi-line reasoning (and editing) and edge-case handling, suggesting that incorporating issue and code semantics into APR pipelines can lead to robust and semantically consistent repairs.

Large language models (LLMs), such as OpenAI's Codex, have demonstrated their potential to generate code from natural language descriptions across a wide range of programming tasks. Several benchmarks have recently emerged to evaluate the ability of LLMs to generate functionally correct code from natural language intent with respect to a set of hidden test cases. This has enabled the research community to identify significant and reproducible advancements in LLM capabilities. However, there is currently a lack of benchmark datasets for assessing the ability of LLMs to generate functionally correct code edits based on natural language descriptions of intended changes. This paper aims to address this gap by motivating the problem NL2Fix of translating natural language descriptions of code changes (namely bug fixes described in Issue reports in repositories) into correct code fixes. To this end, we introduce Defects4J-NL2Fix, a dataset of 283 Java programs from the popular Defects4J dataset augmented with high-level descriptions of bug fixes, and empirically evaluate the performance of several state-of-the-art LLMs for the this task. Results show that these LLMS together are capable of generating plausible fixes for 64.6% of the bugs, and the best LLM-based technique can achieve up to 21.20% top-1 and 35.68% top-5 accuracy on this benchmark.

Background: The positive predictive value (PPV) of large language model (LLM)-based proofreading for radiology reports is limited due to the low error prevalence. Purpose: To assess whether a three-pass LLM framework enhances PPV and reduces operational costs compared with baseline approaches. Materials and Methods: A retrospective analysis was performed on 1,000 consecutive radiology reports (250 each: radiography, ultrasonography, CT, MRI) from the MIMIC-III database. Two external datasets (CheXpert and Open-i) were validation sets. Three LLM frameworks were tested: (1) single-prompt detector; (2) extractor plus detector; and (3) extractor, detector, and false-positive verifier. Precision was measured by PPV and absolute true positive rate (aTPR). Efficiency was calculated from model inference charges and reviewer remuneration. Statistical significance was tested using cluster bootstrap, exact McNemar tests, and Holm-Bonferroni correction. Results: Framework PPV increased from 0.063 (95% CI, 0.036-0.101, Framework 1) to 0.079 (0.049-0.118, Framework 2), and significantly to 0.159 (0.090-0.252, Framework 3; P<.001 vs. baselines). aTPR remained stable (0.012-0.014; P>=.84). Operational costs per 1,000 reports dropped to USD 5.58 (Framework 3) from USD 9.72 (Framework 1) and USD 6.85 (Framework 2), reflecting reductions of 42.6% and 18.5%, respectively. Human-reviewed reports decreased from 192 to 88. External validation supported Framework 3's superior PPV (CheXpert 0.133, Open-i 0.105) and stable aTPR (0.007). Conclusion: A three-pass LLM framework significantly enhanced PPV and reduced operational costs, maintaining detection performance, providing an effective strategy for AI-assisted radiology report quality assurance.

This paper proposes one of the first clinical applications of multimodal large language models (LLMs) as an assistant for radiologists to check errors in their reports. We created an evaluation dataset from two real-world radiology datasets (MIMIC-CXR and IU-Xray), with 1,000 subsampled reports each. A subset of original reports was modified to contain synthetic errors by introducing various type of mistakes. The evaluation contained two difficulty levels: SIMPLE for binary error-checking and COMPLEX for identifying error types. LLaVA (Large Language and Visual Assistant) variant models, including our instruction-tuned model, were used for the evaluation. Additionally, a domain expert evaluation was conducted on a small test set. At the SIMPLE level, the LLaVA v1.5 model outperformed other publicly available models. Instruction tuning significantly enhanced performance by 47.4% and 25.4% on MIMIC-CXR and IU-Xray data, respectively. The model also surpassed the domain experts accuracy in the MIMIC-CXR dataset by 1.67%. Notably, among the subsets (N=21) of the test set where a clinician did not achieve the correct conclusion, the LLaVA ensemble mode correctly identified 71.4% of these cases. This study marks a promising step toward utilizing multi-modal LLMs to enhance diagnostic accuracy in radiology. The ensemble model demonstrated comparable performance to clinicians, even capturing errors overlooked by humans. Nevertheless, future work is needed to improve the model ability to identify the types of inconsistency.

The remarkable success of Large Language Models (LLMs) has illuminated a promising pathway toward achieving Artificial General Intelligence for both academic and industrial communities, owing to their unprecedented performance across various applications. As LLMs continue to gain prominence in both research and commercial domains, their security and safety implications have become a growing concern, not only for researchers and corporations but also for every nation. Currently, existing surveys on LLM safety primarily focus on specific stages of the LLM lifecycle, e.g., deployment phase or fine-tuning phase, lacking a comprehensive understanding of the entire "lifechain" of LLMs. To address this gap, this paper introduces, for the first time, the concept of "full-stack" safety to systematically consider safety issues throughout the entire process of LLM training, deployment, and eventual commercialization. Compared to the off-the-shelf LLM safety surveys, our work demonstrates several distinctive advantages: (I) Comprehensive Perspective. We define the complete LLM lifecycle as encompassing data preparation, pre-training, post-training, deployment and final commercialization. To our knowledge, this represents the first safety survey to encompass the entire lifecycle of LLMs. (II) Extensive Literature Support. Our research is grounded in an exhaustive review of over 800+ papers, ensuring comprehensive coverage and systematic organization of security issues within a more holistic understanding. (III) Unique Insights. Through systematic literature analysis, we have developed reliable roadmaps and perspectives for each chapter. Our work identifies promising research directions, including safety in data generation, alignment techniques, model editing, and LLM-based agent systems. These insights provide valuable guidance for researchers pursuing future work in this field.

High-quality, error-free datasets are a key ingredient in building reliable, accurate, and unbiased machine learning (ML) models. However, real world datasets often suffer from errors due to sensor malfunctions, data entry mistakes, or improper data integration across multiple sources that can severely degrade model performance. Detecting and correcting these issues typically require tailor-made solutions and demand extensive domain expertise. Consequently, automation is challenging, rendering the process labor-intensive and tedious. In this study, we investigate whether Large Language Models (LLMs) can help alleviate the burden of manual data cleaning. We set up an experiment in which an LLM, paired with Python, is tasked with cleaning the training dataset to improve the performance of a learning algorithm without having the ability to modify the training pipeline or perform any feature engineering. We run this experiment on multiple Kaggle datasets that have been intentionally corrupted with errors. Our results show that LLMs can identify and correct erroneous entries, such as illogical values or outlier, by leveraging contextual information from other features within the same row, as well as feedback from previous iterations. However, they struggle to detect more complex errors that require understanding data distribution across multiple rows, such as trends and biases.

An accurate differential diagnosis (DDx) is a cornerstone of medical care, often reached through an iterative process of interpretation that combines clinical history, physical examination, investigations and procedures. Interactive interfaces powered by Large Language Models (LLMs) present new opportunities to both assist and automate aspects of this process. In this study, we introduce an LLM optimized for diagnostic reasoning, and evaluate its ability to generate a DDx alone or as an aid to clinicians. 20 clinicians evaluated 302 challenging, real-world medical cases sourced from the New England Journal of Medicine (NEJM) case reports. Each case report was read by two clinicians, who were randomized to one of two assistive conditions: either assistance from search engines and standard medical resources, or LLM assistance in addition to these tools. All clinicians provided a baseline, unassisted DDx prior to using the respective assistive tools. Our LLM for DDx exhibited standalone performance that exceeded that of unassisted clinicians (top-10 accuracy 59.1% vs 33.6%, [p = 0.04]). Comparing the two assisted study arms, the DDx quality score was higher for clinicians assisted by our LLM (top-10 accuracy 51.7%) compared to clinicians without its assistance (36.1%) (McNemar's Test: 45.7, p < 0.01) and clinicians with search (44.4%) (4.75, p = 0.03). Further, clinicians assisted by our LLM arrived at more comprehensive differential lists than those without its assistance. Our study suggests that our LLM for DDx has potential to improve clinicians' diagnostic reasoning and accuracy in challenging cases, meriting further real-world evaluation for its ability to empower physicians and widen patients' access to specialist-level expertise.

Clinical decision-making in emergency medicine demands rapid, accurate diagnoses under uncertainty. Despite benchmark progress, evidence for LLMs as interactive aids in live physician workflows remains sparse. MedSyn lets physicians iteratively query an LLM provided with the full clinical record while initially viewing only the chief complaint. Seven physicians (three seniors, four residents) completed baseline and AI-assisted sessions across 52 MIMIC-IV cases stratified by difficulty. Blinded evaluation showed residents' Hard-case correctness rose from 0.589 to 0.734; difficulty-standardised completely-correct rates confirmed a medium effect (Δ = 0.092; p = 0.071; d = 0.47). Automated metrics corroborated these gains: standardised any-match accuracy improved by 0.156 (p < 0.0001), and residents showed the largest F1 gain (Δ = 0.138; p < 0.0001). Dialogue analysis revealed expertise-dependent strategies (seniors asked targeted, hypothesis-driven questions; residents relied on broader queries) and cross-expertise concordance increased (Δ = 0.145; p < 0.0001). Interactive LLM support meaningfully enhances diagnostic reasoning.

Large language models (LLMs) have been widely applied to assist test generation with the source code under test provided as the context. This paper aims to answer the question: If the source code under test is incorrect, will LLMs be misguided when generating tests? The effectiveness of test cases is measured by their accuracy, coverage, and bug detection effectiveness. Our evaluation results with five open- and six closed-source LLMs on four datasets demonstrate that incorrect code can significantly mislead LLMs in generating correct, high-coverage, and bug-revealing tests. For instance, in the HumanEval dataset, LLMs achieve 80.45% test accuracy when provided with task descriptions and correct code, but only 57.12% when given task descriptions and incorrect code. For the APPS dataset, prompts with correct code yield tests that detect 39.85% of the bugs, while prompts with incorrect code detect only 19.61%. These findings have important implications for the deployment of LLM-based testing: using it on mature code may help protect against future regression, but on early-stage immature code, it may simply bake in errors. Our findings also underscore the need for further research to improve LLMs resilience against incorrect code in generating reliable and bug-revealing tests.

The strong performance of large language models (LLMs) on natural language processing tasks raises extensive discussion on their application to code generation. Recent work suggests multiple sampling approaches to improve initial code generation accuracy or program repair approaches to refine the code. However, these methods suffer from LLMs' inefficiencies and limited reasoning capacity. In this work, we propose an LLM programming workflow (LPW) designed to improve both initial code generation and subsequent refinements within a structured two-phase workflow. Specifically, in the solution generation phase, the LLM first outlines a solution plan that decomposes the problem into manageable sub-problems and then verifies the generated solution plan through visible test cases. Subsequently, in the code implementation phase, the LLM initially drafts a code according to the solution plan and its verification. If the generated code fails the visible tests, the plan verification serves as the intended natural language solution to inform the refinement process for correcting bugs. We further introduce SLPW, a sampling variant of LPW, which initially generates multiple solution plans and plan verifications, produces a program for each plan and its verification, and refines each program as necessary until one successfully passes the visible tests. Compared to the state-of-the-art methods across various existing LLMs, our experimental results show that LPW significantly improves the Pass@1 accuracy by up to 16.4% on well-established text-to-code generation benchmarks, especially with a notable improvement of around 10% on challenging benchmarks. Additionally, SLPW demonstrates up to a 5.6% improvement over LPW and sets new state-of-the-art Pass@1 accuracy on various benchmarks, e.g., 98.2% on HumanEval, 84.8% on MBPP, 64.0% on APPS, and 35.3% on CodeContest, using GPT-4o as the backbone.

The field of efficient Large Language Model (LLM) inference is rapidly evolving, presenting a unique blend of opportunities and challenges. Although the field has expanded and is vibrant, there hasn't been a concise framework that analyzes the various methods of LLM Inference to provide a clear understanding of this domain. Our survey stands out from traditional literature reviews by not only summarizing the current state of research but also by introducing a framework based on roofline model for systematic analysis of LLM inference techniques. This framework identifies the bottlenecks when deploying LLMs on hardware devices and provides a clear understanding of practical problems, such as why LLMs are memory-bound, how much memory and computation they need, and how to choose the right hardware. We systematically collate the latest advancements in efficient LLM inference, covering crucial areas such as model compression (e.g., Knowledge Distillation and Quantization), algorithm improvements (e.g., Early Exit and Mixture-of-Expert), and both hardware and system-level enhancements. Our survey stands out by analyzing these methods with roofline model, helping us understand their impact on memory access and computation. This distinctive approach not only showcases the current research landscape but also delivers valuable insights for practical implementation, positioning our work as an indispensable resource for researchers new to the field as well as for those seeking to deepen their understanding of efficient LLM deployment. The analyze tool, LLM-Viewer, is open-sourced.

Machine translation is indispensable in healthcare for enabling the global dissemination of medical knowledge across languages. However, complex medical terminology poses unique challenges to achieving adequate translation quality and accuracy. This study introduces a novel "LLMs-in-the-loop" approach to develop supervised neural machine translation models optimized specifically for medical texts. While large language models (LLMs) have demonstrated powerful capabilities, this research shows that small, specialized models trained on high-quality in-domain (mostly synthetic) data can outperform even vastly larger LLMs. Custom parallel corpora in six languages were compiled from scientific articles, synthetically generated clinical documents, and medical texts. Our LLMs-in-the-loop methodology employs synthetic data generation, rigorous evaluation, and agent orchestration to enhance performance. We developed small medical translation models using the MarianMT base model. We introduce a new medical translation test dataset to standardize evaluation in this domain. Assessed using BLEU, METEOR, ROUGE, and BERT scores on this test set, our MarianMT-based models outperform Google Translate, DeepL, and GPT-4-Turbo. Results demonstrate that our LLMs-in-the-loop approach, combined with fine-tuning high-quality, domain-specific data, enables specialized models to outperform general-purpose and some larger systems. This research, part of a broader series on expert small models, paves the way for future healthcare-related AI developments, including deidentification and bio-medical entity extraction models. Our study underscores the potential of tailored neural translation models and the LLMs-in-the-loop methodology to advance the field through improved data generation, evaluation, agent, and modeling techniques.

Reliable evaluation of large language models in surgery remains underdeveloped. Broad medical benchmarks test clinical knowledge, while surgery requires procedural reasoning, management trade-offs, negation handling, and selection among plausible operative decisions. We present SurgiQ, a text-only, source-grounded benchmark of 13,055 four-option multiple-choice questions spanning six surgical domains and four question formats: case-based, reasoning, best-option, and negative. SurgiQ is constructed from surgical textbooks, open-access papers, and examination material using a multi-stage generation, verification, and expert-audit pipeline. We evaluate 35 open-weight LLMs under a unified log-likelihood protocol. Our results show substantial remaining headroom: smaller models often remain near the 25\% random baseline, while the best model reaches 68.1\% accuracy. General-purpose models, especially Qwen2.5, outperform most biomedical models, suggesting that current medical specialization does not yet provide sufficiently broad surgical coverage. Calibration and error analysis further show that even strong models make confident mistakes on clinically plausible distractors, motivating more reliable and broader surgical LLM evaluation.

Large language models (LLMs), such as ChatGPT, have received substantial attention due to their impressive human language understanding and generation capabilities. Therefore, the application of LLMs in medicine to assist physicians and patient care emerges as a promising research direction in both artificial intelligence and clinical medicine. To reflect this trend, this survey provides a comprehensive overview of the principles, applications, and challenges faced by LLMs in medicine. Specifically, we aim to address the following questions: 1) How can medical LLMs be built? 2) What are the downstream performances of medical LLMs? 3) How can medical LLMs be utilized in real-world clinical practice? 4) What challenges arise from the use of medical LLMs? and 5) How can we better construct and utilize medical LLMs? As a result, this survey aims to provide insights into the opportunities and challenges of LLMs in medicine and serve as a valuable resource for constructing practical and effective medical LLMs. A regularly updated list of practical guides on medical LLMs can be found at https://github.com/AI-in-Health/MedLLMsPracticalGuide.

Recent large language models (LLMs) such as ChatGPT and LLaMA have shown great promise in many AI applications. However, their performance on medical tasks is suboptimal and can be improved by training on extensive domain-specific datasets. This study introduces Me LLaMA, a medical LLM family that includes foundation models - Me LLaMA 13/70B, along with their chat-enhanced versions - Me LLaMA 13/70B-chat, developed through continual pre-training and instruction tuning of LLaMA2 using large medical datasets. Our domain-specific data suite for training and evaluation includes a large-scale, continual pre-training dataset with 129B tokens, an instruction tuning dataset with 214k samples, and a new medical evaluation benchmark (MIBE) across six tasks with 12 datasets. Our extensive evaluation using the MIBE shows that Me LLaMA models achieve overall better performance than existing open-source medical LLMs in zero-shot, few-shot and supervised learning abilities. Their zero-shot performance is comparable with ChatGPT across 7 out of 8 datasets, with a slight variance of within 3%, and yet falls short when compared to GPT-4. In addition, we investigated the catastrophic forgetting problem, and our results show that Me LLaMA models outperform other open-source medical LLMs in mitigating this issue. Me LLaMA is one of the largest open-source medical foundation LLMs that use both biomedical and clinical data. It exhibits superior performance across both general and medical tasks compared to other open-source medical LLMs, rendering it an attractive choice for medical AI applications. We release our models, datasets, and evaluation scripts at: https://github.com/BIDS-Xu-Lab/Me-LLaMA.

The integration of large language model (LLM) and data management (DATA) is rapidly redefining both domains. In this survey, we comprehensively review the bidirectional relationships. On the one hand, DATA4LLM, spanning large-scale data processing, storage, and serving, feeds LLMs with high quality, diversity, and timeliness of data required for stages like pre-training, post-training, retrieval-augmented generation, and agentic workflows: (i) Data processing for LLMs includes scalable acquisition, deduplication, filtering, selection, domain mixing, and synthetic augmentation; (ii) Data Storage for LLMs focuses on efficient data and model formats, distributed and heterogeneous storage hierarchies, KV-cache management, and fault-tolerant checkpointing; (iii) Data serving for LLMs tackles challenges in RAG (e.g., knowledge post-processing), LLM inference (e.g., prompt compression, data provenance), and training strategies (e.g., data packing and shuffling). On the other hand, in LLM4DATA, LLMs are emerging as general-purpose engines for data management. We review recent advances in (i) data manipulation, including automatic data cleaning, integration, discovery; (ii) data analysis, covering reasoning over structured, semi-structured, and unstructured data, and (iii) system optimization (e.g., configuration tuning, query rewriting, anomaly diagnosis), powered by LLM techniques like retrieval-augmented prompting, task-specialized fine-tuning, and multi-agent collaboration.

Accident, defect and outage investigations end with a decision that ordinary question answering never faces: whether the evidence gathered so far is enough to close the case. We study this decision for LLM investigators, which request evidence from a case file, revise their hypotheses, and either close the case with a conclusion grounded in what they read or leave it open and name what is missing. This judgment does not come with capability: an untrained 9B model overstates its evidence in 97% of its answers, and a frontier model that identifies the right cause in 84% of cases still overstates in 91% and closes 17 of the 41 cases whose official finding is "cause undetermined". Measuring it is also non-trivial: the source of a case largely predicts its label, and a rule that reads only the source reaches 83.0 balanced accuracy on our test cases. We therefore evaluate closure with three tests: closure accuracy, reported against this rule and within each source; evidence dependence, which removes the grounds of a conclusion and checks whether the model stops closing; and conclusion and gap quality, a judged checklist of what the model asserts and what it says is missing. We build Nautil, 731 audited cases from aviation, rail, maritime, chemical-safety and vehicle-defect reports and production server incidents, with teacher trajectories, an out-of-distribution test set and counterfactual evidence versions. Fine-tuning a 9B model on these trajectories makes its closures follow the evidence: removing the grounds lowers its closure rate by 26 points relative to a matched control, overstatement falls from 97% to 35%, and correct, non-overstated conclusions rise from 3% to 43%. Reinforcement learning that rewards only the closure decision then raises balanced accuracy from 69.2 to 83.3, on par with the teacher, and within-source accuracy from 60.4 to 74.1, at some cost in evidence dependence.

Platform-orchestrated agentic workflows have become a popular paradigm for developing LLM-based applications. However, their reliability remains a major challenge due to the uncertainty of LLM outputs, complex inter-node dependencies, and heterogeneous tool interactions. Existing agentic workflow optimization and agent enhancement methods primarily rely on trajectory-level feedback. Without explicitly identifying the underlying failure root causes, their resulting repair plans are often insufficiently targeted. We propose FlowFixer, a diagnosis-driven automated repair framework for agentic workflows. FlowFixer first transforms workflow executions into unified symbolic traces and performs symbolic inference to derive executable behavioral specifications that capture node correctness, temporal dependencies, and causal relationships. Based on specification verification, it conducts failure attribution and root cause analysis, and then generates targeted repair patches. To reduce verification costs, FlowFixer further employs a multi-dimensional pre-execution assessment to filter infeasible repairs before dynamic verification. We evaluate FlowFixer on workflow failures collected from three popular development platforms: Dify, Coze and n8n. Results show that FlowFixer achieves a repair success rate of 71.3%, outperforming state-of-the-art baselines by 11.9% to 27.6%. It also improves failure attribution accuracy by 4.8% to 33.1% and root cause analysis accuracy by 15.3% to 38.8%. This work offers a new perspective on reliable diagnosis and repair of agentic workflows through symbolic modeling and inference.

Large language model (LLM)-based software engineering agents are increasingly developed to resolve software issues by generating patches from issue reports and code repositories. Bug reproduction tests (BRTs) are an important building block for such agents and have been shown useful for patch validation. However, it remains unclear whether BRTs can also help the more central stage of patch generation. We first conduct a preliminary study and find that directly using advanced BRT generators to guide patch generation is not beneficial: fail-to-fail BRTs can mislead agents, while even fail-to-pass BRTs bring limited or negative gains. Our analysis reveals two reasons: fail-to-pass BRTs may cover only one manifestation of the reported issue, leading to partial patches, whereas fail-to-fail BRTs are unreliable as direct patch-generation targets. Motivated by these insights, we propose SWE-Doctor, a software issue resolution agent that guides patch generation with runtime diagnoses derived from multi-faceted BRT executions. SWE-Doctor first generates multi-faceted BRTs for different behavioral requirements stated in the issue, then executes and debugs these BRTs to construct runtime-grounded diagnosis records, and finally uses the diagnoses together with localization information inferred during BRT generation to guide patch generation and reduce partial patches. We evaluate SWE-Doctor on Python bug-fixing issues from the widely adopted SWE-bench Verified and SWE-bench Pro across five LLM backends. SWE-Doctor consistently outperforms existing agents across all 10 LLM-benchmark combinations, achieving average resolution rates of 75.7% on SWE-bench Verified and 59.4% on SWE-bench Pro. In particular, on the more challenging SWE-bench Pro, SWE-Doctor improves the average resolution rate by 8.0-8.9 percentage points over the baseline agents.

Large Language Models (LLMs) have exhibited significant proficiency in code debugging, especially in automatic program repair, which may substantially reduce the time consumption of developers and enhance their efficiency. Significant advancements in debugging datasets have been made to promote the development of code debugging. However, these datasets primarily focus on assessing the LLM's function-level code repair capabilities, neglecting the more complex and realistic repository-level scenarios, which leads to an incomplete understanding of the LLM's challenges in repository-level debugging. While several repository-level datasets have been proposed, they often suffer from limitations such as limited diversity of tasks, languages, and error types. To mitigate this challenge, this paper introduces RepoDebug, a multi-task and multi-language repository-level code debugging dataset with 22 subtypes of errors that supports 8 commonly used programming languages and 3 debugging tasks. Furthermore, we conduct evaluation experiments on 10 LLMs, where Claude 3.5 Sonnect, the best-performing model, still cannot perform well in repository-level debugging.

Open-source libraries and tools are widely reused, but compatibility maintenance is expensive. Once maintainers leave, useful repositories can stop working as runtimes and dependencies evolve. We study whether LLM agents can adapt old repositories to modern environments, a task we call compatibility rescue. Unlike bug repair, compatibility rescue starts from a repository that worked in its original environment but fails after ecosystem drift. RepoRescue gives agents only the repository and its failing modern environment; the agent must diagnose the failure, locate affected code, and produce a source-code rescue that restores the historical test suite. We build RepoRescue from 193 Python and 122 Java repositories, each verified to pass historically and fail after modernization. We evaluate five deployed agent systems on Python and three on Java. Beyond full-patch pass rate, we rerun patches after removing test-file edits to measure source-only repair, add a runtime-enforced regime that blocks test edits, and validate practical use for repositories whose suites pass after rescue. We find that Claude Code systems sometimes edit failing tests even when prompted not to; with runtime blocking, Kimi still rescues 41.5% of repositories. Systems are complementary: their union reaches 62.7%, exceeding the best single system by 10.9 points. Difficulty concentrates in cross-file coordination: on 14 repositories requiring coordinated whole-codebase changes, GPT-5.2 through Codex passes all 14, while every Claude Code system passes at most two. Finally, a passing suite is only an initial signal: among 34 unmaintained Python candidates whose suites pass after rescue, 22 work in realistic scenarios and 12 pass bug-hunt with patches that address the compatibility failure. RepoRescue benchmarks compatibility rescue with source-only auditing, runtime enforcement, practical validation, and reasoning labels.