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Aug 10

OpenBioRQ: Unsolved Biomedical Research Questions for Agents

A working citation looks like proof -- but the fact that a link resolves does not mean the cited paper supports the claim. I find that current agentic models rarely fabricate citations (over 99% resolve), yet roughly 15.9% link to the wrong paper. Existing benchmarks miss this failure mode: when a question has a fixed answer key, a model can reproduce the expected source from that key rather than independently verifying that the source supports the claim. I introduce \openbiorq{}, a retrieval-grounded agentic benchmark of 12{,}553 unsolved biomedical research questions across 12 domains that treats open questions as a faithfulness-and-abstention probe. To my knowledge, this is the first biomedical benchmark to combine an agentic setting -- where the model must issue multiple tool calls -- with unsolved questions that have no answer key. Openness is verified against real follow-up evidence rather than a model's parametric knowledge. Difficulty is empirical: I anchor it on questions that three open-weight reference models fail to answer, rather than on subjective hardness labels. On this hardest subset, held-out models from the same lineage as the difficulty anchors solve only ~17%, while three independent frontier agents (Gemini-3-Pro, Opus-4.7, GPT-5.5) span a wide 29-60% range. The benchmark is thus hard, non-saturating (the best agent still leaves ~33-40\% unsolved), and discriminating across capability tiers. Beyond difficulty, I observe agentic collapse on the hardest questions, where agents stop using their tools. For the most collapse-prone model, blocking tool access entirely barely changes its score -- so tools stop paying off exactly where they are needed most. A frozen per-question checklist raises inter-judge agreement from Spearman 0.35 to 0.82.

  • 1 authors
·
Jun 19 2

Claudini: Autoresearch Discovers State-of-the-Art Adversarial Attack Algorithms for LLMs

LLM agents like Claude Code can not only write code but also be used for autonomous AI research and engineering rank2026posttrainbench, novikov2025alphaevolve. We show that an autoresearch-style pipeline karpathy2026autoresearch powered by Claude Code discovers novel white-box adversarial attack algorithms that significantly outperform all existing (30+) methods in jailbreaking and prompt injection evaluations. Starting from existing attack implementations, such as GCG~zou2023universal, the agent iterates to produce new algorithms achieving up to 40\% attack success rate on CBRN queries against GPT-OSS-Safeguard-20B, compared to leq10\% for existing algorithms (fig:teaser, left). The discovered algorithms generalize: attacks optimized on surrogate models transfer directly to held-out models, achieving 100\% ASR against Meta-SecAlign-70B chen2025secalign versus 56\% for the best baseline (fig:teaser, middle). Extending the findings of~carlini2025autoadvexbench, our results are an early demonstration that incremental safety and security research can be automated using LLM agents. White-box adversarial red-teaming is particularly well-suited for this: existing methods provide strong starting points, and the optimization objective yields dense, quantitative feedback. We release all discovered attacks alongside baseline implementations and evaluation code at https://github.com/romovpa/claudini.

  • 6 authors
·
Mar 24

AdvancedMathBench: A Benchmark Suite for Advanced Mathematical Proof Generation and Verification

Large language models (LLMs) have achieved remarkable performance on high-school and olympiad-style mathematics, yet their capabilities on advanced mathematics remain poorly understood. Existing benchmarks, however, fall short in both scope and evaluation granularity: they provide limited disciplinary coverage and often rely on final-answer correctness or coarse judgments, leaving the validity of the reasoning process inadequately assessed. To bridge this gap, we introduce AdvancedMathBench, a benchmark suite designed to evaluate advanced mathematical reasoning capabilities. Its core proof-generation benchmark, ProverBench, contains 296 problems spanning undergraduate and doctoral qualifying-exam levels. To provide reliable evaluation of the proofs, we develop a dedicated automatic verification pipeline trained on large-scale expert annotations to produce both correctness verdicts and fine-grained assessments of proof errors, which exhibits strong agreement with human experts on held-out proof trajectories. We further introduce VerifierBench, consisting of 888 model-generated proof trajectories paired with expert ground truth, to evaluate whether models can correctly judge proof validity and provide sound verification rationales. Experiments show that AdvancedMathBench remains challenging for frontier models. On proof generation, the best-performing model, GPT-5.5-xhigh, achieves only 75.8 and 66.1 on the UGD and QE splits, respectively, indicating substantial room for improvement on advanced mathematical proof construction. On proof verification, the best model attains a Balanced F1 of only 65.1, and models generally exhibit low true negative rates, suggesting that critical error detection remains a major bottleneck.

Round-Trip Consistency: Bidirectional Diffusion Models Can Predict Their Own Rollout Errors

Autoregressive models accumulate error over long rollouts, yet at deployment there is no ground truth to measure it against. We train a single conditional latent diffusion model that steps a dynamical system forward or backward in time via a direction flag, and show that this bidirectionality supplies a measurement-free test-time error signal: rolling forward i steps and then backward i steps must return the model to its start, so the round-trip discrepancy C_i is a self-supervised proxy for the unobservable rollout error: no ensembles, no held-out data, no governing equations, for one extra rollout. We validate on compressible magnetohydrodynamics (MHD), an astrophysical turbulent radiative mixing layer, and natural face videos (CelebV-HQ). On held-out MHD trajectories, C_i ranks rollout error (Spearman 0.91-0.98 at fixed depth; 0.69 pm 0.16 within trajectories), and a simple calibrator fit on training rollouts predicts its magnitude to within 1.14times (68%) and 1.29times (95%) with near-nominal coverage - one nat beyond a depth-only predictor, transferring to all six decoded physical fields. The same signal flags the out-of-distribution Orszag-Tang vortex (AUROC 0.98; 1.0 by depth 10) exactly where sampling-dispersion baselines invert, and it cuts incurred error by 15% at 80% coverage - three times the depth-only baseline. Bidirectional training comes at negative cost, beating direction specialists in both directions, and the backward direction doubles as a fast inverse solver. On LE-PDE-UQ's turbulent Navier-Stokes benchmark, a single bidirectional model reaches accuracy within 1.3times of their ten-model ensemble at a tenth of the training cost, with the best training-free pixel-level calibration. Round-trip consistency turns reversibility into a practical trust signal for generative models.

  • 1 authors
·
Aug 1 2

Test-Time Compositional Generalization in Diffusion Models via Concept Discovery

Compositional generalization requires models to produce novel configurations from familiar parts. In diffusion models, prior compositional generation methods typically assume that the relevant concepts or conditioning signals are already available. We instead ask whether a pretrained diffusion model can discover query-specific concepts from the time-indexed scores it learns for the noisy marginals p_t(x_t) and compose them at test time. Given a single out-of-distribution query, our method performs gradient ascent on s_θ(x_t,t) approx nabla_{x_t}log p_t(x_t) at multiple noising timesteps to recover local density modes, maps these modes into clean-space Gaussians, greedily selects relevant prototypes with a submodular likelihood objective, and combines them into a product-of-experts (PoE) teacher model with an analytic score. This teacher model can be sampled directly through classifier-free guidance or used to generate a sample pool for training a new class embedding and low-rank adapter. On held-out composition benchmarks built from ColorMNIST and CelebA, both the analytic PoE sampler and the low-rank adapted model outperform query-only and nearest trained-class baselines. These results suggest that the time-indexed score geometry of the diffusion model contains reusable density-mode concepts that support test-time compositional generation without a predefined concept library.

  • 4 authors
·
May 7

Large Language Models and Synthetic Data for Monitoring Dataset Mentions in Research Papers

Tracking how data is mentioned and used in research papers provides critical insights for improving data discoverability, quality, and production. However, manually identifying and classifying dataset mentions across vast academic literature is resource-intensive and not scalable. This paper presents a machine learning framework that automates dataset mention detection across research domains by leveraging large language models (LLMs), synthetic data, and a two-stage fine-tuning process. We employ zero-shot extraction from research papers, an LLM-as-a-Judge for quality assessment, and a reasoning agent for refinement to generate a weakly supervised synthetic dataset. The Phi-3.5-mini instruct model is pre-fine-tuned on this dataset, followed by fine-tuning on a manually annotated subset. At inference, a ModernBERT-based classifier efficiently filters dataset mentions, reducing computational overhead while maintaining high recall. Evaluated on a held-out manually annotated sample, our fine-tuned model outperforms NuExtract-v1.5 and GLiNER-large-v2.1 in dataset extraction accuracy. Our results highlight how LLM-generated synthetic data can effectively address training data scarcity, improving generalization in low-resource settings. This framework offers a pathway toward scalable monitoring of dataset usage, enhancing transparency, and supporting researchers, funders, and policymakers in identifying data gaps and strengthening data accessibility for informed decision-making.

  • 3 authors
·
Feb 14, 2025

Program Synthesis with Large Language Models

This paper explores the limits of the current generation of large language models for program synthesis in general purpose programming languages. We evaluate a collection of such models (with between 244M and 137B parameters) on two new benchmarks, MBPP and MathQA-Python, in both the few-shot and fine-tuning regimes. Our benchmarks are designed to measure the ability of these models to synthesize short Python programs from natural language descriptions. The Mostly Basic Programming Problems (MBPP) dataset contains 974 programming tasks, designed to be solvable by entry-level programmers. The MathQA-Python dataset, a Python version of the MathQA benchmark, contains 23914 problems that evaluate the ability of the models to synthesize code from more complex text. On both datasets, we find that synthesis performance scales log-linearly with model size. Our largest models, even without finetuning on a code dataset, can synthesize solutions to 59.6 percent of the problems from MBPP using few-shot learning with a well-designed prompt. Fine-tuning on a held-out portion of the dataset improves performance by about 10 percentage points across most model sizes. On the MathQA-Python dataset, the largest fine-tuned model achieves 83.8 percent accuracy. Going further, we study the model's ability to engage in dialog about code, incorporating human feedback to improve its solutions. We find that natural language feedback from a human halves the error rate compared to the model's initial prediction. Additionally, we conduct an error analysis to shed light on where these models fall short and what types of programs are most difficult to generate. Finally, we explore the semantic grounding of these models by fine-tuning them to predict the results of program execution. We find that even our best models are generally unable to predict the output of a program given a specific input.

  • 11 authors
·
Aug 15, 2021

Pramana: Fine-Tuning Large Language Models for Epistemic Reasoning through Navya-Nyaya

Large language models produce fluent text but struggle with systematic reasoning, often hallucinating confident but unfounded claims. When Apple researchers added irrelevant context to mathematical problems, LLM performance degraded by 65% Apple Machine Learning Research, exposing brittle pattern-matching beneath apparent reasoning. This epistemic gap, the inability to ground claims in traceable evidence, limits AI reliability in domains requiring justification. We introduce Pramana, a novel approach that teaches LLMs explicit epistemological methodology by fine-tuning on Navya-Nyaya logic, a 2,500-year-old Indian reasoning framework. Unlike generic chain-of-thought prompting, Navya-Nyaya enforces structured 6-phase reasoning: SAMSHAYA (doubt analysis), PRAMANA (evidence source identification), PANCHA AVAYAVA (5-member syllogism with universal rules), TARKA (counterfactual verification), HETVABHASA (fallacy detection), and NIRNAYA (ascertainment distinguishing knowledge from hypothesis). This integration of logic and epistemology provides cognitive scaffolding absent from standard reasoning approaches. We fine-tune Llama 3.2-3B and DeepSeek-R1-Distill-Llama-8B on 55 Nyaya-structured logical problems (constraint satisfaction, Boolean SAT, multi-step deduction). Stage 1 achieves 100% semantic correctness on held-out evaluation despite only 40% strict format adherence revealing that models internalize reasoning content even when structural enforcement is imperfect. Ablation studies show format prompting and temperature critically affect performance, with optimal configurations differing by stage. We release all models, datasets, and training infrastructure on Hugging Face to enable further research on epistemic frameworks for AI reasoning.

  • 1 authors
·
Feb 13

Can Models Learn Skill Composition from Examples?

As large language models (LLMs) become increasingly advanced, their ability to exhibit compositional generalization -- the capacity to combine learned skills in novel ways not encountered during training -- has garnered significant attention. This type of generalization, particularly in scenarios beyond training data, is also of great interest in the study of AI safety and alignment. A recent study introduced the SKILL-MIX evaluation, where models are tasked with composing a short paragraph demonstrating the use of a specified k-tuple of language skills. While small models struggled with composing even with k=3, larger models like GPT-4 performed reasonably well with k=5 and 6. In this paper, we employ a setup akin to SKILL-MIX to evaluate the capacity of smaller models to learn compositional generalization from examples. Utilizing a diverse set of language skills -- including rhetorical, literary, reasoning, theory of mind, and common sense -- GPT-4 was used to generate text samples that exhibit random subsets of k skills. Subsequent fine-tuning of 7B and 13B parameter models on these combined skill texts, for increasing values of k, revealed the following findings: (1) Training on combinations of k=2 and 3 skills results in noticeable improvements in the ability to compose texts with k=4 and 5 skills, despite models never having seen such examples during training. (2) When skill categories are split into training and held-out groups, models significantly improve at composing texts with held-out skills during testing despite having only seen training skills during fine-tuning, illustrating the efficacy of the training approach even with previously unseen skills. This study also suggests that incorporating skill-rich (potentially synthetic) text into training can substantially enhance the compositional capabilities of models.

  • 5 authors
·
Sep 29, 2024 2

Foundational Autoraters: Taming Large Language Models for Better Automatic Evaluation

As large language models (LLMs) advance, it becomes more challenging to reliably evaluate their output due to the high costs of human evaluation. To make progress towards better LLM autoraters, we introduce FLAMe, a family of Foundational Large Autorater Models. FLAMe is trained on our large and diverse collection of 100+ quality assessment tasks comprising 5M+ human judgments, curated and standardized using publicly released human evaluations from previous research. FLAMe significantly improves generalization to a wide variety of held-out tasks, outperforming LLMs trained on proprietary data like GPT-4 and Claude-3 on many tasks. We show that FLAMe can also serve as a powerful starting point for further downstream fine-tuning, using reward modeling evaluation as a case study (FLAMe-RM). Notably, on RewardBench, our FLAMe-RM-24B model (with an accuracy of 87.8%) is the top-performing generative model trained exclusively on permissively licensed data, outperforming both GPT-4-0125 (85.9%) and GPT-4o (84.7%). Additionally, we explore a more computationally efficient approach using a novel tail-patch fine-tuning strategy to optimize our FLAMe multitask mixture for reward modeling evaluation (FLAMe-Opt-RM), offering competitive RewardBench performance while requiring approximately 25x less training datapoints. Overall, our FLAMe variants outperform all popular proprietary LLM-as-a-Judge models we consider across 8 out of 12 autorater evaluation benchmarks, encompassing 53 quality assessment tasks, including RewardBench and LLM-AggreFact. Finally, our analysis reveals that FLAMe is significantly less biased than these LLM-as-a-Judge models on the CoBBLEr autorater bias benchmark, while effectively identifying high-quality responses for code generation.

  • 6 authors
·
Jul 15, 2024 8

Scaling Laws for Robust Comparison of Open Foundation Language-Vision Models and Datasets

In studies of transferable learning, scaling laws are obtained for various important foundation models to predict their properties and performance at larger scales. We show here how scaling law derivation can also be used for model and dataset comparison, allowing to decide which procedure is to be preferred for pre-training. For the first time, full scaling laws based on dense measurements across a wide span of model and samples seen scales are derived for two important language-vision learning procedures, CLIP and MaMMUT, that use either contrastive only or contrastive and captioning text generative loss. Ensuring sufficient prediction accuracy for held out points, we use derived scaling laws to compare both models, obtaining evidence for MaMMUT's stronger improvement with scale and better sample efficiency than standard CLIP. To strengthen validity of the comparison, we show scaling laws for various downstream tasks, classification, retrieval, and segmentation, and for different open datasets, DataComp, DFN and Re-LAION, observing consistently the same trends. We show that comparison can also be performed when deriving scaling laws with a constant learning rate schedule, reducing compute cost. Accurate derivation of scaling laws provides thus means to perform model and dataset comparison across scale spans, avoiding misleading conclusions based on measurements from single reference scales only, paving the road for systematic comparison and improvement of open foundation models and datasets for their creation. We release all the pre-trained models with their intermediate checkpoints, including openMaMMUT-L/14, which achieves 80.3% zero-shot ImageNet-1k accuracy, trained on 12.8B samples from DataComp-1.4B. Code for reproducing experiments in the paper and raw experiments data can be found at https://github.com/LAION-AI/scaling-laws-for-comparison.

  • 7 authors
·
Jun 4, 2025 2

RetailSMV: Exocentric vs. Egocentric Adaptation of Foundation Video World Models in Retail

Foundation video diffusion models are increasingly viewed as world simulators for embodied agents, yet their pretraining on internet-scale generic video leaves them poorly aligned with real-world deployment domains. We study parameter-efficient adaptation of a pretrained foundation video world model to retail scenes: when synchronized egocentric and exocentric video of the same activity are available, which viewpoint of training data produces the strongest adapted model? We introduce RetailSMV (Retail Synchronized Multi-View), a corpus of 32,105 captioned retail clips from five supermarkets with synchronized ego/exo capture from the store-staff perspective (stocking, arranging, weighing, managing supply carts, scanning at checkout), rather than the customer-centric framing of prior retail video corpora, and train three matched Low-Rank Adaptation (LoRA) configurations of Cosmos3-Nano (egocentric-only, exocentric-only, combined) under identical hyperparameters. On a 200-clip held-out test set evaluated with seven complementary metrics under a strict paired statistical protocol, exocentric-only adaptation matches or exceeds combined adaptation on six of seven point estimates and is significantly better on LPIPS, PSNR, and DreamSim, despite training on only 15,985 exocentric clips (versus 32,105 for combined). A symmetric paired comparison further shows that adding exocentric data to egocentric-only training helps while adding egocentric data to exocentric-only training hurts. The absolute adaptation gap is largest at the shortest rollout time, identifying the near-horizon prediction window as the regime in which adaptation is most beneficial.

  • 5 authors
·
Jun 30

Leveraging Generic Foundation Models for Multimodal Surgical Data Analysis

We investigate how both the adaptation of a generic foundation model via transfer learning and the integration of complementary modalities from the operating room (OR) can support surgical data science. To this end, we use V-JEPA as the single-modality foundation of a multimodal model for minimally invasive surgery support. We analyze how the model's downstream performance can benefit (a) from finetuning on unlabeled surgical video data and (b) from providing additional time-resolved data streams from the OR in a multimodal setup. In an in-house dataset of liver surgery videos, we analyze the tasks of predicting hospital length of stay and postoperative complications. In videos of the public HeiCo dataset, we analyze the task of surgical phase recognition. As a baseline, we apply pretrained V-JEPA to all tasks. We then finetune it on unlabeled, held-out videos to investigate its change in performance after domain adaptation. Following the idea of modular decision support networks, we integrate additional data streams from the OR by training a separate encoder to form a shared representation space with V-JEPA's embeddings. Our experiments show that finetuning on domain-specific data increases model performance. On the in-house data, integrating additional time-resolved data likewise benefits the model. On the HeiCo data, accuracy of the pretrained video-only, single-modality baseline setup is on par with the top-performing submissions of the EndoVis2017 challenge, while finetuning on domain-specific data increases accuracy further. Our results thus demonstrate how surgical data science can leverage public, generic foundation models. Likewise, they indicate the potential of domain adaptation and of integrating suitable complementary data streams from the OR. To support further research, we release our code and model weights at https://github.com/DigitalSurgeryLab-Basel/ML-CDS-2025.

  • 5 authors
·
Sep 8, 2025

Self-supervision drives representational convergence in medical foundation models more than clinical supervision

Medical image encoders from different groups are increasingly treated as interchangeable, on the assumption that scale and clinical supervision concentrate their representations onto a shared structure. Whether this convergence is real, what produces it, and whether it is clinically usable are untested, and the similarity measures behind such claims are fragile. We present a controlled dissection across 18 image and 7 text encoders, all open-weight and run locally, spanning 7M to 27B parameters and five imaging modalities, including 650,982 chest radiographs from six datasets. To isolate cause, we train encoders that vary only the objective under fixed data, architecture, and scale, and reproduce the effect in a synthetic model. Convergence is modest but above a random floor, driven by the self-supervised objective, not clinical supervision: matched self-supervised encoders aligned most (40.4% on chest radiography), with label-supervised (21.1%) and image-text (3.3%) far lower, and did not grow with size (Spearman 0.302, p=0.223) or capability. It is within-modality, does not reach clinical language, and does not reproduce how radiologists judge case similarity. Yet a linear classifier transfers across encoders and to five held-out hospitals, retaining about 85% of within-encoder performance. Convergence in medical imaging is therefore set by the pretraining objective, not inherited from scale or clinical supervision. Interoperability is accordingly something to design for through that objective, and to validate where the shared geometry is weakest, across patient subgroups and against clinical judgment.

  • 7 authors
·
Jul 21

Alignment Whack-a-Mole : Finetuning Activates Verbatim Recall of Copyrighted Books in Large Language Models

Frontier LLM companies have repeatedly assured courts and regulators that their models do not store copies of training data. They further rely on safety alignment strategies via RLHF, system prompts, and output filters to block verbatim regurgitation of copyrighted works, and have cited the efficacy of these measures in their legal defenses against copyright infringement claims. We show that finetuning bypasses these protections: by training models to expand plot summaries into full text, a task naturally suited for commercial writing assistants, we cause GPT-4o, Gemini-2.5-Pro, and DeepSeek-V3.1 to reproduce up to 85-90% of held-out copyrighted books, with single verbatim spans exceeding 460 words, using only semantic descriptions as prompts and no actual book text. This extraction generalizes across authors: finetuning exclusively on Haruki Murakami's novels unlocks verbatim recall of copyrighted books from over 30 unrelated authors. The effect is not specific to any training author or corpus: random author pairs and public-domain finetuning data produce comparable extraction, while finetuning on synthetic text yields near-zero extraction, indicating that finetuning on individual authors' works reactivates latent memorization from pretraining. Three models from different providers memorize the same books in the same regions (r ge 0.90), pointing to an industry-wide vulnerability. Our findings offer compelling evidence that model weights store copies of copyrighted works and that the security failures that manifest after finetuning on individual authors' works undermine a key premise of recent fair use rulings, where courts have conditioned favorable outcomes on the adequacy of measures preventing reproduction of protected expression.

  • 4 authors
·
Mar 27

AI Sandbagging: Language Models can Strategically Underperform on Evaluations

Trustworthy capability evaluations are crucial for ensuring the safety of AI systems, and are becoming a key component of AI regulation. However, the developers of an AI system, or the AI system itself, may have incentives for evaluations to understate the AI's actual capability. These conflicting interests lead to the problem of sandbagging, which we define as strategic underperformance on an evaluation. In this paper we assess sandbagging capabilities in contemporary language models (LMs). We prompt frontier LMs, like GPT-4 and Claude 3 Opus, to selectively underperform on dangerous capability evaluations, while maintaining performance on general (harmless) capability evaluations. Moreover, we find that models can be fine-tuned, on a synthetic dataset, to hide specific capabilities unless given a password. This behaviour generalizes to high-quality, held-out benchmarks such as WMDP. In addition, we show that both frontier and smaller models can be prompted or password-locked to target specific scores on a capability evaluation. We have mediocre success in password-locking a model to mimic the answers a weaker model would give. Overall, our results suggest that capability evaluations are vulnerable to sandbagging. This vulnerability decreases the trustworthiness of evaluations, and thereby undermines important safety decisions regarding the development and deployment of advanced AI systems.

  • 5 authors
·
Feb 5, 2025

InstructBLIP: Towards General-purpose Vision-Language Models with Instruction Tuning

General-purpose language models that can solve various language-domain tasks have emerged driven by the pre-training and instruction-tuning pipeline. However, building general-purpose vision-language models is challenging due to the increased task discrepancy introduced by the additional visual input. Although vision-language pre-training has been widely studied, vision-language instruction tuning remains relatively less explored. In this paper, we conduct a systematic and comprehensive study on vision-language instruction tuning based on the pre-trained BLIP-2 models. We gather a wide variety of 26 publicly available datasets, transform them into instruction tuning format and categorize them into two clusters for held-in instruction tuning and held-out zero-shot evaluation. Additionally, we introduce instruction-aware visual feature extraction, a crucial method that enables the model to extract informative features tailored to the given instruction. The resulting InstructBLIP models achieve state-of-the-art zero-shot performance across all 13 held-out datasets, substantially outperforming BLIP-2 and the larger Flamingo. Our models also lead to state-of-the-art performance when finetuned on individual downstream tasks (e.g., 90.7% accuracy on ScienceQA IMG). Furthermore, we qualitatively demonstrate the advantages of InstructBLIP over concurrent multimodal models. All InstructBLIP models have been open-sourced at https://github.com/salesforce/LAVIS/tree/main/projects/instructblip.

  • 9 authors
·
May 10, 2023

TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

  • 16 authors
·
Mar 5, 2025

OpenMedReason: Scientific Reasoning Supervision for Medical Vision-Language Models

High-stakes clinical use of large vision-language models (LVLMs) requires reasoning that is grounded in visual evidence and clinical knowledge, not just correct final answers. We introduce OpenMedReason, a large-scale, open multimodal medical reasoning corpus comprising approximately 450K image-question-answer instances whose reasoning traces are primarily derived from curated biomedical, human-authored scientific articles. OpenMedReason provides high-fidelity supervision beyond synthetic chains of thought, covering diverse medical domain vision modalities such as radiological scans, microscopic images, visible light photographs, charts, and others. We complement it with OpenMedReason-Bench, a held-out benchmark that allows fine-grained evaluation of LVLMs along three complementary axes of capability, including perception, medical knowledge, and rationale, enabling diagnostic evaluation beyond final-answer accuracy. OpenMedReason is a rich training resource that exhibits its effectiveness in both supervised fine-tuning (SFT) and reinforcement-based alignment. Training with OpenMedReason yields a 20% average improvement in VQA accuracy over the base model and achieves performance within 4.2% of the strongest comparable-scale medical LVLMs. Fine-grained performance analysis confirms that the gains are not concentrated in any single axis: OpenMedReason improves perception, medical knowledge, and rationale jointly, and its reasoning traces are preferred over those of the base model in 86.1% of pairwise comparisons. We release the code and dataset at huggingface.co/datasets/neginb/OpenMedReason.

  • 9 authors
·
Jun 10

Pando: Do Interpretability Methods Work When Models Won't Explain Themselves?

Mechanistic interpretability is often motivated for alignment auditing, where a model's verbal explanations can be absent, incomplete, or misleading. Yet many evaluations do not control whether black-box prompting alone can recover the target behavior, so apparent gains from white-box tools may reflect elicitation rather than internal signal; we call this the elicitation confounder. We introduce Pando, a model-organism benchmark that breaks this confound via an explanation axis: models are trained to produce either faithful explanations of the true rule, no explanation, or confident but unfaithful explanations of a disjoint distractor rule. Across 720 finetuned models implementing hidden decision-tree rules, agents predict held-out model decisions from 10 labeled query-response pairs, optionally augmented with one interpretability tool output. When explanations are faithful, black-box elicitation matches or exceeds all white-box methods; when explanations are absent or misleading, gradient-based attribution improves accuracy by 3-5 percentage points, and relevance patching, RelP, gives the largest gains, while logit lens, sparse autoencoders, and circuit tracing provide no reliable benefit. Variance decomposition suggests gradients track decision computation, which fields causally drive the output, whereas other readouts are dominated by task representation, biases toward field identity and value. We release all models, code, and evaluation infrastructure.

  • 5 authors
·
Apr 12

Grading Handwritten Engineering Exams with Multimodal Large Language Models

Handwritten STEM exams capture open-ended reasoning and diagrams, but manual grading is slow and difficult to scale. We present an end-to-end workflow for grading scanned handwritten engineering quizzes with multimodal large language models (LLMs) that preserves the standard exam process (A4 paper, unconstrained student handwriting). The lecturer provides only a handwritten reference solution (100%) and a short set of grading rules; the reference is converted into a text-only summary that conditions grading without exposing the reference scan. Reliability is achieved through a multi-stage design with a format/presence check to prevent grading blank answers, an ensemble of independent graders, supervisor aggregation, and rigid templates with deterministic validation to produce auditable, machine-parseable reports. We evaluate the frozen pipeline in a clean-room protocol on a held-out real course quiz in Slovenian, including hand-drawn circuit schematics. With state-of-the-art backends (GPT-5.2 and Gemini-3 Pro), the full pipeline achieves approx8-point mean absolute difference to lecturer grades with low bias and an estimated manual-review trigger rate of approx17% at D_{max}=40. Ablations show that trivial prompting and removing the reference solution substantially degrade accuracy and introduce systematic over-grading, confirming that structured prompting and reference grounding are essential.

  • 4 authors
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Jan 2

Structured State Space Models for In-Context Reinforcement Learning

Structured state space sequence (S4) models have recently achieved state-of-the-art performance on long-range sequence modeling tasks. These models also have fast inference speeds and parallelisable training, making them potentially useful in many reinforcement learning settings. We propose a modification to a variant of S4 that enables us to initialise and reset the hidden state in parallel, allowing us to tackle reinforcement learning tasks. We show that our modified architecture runs asymptotically faster than Transformers in sequence length and performs better than RNN's on a simple memory-based task. We evaluate our modified architecture on a set of partially-observable environments and find that, in practice, our model outperforms RNN's while also running over five times faster. Then, by leveraging the model's ability to handle long-range sequences, we achieve strong performance on a challenging meta-learning task in which the agent is given a randomly-sampled continuous control environment, combined with a randomly-sampled linear projection of the environment's observations and actions. Furthermore, we show the resulting model can adapt to out-of-distribution held-out tasks. Overall, the results presented in this paper show that structured state space models are fast and performant for in-context reinforcement learning tasks. We provide code at https://github.com/luchris429/popjaxrl.

  • 7 authors
·
Mar 7, 2023

ECHO: Terminal Agents Learn World Models for Free

CLI agents are the closest thing language models have to an embodied setting: the model emits commands, the terminal executes them, and the returned stream -- stdout, errors, files, logs, and traces -- records the consequences. We argue that this stream is a supervision signal, but standard agent RL discards it: GRPO-style training updates action tokens with sparse outcome-level rewards while ignoring environment responses already in the rollout. Failed rollouts provide little policy-gradient signal despite containing rich evidence about how the environment responds. We introduce ECHO (Environment Cross-entropy Hybrid Objective), a hybrid objective that combines the standard policy-gradient loss on action tokens with an auxiliary loss that trains the policy to predict environment observation tokens resulting from its own actions. ECHO reuses the same forward pass as GRPO, requires no additional rollouts, and turns terminal feedback into dense supervision for all rollouts. ECHO doubles GRPO pass@1 on TerminalBench-2.0: Qwen3-8B improves from 2.70% to 5.17%, and Qwen3-14B from 5.17% to 10.79%. ECHO also produces policies that better predict terminal dynamics, even on trajectories they did not generate: across held-out rollouts, it sharply reduces environment-token cross-entropy while GRPO alone barely changes it. From base Qwen3-8B, ECHO matches expert-SFT-then-GRPO performance on held-out terminal tasks without expert demonstrations, and recovers roughly half of the expert-SFT initialization benefit on TerminalBench-2.0. In some settings, the environment prediction loss alone enables verifier-free self-improvement, allowing policies to improve on unseen OOD tasks by learning only from environment interactions. Together, these results suggest that environment observations are not merely context for future actions, but a dense, on-policy supervision signal already present in every rollout.

Small Foundation Models of Human Cognition and Behaviour

Large language models fine-tuned on human behavioural data have emerged as general-purpose cognitive proxies, but the scale this requires, and whether these models process task structure or exploit statistical shortcuts, remain open questions. We train fourteen models from 135M to 14B parameters across four architecture families on Psych-101, a dataset of 10.7 million trial-level choices from 160 experiments. In-distribution, scale barely matters. The models fall within a narrow band, as though against a ceiling, and 0.6B to 1B parameters suffice to match a 70B baseline on held-out participants. Out-of-distribution, that band opens into a markedly steeper scaling gradient, with larger models clearly advantaged in generalisation to novel task structure. To determine what information these models use, we run two diagnostics. We progressively strip four prompt channels -- task instructions, experimental stimuli, outcome feedback, and choice history -- across 27 experiments, and permute trial order. Masking the content of stimuli and feedback destroys 75.7% of learned information and pushes models below chance, demonstrating that choice history alone does not account for performance. Permutation reveals invariance on tasks with independent trials but sensitivity where trial order is determined by prior responses. Small cognitively fine-tuned models therefore show promise as noise ceiling estimators for psychological experiments, though their scope remains bounded by the paradigms seen in training.

  • 2 authors
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Aug 4

Fine-tuning Language Models for Factuality

The fluency and creativity of large pre-trained language models (LLMs) have led to their widespread use, sometimes even as a replacement for traditional search engines. Yet language models are prone to making convincing but factually inaccurate claims, often referred to as 'hallucinations.' These errors can inadvertently spread misinformation or harmfully perpetuate misconceptions. Further, manual fact-checking of model responses is a time-consuming process, making human factuality labels expensive to acquire. In this work, we fine-tune language models to be more factual, without human labeling and targeting more open-ended generation settings than past work. We leverage two key recent innovations in NLP to do so. First, several recent works have proposed methods for judging the factuality of open-ended text by measuring consistency with an external knowledge base or simply a large model's confidence scores. Second, the direct preference optimization algorithm enables straightforward fine-tuning of language models on objectives other than supervised imitation, using a preference ranking over possible model responses. We show that learning from automatically generated factuality preference rankings, generated either through existing retrieval systems or our novel retrieval-free approach, significantly improves the factuality (percent of generated claims that are correct) of Llama-2 on held-out topics compared with RLHF or decoding strategies targeted at factuality. At 7B scale, compared to Llama-2-chat, we observe 58% and 40% reduction in factual error rate when generating biographies and answering medical questions, respectively.

  • 5 authors
·
Nov 14, 2023 2

What do Language Models Learn and When? The Implicit Curriculum Hypothesis

Large language models (LLMs) can perform remarkably complex tasks, yet the fine-grained details of how these capabilities emerge during pretraining remain poorly understood. Scaling laws on validation loss tell us how much a model improves with additional compute, but not what skills it acquires in which order. To remedy this, we propose the Implicit Curriculum Hypothesis: pretraining follows a compositional and predictable curriculum across models and data mixtures. We test this by designing a suite of simple, composable tasks spanning retrieval, morphological transformations, coreference, logical reasoning, and mathematics. Using these tasks, we track emergence points across four model families spanning sizes from 410M-13B parameters. We find that emergence orderings of when models reach fixed accuracy thresholds are strikingly consistent (ρ= .81 across 45 model pairs), and that composite tasks most often emerge after their component tasks. Furthermore, we find that this structure is encoded in model representations: tasks with similar function vector representations also tend to follow similar trajectories in training. By using the space of representations derived from our task set, we can effectively predict the training trajectories of simple held-out compositional tasks throughout the course of pretraining (R^2 = .68-.84 across models) without previously evaluating them. Together, these results suggest that pretraining is more structured than loss curves reveal: skills emerge in a compositional order that is consistent across models and readable from their internals.

Cross-modal linkage risk in clinical vision-language models

Vision-language models (VLMs) trained on paired chest radiographs and radiology reports learn a shared embedding space that can preserve instance-level image-report correspondence. This poses a privacy risk in settings where radiographs and reports are deliberately kept separate after acquisition, such as image-only data sharing or access-controlled reports, because a de-identified image may be re-linked to its original narrative report through cosine similarity alone. We formalized this as image-to-report retrieval and used public paired cohorts, in which the true pairing is known by design, as ground-truth benchmarks to audit the risk rather than as the privacy scenario. Evaluating VLMs of increasing clinical specialization on 406,241 paired examples from 126,804 patients across MIMIC-CXR (43,793 held-out pairs) and external CheXpert Plus (29,296 pairs), we found that re-linkage rose systematically with specialization: the strongest VLM retrieved the correct report at 15 times chance at a candidate pool of N = 100, 50 times chance at N = 10,000, and well above chance at full-database scale. The signal persisted under pathology-matched hard negatives that removed disease-label shortcuts, indicating correspondence beyond broad diagnostic categories. To reduce it without retraining, we froze both encoders and applied differentially private optimization only to the projection heads defining the alignment layer (epsilon = 0.34, delta = 6x10-6). This reduced Recall@1 by 61.8% at N = 10,000 on MIMIC-CXR and transferred to CheXpert Plus without retraining, while image-side utility was largely preserved: macro AUROC for linear-probe classification across 14 labels shifted only from 79.63% to 79.43%. Targeted DP finetuning of the shared alignment layer can substantially reduce cross-modal re-linkage without materially degrading the image representations that make these models clinically useful.

  • 4 authors
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May 31

Language Models Without a Trainable Input Embedding Table: Learning from Fixed Minimal Binary Token Codes

Trainable input embedding tables are a standard component of modern language models. We ask whether they are actually necessary at the input interface. For a vocabulary of size V, exact token identity requires only K=lceil log_2 Vrceil bits. We replace the usual trainable Vtimes d_{model} input embedding matrix with fixed minimal binary token codes and a zero-parameter lift to model width. In our main setting, V=65{,}536, so K=16, and tokens are represented by fixed 16-dimensional binary codes tiled to d_{model}=1024. We also evaluate a fully table-free variant in which codes are generated from token IDs on the fly and randomly recoded by an invertible affine transform over F_2^K. Across matched 32-layer decoder-only models trained on approximately 17B tokens and evaluated over three independent training seeds, fixed minimal codes achieve comparable held-out validation perplexity to a standard learned-input baseline while removing 67.1M trainable input parameters. The fixed-code runs have a lower mean validation perplexity in our experiments, 2.36 versus 2.44, but the observed gap is within the measured seed-to-seed variation of 4.8\%; we therefore interpret the result as evidence that the trainable input table is not necessary, rather than as a statistically resolved superiority claim. The table-free affine-recoded variant remains close at 2.39 despite a slightly shorter training run. These results show that, in this regime, a trainable input embedding table is not necessary for useful language modeling. The output projection remains standard and trainable.

  • 1 authors
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May 9

From scratch to silver: Creating trustworthy training data for patent-SDG classification using Large Language Models

Classifying patents by their relevance to the UN Sustainable Development Goals (SDGs) is crucial for tracking how innovation addresses global challenges. However, the absence of a large, labeled dataset limits the use of supervised learning. Existing methods, such as keyword searches, transfer learning, and citation-based heuristics, lack scalability and generalizability. This paper frames patent-to-SDG classification as a weak supervision problem, using citations from patents to SDG-tagged scientific publications (NPL citations) as a noisy initial signal. To address its sparsity and noise, we develop a composite labeling function (LF) that uses large language models (LLMs) to extract structured concepts, namely functions, solutions, and applications, from patents and SDG papers based on a patent ontology. Cross-domain similarity scores are computed and combined using a rank-based retrieval approach. The LF is calibrated via a custom positive-only loss that aligns with known NPL-SDG links without penalizing discovery of new SDG associations. The result is a silver-standard, soft multi-label dataset mapping patents to SDGs, enabling the training of effective multi-label regression models. We validate our approach through two complementary strategies: (1) internal validation against held-out NPL-based labels, where our method outperforms several baselines including transformer-based models, and zero-shot LLM; and (2) external validation using network modularity in patent citation, co-inventor, and co-applicant graphs, where our labels reveal greater thematic, cognitive, and organizational coherence than traditional technological classifications. These results show that weak supervision and semantic alignment can enhance SDG classification at scale.

  • 2 authors
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Sep 11, 2025

DLLM-JEPA: Joint Embedding Predictive Architectures for Masked Diffusion Language Models

Joint Embedding Predictive Architectures (JEPAs) have reshaped self-supervised representation learning in vision. The recent LLM-JEPA ported JEPA to autoregressive language models but inherited two steep costs from the causal-attention substrate: it demands explicit multi-view data (e.g., text-code pairs), and it requires two gradient-carrying forward passes per step. We introduce DLLM-JEPA, which pairs JEPA with masked-diffusion language models to eliminate both costs at once. The bidirectional attention of diffusion models yields two semantically distinct views of the same input via different masking rates -- no explicit pairs needed -- and supports a single gradient-carrying forward pass, cutting training FLOPs by 33% relative to LLM-JEPA. DLLM-JEPA improves over diffusion-only fine-tuning in every (task, architecture) combination we evaluate: up to +18.7 pp on LLaDA-8B GSM8K and +11.4 pp on Dream-7B GSM8K, with consistent positive gains on Spider, NL-RX-SYNTH, and Django. Beyond accuracy, DLLM-JEPA exhibits a dual-win property: on LLaDA-8B with the Wide-t configuration, it simultaneously raises GSM8K accuracy (67.1 vs. 65.2, +1.8 pp), drives held-out Wikitext loss below the pre-trained base, and preserves MMLU accuracy at base level across three fine-tuning seeds -- whereas an L2-to-base parameter anchor matches baseline accuracy with no task gain. Layer-wise probing reveals the mechanism: a geometric-functional drift dissociation in which the fine-tuned backbone moves further from the pre-trained weights than the baseline yet forgets less on held-out Wikitext, with the amplification concentrated in middle transformer layers. The pattern appears on Dream-7B as well, indicating the phenomenon is not specific to a single backbone.

  • 1 authors
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May 23

Chain of Risk: Safety Failures in Large Reasoning Models and Mitigation via Adaptive Multi-Principle Steering

Large reasoning models (LRMs) increasingly expose chain-of-thought-like reasoning for transparency, verification, and deliberate problem solving. This creates a safety blind spot: harmful or policy-violating content may appear in reasoning traces even when final answers appear safe. We test whether final-answer safety is a sufficient proxy for the full reasoning-answer trajectory by scoring both stages under a unified twenty-principle safety rubric. Using prompts from seven public harmfulness and jailbreak sources, plus four out-of-distribution (OOD) sources, we evaluate 15 open-weight and API-based LRMs across 41K prompts per model. Reasoning traces consistently reveal additional safety risks beyond final answers, especially in high-severity stage-wise failures: leak cases, where unsafe reasoning precedes a safe-looking answer, and escape cases, where benign-looking reasoning precedes an unsafe final response. Principle-level analysis shows that risk concentrates in misinformation, legal compliance, discrimination, physical harm, and psychological harm. We further propose adaptive multi-principle steering, a white-box test-time mitigation that learns one unsafe-to-safe activation direction per safety principle and activates only directions whose current hidden state is closer to the unsafe than safe centroid. On three steerable open reasoning models, adaptive steering reduces unsafe counts in both reasoning traces and final answers on held-out and OOD benchmarks. DeepSeek-R1-Qwen-7B achieves a 40.8% average unsafe-count reduction while retaining 97.7% macro-averaged accuracy on BBH, GSM8K, and MMLU. These results suggest that LRM safety should be evaluated and mitigated over the full exposed reasoning-answer trajectory, not only at the final-answer stage.

  • 9 authors
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May 6

U-Mamba2: Scaling State Space Models for Dental Anatomy Segmentation in CBCT

Cone-Beam Computed Tomography (CBCT) is a widely used 3D imaging technique in dentistry, providing volumetric information about the anatomical structures of jaws and teeth. Accurate segmentation of these anatomies is critical for clinical applications such as diagnosis and surgical planning, but remains time-consuming and challenging. In this paper, we present U-Mamba2, a new neural network architecture designed for multi-anatomy CBCT segmentation in the context of the ToothFairy3 challenge. U-Mamba2 integrates the Mamba2 state space models into the U-Net architecture, enforcing stronger structural constraints for higher efficiency without compromising performance. In addition, we integrate interactive click prompts with cross-attention blocks, pre-train U-Mamba2 using self-supervised learning, and incorporate dental domain knowledge into the model design to address key challenges of dental anatomy segmentation in CBCT. Extensive experiments, including independent tests, demonstrate that U-Mamba2 is both effective and efficient, securing first place in both tasks of the Toothfairy3 challenge. In Task 1, U-Mamba2 achieved a mean Dice of 0.84, HD95 of 38.17 with the held-out test data, with an average inference time of 40.58s. In Task 2, U-Mamba2 achieved the mean Dice of 0.87 and HD95 of 2.15 with the held-out test data. The code is publicly available at https://github.com/zhiqin1998/UMamba2.

  • 4 authors
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Sep 15, 2025

Model soups: averaging weights of multiple fine-tuned models improves accuracy without increasing inference time

The conventional recipe for maximizing model accuracy is to (1) train multiple models with various hyperparameters and (2) pick the individual model which performs best on a held-out validation set, discarding the remainder. In this paper, we revisit the second step of this procedure in the context of fine-tuning large pre-trained models, where fine-tuned models often appear to lie in a single low error basin. We show that averaging the weights of multiple models fine-tuned with different hyperparameter configurations often improves accuracy and robustness. Unlike a conventional ensemble, we may average many models without incurring any additional inference or memory costs -- we call the results "model soups." When fine-tuning large pre-trained models such as CLIP, ALIGN, and a ViT-G pre-trained on JFT, our soup recipe provides significant improvements over the best model in a hyperparameter sweep on ImageNet. The resulting ViT-G model, which attains 90.94% top-1 accuracy on ImageNet, achieved a new state of the art. Furthermore, we show that the model soup approach extends to multiple image classification and natural language processing tasks, improves out-of-distribution performance, and improves zero-shot performance on new downstream tasks. Finally, we analytically relate the performance similarity of weight-averaging and logit-ensembling to flatness of the loss and confidence of the predictions, and validate this relation empirically. Code is available at https://github.com/mlfoundations/model-soups.

  • 11 authors
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Mar 10, 2022

Learning to Predict Future-Aligned Research Proposals with Language Models

Large language models (LLMs) are increasingly used to assist ideation in research, but evaluating the quality of LLM-generated research proposals remains difficult: novelty and soundness are hard to measure automatically, and large-scale human evaluation is costly. We propose a verifiable alternative by reframing proposal generation as a time-sliced scientific forecasting problem. Given a research question and inspiring papers available before a cutoff time, the model generates a structured proposal and is evaluated by whether it anticipates research directions that appear in papers published after the time. We operationalize this objective with the Future Alignment Score (FAS), computed via retrieval and LLM-based semantic scoring against a held-out future corpus. To train models, we build a time-consistent dataset of 17,771 papers from targets and their pre-cutoff citations, and synthesize reasoning traces that teach gap identification and inspiration borrowing. Across Llama-3.1 and Qwen2.5 models, future-aligned tuning improves future alignment over unaligned baselines (up to +10.6% overall FAS), and domain-expert human evaluation corroborates improved proposal quality. Finally, we demonstrate practical impact by implementing two model-generated proposals with a code agent, obtaining 4.17% accuracy gain on MATH from a new prompting strategy and consistent improvements for a novel model-merging method.

  • 7 authors
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Apr 5

Nature-Inspired Population-Based Evolution of Large Language Models

Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formally defines a newly emerging problem -- the population-based evolution of large language models (LLMs) -- and introduces a novel framework. Starting with a population of parent LLMs, our framework enables the population to evolve through four key operations: (i) crossover, merging the weights of different parents to create offspring LLMs, (ii) mutation, introducing small, random changes to model weights to foster diversity, (iii) selection, prioritizing high-performing models, and (iv) succession, transferring the learned experience from parent to offspring LLMs. With only 200 samples per new task, the LLM population evolves rapidly to adapt to the task at hand, without any gradients. Experiments on 12 datasets show that our framework consistently outperforms existing multi-LLM merging and adaptation methods, achieving accuracy gains of up to 54.8% over the best LLM in the initial population. Moreover, our framework allows for the evolution of LLMs across multiple new tasks simultaneously, scaling effectively with populations of up to 40 LLMs, and even zero-shot generalization to unseen held-out tasks. We have open-sourced the code on GitHub and released the weights of 10 parent LLMs, fine-tuned from gemma-2-2b-it, on HuggingFace$, enabling reproduction of our proposed framework using just a single 4090 GPU with 24GB memory, without any performance degradation.

  • 8 authors
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Mar 2, 2025

H2LooP Spark Preview: Continual Pretraining of Large Language Models for Low-Level Embedded Systems Code

Large language models (LLMs) demonstrate strong code generation abilities in general-purpose programming languages but remain limited in specialized domains such as low-level embedded systems programming. This domain involves hardware register manipulation, vendor-specific SDKs, real-time operating system APIs, and hardware abstraction layers that are underrepresented in standard pretraining corpora. We introduce H2LooP Spark Preview, a continual pretraining (CPT) pipeline that adapts the OLMo-3-7B-a fully open language model to the embedded systems domain using BF16 LoRA with rank-stabilized scaling on 8 NVIDIA H100 GPUs. Our training corpus is constructed from repository-datasheet pairs covering 100B tokens of raw embedded systems data across 117 manufacturers, processed using the hierarchical datasheet-to-code mapping approach proposed in SpecMap (Nipane et al., 2026). The resulting curated dataset split contains 23.5B tokens across 13 embedded domains. Continual pretraining with high-rank LoRA (r=512) yields substantial gains, reducing in-domain perplexity by 70.4% and held-out repository perplexity by 66.1%. On generative code completion benchmarks spanning 13 embedded domains, our 7B model outperforms Claude Opus 4.6 and Qwen3-Coder-30B on 8 categories in token accuracy, showing that targeted continual pretraining enables smaller open-weight models to rival frontier systems on specialized technical tasks. We release the production training checkpoint on Huggingface as an open-source artifact.

  • 5 authors
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Mar 12

Domain-specific optimization and diverse evaluation of self-supervised models for histopathology

Task-specific deep learning models in histopathology offer promising opportunities for improving diagnosis, clinical research, and precision medicine. However, development of such models is often limited by availability of high-quality data. Foundation models in histopathology that learn general representations across a wide range of tissue types, diagnoses, and magnifications offer the potential to reduce the data, compute, and technical expertise necessary to develop task-specific deep learning models with the required level of model performance. In this work, we describe the development and evaluation of foundation models for histopathology via self-supervised learning (SSL). We first establish a diverse set of benchmark tasks involving 17 unique tissue types and 12 unique cancer types and spanning different optimal magnifications and task types. Next, we use this benchmark to explore and evaluate histopathology-specific SSL methods followed by further evaluation on held out patch-level and weakly supervised tasks. We found that standard SSL methods thoughtfully applied to histopathology images are performant across our benchmark tasks and that domain-specific methodological improvements can further increase performance. Our findings reinforce the value of using domain-specific SSL methods in pathology, and establish a set of high quality foundation models to enable further research across diverse applications.

  • 16 authors
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Oct 19, 2023

Perception Test: A Diagnostic Benchmark for Multimodal Video Models

We propose a novel multimodal video benchmark - the Perception Test - to evaluate the perception and reasoning skills of pre-trained multimodal models (e.g. Flamingo, BEiT-3, or GPT-4). Compared to existing benchmarks that focus on computational tasks (e.g. classification, detection or tracking), the Perception Test focuses on skills (Memory, Abstraction, Physics, Semantics) and types of reasoning (descriptive, explanatory, predictive, counterfactual) across video, audio, and text modalities, to provide a comprehensive and efficient evaluation tool. The benchmark probes pre-trained models for their transfer capabilities, in a zero-shot / few-shot or limited finetuning regime. For these purposes, the Perception Test introduces 11.6k real-world videos, 23s average length, designed to show perceptually interesting situations, filmed by around 100 participants worldwide. The videos are densely annotated with six types of labels (multiple-choice and grounded video question-answers, object and point tracks, temporal action and sound segments), enabling both language and non-language evaluations. The fine-tuning and validation splits of the benchmark are publicly available (CC-BY license), in addition to a challenge server with a held-out test split. Human baseline results compared to state-of-the-art video QA models show a significant gap in performance (91.4% vs 43.6%), suggesting that there is significant room for improvement in multimodal video understanding. Dataset, baselines code, and challenge server are available at https://github.com/deepmind/perception_test

  • 24 authors
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May 23, 2023

Learning the Signature of Memorization in Autoregressive Language Models

All prior membership inference attacks for fine-tuned language models use hand-crafted heuristics (e.g., loss thresholding, Min-K\%, reference calibration), each bounded by the designer's intuition. We introduce the first transferable learned attack, enabled by the observation that fine-tuning any model on any corpus yields unlimited labeled data, since membership is known by construction. This removes the shadow model bottleneck and brings membership inference into the deep learning era: learning what matters rather than designing it, with generalization through training diversity and scale. We discover that fine-tuning language models produces an invariant signature of memorization detectable across architectural families and data domains. We train a membership inference classifier exclusively on transformer-based models. It transfers zero-shot to Mamba (state-space), RWKV-4 (linear attention), and RecurrentGemma (gated recurrence), achieving 0.963, 0.972, and 0.936 AUC respectively. Each evaluation combines an architecture and dataset never seen during training, yet all three exceed performance on held-out transformers (0.908 AUC). These four families share no computational mechanisms, their only commonality is gradient descent on cross-entropy loss. Even simple likelihood-based methods exhibit strong transfer, confirming the signature exists independently of the detection method. Our method, Learned Transfer MIA (LT-MIA), captures this signal most effectively by reframing membership inference as sequence classification over per-token distributional statistics. On transformers, LT-MIA achieves 2.8times higher TPR at 0.1\% FPR than the strongest baseline. The method also transfers to code (0.865 AUC) despite training only on natural language texts. Code and trained classifier available at https://github.com/JetBrains-Research/learned-mia.

  • 4 authors
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Apr 2

Layer-Targeted Multilingual Knowledge Erasure in Large Language Models

Recent work has demonstrated that machine unlearning in Large Language Models (LLMs) fails to generalize across languages: knowledge erased in one language frequently remains accessible through others. However, the underlying cause of this failure and a principled solution remain open. In this work, we identify intervention depth as the key factor determining multilingual generalization. Through systematic layer-wise experiments, we characterize two distinct failure modes: shallow-layer interventions achieve erasure but collapse multilingual capabilities in held-out languages, while deep-layer interventions preserve utility but fail to erase target knowledge even in source languages. These findings reveal that the choice of intervention layer is not a free parameter; it fundamentally determines whether multilingual unlearning succeeds. We propose MUTE (Multilingual Unlearning via Targeted Erasure), a framework that uses Centered Kernel Alignment (CKA) and Linguistic Regions Development Score (LRDS) to identify intermediate, language-agnostic layers where cross-lingual representations converge. By restricting unlearning updates to these layers, MUTE achieves robust multilingual knowledge erasure while optimizing on only a small set of source languages. Extensive experiments across three LLM architectures and three unlearning algorithms validate our approach, with mechanistic analysis via Logit Lens probing confirming genuine knowledge removal rather than output-level suppression.

  • 3 authors
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Feb 25

$μ$VLA: On Recurrent Memory for Partially Observable Manipulation in VLA Models

Vision-language-action (VLA) models predict chunks of future actions from the current observation, an assumption that fails under partial observability, where decisions depend on information no longer visible. Existing memory-augmented VLAs simultaneously introduce recurrence, retrieval, compression modules, auxiliary objectives, hierarchical memory, or task-specific architectural changes, so the contribution of recurrence itself remains entangled with surrounding machinery. We present a controlled isolation study of recurrence in a strong pretrained VLA backbone. Our formulation augments the transformer with a small set of learnable memory tokens carried across timesteps and updated through self-attention, trained end to end with truncated backpropagation through time, with no auxiliary losses and no architectural changes. We instantiate this as μVLA, a family of OpenVLA-OFT variants parameterized by memory width m, TBPTT length K, and the memory update rule (cross-step gradients or a detached EMA), so that recurrence is the only varying factor. On MIKASA-Robo, μVLA improves average success rate on five training tasks from 0.42 to 0.84 at the strongest setting and reaches 0.23 on held-out tasks with the same memory structure versus 0.07 for the memoryless baseline. On tasks requiring different memory structure, performance remains near baseline. On LIBERO, the strongest recurrent variant achieves 96.2% average success, indicating no regression under full observability. We interpret these results as a calibration of the capability envelope of minimal in-backbone recurrence, identifying the regime in which it is sufficient and the regime where additional memory structure is required. Demos and videos can be found in https://avanturist322.github.io/mu-vla/.

  • 9 authors
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Jun 9

Identifying and Mitigating the Influence of the Prior Distribution in Large Language Models

Large language models (LLMs) sometimes fail to respond appropriately to deterministic tasks -- such as counting or forming acronyms -- because the implicit prior distribution they have learned over sequences of tokens influences their responses. In this work, we show that, in at least some cases, LLMs actually compute the information needed to perform these tasks correctly, and we identify some interventions that can allow them to access this information to improve their performance. First, we show that simply prompting the language model to not rely on its prior knowledge leads to dramatic improvements in prior-dominated tasks. We then use mechanistic interpretability techniques to localize the prior within the LLM and manipulate the extent to which that prior influences its responses. Specifically, we show that it is possible to identify layers of the underlying neural network that correlate with the prior probability of a response and that lightweight finetuning of these layers with basic prompts on prior-dominated tasks achieves high performance on held-out answers. These results suggest that the information required to produce a correct response is contained within the representations of the problems formed by the models. Furthermore, we show that this finetuning is significantly more effective for prior-dominated tasks, and that the error after finetuning is no longer correlated with the prior. Our results suggest that it may be possible to define effective methods for manipulating the extent to which LLMs rely upon their priors in solving problems, potentially increasing their performance in settings where LLMs hallucinate for reasons related to the prior probability of token sequences.

  • 4 authors
·
Apr 16, 2025

Security Vulnerability Detection with Multitask Self-Instructed Fine-Tuning of Large Language Models

Software security vulnerabilities allow attackers to perform malicious activities to disrupt software operations. Recent Transformer-based language models have significantly advanced vulnerability detection, surpassing the capabilities of static analysis based deep learning models. However, language models trained solely on code tokens do not capture either the explanation of vulnerability type or the data flow structure information of code, both of which are crucial for vulnerability detection. We propose a novel technique that integrates a multitask sequence-to-sequence LLM with pro-gram control flow graphs encoded as a graph neural network to achieve sequence-to-classification vulnerability detection. We introduce MSIVD, multitask self-instructed fine-tuning for vulnerability detection, inspired by chain-of-thought prompting and LLM self-instruction. Our experiments demonstrate that MSIVD achieves superior performance, outperforming the highest LLM-based vulnerability detector baseline (LineVul), with a F1 score of 0.92 on the BigVul dataset, and 0.48 on the PreciseBugs dataset. By training LLMs and GNNs simultaneously using a combination of code and explanatory metrics of a vulnerable program, MSIVD represents a promising direction for advancing LLM-based vulnerability detection that generalizes to unseen data. Based on our findings, we further discuss the necessity for new labelled security vulnerability datasets, as recent LLMs have seen or memorized prior datasets' held-out evaluation data.

  • 5 authors
·
Jun 9, 2024

The Granularity Axis: A Micro-to-Macro Latent Direction for Social Roles in Language Models

Large language models (LLMs) are routinely prompted to take on social roles ranging from individuals to institutions, yet it remains unclear whether their internal representations encode the granularity of such roles, from micro-level individual experience to macro-level organizational, institutional, or national reasoning. We show that they do. We define a contrast-based Granularity Axis as the difference between mean macro- and micro-role hidden states. In Qwen3-8B, this axis aligns with the principal axis (PC1) of the role representation space at cosine 0.972 and accounts for 52.6% of its variance, indicating that granularity is the dominant geometric axis organizing prompted social roles. We construct 75 social roles across five granularity levels and collect 91,200 role-conditioned responses over shared questions and prompt variants, then extract role-level hidden states and project them onto the axis. Role projections increase monotonically across all five levels, remain stable across layers, prompt variants, endpoint definitions, held-out splits, and score-filtered subsets, and transfer to Llama-3.1-8B-Instruct. The axis is also causally relevant: activation steering along it shifts response granularity in the predicted direction, with Llama moving from 2.00 to 3.17 on a five-point macro scale under positive steering on prompts that admit local responses. The two models differ in controllability, suggesting that steering depends on each model's default operating regime. Overall, our findings suggest that social role granularity is not merely a stylistic surface feature, but a structured, ordered, and causally manipulable latent direction in role-conditioned language model behavior.

Prior-Aligned Data Cleaning for Tabular Foundation Models

Tabular Foundation Models (TFMs) achieve state-of-the-art zero-shot accuracy on small tabular datasets by meta-learning over synthetic data-generating processes -- making them highly attractive for practitioners who cannot afford large annotated corpora. However, their in-context learning mechanism assumes approximately clean inputs: missing values, outliers, and duplicates in the real-world data create a prior mismatch that degrades both accuracy and confidence calibration simultaneously. Correcting this mismatch requires sequential decisions over cleaning operators whose interactions no static preprocessing rule can anticipate -a natural fit for reinforcement learning~(RL). We introduce L2C2, the first deep RL framework framing tabular data cleaning as prior alignment: a learned policy sequences operators to minimize the distributional gap between dirty input and the TFM's synthetic prior. Six experiments on ten OpenML benchmark datasets establish: 1) three of seven reward designs collapse to degenerate trivial cleaning strategies -- principled reward engineering is scientifically non-trivial; 2) the novel TFMAwareReward reward we propose selects structurally distinct pipelines on 4/10 datasets and achieves higher TabPFN accuracy on those diverging cases (mean 0.851 vs. 0.843; Wilcoxon p=0.063, n=4) while never underperforming; 3) parameterized cleaning actions improve best-found pipeline reward on 9/10 datasets (Wilcoxon p=0.004); and 4) a policy pre-trained on one single source dataset exceeds scratch training at the 2,000-step fine-tuning checkpoint on all three held-out datasets (up to +28.8% after full fine-tuning) demonstrating cross-dataset transfer of prior-alignment knowledge. These findings establish that prior alignment is a principled data preparation strategy for TFM deployment on real-world tabular data.

  • 1 authors
·
Apr 27 2

Perfect Detection, Failed Control: The Geometry of Knowing vs. Steering in Language Models

A central aspiration of mechanistic interpretability is controllability: if we know where a behavior is represented in a model's activations, we should be able to modify it. This rests on a hidden premise -- that the direction which detects a behavior and the direction which controls it are the same, or close. We test this geometrically: what is the angle between the direction that best detects a behavior and the one that best causes it? If detection implies control the cosine is near 1; otherwise it quantifies a detection-intervention gap. On Gemma 2-2B-it, output format (clean JSON vs markdown fencing) collapses both roles onto one axis. Hallucination does not: the model detects fake entities with perfect linear separability (AUC = 1.000 from layer 5), yet that direction sits at cos = 0.12 (about 83 degrees) from the direction producing a refusal -- a small, reproducible alignment, far from the cos = 1 that "detection is control" would require. A detector built from activations, with no chosen tokens, likewise fails to align (cos = -0.06). The gap generalizes: across four models from three families and two scales (1B-9B), cos stays in [0.12, 0.20], identical before and after instruction tuning (0.1197 vs 0.1200), placing its origin in pretraining. A 15-degree rotation toward the refusal direction partially bridges it -- 73% and 60% refusal on two held-out fake-entity categories at 1.8% false positives. We then ask whether this cosine predicts steerability, and it does not: detection is a high-dimensional class, not a single direction, and what separates the steerable case is functional, not readable from a static angle. The cosine is a weight-computable signature of the dissociation between knowing and steering, not a predictor of it.

  • 5 authors
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Jun 22

iSight: Towards expert-AI co-assessment for improved immunohistochemistry staining interpretation

Immunohistochemistry (IHC) provides information on protein expression in tissue sections and is commonly used to support pathology diagnosis and disease triage. While AI models for H\&E-stained slides show promise, their applicability to IHC is limited due to domain-specific variations. Here we introduce HPA10M, a dataset that contains 10,495,672 IHC images from the Human Protein Atlas with comprehensive metadata included, and encompasses 45 normal tissue types and 20 major cancer types. Based on HPA10M, we trained iSight, a multi-task learning framework for automated IHC staining assessment. iSight combines visual features from whole-slide images with tissue metadata through a token-level attention mechanism, simultaneously predicting staining intensity, location, quantity, tissue type, and malignancy status. On held-out data, iSight achieved 85.5\% accuracy for location, 76.6\% for intensity, and 75.7\% for quantity, outperforming fine-tuned foundation models (PLIP, CONCH) by 2.5--10.2\%. In addition, iSight demonstrates well-calibrated predictions with expected calibration errors of 0.0150-0.0408. Furthermore, in a user study with eight pathologists evaluating 200 images from two datasets, iSight outperformed initial pathologist assessments on the held-out HPA dataset (79\% vs 68\% for location, 70\% vs 57\% for intensity, 68\% vs 52\% for quantity). Inter-pathologist agreement also improved after AI assistance in both held-out HPA (Cohen's κ increased from 0.63 to 0.70) and Stanford TMAD datasets (from 0.74 to 0.76), suggesting expert--AI co-assessment can improve IHC interpretation. This work establishes a foundation for AI systems that can improve IHC diagnostic accuracy and highlights the potential for integrating iSight into clinical workflows to enhance the consistency and reliability of IHC assessment.

  • 20 authors
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Feb 3

FUSE : A Ridge and Random Forest-Based Metric for Evaluating MT in Indigenous Languages

This paper presents the winning submission of the RaaVa team to the AmericasNLP 2025 Shared Task 3 on Automatic Evaluation Metrics for Machine Translation (MT) into Indigenous Languages of America, where our system ranked first overall based on average Pearson correlation with the human annotations. We introduce Feature-Union Scorer (FUSE) for Evaluation, FUSE integrates Ridge regression and Gradient Boosting to model translation quality. In addition to FUSE, we explore five alternative approaches leveraging different combinations of linguistic similarity features and learning paradigms. FUSE Score highlights the effectiveness of combining lexical, phonetic, semantic, and fuzzy token similarity with learning-based modeling to improve MT evaluation for morphologically rich and low-resource languages. MT into Indigenous languages poses unique challenges due to polysynthesis, complex morphology, and non-standardized orthography. Conventional automatic metrics such as BLEU, TER, and ChrF often fail to capture deeper aspects like semantic adequacy and fluency. Our proposed framework, formerly referred to as FUSE, incorporates multilingual sentence embeddings and phonological encodings to better align with human evaluation. We train supervised models on human-annotated development sets and evaluate held-out test data. Results show that FUSE consistently achieves higher Pearson and Spearman correlations with human judgments, offering a robust and linguistically informed solution for MT evaluation in low-resource settings.

  • 2 authors
·
Mar 28, 2025

Automatic Differential Diagnosis using Transformer-Based Multi-Label Sequence Classification

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

  • 3 authors
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Aug 28, 2024 1

Predictive Radiomics for Evaluation of Cancer Immune SignaturE in Glioblastoma: the PRECISE-GBM study

Background: Radiogenomics allows identification of radiological biomarkers for genomic phenotypes. In glioblastoma, these biomarkers could potentially complement patient stratification strategies. We aim to develop and analytically validate radiological biomarkers that capture immune cell signatures within IDH-wildtype glioblastoma microenvironment using radiogenomic analysis. Methods: This was a retrospective multicenter study using curated open-access anonymized imaging and genomic data from TCGA-GBM, CPTAC, IvyGAP, REMBRANDT and CGGA datasets. Imaging data consisted of MRI-based radiomic features extracted from necrotic core, enhancing and edema regions of deep learning-based auto-segmented tumors. Radiomic feature selections were performed using nested cross-validated LASSO. Support vector machine and ensemble models were trained using seventeen immune and cell-specific score labels extracted from deconvoluted transcriptomic data using pan-cancer and glioblastoma immune signature matrices as reference standards. Seventeen classifier models trained in three cross-cohort strategies were validated on three held-out datasets assessing stability and generalizability. Results: One-hundred-and-seventy-six patients were included in the study. The immune-related radiomic signatures obtained after feature selection were shape, first order and higher order radiomic features. Models predicting macrophage subtype immune signature showed stable mean performance on balanced accuracy (0.67) and precision (0.89) metrics for three independent holdout datasets with ensemble model outperforming support vector machine model. Conclusion: Radiogenomic models non-invasively predicted the macrophage subtype M0 immune signature in IDH-wildtype glioblastoma. These biomarkers have the potential to stratify patients for immunotherapy within prospective glioblastoma clinical trials.

  • 5 authors
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May 10

VISTA-PATH: An interactive foundation model for pathology image segmentation and quantitative analysis in computational pathology

Accurate semantic segmentation for histopathology image is crucial for quantitative tissue analysis and downstream clinical modeling. Recent segmentation foundation models have improved generalization through large-scale pretraining, yet remain poorly aligned with pathology because they treat segmentation as a static visual prediction task. Here we present VISTA-PATH, an interactive, class-aware pathology segmentation foundation model designed to resolve heterogeneous structures, incorporate expert feedback, and produce pixel-level segmentation that are directly meaningful for clinical interpretation. VISTA-PATH jointly conditions segmentation on visual context, semantic tissue descriptions, and optional expert-provided spatial prompts, enabling precise multi-class segmentation across heterogeneous pathology images. To support this paradigm, we curate VISTA-PATH Data, a large-scale pathology segmentation corpus comprising over 1.6 million image-mask-text triplets spanning 9 organs and 93 tissue classes. Across extensive held-out and external benchmarks, VISTA-PATH consistently outperforms existing segmentation foundation models. Importantly, VISTA-PATH supports dynamic human-in-the-loop refinement by propagating sparse, patch-level bounding-box annotation feedback into whole-slide segmentation. Finally, we show that the high-fidelity, class-aware segmentation produced by VISTA-PATH is a preferred model for computational pathology. It improve tissue microenvironment analysis through proposed Tumor Interaction Score (TIS), which exhibits strong and significant associations with patient survival. Together, these results establish VISTA-PATH as a foundation model that elevates pathology image segmentation from a static prediction to an interactive and clinically grounded representation for digital pathology. Source code and demo can be found at https://github.com/zhihuanglab/VISTA-PATH.

zhihuanglab Zhi Huang Lab
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Jan 23 3

AgentFairBench: Do LLM Agents Discriminate When They Act?

Large language model (LLM) agents increasingly take actions (screening applicants, recommending credit, triaging patients), yet fairness for LLMs is still measured by grading answers. We introduce AgentFairBench, a cheap, reproducible, multi-domain benchmark for demographic disparity in the actions of LLM agents. Grounded in a companion framework, the Bias Conduction Framework (BCF, restated here), it spans three regulator-anchored domains: hiring, lending, and medical triage. Synthetic, demographic-neutral profiles are evaluated in counterfactual matched sets that vary only a name-coded race x gender signal (in the Bertrand Mullainathan tradition), under four agent scaffolds of increasing agency (direct, chain-of-thought, multi-agent deliberation, tool-augmented). A NumPy-only harness computes counterfactual flip rate, mean absolute score difference (MASD), action-rate disparity, and tool-invocation disparity, with bootstrap confidence intervals, paired tests, and false-discovery-rate control, for single-digit dollars per model. A live leaderboard with a held-out private split and a contamination canary admits external models by submission. Our pilot (864 decisions plus a test-retest replication) carries a methodological lesson: comparing a six-group score spread against a two-run noise difference overstates disparity by ~ 2.4X through statistic arity alone. Against an arity matched noise floor and an omnibus group test, claude haiku 4 5 shows no demographic effect above sampling noise (0 of 120 pairwise and 0 of 9 omnibus contrasts survive correction); a planted-bias test confirms the instrument detects disparity when present. The contribution is a sound, sensitive, adoption-ready instrument, the arity matched null methodology, and open artifacts to scale it. Code, data, and harness are released under open licenses, with an anonymized review artifact.

  • 4 authors
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Jun 14

What Matters for Model Merging at Scale?

Model merging aims to combine multiple expert models into a more capable single model, offering benefits such as reduced storage and serving costs, improved generalization, and support for decentralized model development. Despite its promise, previous studies have primarily focused on merging a few small models. This leaves many unanswered questions about the effect of scaling model size and how it interplays with other key factors -- like the base model quality and number of expert models -- , to affect the merged model's performance. This work systematically evaluates the utility of model merging at scale, examining the impact of these different factors. We experiment with merging fully fine-tuned models using 4 popular merging methods -- Averaging, Task~Arithmetic, Dare, and TIES -- across model sizes ranging from 1B-64B parameters and merging up to 8 different expert models. We evaluate the merged models on both held-in tasks, i.e., the expert's training tasks, and zero-shot generalization to unseen held-out tasks. Our experiments provide several new insights about model merging at scale and the interplay between different factors. First, we find that merging is more effective when experts are created from strong base models, i.e., models with good zero-shot performance. Second, larger models facilitate easier merging. Third merging consistently improves generalization capabilities. Notably, when merging 8 large expert models, the merged models often generalize better compared to the multitask trained models. Fourth, we can better merge more expert models when working with larger models. Fifth, different merging methods behave very similarly at larger scales. Overall, our findings shed light on some interesting properties of model merging while also highlighting some limitations. We hope that this study will serve as a reference point on large-scale merging for upcoming research.

  • 7 authors
·
Oct 4, 2024 2

RLVR Datasets and Where to Find Them: Tracing Data Lineage for Better Training Data

The proliferation of Reinforcement Learning from Verifiable Rewards (RLVR) datasets has exacerbated provenance collapse due to unclear lineage among existing datasets. To bridge this fragmented RLVR data landscape, we propose Atomic-source Tracing via Lineage-Aware Search (ATLAS), a systematic framework for tracing RLVR datasets back to their atomic sources, attributing over 99.7% of 1.45M instances to 20 atomic sources. Our analysis reveals that most RLVR datasets are variants of a small set of shared upstream sources, with few introducing genuinely new data, and many facing data contamination risks. These findings naturally motivate us to curate a new RLVR dataset, DAPO++, and to benchmark existing datasets from a lineage-aware perspective. To this end, we propose Source-level Counterfactual Attribution (SCA) as a guiding principle to curate a decontaminated training dataset with concentrated learning signals. Essentially, SCA measures a sample's marginal utility by comparing per-atomic-source RL checkpoints against a shared base model. Building upon these attribution signals, we further design a composite dataset quality score Q that strongly correlates with downstream RLVR performance. Experiments on Qwen3 series models verify that DAPO++ consistently improves performance on held-out benchmarks, while Q reliably predicts downstream RLVR training effectiveness. Our code and data is available at https://github.com/Celine-hxy/ATLAS.

  • 8 authors
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May 25

ShapeGlot: Learning Language for Shape Differentiation

In this work we explore how fine-grained differences between the shapes of common objects are expressed in language, grounded on images and 3D models of the objects. We first build a large scale, carefully controlled dataset of human utterances that each refers to a 2D rendering of a 3D CAD model so as to distinguish it from a set of shape-wise similar alternatives. Using this dataset, we develop neural language understanding (listening) and production (speaking) models that vary in their grounding (pure 3D forms via point-clouds vs. rendered 2D images), the degree of pragmatic reasoning captured (e.g. speakers that reason about a listener or not), and the neural architecture (e.g. with or without attention). We find models that perform well with both synthetic and human partners, and with held out utterances and objects. We also find that these models are amenable to zero-shot transfer learning to novel object classes (e.g. transfer from training on chairs to testing on lamps), as well as to real-world images drawn from furniture catalogs. Lesion studies indicate that the neural listeners depend heavily on part-related words and associate these words correctly with visual parts of objects (without any explicit network training on object parts), and that transfer to novel classes is most successful when known part-words are available. This work illustrates a practical approach to language grounding, and provides a case study in the relationship between object shape and linguistic structure when it comes to object differentiation.

  • 5 authors
·
May 7, 2019

Spatiotemporal Pyramid Flow Matching for Climate Emulation

Generative models have the potential to transform the way we emulate Earth's changing climate. Previous generative approaches rely on weather-scale autoregression for climate emulation, but this is inherently slow for long climate horizons and has yet to demonstrate stable rollouts under nonstationary forcings. Here, we introduce Spatiotemporal Pyramid Flows (SPF), a new class of flow matching approaches that model data hierarchically across spatial and temporal scales. Inspired by cascaded video models, SPF partitions the generative trajectory into a spatiotemporal pyramid, progressively increasing spatial resolution to reduce computation and coupling each stage with an associated timescale to enable direct sampling at any temporal level in the pyramid. This design, together with conditioning each stage on prescribed physical forcings (e.g., greenhouse gases or aerosols), enables efficient, parallel climate emulation at multiple timescales. On ClimateBench, SPF outperforms strong flow matching baselines and pre-trained models at yearly and monthly timescales while offering fast sampling, especially at coarser temporal levels. To scale SPF, we curate ClimateSuite, the largest collection of Earth system simulations to date, comprising over 33,000 simulation-years across ten climate models and the first dataset to include simulations of climate interventions. We find that the scaled SPF model demonstrates good generalization to held-out scenarios across climate models. Together, SPF and ClimateSuite provide a foundation for accurate, efficient, probabilistic climate emulation across temporal scales and realistic future scenarios. Data and code is publicly available at https://github.com/stanfordmlgroup/spf .

  • 9 authors
·
Nov 30, 2025

Long-horizon Reasoning Agent for Olympiad-Level Mathematical Problem Solving

Large language models (LLMs) have achieved significant progress in solving complex reasoning tasks by Reinforcement Learning with Verifiable Rewards (RLVR). This advancement is also inseparable from the oversight automated by reliable verifiers. However, current outcome-based verifiers (OVs) are unable to inspect the unreliable intermediate steps in the long reasoning chains of thought (CoTs). Meanwhile, current process-based verifiers (PVs) have difficulties in reliably detecting errors in the complex long CoTs, limited by the scarcity of high-quality annotations due to the prohibitive costs of human annotations. Therefore, we propose the Outcome-based Process Verifier (OPV), which verifies the rationale process of summarized outcomes from long CoTs to achieve both accurate and efficient verification and enable large-scale annotation. To empower the proposed verifier, we adopt an iterative active learning framework with expert annotations to progressively improve the verification capability of OPV with fewer annotation costs. Specifically, in each iteration, the most uncertain cases of the current best OPV are annotated and then subsequently used to train a new OPV through Rejection Fine-Tuning (RFT) and RLVR for the next round. Extensive experiments demonstrate OPV's superior performance and broad applicability. It achieves new state-of-the-art results on our held-out \thisbench, outperforming much larger open-source models such as Qwen3-Max-Preview with an F1 score of 83.1 compared to 76.3. Furthermore, OPV effectively detects false positives within synthetic dataset, closely align with expert assessment. When collaborating with policy models, OPV consistently yields performance gains, e.g., raising the accuracy of DeepSeek-R1-Distill-Qwen-32B from 55.2\% to 73.3\% on AIME2025 as the compute budget scales.

ShanghaiAiLab shanghai ailab
·
Dec 11, 2025 4

OPV: Outcome-based Process Verifier for Efficient Long Chain-of-Thought Verification

Large language models (LLMs) have achieved significant progress in solving complex reasoning tasks by Reinforcement Learning with Verifiable Rewards (RLVR). This advancement is also inseparable from the oversight automated by reliable verifiers. However, current outcome-based verifiers (OVs) are unable to inspect the unreliable intermediate steps in the long reasoning chains of thought (CoTs). Meanwhile, current process-based verifiers (PVs) have difficulties in reliably detecting errors in the complex long CoTs, limited by the scarcity of high-quality annotations due to the prohibitive costs of human annotations. Therefore, we propose the Outcome-based Process Verifier (OPV), which verifies the rationale process of summarized outcomes from long CoTs to achieve both accurate and efficient verification and enable large-scale annotation. To empower the proposed verifier, we adopt an iterative active learning framework with expert annotations to progressively improve the verification capability of OPV with fewer annotation costs. Specifically, in each iteration, the most uncertain cases of the current best OPV are annotated and then subsequently used to train a new OPV through Rejection Fine-Tuning (RFT) and RLVR for the next round. Extensive experiments demonstrate OPV's superior performance and broad applicability. It achieves new state-of-the-art results on our held-out OPV-Bench, outperforming much larger open-source models such as Qwen3-Max-Preview with an F1 score of 83.1 compared to 76.3. Furthermore, OPV effectively detects false positives within synthetic dataset, closely align with expert assessment. When collaborating with policy models, OPV consistently yields performance gains, e.g., raising the accuracy of DeepSeek-R1-Distill-Qwen-32B from 55.2% to 73.3% on AIME2025 as the compute budget scales.

ShanghaiAiLab shanghai ailab
·
Dec 11, 2025 2

Endless Terminals: Scaling RL Environments for Terminal Agents

Environments are the bottleneck for self-improving agents. Current terminal benchmarks were built for evaluation, not training; reinforcement learning requires a scalable pipeline, not just a dataset. We introduce Endless Terminals, a fully autonomous pipeline that procedurally generates terminal-use tasks without human annotation. The pipeline has four stages: generating diverse task descriptions, building and validating containerized environments, producing completion tests, and filtering for solvability. From this pipeline we obtain 3255 tasks spanning file operations, log management, data processing, scripting, and database operations. We train agents using vanilla PPO with binary episode level rewards and a minimal interaction loop: no retrieval, multi-agent coordination, or specialized tools. Despite this simplicity, models trained on Endless Terminals show substantial gains: on our held-out dev set, Llama-3.2-3B improves from 4.0% to 18.2%, Qwen2.5-7B from 10.7% to 53.3%, and Qwen3-8B-openthinker-sft from 42.6% to 59.0%. These improvements transfer to human-curated benchmarks: models trained on Endless Terminals show substantial gains on held out human curated benchmarks: on TerminalBench 2.0, Llama-3.2-3B improves from 0.0% to 2.2%, Qwen2.5-7B from 2.2% to 3.4%, and Qwen3-8B-openthinker-sft from 1.1% to 6.7%, in each case outperforming alternative approaches including models with more complex agentic scaffolds. These results demonstrate that simple RL succeeds when environments scale.

Self-Harness: Harnesses That Improve Themselves

The performance of LLM-based agents is jointly shaped by their base models and the harnesses that mediate their interaction with the environment. Because different models exhibit distinct behaviors, effective harness design is inherently model-specific. Yet agent harnesses are still largely engineered by human experts, a paradigm that scales poorly as modern LLMs become increasingly diverse and rapidly evolving. In this paper, we introduce Self-Harness, a new paradigm in which an LLM-based agent improves its own operating harness, without relying on human engineers or stronger external agents. We operationalize Self-Harness as an iterative loop with three stages: Weakness Mining, which identifies model-specific failure patterns from execution traces; Harness Proposal, which generates diverse yet minimal harness modifications tied to these failures; and Proposal Validation, which accepts candidate edits only after regression testing. We instantiate Self-Harness on Terminal-Bench-2.0 using a minimal initial harness and three base models from diverse families: MiniMax M2.5, Qwen3.5-35B-A3B, and GLM-5. Across all three models, Self-Harness consistently improves performance, with held-out pass rates increasing from 40.5% to 61.9%, 23.8% to 38.1%, and 42.9% to 57.1%, respectively. Qualitative analyses further show that Self-Harness does not simply add generic instructions, but effectively turns model-specific weaknesses into concrete, executable harness changes. These results suggest a path toward LLM-based agents that are not merely shaped by their harnesses, but can also participate in reshaping them.

  • 8 authors
·
Jun 7 1

HydroAgent: Closing the Gap Between Frontier LLMs and Human Experts in Hydrologic Model Calibration via Simulator-Grounded RL

Calibrating distributed hydrologic models is a critical bottleneck across operational water resources management - streamflow prediction, reservoir operation, drought monitoring, infrastructure design, and flood forecasting all depend on it. Each basin demands an expert to translate hydrograph signatures into adjustments of a high-dimensional parameter vector, and the resulting workflow does not transfer between watersheds. We ask: can frontier large language model (LLM) agents replace the human hydrologic modeler, and if not, what would it take? We benchmark nine frontier LLM agents - Claude Opus 4.6/4.7, Sonnet 4.6, GPT-5/5.4/5.4-pro, and Gemini 2.5-pro/3.1-pro/3-flash - on the operational CREST distributed hydrologic model used by the U.S. National Weather Service for flash-flood forecasting. Best-of-twenty-rounds Nash-Sutcliffe Efficiency (NSE) across four held-out gauges spanning 329-40,792 km2 ranges from -0.16 (GPT-5.4) to 0.75 (Sonnet 4.6); the ceiling reproduces across all three vendors and capability tiers, with the strongest models concentrating in the 0.65-0.75 band, and no model reaches the human-expert reference except Opus-4.7 on one gauge. We argue this gap is not a parameter-count problem but a domain-grounding problem. We then propose HYDROAGENT, fine-tuning open-weight Qwen3-4B with supervised fine-tuning on 2,576 expert calibration trajectories and Group-Relative Policy Optimization using NSE as a verifiable reward from online CREST simulations - reinforcement learning with simulation feedback (RLSF). For Earth system science, a small domain-tuned policy with simulator-in-the-loop RL is a more compute-efficient and physically faithful path than scaling generic frontier models, and the multi-modal richness of Earth data - remote sensing, in-situ time series, and forecaster narrative - makes domain agents a leveraged direction for AI in physical science.

  • 7 authors
·
May 17

Glider: Global and Local Instruction-Driven Expert Router

The availability of performant pre-trained models has led to a proliferation of fine-tuned expert models that are specialized to particular domains. This has enabled the creation of powerful and adaptive routing-based "Model MoErging" methods with the goal of using expert modules to create an aggregate system with improved performance or generalization. However, existing MoErging methods often prioritize generalization to unseen tasks at the expense of performance on held-in tasks, which limits its practical applicability in real-world deployment scenarios. We observe that current token-level routing mechanisms neglect the global semantic context of the input task. This token-wise independence hinders effective expert selection for held-in tasks, as routing decisions fail to incorporate the semantic properties of the task. To address this, we propose, Global and Local Instruction Driven Expert Router (GLIDER) that integrates a multi-scale routing mechanism, encompassing a semantic global router and a learned local router. The global router leverages LLM's advanced reasoning capabilities for semantic-related contexts to enhance expert selection. Given the input query and LLM, the router generates semantic task instructions that guide the retrieval of the most relevant experts across all layers. This global guidance is complemented by a local router that facilitates token-level routing decisions within each module, enabling finer control and enhanced performance on unseen tasks. Our experiments using T5-based models for T0 and FLAN tasks demonstrate that GLIDER achieves substantially improved held-in performance while maintaining strong generalization on held-out tasks. We also perform ablations experiments to dive deeper into the components of GLIDER. Our experiments highlight the importance of our multi-scale routing that leverages LLM-driven semantic reasoning for MoErging methods.

  • 7 authors
·
Oct 9, 2024

MELD: Multi-Task Equilibrated Learning Detector for AI-Generated Text

Large language models are now embedded in everyday writing workflows, making reliable AI-generated text detection important for academic integrity, content moderation, and provenance tracking. In practice, however, a detector must do more than achieve high aggregate AUROC on clean, in-distribution human and AI text: it should remain robust to attacks and adversarial rewrites, transfer to unseen generators and domains, and operate at low false-positive rates (FPR). Most existing detectors optimize a single AI/Human objective, giving the representation little incentive to learn generator, attack, or domain structure once the binary task saturates. We introduce MELD (Multi-Task Equilibrated Learning Detector), a deployable detector for AI-generated text that enriches binary detection with auxiliary supervision. MELD attaches generator-family, attack-type, and source-domain heads to a shared encoder, and balances the four losses with learned homoscedastic uncertainty weights. To improve robustness, an EMA teacher predicts on clean inputs while an attack-augmented student is distilled toward the teacher. MELD further uses a hard-negative pairwise ranking loss to enlarge the score margin between AI-generated texts and the most confusable human texts. At inference, all auxiliary heads are discarded, giving MELD the same interface and cost as a standard detector. On the public RAID leaderboard, MELD is the strongest open-source detector and is competitive with leading commercial models, especially under attack and at low FPR. Across standard held-out benchmarks, MELD matches or outperforms supervised baselines. We further introduce MELD-eval, a held-out evaluation pool built from recent chat models released by four major LLM providers. Without additional finetuning, MELD achieves 99.9% TPR at 1% FPR on MELD-eval, while many baselines degrade sharply.

  • 3 authors
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May 6

Induction Signatures Are Not Enough: A Matched-Compute Study of Load-Bearing Structure in In-Context Learning

Mechanism-targeted synthetic data is increasingly proposed as a way to steer pretraining toward desirable capabilities, but it remains unclear how such interventions should be evaluated. We study this question for in-context learning (ICL) under matched compute (iso-FLOPs) using Bi-Induct, a lightweight data rewrite that interleaves short directional copy snippets into a natural pretraining stream: forward-copy (induction), backward-copy (anti-induction, as a directional control), or a balanced mix. Across 0.13B-1B decoder-only models, we evaluate (i) few-shot performance on standard LM benchmarks and function-style ICL probes, (ii) head-level copy telemetry, and (iii) held-out perplexity as a guardrail. Bi-Induct reliably increases induction-head activity, but this does not translate into consistent improvements in few-shot generalization: on standard LM benchmarks, Bi-Induct is largely performance-neutral relative to natural-only training, while on function-style probes the 1B natural-only model performs best. Despite explicit backward-copy cues, anti-induction scores remain near zero across scales, revealing a strong forward/backward asymmetry. Targeted ablations show a sharper distinction: removing the top 2% induction heads per layer harms ICL more than matched random ablations, with the largest relative drop occurring in the natural-only models. This indicates that natural-only training produces more centralized, load-bearing induction circuitry, whereas Bi-Induct tends to create more distributed and redundant induction activity. Our main conclusion is that eliciting a mechanism is not the same as making it load-bearing. For data-centric foundation model design, this suggests that synthetic data interventions should be evaluated not only by signature amplification, but by whether they create causally necessary computation while preserving natural-data modeling quality.

  • 2 authors
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Mar 13

AHD Agent: Agentic Reinforcement Learning for Automatic Heuristic Design

Automatic heuristic design (AHD) has emerged as a promising paradigm for solving NP-hard combinatorial optimization problems (COPs). Recent works show that large language models (LLMs), when integrated into well-designed frameworks (i.e., LLM-AHD), can autonomously discover high-performing heuristics. However, existing LLM-AHD frameworks typically treat LLMs as passive generators within fixed workflows, where the model generates heuristics from manually designed, limited context. Such context may fail to capture state-dependent information (e.g., specific failure modes), leading to inefficient trial-and-error exploration. To overcome these limitations, we propose AHD Agent, a novel tool-integrated, multi-turn framework that empowers LLMs to proactively decide whether to generate heuristics or invoke tools to retrieve targeted evidence from the solving environment. To effectively train such a dynamic decision-making agent, we introduce an agentic reinforcement learning (RL) system, which leverages a novel environment synthesis pipeline to optimize a compact model's generalizable AHD capabilities. Experiments across eight diverse domains, including four held-out tasks, demonstrate that our 4B-parameter agent matches or surpasses state-of-the-art baselines using much larger models, while requiring significantly fewer evaluations. Model and inference scaling analysis further reveals that AHD Agent offers an effective trajectory toward truly autonomous heuristic design.

  • 4 authors
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May 8

Can a Language Model Learn Facts Continually in Its Weights?

Continual learning promises a language model that keeps acquiring knowledge after training, with each new fact written into its weights. Whether weight writes can support accumulation remains undecided. We follow invented facts written into Qwen3 models from creation through sequences of twenty to one hundred later writes, using held-out questions of five types, with the original model given the fact in its prompt as the reference. Across these experiments, the breadth of the training data determines the kind of knowledge created. Bare-statement training produces recitation, while diverse restatements reduce the recitation-to-use gap from 27.4 to 5.4 points without showing the model a conclusion. This difference carries into later writes: after twenty sequential writes, bare-statement facts retain 1% accuracy while facts written from broad study data retain 46%. We also find that facts can be behaviourally forgotten without being erased. Forgotten facts keep most of the log-probability added by their write, and under bare-statement training 70% of wrong answers about them contain the most recently written fact. The same writes barely degrade the model's use of facts in context, and a forgotten study fact supplied in the prompt recovers to 77-80% on its questions. These results describe knowledge that is stored but question-keyed: later writes redirect the questions that reached it. Damage to unrelated abilities tracks KL divergence from the original model, and the later writes cause interference regardless of how the earlier fact was stored. Broad data can create usable knowledge, and a frozen reference can preserve capability, but no intervention we tested, including those built on accurate local measurements of each write, keeps earlier facts reachable. When facts must be composed or survive later writes, the reliable channel is context rather than the weights.

  • 1 authors
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Jul 13

Spectrum Tuning: Post-Training for Distributional Coverage and In-Context Steerability

Language model post-training has enhanced instruction-following and performance on many downstream tasks, but also comes with an often-overlooked cost on tasks with many possible valid answers. We characterize three desiderata for conditional distributional modeling: in-context steerability, valid output space coverage, and distributional alignment, and document across three model families how current post-training can reduce these properties. In particular, we disambiguate between two kinds of in-context learning: ICL for eliciting existing underlying knowledge or capabilities, and in-context steerability, where a model must use in-context information to override its priors and steer to a novel data generating distribution. To better evaluate and improve these desiderata, we introduce Spectrum Suite, a large-scale resource compiled from >40 data sources and spanning >90 tasks requiring models to steer to and match diverse distributions ranging from varied human preferences to numerical distributions and more. We find that while current post-training techniques help elicit underlying capabilities and knowledge, they hurt models' ability to flexibly steer in-context. To mitigate these issues, we propose Spectrum Tuning, a post-training method using Spectrum Suite to improve steerability and distributional coverage. We find that Spectrum Tuning often improves over pretrained models and their instruction-tuned counterparts, enhancing steerability, spanning more of the output space, and improving distributional alignment on held-out datasets.

  • 8 authors
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Oct 7, 2025

Evolution Fine-Tuning: Learning to Discover Across 371 Optimization Tasks

Would experience designing faster GPU kernels also help close in on a long-standing open mathematical conjecture? Large Language Models (LLMs) integrated into evolutionary search have recently produced state-of-the-art solutions on optimization tasks, including open mathematical conjectures, GPU kernel design, scientific law discovery, and combinatorial puzzles. To achieve this, prior work applied search scaffolds to one target task at a time, so every new problem is approached from scratch and the experience accumulated during search is discarded once the model finishes its attempt. This leaves the capability of iteratively evolving a solution (e.g., knowing which part to mutate and how, deciding when to backtrack) entirely in the scaffold rather than in the model itself. Whether the model itself could acquire this capability and reuse it across different tasks has been largely unexamined. To address this, we introduce Evolution Fine-Tuning (EFT), a mid-training paradigm that teaches LLMs to evolve solutions across tasks by converting evolutionary search trajectories into supervision. We construct Finch Collection, a 156K-trajectory dataset spanning 10 domains and 371 optimization tasks, and fine-tune open-source LLMs from 2B to 9B parameters. Empirically, EFT confers cross-task generalization: across 22 held-out tasks, our models surpass their base counterparts by 10.22% on average. Furthermore, when paired with test-time RL, our model matches state-of-the-art performance on two circle-packing tasks and outperforms its base-model counterpart on the Erdős minimum-overlap problem. EFT thus serves as a "practice phase" for general-purpose discovery agents that do not solve new problems from scratch.

minnesotanlp Minnesota NLP
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Jun 26 2

UnityMAS-O: A General RL Optimization Framework for LLM-Based Multi-Agent Systems

LLM-based multi-agent systems decompose complex tasks into interacting roles, but most remain manually orchestrated by prompts, tools, and control rules, while agents are rarely optimized through a unified reinforcement learning interface. Existing RL post-training frameworks mainly target single-policy optimization and lack abstractions for user-defined multi-agent workflows, structured interaction, role-specific credit assignment, and configurable parameter sharing. We present UnityMAS-O, a general RL optimization framework for LLM-based multi-agent systems. UnityMAS-O treats the complete workflow as the optimization unit, rather than a single response or policy trajectory. It represents workflows through four first-class objects: logical agent roles, graph trajectories, user-defined rewards, and agent--model mappings. This decouples logical agents from physical model parameters, supporting full sharing, full separation, and partial sharing, with rewards assigned at role, turn, and trajectory levels. UnityMAS-O extends verl with a Ray-based star-topology runtime. A central controller executes workflows, invokes tools, records structured trajectories, and assembles rewards; model-local worker groups handle rollout, buffering, advantage computation, and distributed PPO-style updates. Users can define agents, workflows, model mappings, and rewards without rewriting the optimization infrastructure. We instantiate UnityMAS-O on retrieval-augmented QA, iterative agentic search, and reflective code generation. Across Natural Questions, HotpotQA, and held-out code tasks, multi-agent RL improves manually specified workflows after optimization, with especially large gains for smaller models and strict code all-passed metrics. These results show that UnityMAS-O can serve as a reusable substrate for converting diverse LLM-based multi-agent workflows into trainable multi-agent RL systems.

  • 17 authors
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May 25

2DNMRGym: An Annotated Experimental Dataset for Atom-Level Molecular Representation Learning in 2D NMR via Surrogate Supervision

Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties. However, accurately interpreting 2D NMR data remains labor-intensive and error-prone, requiring highly trained domain experts, especially for complex molecules. Machine Learning (ML) holds significant potential in 2D NMR analysis by learning molecular representations and recognizing complex patterns from data. However, progress has been limited by the lack of large-scale and high-quality annotated datasets. In this work, we introduce 2DNMRGym, the first annotated experimental dataset designed for ML-based molecular representation learning in 2D NMR. It includes over 22,000 HSQC spectra, along with the corresponding molecular graphs and SMILES strings. Uniquely, 2DNMRGym adopts a surrogate supervision setup: models are trained using algorithm-generated annotations derived from a previously validated method and evaluated on a held-out set of human-annotated gold-standard labels. This enables rigorous assessment of a model's ability to generalize from imperfect supervision to expert-level interpretation. We provide benchmark results using a series of 2D and 3D GNN and GNN transformer models, establishing a strong foundation for future work. 2DNMRGym supports scalable model training and introduces a chemically meaningful benchmark for evaluating atom-level molecular representations in NMR-guided structural tasks. Our data and code is open-source and available on Huggingface and Github.

  • 3 authors
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May 16, 2025

GRAID: Enhancing Spatial Reasoning of VLMs Through High-Fidelity Data Generation

Vision Language Models (VLMs) achieve strong performance on many vision-language tasks but often struggle with spatial reasoningx2014a prerequisite for many applications. Empirically, we find that a dataset produced by a current training data generation pipeline has a 57.6% human validation rate. These rates stem from current limitations: single-image 3D reconstruction introduces cascading modeling errors and requires wide answer tolerances, while caption-based methods require hyper-detailed annotations and suffer from generative hallucinations. We present GRAID, built on the key insight that qualitative spatial relationships can be reliably determined from 2D geometric primitives alone. By operating exclusively on 2D bounding boxes from standard object detectors, GRAID avoids both 3D reconstruction errors and generative hallucinations, resulting in datasets that are of higher quality than existing tools that produce similar datasets as validated by human evaluations. We apply our framework to the BDD100k, NuImages, and Waymo datasets, generating over 8.5 million high-quality VQA pairs creating questions spanning spatial relations, counting, ranking, and size comparisons. We evaluate one of the datasets and find it achieves 91.16% human-validated accuracyx2014compared to 57.6% on a dataset generated by recent work. Critically, we demonstrate that when trained on GRAID data, models learn spatial reasoning concepts that generalize: models fine-tuned on 6 question types improve on over 10 held-out types, with accuracy gains of 47.5% on BDD and 37.9% on NuImages for Llama 3.2B 11B, and when trained on all questions types, achieve improvements on several existing benchmarks such as BLINK. The GRAID framework, datasets, and additional information can be found this https URL{here}.

  • 6 authors
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Oct 24, 2025