Daily Papers

Many tasks revolve around editing a document, whether code or text. We formulate the revision similarity problem to unify a wide range of machine learning evaluation problems whose goal is to assess a revision to an existing document. We observe that revisions usually change only a small portion of an existing document, so the existing document and its immediate revisions share a majority of their content. We formulate five adequacy criteria for revision similarity measures, designed to align them with human judgement. We show that popular pairwise measures, like BLEU, fail to meet these criteria, because their scores are dominated by the shared content. They report high similarity between two revisions when humans would assess them as quite different. This is a fundamental flaw we address. We propose a novel static measure, Excision Score (ES), which computes longest common subsequence (LCS) to remove content shared by an existing document with the ground truth and predicted revisions, before comparing only the remaining divergent regions. This is analogous to a surgeon creating a sterile field to focus on the work area. We use approximation to speed the standard cubic LCS computation to quadratic. In code-editing evaluation, where static measures are often used as a cheap proxy for passing tests, we demonstrate that ES surpasses existing measures. When aligned with test execution on HumanEvalFix, ES improves over its nearest competitor, SARI, by 12% Pearson correlation and by >21% over standard measures like BLEU. The key criterion is invariance to shared context; when we perturb HumanEvalFix with increased shared context, ES' improvement over SARI increases to 20% and >30% over standard measures. ES also handles other corner cases that other measures do not, such as correctly aligning moved code blocks, and appropriately rewarding matching insertions or deletions.

We address the problem of runtime trajectory anomaly detection, a critical capability for enabling trustworthy LLM agents. Current safety measures predominantly focus on static input/output filtering. However, we argue that ensuring LLM agents reliability requires auditing the intermediate execution process. In this work, we formulate the task of Trajectory Anomaly Detection. The goal is not merely detection, but precise error localization. This capability is essential for enabling efficient rollback-and-retry. To achieve this, we construct TrajBench, a dataset synthesized via a perturb-and-complete strategy to cover diverse procedural anomalies. Using this benchmark, we investigate the capability of models in process supervision. We observe that general-purpose LLMs, even with zero-shot prompting, struggle to identify and localize these anomalies. This reveals that generalized capabilities do not automatically translate to process reliability. To address this, we propose TrajAD, a specialized verifier trained with fine-grained process supervision. Our approach outperforms baselines, demonstrating that specialized supervision is essential for building trustworthy agents.

Developing robust artificial intelligence models for 4D (3D + time) medical imaging is constrained by limited annotated data, inter-device domain shifts, and privacy restrictions. To address this, we propose a 4D controllable generative framework for anatomically consistent data augmentation. A semi-supervised variational autoencoder learns a compact latent representation of anatomical volumes while jointly predicting aligned segmentation masks in a unified framework. Anatomical structure is then disentangled from temporal dynamics through a cascaded latent diffusion model (LDM). A static LDM generates subject-specific anatomy conditioned on clinical priors (diagnosis and volumes measures) and a subsequent motion LDM estimates residual latent motions, ensuring strict temporal coherence across the 4D sequence. The proposed approach was evaluated on cine cardiac MRI as a representative 4D imaging application. Experiments across multiple datasets demonstrate high controllability of static anatomy (Pearson r > 0.8) and strong temporal coherence (FVD = 288.08). In cross-vendor generalization experiments, augmenting training sets with synthetic 4D sequences significantly improves downstream segmentation performance. Using nnU-Net, the proposed augmentation strategy improves the average Dice score by 1.4% and reduces the Hausdorff Distance by 3.0mm compared to training on real data alone, for the left ventricle, Dice improves by 2.8% with a 5.4mm reduction in boundary error. Overall, this framework provides a scalable and controllable solution for 4D medical image synthesis, supporting the development of more robust models with limited annotations and cross-vendor variability. Code available on https://github.com/cyiheng/4DCardiacMRISynthesis.

Modern Large Language Models (LLMs) are often criticized for producing repetitive and homogeneous text, despite possessing vast latent vocabularies. While previous research has focused on model knowledge and training data, we investigate the role of decoding mechanics in suppressing linguistic diversity. We introduce the Word Coverage Score (WCS), a metric that quantifies the extent to which contextually appropriate human vocabulary is mathematically pruned by standard sampling filters (e.g., Top-p, Top-k, and Min-p). Rather than assessing static knowledge, the WCS measures the lexical survival rate of low-frequency, high-information human words as a function of sampling parameters. By auditing open-weight models on human-authored corpus fragments, we identify which logical lexical choices are rendered unreachable by the decoder, even when they reside within the probability space. Our results provide quantitative evidence that industry-standard sampling defaults act as unintended censorship mechanisms, smoothing the unique textures of human expression into a homogenized discourse. The WCS offers a rigorous framework for optimizing the trade-off between text coherence and lexical richness, providing a diagnostic tool for preserving the diversity of human language in generative models.

Recommender systems are essential components of modern online platforms which presents personalized content in various domain. The traditional collaborative filtering methods depends on static user-item interaction graphs and a limited subset of similarity measures which fail to capture the changing nature of preferences of an individual. Recent graph neural network (GNN) based approaches focus on user-item bipartite graphs which do not use explicit user-user relational modelling and dynamic graph evolution during training. To address these limitations, this paper proposes a Dynamic Graph SimilarityAware Attention Graph Neural Network (DG-SA-GNN) framework that integrates dynamic user similarity graph construction with multi-similarity propagation and attention-based aggregation. The proposed architecture constructs four parallel user similarity graphs using Cosine, Jaccard, Discounted Pearson Correlation Coefficient (Discount PCC), and IPIJ similarity functions, each processed by a dedicated UserGNN module. A Graph Transformer fuses the four graph views, and a CrossAttention module refines user embeddings through interaction with item embeddings. Crucially, the graphs are reconstructed at scheduled epochs during training, enabling the model to adapt to the learned embedding space constituting the dynamic graph component. Mini-batch training with hard negative sampling improves scalability and convergence. Experiments on the MovieLens100K benchmark demonstrate that DG-SA-GNN achieves a Recall@20 of 0.162 and NDCG@20 of 0.065 which is better than the LightGCN baseline in recall. The results validate that dynamic multi-similarity graph construction coupled with attention-based fusion which produce recommendation performance

While large language models have significantly accelerated scientific code generation, comprehensively evaluating the generated code remains a major challenge. Traditional benchmarks reduce evaluation to test-case matching, an approach insufficient for library code in HPC where solver selection, API conventions, memory management, and performance are just as critical as functional correctness. To address this gap, we introduce petscagent-bench, an agentic framework built on an agents-evaluating-agents paradigm. Instead of relying on static scripts, petscagent-bench deploys a tool-augmented evaluator agent that compiles, executes, and measures code produced by a separate model-under-test agent, orchestrating a 14-evaluator pipeline across five scoring categories: correctness, performance, code quality, algorithmic appropriateness, and library-specific conventions. Because the agents communicate through standardized protocols (A2A and MCP), the framework enables black-box evaluation of any coding agent without requiring access to its source code. We demonstrate the framework on a benchmark suite of realistic problems using the PETSc library for HPC. Our empirical analysis of frontier models reveals that while current models generate readable, well-structured code, they consistently struggle with library-specific conventions that traditional pass/fail metrics completely miss.

This work addresses minimum-weight design of undamped Euler-Bernoulli frame structures under subresonant single-frequency harmonic excitations, focusing on (robust) dynamic compliance and (robust) peak input power with ellipsoidal load uncertainty. We develop a semidefinite reformulation of robust dynamic compliance for subresonant single-frequency excitation and prove its equivalence to robust peak input power. We show that both these response measures admit an exact reformulation as a free-vibration eigenvalue constraint with design-independent mass augmentation, unifying static, dynamic, and modal requirements. Despite the nonconvex polynomial dependence on cross-sectional areas, certified bounds on global minimizers are obtained via the moment-sum-of-squares hierarchy of semidefinite relaxations. Benchmark studies on 10- and 35-segment frames corroborate the theory. For the 10-segment problem, we obtain the global optimum; for the 35-segment frame, we find high-quality locally-optimal designs that substantially improve on the best known one. We further fabricate and experimentally validate an additional design that closely matches the predictions of the model.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

While Large Language Models (LLMs) have achieved remarkable performance, they remain vulnerable to jailbreak. The integration of Large Language Models (LLMs) with external tools via protocols such as the Model Context Protocol (MCP) introduces critical security vulnerabilities, including prompt injection, data exfiltration, and other threats. To counter these challenges, we propose MCP-GUARD, a robust, layered defense architecture designed for LLM-tool interactions. MCP-GUARD employs a three-stage detection pipeline that balances efficiency with accuracy: it progresses from lightweight static scanning for overt threats and a deep neural detector for semantic attacks, to our fine-tuned E5-based model which achieves 96.01\% accuracy in identifying adversarial prompts. Finally, an LLM arbitrator synthesizes these signals to deliver the final decision. To enable rigorous training and evaluation, we introduce MCP-ATTACKBENCH, a comprehensive benchmark comprising 70,448 samples augmented by GPT-4. This benchmark simulates diverse real-world attack vectors that circumvent conventional defenses in the MCP paradigm, thereby laying a solid foundation for future research on securing LLM-tool ecosystems.

Remote Code Execution (RCE) exploits pose a significant threat to AI and ML systems, particularly in GPU-accelerated environments where the computational power of GPUs can be misused for malicious purposes. This paper focuses on RCE attacks leveraging deserialization vulnerabilities and custom layers, such as TensorFlow Lambda layers, which are often overlooked due to the complexity of monitoring GPU workloads. These vulnerabilities enable attackers to execute arbitrary code, blending malicious activity seamlessly into expected model behavior and exploiting GPUs for unauthorized tasks such as cryptocurrency mining. Unlike traditional CPU-based attacks, the parallel processing nature of GPUs and their high resource utilization make runtime detection exceptionally challenging. In this work, we provide a comprehensive examination of RCE exploits targeting GPUs, demonstrating an attack that utilizes these vulnerabilities to deploy a crypto miner on a GPU. We highlight the technical intricacies of such attacks, emphasize their potential for significant financial and computational costs, and propose strategies for mitigation. By shedding light on this underexplored attack vector, we aim to raise awareness and encourage the adoption of robust security measures in GPU-driven AI and ML systems, with an emphasis on static and model scanning as an easier way to detect exploits.

Large language models (LLMs) have empowered nodes within multi-agent networks with intelligence, showing growing applications in both academia and industry. However, how to prevent these networks from generating malicious information remains unexplored with previous research on single LLM's safety be challenging to transfer. In this paper, we focus on the safety of multi-agent networks from a topological perspective, investigating which topological properties contribute to safer networks. To this end, we propose a general framework, NetSafe along with an iterative RelCom interaction to unify existing diverse LLM-based agent frameworks, laying the foundation for generalized topological safety research. We identify several critical phenomena when multi-agent networks are exposed to attacks involving misinformation, bias, and harmful information, termed as Agent Hallucination and Aggregation Safety. Furthermore, we find that highly connected networks are more susceptible to the spread of adversarial attacks, with task performance in a Star Graph Topology decreasing by 29.7%. Besides, our proposed static metrics aligned more closely with real-world dynamic evaluations than traditional graph-theoretic metrics, indicating that networks with greater average distances from attackers exhibit enhanced safety. In conclusion, our work introduces a new topological perspective on the safety of LLM-based multi-agent networks and discovers several unreported phenomena, paving the way for future research to explore the safety of such networks.

We identify the task of measuring data to quantitatively characterize the composition of machine learning data and datasets. Similar to an object's height, width, and volume, data measurements quantify different attributes of data along common dimensions that support comparison. Several lines of research have proposed what we refer to as measurements, with differing terminology; we bring some of this work together, particularly in fields of computer vision and language, and build from it to motivate measuring data as a critical component of responsible AI development. Measuring data aids in systematically building and analyzing machine learning (ML) data towards specific goals and gaining better control of what modern ML systems will learn. We conclude with a discussion of the many avenues of future work, the limitations of data measurements, and how to leverage these measurement approaches in research and practice.

AI for scientific discovery is entering an agentic era, where protein-engineering systems are expected to prioritize future wet-lab experiments rather than merely fit static measurements. We introduce TadA-Bench, a million-variant wet-lab replay benchmark from 31 TadA directed-evolution rounds for future-round discovery toward agentic protein engineering. TadA-Bench preserves the campaign chronology and defines a fixed-data replay task: given earlier experimental rounds, models rank variants that appear only in later rounds. It provides aligned DNA, RNA, and protein views, and uses Seq2Graph, a graph-based label-unification pipeline, to reconcile noisy enrichment measurements into consistent cross-round activity labels. Random-split controls show strong interpolation, but future-round ranking and finite-budget candidate selection are much weaker. Controlled analyses suggest that evolutionary coverage is more informative than local data density, positioning TadA-Bench as a reproducible wet-lab replay substrate for future-round discovery toward agentic protein engineering; the data and code are released on Hugging Face and GitHub.

Static analysis is a cornerstone for software vulnerability detection, yet it often struggles with the classic precision-scalability trade-off. In practice, such tools often produce high false positive rates, particularly in large codebases like the Linux kernel. This imprecision can arise from simplified vulnerability modeling and over-approximation of path and data constraints. While large language models (LLMs) show promise in code understanding, their naive application to program analysis yields unreliable results due to inherent reasoning limitations. We introduce BugLens, a post-refinement framework that significantly improves static analysis precision. BugLens guides an LLM to follow traditional analysis steps by assessing buggy code patterns for security impact and validating the constraints associated with static warnings. Evaluated on real-world Linux kernel bugs, BugLens raises precision from 0.10 (raw) and 0.50 (semi-automated refinement) to 0.72, substantially reducing false positives and revealing four previously unreported vulnerabilities. Our results suggest that a structured LLM-based workflow can meaningfully enhance the effectiveness of static analysis tools.