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Jun 5

Reward Modeling for Scientific Writing Evaluation

Scientific writing is an expert-domain task that demands deep domain knowledge, task-specific requirements and reasoning capabilities that leverage the domain knowledge to satisfy the task specifications. While scientific text generation has been widely studied, its evaluation remains a challenging and open problem. It is critical to develop models that can be reliably deployed for evaluating diverse open-ended scientific writing tasks while adhering to their distinct requirements. However, existing LLM-based judges and reward models are primarily optimized for general-purpose benchmarks with fixed scoring rubrics and evaluation criteria. Consequently, they often fail to reason over sparse knowledge of scientific domains when interpreting task-dependent and multi-faceted criteria. Moreover, fine-tuning for each individual task is costly and impractical for low-resource settings. To bridge these gaps, we propose cost-efficient, open-source reward models tailored for scientific writing evaluation. We introduce a two-stage training framework that initially optimizes scientific evaluation preferences and then refines reasoning capabilities. Our multi-aspect evaluation design and joint training across diverse tasks enable fine-grained assessment and robustness to dynamic criteria and scoring rubrics. Experimental analysis shows that our training regime strongly improves LLM-based scientific writing evaluation. Our models generalize effectively across tasks and to previously unseen scientific writing evaluation settings, allowing a single trained evaluator to be reused without task-specific retraining.

  • 3 authors
·
Jan 15

LLM-Based Evaluation of Low-Resource Machine Translation: A Reference-less Dialect Guided Approach with a Refined Sylheti-English Benchmark

Evaluating machine translation (MT) for low-resource languages poses a persistent challenge, primarily due to the limited availability of high quality reference translations. This issue is further exacerbated in languages with multiple dialects, where linguistic diversity and data scarcity hinder robust evaluation. Large Language Models (LLMs) present a promising solution through reference-free evaluation techniques; however, their effectiveness diminishes in the absence of dialect-specific context and tailored guidance. In this work, we propose a comprehensive framework that enhances LLM-based MT evaluation using a dialect guided approach. We extend the ONUBAD dataset by incorporating Sylheti-English sentence pairs, corresponding machine translations, and Direct Assessment (DA) scores annotated by native speakers. To address the vocabulary gap, we augment the tokenizer vocabulary with dialect-specific terms. We further introduce a regression head to enable scalar score prediction and design a dialect-guided (DG) prompting strategy. Our evaluation across multiple LLMs shows that the proposed pipeline consistently outperforms existing methods, achieving the highest gain of +0.1083 in Spearman correlation, along with improvements across other evaluation settings. The dataset and the code are available at https://github.com/180041123-Atiq/MTEonLowResourceLanguage.

  • 3 authors
·
May 18, 2025

LIBERO-PRO: Towards Robust and Fair Evaluation of Vision-Language-Action Models Beyond Memorization

LIBERO has emerged as a widely adopted benchmark for evaluating Vision-Language-Action (VLA) models; however, its current training and evaluation settings are problematic, often leading to inflated performance estimates and preventing fair model comparison. To address these issues, we introduce LIBERO-PRO, an extended LIBERO benchmark that systematically evaluates model performance under reasonable perturbations across four dimensions: manipulated objects, initial states, task instructions, and environments. Experimental results reveal that, although existing models achieve over 90% accuracy under the standard LIBERO evaluation, their performance collapses to 0.0% under our generalized setting. Crucially, this discrepancy exposes the models' reliance on rote memorization of action sequences and environment layouts from the training set, rather than genuine task understanding or environmental perception. For instance, models persist in executing grasping actions when the target object is replaced with irrelevant items, and their outputs remain unchanged even when given corrupted instructions or even messy tokens. These findings expose the severe flaws in current evaluation practices, and we call on the community to abandon misleading methodologies in favor of robust assessments of model generalization and comprehension. Our code is available at: https://github.com/Zxy-MLlab/LIBERO-PRO.

  • 8 authors
·
Oct 4, 2025

BIRD-INTERACT: Re-imagining Text-to-SQL Evaluation for Large Language Models via Lens of Dynamic Interactions

Large language models (LLMs) have demonstrated remarkable performance on single-turn text-to-SQL tasks, but real-world database applications predominantly require multi-turn interactions to handle ambiguous queries, execution errors, and evolving user requirements. Existing multi-turn benchmarks fall short by treating conversation histories as static context or limiting evaluation to read-only operations, failing to reflect production-grade database assistant challenges. We introduce BIRD-INTERACT, a benchmark that restores this realism through: (1) a comprehensive interaction environment coupling each database with a hierarchical knowledge base, metadata files, and a function-driven user simulator, enabling models to solicit clarifications, retrieve knowledge, and recover from errors without human supervision; (2) two evaluation settings consisting of a pre-defined conversational protocol (c-Interact) and an open-ended agentic setting (a-Interact) where models autonomously decide when to query the user simulator or explore the environment; (3) a challenging task suite covering the full CRUD spectrum for business-intelligence and operational use cases, guarded by executable test cases. Each task features ambiguous and follow-up sub-tasks requiring dynamic interaction. The suite comprises BIRD-INTERACT-FULL (600 tasks, up to 11,796 interactions) for comprehensive performance assessment, and BIRD-INTERACT-LITE (300 tasks with simplified databases) for detailed behavioral analysis and rapid method development. Our empirical results highlight BIRD-INTERACT's difficulty: GPT-5 completes only 8.67% of tasks in c-Interact and 17.00% in a-Interact. Analysis via memory grafting and Interaction Test-time Scaling validates the importance of effective interaction for complex, dynamic text-to-SQL tasks.

birdsql The BIRD Team
·
Oct 6, 2025 2

Evaluating the Search Agent in a Parallel World

Integrating web search tools has significantly extended the capability of LLMs to address open-world, real-time, and long-tail problems. However, evaluating these Search Agents presents formidable challenges. First, constructing high-quality deep search benchmarks is prohibitively expensive, while unverified synthetic data often suffers from unreliable sources. Second, static benchmarks face dynamic obsolescence: as internet information evolves, complex queries requiring deep research often degrade into simple retrieval tasks due to increased popularity, and ground truths become outdated due to temporal shifts. Third, attribution ambiguity confounds evaluation, as an agent's performance is often dominated by its parametric memory rather than its actual search and reasoning capabilities. Finally, reliance on specific commercial search engines introduces variability that hampers reproducibility. To address these issues, we propose a novel framework, Mind-ParaWorld, for evaluating Search Agents in a Parallel World. Specifically, MPW samples real-world entity names to synthesize future scenarios and questions situated beyond the model's knowledge cutoff. A ParaWorld Law Model then constructs a set of indivisible Atomic Facts and a unique ground-truth for each question. During evaluation, instead of retrieving real-world results, the agent interacts with a ParaWorld Engine Model that dynamically generates SERPs grounded in these inviolable Atomic Facts. We release MPW-Bench, an interactive benchmark spanning 19 domains with 1,608 instances. Experiments across three evaluation settings show that, while search agents are strong at evidence synthesis given complete information, their performance is limited not only by evidence collection and coverage in unfamiliar search environments, but also by unreliable evidence sufficiency judgment and when-to-stop decisions-bottlenecks.

GPCR-Filter: a deep learning framework for efficient and precise GPCR modulator discovery

G protein-coupled receptors (GPCRs) govern diverse physiological processes and are central to modern pharmacology. Yet discovering GPCR modulators remains challenging because receptor activation often arises from complex allosteric effects rather than direct binding affinity, and conventional assays are slow, costly, and not optimized for capturing these dynamics. Here we present GPCR-Filter, a deep learning framework specifically developed for GPCR modulator discovery. We assembled a high-quality dataset of over 90,000 experimentally validated GPCR-ligand pairs, providing a robust foundation for training and evaluation. GPCR-Filter integrates the ESM-3 protein language model for high-fidelity GPCR sequence representations with graph neural networks that encode ligand structures, coupled through an attention-based fusion mechanism that learns receptor-ligand functional relationships. Across multiple evaluation settings, GPCR-Filter consistently outperforms state-of-the-art compound-protein interaction models and exhibits strong generalization to unseen receptors and ligands. Notably, the model successfully identified micromolar-level agonists of the 5-HT1A receptor with distinct chemical frameworks. These results establish GPCR-Filter as a scalable and effective computational approach for GPCR modulator discovery, advancing AI-assisted drug development for complex signaling systems.

SenseMath: Do LLMs Have Number Sense? Evaluating Shortcut Use, Judgment, and Generation

Large language models often default to step-by-step computation even when efficient numerical shortcuts are available. This raises a basic question: do they exhibit number sense in a human-like behavioral sense, i.e., the ability to recognize numerical structure, apply shortcuts when appropriate, and avoid them when they are not? We introduce SenseMath, a controlled benchmark for evaluating structure-sensitive numerical reasoning in LLMs. SenseMath contains 4,800 items spanning eight shortcut categories and four digit scales, with matched strong-shortcut, weak-shortcut, and control variants. It supports three evaluation settings of increasing cognitive demand: Shortcut Use (whether models can apply shortcuts on shortcut-amenable problems); Applicability Judgment (whether they can recognize when a shortcut is appropriate or misleading); and Problem Generation (whether they can generate new problem items that correctly admit a given type of shortcut). Our evaluation across five LLMs, ranging from GPT-4o-mini to Llama-3.1-8B, shows a consistent pattern: when explicitly prompted, models readily adopt shortcut strategies and achieve substantial accuracy gains on shortcut-amenable items (up to 15%), yet under standard chain-of-thought prompting they spontaneously employ such strategies in fewer than 40% of cases, even when they demonstrably possess the requisite capability. Moreover, this competence is confined to the Use level; models systematically over-generalise shortcuts to problems where they do not apply, and fail to generate valid shortcut-bearing problems from scratch. Together, these results suggest that current LLMs exhibit procedural shortcut fluency without the structural understanding of when and why shortcuts work that underlies human number sense.

  • 5 authors
·
Apr 1

Full-Body Articulated Human-Object Interaction

Fine-grained capturing of 3D HOI boosts human activity understanding and facilitates downstream visual tasks, including action recognition, holistic scene reconstruction, and human motion synthesis. Despite its significance, existing works mostly assume that humans interact with rigid objects using only a few body parts, limiting their scope. In this paper, we address the challenging problem of f-AHOI, wherein the whole human bodies interact with articulated objects, whose parts are connected by movable joints. We present CHAIRS, a large-scale motion-captured f-AHOI dataset, consisting of 16.2 hours of versatile interactions between 46 participants and 81 articulated and rigid sittable objects. CHAIRS provides 3D meshes of both humans and articulated objects during the entire interactive process, as well as realistic and physically plausible full-body interactions. We show the value of CHAIRS with object pose estimation. By learning the geometrical relationships in HOI, we devise the very first model that leverage human pose estimation to tackle the estimation of articulated object poses and shapes during whole-body interactions. Given an image and an estimated human pose, our model first reconstructs the pose and shape of the object, then optimizes the reconstruction according to a learned interaction prior. Under both evaluation settings (e.g., with or without the knowledge of objects' geometries/structures), our model significantly outperforms baselines. We hope CHAIRS will promote the community towards finer-grained interaction understanding. We will make the data/code publicly available.

  • 9 authors
·
Dec 20, 2022

Replayable Financial Agents: A Determinism-Faithfulness Assurance Harness for Tool-Using LLM Agents

LLM agents struggle with regulatory audit replay: when asked to reproduce a flagged transaction decision with identical inputs, many deployments fail to return consistent results. We introduce the Determinism-Faithfulness Assurance Harness (DFAH), a framework for measuring trajectory determinism, decision determinism, and evidence-conditioned faithfulness in tool-using agents deployed in financial services. Across 4,700+ agentic runs (7 models, 4 providers, 3 financial benchmarks with 50 cases each at T=0.0), we find that decision determinism and task accuracy are not detectably correlated (r = -0.11, 95% CI [-0.49, 0.31], p = 0.63, n = 21 configurations): models can be deterministic without being accurate, and accurate without being deterministic. Because neither metric predicts the other in our sample, both must be measured independently, which is precisely what DFAH provides. Small models (7-20B) achieve near-perfect determinism through rigid pattern matching at the cost of accuracy (20-42%), while frontier models show moderate determinism (50-96%) with variable accuracy. No model achieves both perfect determinism and high accuracy, supporting DFAH's multi-dimensional measurement approach. We provide three financial benchmarks (compliance triage, portfolio constraints, and DataOps exceptions; 50 cases each) together with an open-source stress-test harness. Across these benchmarks and DFAH evaluation settings, Tier 1 models with schema-first architectures achieved determinism levels consistent with audit replay requirements.

  • 1 authors
·
Mar 6

AutoRedTeamer: Autonomous Red Teaming with Lifelong Attack Integration

As large language models (LLMs) become increasingly capable, security and safety evaluation are crucial. While current red teaming approaches have made strides in assessing LLM vulnerabilities, they often rely heavily on human input and lack comprehensive coverage of emerging attack vectors. This paper introduces AutoRedTeamer, a novel framework for fully automated, end-to-end red teaming against LLMs. AutoRedTeamer combines a multi-agent architecture with a memory-guided attack selection mechanism to enable continuous discovery and integration of new attack vectors. The dual-agent framework consists of a red teaming agent that can operate from high-level risk categories alone to generate and execute test cases and a strategy proposer agent that autonomously discovers and implements new attacks by analyzing recent research. This modular design allows AutoRedTeamer to adapt to emerging threats while maintaining strong performance on existing attack vectors. We demonstrate AutoRedTeamer's effectiveness across diverse evaluation settings, achieving 20% higher attack success rates on HarmBench against Llama-3.1-70B while reducing computational costs by 46% compared to existing approaches. AutoRedTeamer also matches the diversity of human-curated benchmarks in generating test cases, providing a comprehensive, scalable, and continuously evolving framework for evaluating the security of AI systems.

  • 10 authors
·
Mar 19, 2025

A Scalable Framework for Evaluating Health Language Models

Large language models (LLMs) have emerged as powerful tools for analyzing complex datasets. Recent studies demonstrate their potential to generate useful, personalized responses when provided with patient-specific health information that encompasses lifestyle, biomarkers, and context. As LLM-driven health applications are increasingly adopted, rigorous and efficient one-sided evaluation methodologies are crucial to ensure response quality across multiple dimensions, including accuracy, personalization and safety. Current evaluation practices for open-ended text responses heavily rely on human experts. This approach introduces human factors and is often cost-prohibitive, labor-intensive, and hinders scalability, especially in complex domains like healthcare where response assessment necessitates domain expertise and considers multifaceted patient data. In this work, we introduce Adaptive Precise Boolean rubrics: an evaluation framework that streamlines human and automated evaluation of open-ended questions by identifying gaps in model responses using a minimal set of targeted rubrics questions. Our approach is based on recent work in more general evaluation settings that contrasts a smaller set of complex evaluation targets with a larger set of more precise, granular targets answerable with simple boolean responses. We validate this approach in metabolic health, a domain encompassing diabetes, cardiovascular disease, and obesity. Our results demonstrate that Adaptive Precise Boolean rubrics yield higher inter-rater agreement among expert and non-expert human evaluators, and in automated assessments, compared to traditional Likert scales, while requiring approximately half the evaluation time of Likert-based methods. This enhanced efficiency, particularly in automated evaluation and non-expert contributions, paves the way for more extensive and cost-effective evaluation of LLMs in health.

  • 13 authors
·
Mar 30, 2025

VenusX: Unlocking Fine-Grained Functional Understanding of Proteins

Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for understanding protein functional mechanisms and evaluating the biological knowledge captured by models. To address this demand, we introduce VenusX, the first large-scale benchmark for fine-grained functional annotation and function-based protein pairing at the residue, fragment, and domain levels. VenusX comprises three major task categories across six types of annotations, including residue-level binary classification, fragment-level multi-class classification, and pairwise functional similarity scoring for identifying critical active sites, binding sites, conserved sites, motifs, domains, and epitopes. The benchmark features over 878,000 samples curated from major open-source databases such as InterPro, BioLiP, and SAbDab. By providing mixed-family and cross-family splits at three sequence identity thresholds, our benchmark enables a comprehensive assessment of model performance on both in-distribution and out-of-distribution scenarios. For baseline evaluation, we assess a diverse set of popular and open-source models, including pre-trained protein language models, sequence-structure hybrids, structure-based methods, and alignment-based techniques. Their performance is reported across all benchmark datasets and evaluation settings using multiple metrics, offering a thorough comparison and a strong foundation for future research. Code and data are publicly available at https://github.com/ai4protein/VenusX.

  • 6 authors
·
May 16, 2025

Qwen3Guard Technical Report

As large language models (LLMs) become more capable and widely used, ensuring the safety of their outputs is increasingly critical. Existing guardrail models, though useful in static evaluation settings, face two major limitations in real-world applications: (1) they typically output only binary "safe/unsafe" labels, which can be interpreted inconsistently across diverse safety policies, rendering them incapable of accommodating varying safety tolerances across domains; and (2) they require complete model outputs before performing safety checks, making them fundamentally incompatible with streaming LLM inference, thereby preventing timely intervention during generation and increasing exposure to harmful partial outputs. To address these challenges, we present Qwen3Guard, a series of multilingual safety guardrail models with two specialized variants: Generative Qwen3Guard, which casts safety classification as an instruction-following task to enable fine-grained tri-class judgments (safe, controversial, unsafe); and Stream Qwen3Guard, which introduces a token-level classification head for real-time safety monitoring during incremental text generation. Both variants are available in three sizes (0.6B, 4B, and 8B parameters) and support up to 119 languages and dialects, providing comprehensive, scalable, and low-latency safety moderation for global LLM deployments. Evaluated across English, Chinese, and multilingual benchmarks, Qwen3Guard achieves state-of-the-art performance in both prompt and response safety classification. All models are released under the Apache 2.0 license for public use.

Qwen Qwen
·
Oct 16, 2025 2

A Reasoning-Enabled Vision-Language Foundation Model for Chest X-ray Interpretation

Chest X-rays (CXRs) are among the most frequently performed imaging examinations worldwide, yet rising imaging volumes increase radiologist workload and the risk of diagnostic errors. Although artificial intelligence (AI) systems have shown promise for CXR interpretation, most generate only final predictions, without making explicit how visual evidence is translated into radiographic findings and diagnostic predictions. We present CheXOne, a reasoning-enabled vision-language model for CXR interpretation. CheXOne jointly generates diagnostic predictions and explicit, clinically grounded reasoning traces that connect visual evidence, radiographic findings, and these predictions. The model is trained on 14.7 million instruction and reasoning samples curated from 30 public datasets spanning 36 CXR interpretation tasks, using a two-stage framework that combines instruction tuning with reinforcement learning to improve reasoning quality. We evaluate CheXOne in zero-shot settings across visual question answering, report generation, visual grounding and reasoning assessment, covering 17 evaluation settings. CheXOne outperforms existing medical and general-domain foundation models and achieves strong performance on independent public benchmarks. A clinical reader study demonstrates that CheXOne-drafted reports are comparable to or better than resident-written reports in 55% of cases, while effectively addressing clinical indications and enhancing both report writing and CXR interpretation efficiency. Further analyses involving radiologists reveal that the generated reasoning traces show high clinical factuality and provide causal support for the final predictions, offering a plausible explanation for the performance gains. These results suggest that explicit reasoning can improve model performance, interpretability and clinical utility in AI-assisted CXR interpretation.

  • 22 authors
·
Apr 1

LLM The Genius Paradox: A Linguistic and Math Expert's Struggle with Simple Word-based Counting Problems

Interestingly, LLMs yet struggle with some basic tasks that humans find trivial to handle, e.g., counting the number of character r's in the word "strawberry". There are several popular conjectures (e.g., tokenization, architecture and training data) regarding the reason for deficiency of LLMs in simple word-based counting problems, sharing the similar belief that such failure stems from model pretraining hence probably inevitable during deployment. In this paper, we carefully design multiple evaluation settings to investigate validity of prevalent conjectures. Meanwhile, we measure transferability of advanced mathematical and coding reasoning capabilities from specialized LLMs to simple counting tasks. Although specialized LLMs suffer from counting problems as well, we find conjectures about inherent deficiency of LLMs invalid and further seek opportunities to elicit knowledge and capabilities from LLMs that are beneficial to counting tasks. Compared with strategies such as finetuning and in-context learning that are commonly adopted to enhance performance on new or challenging tasks, we show that engaging reasoning is the most robust and efficient way to help LLMs better perceive tasks with more accurate responses. We hope our conjecture validation design could provide insights into the study of future critical failure modes of LLMs. Based on challenges in transferring advanced capabilities to much simpler tasks, we call for more attention to model capability acquisition and evaluation. We also highlight the importance of cultivating consciousness of "reasoning before responding" during model pretraining.

  • 2 authors
·
Oct 18, 2024

DBConformer: Dual-Branch Convolutional Transformer for EEG Decoding

Electroencephalography (EEG)-based brain-computer interfaces (BCIs) transform spontaneous/evoked neural activity into control commands for external communication. While convolutional neural networks (CNNs) remain the mainstream backbone for EEG decoding, their inherently short receptive field makes it difficult to capture long-range temporal dependencies and global inter-channel relationships. Recent CNN-Transformer (Conformers) hybrids partially address this issue, but most adopt a serial design, resulting in suboptimal integration of local and global features, and often overlook explicit channel-wise modeling. To address these limitations, we propose DBConformer, a dual-branch convolutional Transformer network tailored for EEG decoding. It integrates a temporal Conformer to model long-range temporal dependencies and a spatial Conformer to extract inter-channel interactions, capturing both temporal dynamics and spatial patterns in EEG signals. A lightweight channel attention module further refines spatial representations by assigning data-driven importance to EEG channels. Extensive experiments on five motor imagery (MI) datasets and two seizure detection datasets under three evaluation settings demonstrate that DBConformer consistently outperforms 10 competitive baseline models, with over eight times fewer parameters than the high-capacity EEG Conformer baseline. Further, the visualization results confirm that the features extracted by DBConformer are physiologically interpretable and aligned with sensorimotor priors in MI. The superior performance and interpretability of DBConformer make it reliable for robust and explainable EEG decoding. Code is publicized at https://github.com/wzwvv/DBConformer.

  • 6 authors
·
Jun 26, 2025

Reverse Engineering Human Preferences with Reinforcement Learning

The capabilities of Large Language Models (LLMs) are routinely evaluated by other LLMs trained to predict human preferences. This framework--known as LLM-as-a-judge--is highly scalable and relatively low cost. However, it is also vulnerable to malicious exploitation, as LLM responses can be tuned to overfit the preferences of the judge. Previous work shows that the answers generated by a candidate-LLM can be edited post hoc to maximise the score assigned to them by a judge-LLM. In this study, we adopt a different approach and use the signal provided by judge-LLMs as a reward to adversarially tune models that generate text preambles designed to boost downstream performance. We find that frozen LLMs pipelined with these models attain higher LLM-evaluation scores than existing frameworks. Crucially, unlike other frameworks which intervene directly on the model's response, our method is virtually undetectable. We also demonstrate that the effectiveness of the tuned preamble generator transfers when the candidate-LLM and the judge-LLM are replaced with models that are not used during training. These findings raise important questions about the design of more reliable LLM-as-a-judge evaluation settings. They also demonstrate that human preferences can be reverse engineered effectively, by pipelining LLMs to optimise upstream preambles via reinforcement learning--an approach that could find future applications in diverse tasks and domains beyond adversarial attacks.

  • 6 authors
·
May 21, 2025

LongIns: A Challenging Long-context Instruction-based Exam for LLMs

The long-context capabilities of large language models (LLMs) have been a hot topic in recent years. To evaluate the performance of LLMs in different scenarios, various assessment benchmarks have emerged. However, as most of these benchmarks focus on identifying key information to answer questions, which mainly requires the retrieval ability of LLMs, these benchmarks can partially represent the reasoning performance of LLMs from large amounts of information. Meanwhile, although LLMs often claim to have context windows of 32k, 128k, 200k, or even longer, these benchmarks fail to reveal the actual supported length of these LLMs. To address these issues, we propose the LongIns benchmark dataset, a challenging long-context instruction-based exam for LLMs, which is built based on the existing instruction datasets. Specifically, in our LongIns, we introduce three evaluation settings: Global Instruction & Single Task (GIST), Local Instruction & Single Task (LIST), and Local Instruction & Multiple Tasks (LIMT). Based on LongIns, we perform comprehensive evaluations on existing LLMs and have the following important findings: (1). The top-performing GPT-4 with 128k context length performs poorly on the evaluation context window of 16k in our LongIns. (2). For the multi-hop reasoning ability of many existing LLMs, significant efforts are still needed under short context windows (less than 4k).

  • 10 authors
·
Jun 25, 2024 1

Reproducing and Comparing Distillation Techniques for Cross-Encoders

Recent advances in Information Retrieval have established transformer-based cross-encoders as a keystone in IR. Recent studies have focused on knowledge distillation and showed that, with the right strategy, traditional cross-encoders could reach the level of effectiveness of LLM re-rankers. Yet, comparisons with previous training strategies, including distillation from strong cross-encoder teachers, remain unclear. In addition, few studies cover a similar range of backbone encoders, while substantial improvements have been made in this area since BERT. This lack of comprehensive studies in controlled environments makes it difficult to identify robust design choices. In this work, we reproduce schlattRankDistiLLMClosingEffectiveness2025 LLM-based distillation strategy and compare it to hofstatterImprovingEfficientNeural2020 approach based on an ensemble of cross-encoder teachers, as well as other supervised objectives, to fine-tune a large range of cross-encoders, from the original BERT and its follow-ups RoBERTa, ELECTRA and DeBERTa-v3, to the more recent ModernBERT. We evaluate all models on both in-domain (TREC-DL and MS~MARCO dev) and out-of-domain datasets (BEIR, LoTTE, and Robust04). Our results show that objectives emphasizing relative comparisons -- pairwise MarginMSE and listwise InfoNCE -- consistently outperform pointwise baselines across all backbones and evaluation settings, and that objective choice can yield gains comparable to scaling the backbone architecture.

CoMAS: Co-Evolving Multi-Agent Systems via Interaction Rewards

Self-evolution is a central research topic in enabling large language model (LLM)-based agents to continually improve their capabilities after pretraining. Recent research has witnessed a transition from reinforcement learning (RL)-free to RL-based methods. Current RL-based methods either rely on dense external reward signals or extract intrinsic reward signals from LLMs themselves. However, these approaches diverge from the self-evolution mechanisms observed in human intelligence, where individuals learn and improve through mutual discussion and collaboration. In this work, we introduce Co-Evolving Multi-Agent Systems (CoMAS), a novel framework that enables agents to improve autonomously by learning from inter-agent interactions without external supervision. CoMAS generates intrinsic rewards from rich discussion dynamics, employs an LLM-as-a-judge mechanism to formulate these rewards, and optimizes each agent's policy through RL, thereby enabling decentralized and scalable co-evolution. Experimental results demonstrate that CoMAS consistently outperforms untrained agents and achieves state-of-the-art performance across most evaluation settings. Ablation studies confirm the necessity of interaction-based reward signals and reveal promising scalability as the number and diversity of agents increase. These findings establish CoMAS as a novel and effective paradigm for self-evolution in LLM-based agents.

  • 10 authors
·
Oct 9, 2025 2

MarkushGrapher: Joint Visual and Textual Recognition of Markush Structures

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

  • 7 authors
·
Mar 20, 2025

RAFT: Rationale adaptor for few-shot abusive language detection

Abusive language is a concerning problem in online social media. Past research on detecting abusive language covers different platforms, languages, demographies, etc. However, models trained using these datasets do not perform well in cross-domain evaluation settings. To overcome this, a common strategy is to use a few samples from the target domain to train models to get better performance in that domain (cross-domain few-shot training). However, this might cause the models to overfit the artefacts of those samples. A compelling solution could be to guide the models toward rationales, i.e., spans of text that justify the text's label. This method has been found to improve model performance in the in-domain setting across various NLP tasks. In this paper, we propose RAFT (Rationale Adaptor for Few-shoT classification) for abusive language detection. We first build a multitask learning setup to jointly learn rationales, targets, and labels, and find a significant improvement of 6% macro F1 on the rationale detection task over training solely rationale classifiers. We introduce two rationale-integrated BERT-based architectures (the RAFT models) and evaluate our systems over five different abusive language datasets, finding that in the few-shot classification setting, RAFT-based models outperform baseline models by about 7% in macro F1 scores and perform competitively to models finetuned on other source domains. Furthermore, RAFT-based models outperform LIME/SHAP-based approaches in terms of plausibility and are close in performance in terms of faithfulness.

  • 5 authors
·
Nov 30, 2022

Meissa: Multi-modal Medical Agentic Intelligence

Multi-modal large language models (MM-LLMs) have shown strong performance in medical image understanding and clinical reasoning. Recent medical agent systems extend them with tool use and multi-agent collaboration, enabling complex decision-making. However, these systems rely almost entirely on frontier models (e.g., GPT), whose API-based deployment incurs high cost, high latency, and privacy risks that conflict with on-premise clinical requirements. We present Meissa, a lightweight 4B-parameter medical MM-LLM that brings agentic capability offline. Instead of imitating static answers, Meissa learns both when to engage external interaction (strategy selection) and how to execute multi-step interaction (strategy execution) by distilling structured trajectories from frontier models. Specifically, we propose: (1) Unified trajectory modeling: trajectories (reasoning and action traces) are represented within a single state-action-observation formalism, allowing one model to generalize across heterogeneous medical environments. (2) Three-tier stratified supervision: the model's own errors trigger progressive escalation from direct reasoning to tool-augmented and multi-agent interaction, explicitly learning difficulty-aware strategy selection. (3) Prospective-retrospective supervision: pairing exploratory forward traces with hindsight-rationalized execution traces enables stable learning of effective interaction policies. Trained on 40K curated trajectories, Meissa matches or exceeds proprietary frontier agents in 10 of 16 evaluation settings across 13 medical benchmarks spanning radiology, pathology, and clinical reasoning. Using over 25x fewer parameters than typical frontier models like Gemini-3, Meissa operates fully offline with 22x lower end-to-end latency compared to API-based deployment. Data, models, and environments are released at https://github.com/Schuture/Meissa.

ModelLens: Finding the Best for Your Task from Myriads of Models

The open-source model ecosystem now contains hundreds of thousands of pretrained models, yet picking the best model for a new dataset is increasingly infeasible: new models and unbenchmarked datasets emerge continuously, leaving practitioners with no prior records on either side. Existing approaches handle only fragments of this in-the-wild setting: AutoML and transferability estimation select models from small predefined pools or require expensive per-model forward passes on the target dataset, while model routing presupposes a given candidate pool. We introduce ModelLens, a unified framework for model recommendation in the wild. Our key insight is that public leaderboard interactions, though scattered and noisy, collectively trace out an implicit atlas of model capabilities across heterogeneous evaluation settings, a signal rich enough to learn from directly. By learning a performance-aware latent space over model--dataset--metric tuples, ModelLens ranks unseen models on unseen datasets without running candidates on the target dataset. On a new benchmark of 1.62M evaluation records spanning 47K models and 9.6K datasets, ModelLens surpasses baselines that either rely on metadata alone or require running each candidate on the target dataset. Its recommended Top-K pools further improve multiple representative routing methods by up to 81% across diverse QA benchmarks. Case studies on recently released benchmarks further confirm generalization to both text and vision-language tasks.

ucdavis UC Davis
·
May 7 2

Are Video Reasoning Models Ready to Go Outside?

In real-world deployment, vision-language models often encounter disturbances such as weather, occlusion, and camera motion. Under such conditions, their understanding and reasoning degrade substantially, revealing a gap between clean, controlled (i.e., unperturbed) evaluation settings and real-world robustness. To address this limitation, we propose ROVA, a novel training framework that improves robustness by modeling a robustness-aware consistency reward under spatio-temporal corruptions. ROVA introduces a difficulty-aware online training strategy that prioritizes informative samples based on the model's evolving capability. Specifically, it continuously re-estimates sample difficulty via self-reflective evaluation, enabling adaptive training with a robustness-aware consistency reward. We also introduce PVRBench, a new benchmark that injects real-world perturbations into embodied video datasets to assess both accuracy and reasoning quality under realistic disturbances. We evaluate ROVA and baselines on PVRBench, UrbanVideo, and VisBench, where open-source and proprietary models suffer up to 35% and 28% drops in accuracy and reasoning under realistic perturbations. ROVA effectively mitigates performance degradation, boosting relative accuracy by at least 24% and reasoning by over 9% compared with baseline models (QWen2.5/3-VL, InternVL2.5, Embodied-R). These gains transfer to clean standard benchmarks, yielding consistent improvements.

SpaCE-10: A Comprehensive Benchmark for Multimodal Large Language Models in Compositional Spatial Intelligence

Multimodal Large Language Models (MLLMs) have achieved remarkable progress in various multimodal tasks. To pursue higher intelligence in space, MLLMs require integrating multiple atomic spatial capabilities to handle complex and dynamic tasks. However, existing benchmarks struggle to comprehensively evaluate the spatial intelligence of common MLLMs from the atomic level to the compositional level. To fill this gap, we present SpaCE-10, a comprehensive benchmark for compositional spatial evaluations. In SpaCE-10, we define 10 atomic spatial capabilities, which are combined to form 8 compositional capabilities. Based on these definitions, we propose a novel hierarchical annotation pipeline to generate high-quality and diverse question-answer (QA) pairs. With over 150+ hours of human expert effort, we obtain over 5k QA pairs for 811 real indoor scenes in SpaCE-10, which covers various evaluation settings like point cloud input and multi-choice QA. We conduct an extensive evaluation of common MLLMs on SpaCE-10 and find that even the most advanced MLLM still lags behind humans by large margins. Through our careful study, we also draw several significant findings that benefit the MLLM community. For example, we reveal that the shortcoming of counting capability greatly limits the compositional spatial capabilities of existing MLLMs. The evaluation code and benchmark datasets are available at https://github.com/Cuzyoung/SpaCE-10.

  • 9 authors
·
Jun 9, 2025

A Comprehensive Analysis of Static Word Embeddings for Turkish

Word embeddings are fixed-length, dense and distributed word representations that are used in natural language processing (NLP) applications. There are basically two types of word embedding models which are non-contextual (static) models and contextual models. The former method generates a single embedding for a word regardless of its context, while the latter method produces distinct embeddings for a word based on the specific contexts in which it appears. There are plenty of works that compare contextual and non-contextual embedding models within their respective groups in different languages. However, the number of studies that compare the models in these two groups with each other is very few and there is no such study in Turkish. This process necessitates converting contextual embeddings into static embeddings. In this paper, we compare and evaluate the performance of several contextual and non-contextual models in both intrinsic and extrinsic evaluation settings for Turkish. We make a fine-grained comparison by analyzing the syntactic and semantic capabilities of the models separately. The results of the analyses provide insights about the suitability of different embedding models in different types of NLP tasks. We also build a Turkish word embedding repository comprising the embedding models used in this work, which may serve as a valuable resource for researchers and practitioners in the field of Turkish NLP. We make the word embeddings, scripts, and evaluation datasets publicly available.

  • 3 authors
·
May 13, 2024

MAMMA: Markerless & Automatic Multi-Person Motion Action Capture

We present MAMMA, a markerless motion-capture pipeline that accurately recovers SMPL-X parameters from multi-view video of two-person interaction sequences. Traditional motion-capture systems rely on physical markers. Although they offer high accuracy, their requirements of specialized hardware, manual marker placement, and extensive post-processing make them costly and time-consuming. Recent learning-based methods attempt to overcome these limitations, but most are designed for single-person capture, rely on sparse keypoints, or struggle with occlusions and physical interactions. In this work, we introduce a method that predicts dense 2D contact-aware surface landmarks conditioned on segmentation masks, enabling person-specific correspondence estimation even under heavy occlusion. We employ a novel architecture that exploits learnable queries for each landmark. We demonstrate that our approach can handle complex person--person interaction and offers greater accuracy than existing methods. To train our network, we construct a large, synthetic multi-view dataset combining human motions from diverse sources, including extreme poses, hand motions, and close interactions. Our dataset yields high-variability synthetic sequences with rich body contact and occlusion, and includes SMPL-X ground-truth annotations with dense 2D landmarks. The result is a system capable of capturing human motion without the need for markers. Our approach offers competitive reconstruction quality compared to commercial marker-based motion-capture solutions, without the extensive manual cleanup. Finally, we address the absence of common benchmarks for dense-landmark prediction and markerless motion capture by introducing two evaluation settings built from real multi-view sequences. Our dataset is available in https://mamma.is.tue.mpg.de for research purposes.

  • 10 authors
·
Apr 6

KV Cache Quantization for Self-Forcing Video Generation: A 33-Method Empirical Study

Self-forcing video generation extends a short-horizon video model to longer rollouts by repeatedly feeding generated content back in as context. This scaling path immediately exposes a systems bottleneck: the key-value (KV) cache grows with rollout length, so longer videos require not only better generation quality but also substantially better memory behavior. We present a comprehensive empirical study of KV-cache compression for self-forcing video generation on a Wan2.1-based Self-Forcing stack. Our study covers 33 quantization and cache-policy variants, 610 prompt-level observations, and 63 benchmark-level summaries across two evaluation settings: MovieGen for single-shot 10-second generation and StoryEval for longer narrative-style stability. We jointly evaluate peak VRAM, runtime, realized compression ratio, VBench imaging quality, BF16-referenced fidelity (SSIM, LPIPS, PSNR), and terminal drift. Three findings are robust. First, the strongest practical operating region is a FlowCache-inspired soft-prune INT4 adaptation, which reaches 5.42-5.49x compression while reducing peak VRAM from 19.28 GB to about 11.7 GB with only modest runtime overhead. Second, the highest-fidelity compressed methods, especially PRQ_INT4 and QUAROT_KV_INT4, are not the best deployment choices because they preserve quality at severe runtime or memory cost. Third, nominal compression alone is not sufficient: several methods shrink KV storage but still exceed BF16 peak VRAM because the current integration reconstructs or retains large BF16 buffers during attention and refresh stages. The result is a benchmark harness, analysis workflow, and empirical map of which KV-cache ideas are practical today and which are promising research directions for better memory integration. Code, data products, and the presentation dashboard are available at https://github.com/suraj-ranganath/kv-quant-longhorizon/.

  • 3 authors
·
Mar 28

Are We Making Progress in Multimodal Domain Generalization? A Comprehensive Benchmark Study

Despite the growing popularity of Multimodal Domain Generalization (MMDG) for enhancing model robustness, it remains unclear whether reported performance gains reflect genuine algorithmic progress or are artifacts of inconsistent evaluation protocols. Current research is fragmented, with studies varying significantly across datasets, modality configurations, and experimental settings. Furthermore, existing benchmarks focus predominantly on action recognition, often neglecting critical real-world challenges such as input corruptions, missing modalities, and model trustworthiness. This lack of standardization obscures a reliable assessment of the field's advancement. To address this issue, we introduce MMDG-Bench, the first unified and comprehensive benchmark for MMDG, which standardizes evaluation across six datasets spanning three diverse tasks: action recognition, mechanical fault diagnosis, and sentiment analysis. MMDG-Bench encompasses six modality combinations, nine representative methods, and multiple evaluation settings. Beyond standard accuracy, it systematically assesses corruption robustness, missing-modality generalization, misclassification detection, and out-of-distribution detection. With 7, 402 neural networks trained in total across 95 unique cross-domain tasks, MMDG-Bench yields five key findings: (1) under fair comparisons, recent specialized MMDG methods offer only marginal improvements over ERM baseline; (2) no single method consistently outperforms others across datasets or modality combinations; (3) a substantial gap to upper-bound performance persists, indicating that MMDG remains far from solved; (4) trimodal fusion does not consistently outperform the strongest bimodal configurations; and (5) all evaluated methods exhibit significant degradation under corruption and missing-modality scenarios, with some methods further compromising model trustworthiness.

ethz ETH Zurich
·
May 6 3

Shall We Pretrain Autoregressive Language Models with Retrieval? A Comprehensive Study

Large decoder-only language models (LMs) can be largely improved in terms of perplexity by retrieval (e.g., RETRO), but its impact on text generation quality and downstream task accuracy is unclear. Thus, it is still an open question: shall we pretrain large autoregressive LMs with retrieval? To answer it, we perform a comprehensive study on a scalable pre-trained retrieval-augmented LM (i.e., RETRO) compared with standard GPT and retrieval-augmented GPT incorporated at fine-tuning or inference stages. We first provide the recipe to reproduce RETRO up to 9.5B parameters while retrieving a text corpus with 330B tokens. Based on that, we have the following novel findings: i) RETRO outperforms GPT on text generation with much less degeneration (i.e., repetition), moderately higher factual accuracy, and slightly lower toxicity with a nontoxic retrieval database. ii) On the LM Evaluation Harness benchmark, RETRO largely outperforms GPT on knowledge-intensive tasks, but is on par with GPT on other tasks. Furthermore, we introduce a simple variant of the model, RETRO++, which largely improves open-domain QA results of original RETRO (e.g., EM score +8.6 on Natural Question) and significantly outperforms retrieval-augmented GPT in both fine-tuning and zero-shot evaluation settings. Our findings highlight the promising direction of pretraining autoregressive LMs with retrieval as future foundation models. We release our implementation at: https://github.com/NVIDIA/Megatron-LM#retro.

  • 12 authors
·
Apr 13, 2023

FOS: A Large-Scale Temporal Graph Benchmark for Scientific Interdisciplinary Link Prediction

Interdisciplinary scientific breakthroughs mostly emerge unexpectedly, and forecasting the formation of novel research fields remains a major challenge. We introduce FOS (Future Of Science), a comprehensive time-aware graph-based benchmark that reconstructs annual co-occurrence graphs of 65,027 research sub-fields (spanning 19 general domains) over the period 1827-2024. In these graphs, edges denote the co-occurrence of two fields in a single publication and are timestamped with the corresponding publication year. Nodes are enriched with semantic embeddings, and edges are characterized by temporal and topological descriptors. We formulate the prediction of new field-pair linkages as a temporal link-prediction task, emphasizing the "first-time" connections that signify pioneering interdisciplinary directions. Through extensive experiments, we evaluate a suite of state-of-the-art temporal graph architectures under multiple negative-sampling regimes and show that (i) embedding long-form textual descriptions of fields significantly boosts prediction accuracy, and (ii) distinct model classes excel under different evaluation settings. Case analyses show that top-ranked link predictions on FOS align with field pairings that emerge in subsequent years of academic publications. We publicly release FOS, along with its temporal data splits and evaluation code, to establish a reproducible benchmark for advancing research in predicting scientific frontiers.

  • 7 authors
·
Nov 23, 2025

Calibrating LLMs with Semantic-level Reward

As large language models (LLMs) are deployed in consequential settings such as medical question answering and legal reasoning, the ability to estimate when their outputs are likely to be correct is essential for safe and reliable use, requiring well-calibrated uncertainty. Standard reinforcement learning with verifiable rewards (RLVR) trains models with a binary correctness reward that is indifferent to confidence, providing no penalty for confident but wrong predictions and thereby degrading calibration. Recent work addresses this by training models to produce verbalized confidence scores alongside answers and rewarding agreement with correctness. However, verbalized confidence is calibrated at the token level and thus exhibits inconsistency across textual variations with same semantic meaning. We propose Calibration with Semantic Reward (CSR), a framework that calibrates language models directly in semantic space without a verbalized confidence interface. CSR combines the correctness reward with a novel semantic calibration reward that encourages exploitation among correct rollouts by promoting semantic agreement, and exploration among incorrect ones by discouraging spurious consistency. Experiments across three model families on HotpotQA (in-distribution) and TriviaQA, MSMARCO, and NQ-Open (out-of-distribution) show that CSR consistently achieves lower ECE and higher AUROC than verbalized-confidence baselines across nearly all settings, reducing ECE by up to 40% and improving AUROC by up to 31% over verbalized-confidence baselines, with calibration behavior generalizing robustly across all four evaluation settings.

  • 5 authors
·
May 19

HRBench: Benchmarking and Understanding Thinking-Mode Switch Strategies in Hybrid-Reasoning LLMs

Hybrid-reasoning large language models (LLMs) expose explicit controls over reasoning effort, allowing users or systems to trade off answer quality against inference cost. However, existing methods for adaptive thinking-mode selection are typically evaluated under different models, datasets, and implementation assumptions, making it difficult to compare their practical behavior. We introduce HRBench, a unified evaluation framework for studying thinking-mode switching in hybrid-reasoning LLMs. HRBench organizes the design space along two axes: three switching strategy families, prompt-based selection, external routing, and speculative execution, and four training regimes, training-free, SFT, offline and online RL, yielding 12 controlled evaluation settings. We evaluate these settings across 6 LLMs, from Qwen3.5-2B to Kimi-K2.5-1.1T, and 5 reasoning benchmarks covering mathematics, science, and code, while reimplementing 12+ representative prior methods within the same pipeline. Our analysis characterizes how different switching strategies occupy distinct effectiveness-efficiency trade-off regions: prompt-based methods often provide favorable token-accuracy trade-offs, routing methods offer more stable cost reduction, and speculative methods tend to improve accuracy at higher token cost. We further find that training affects strategies differently, and that the preferred strategy varies with model scale and task domain. HRBench provides reference implementations and a unified evaluation platform to support more controlled research on efficient reasoning in hybrid-reasoning LLMs. Our data, code and repository are available at https://github.com/usail-hkust/HRBench.

tencent Tencent
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May 26 4

Denoising MCMC for Accelerating Diffusion-Based Generative Models

Diffusion models are powerful generative models that simulate the reverse of diffusion processes using score functions to synthesize data from noise. The sampling process of diffusion models can be interpreted as solving the reverse stochastic differential equation (SDE) or the ordinary differential equation (ODE) of the diffusion process, which often requires up to thousands of discretization steps to generate a single image. This has sparked a great interest in developing efficient integration techniques for reverse-S/ODEs. Here, we propose an orthogonal approach to accelerating score-based sampling: Denoising MCMC (DMCMC). DMCMC first uses MCMC to produce samples in the product space of data and variance (or diffusion time). Then, a reverse-S/ODE integrator is used to denoise the MCMC samples. Since MCMC traverses close to the data manifold, the computation cost of producing a clean sample for DMCMC is much less than that of producing a clean sample from noise. To verify the proposed concept, we show that Denoising Langevin Gibbs (DLG), an instance of DMCMC, successfully accelerates all six reverse-S/ODE integrators considered in this work on the tasks of CIFAR10 and CelebA-HQ-256 image generation. Notably, combined with integrators of Karras et al. (2022) and pre-trained score models of Song et al. (2021b), DLG achieves SOTA results. In the limited number of score function evaluation (NFE) settings on CIFAR10, we have 3.86 FID with approx 10 NFE and 2.63 FID with approx 20 NFE. On CelebA-HQ-256, we have 6.99 FID with approx 160 NFE, which beats the current best record of Kim et al. (2022) among score-based models, 7.16 FID with 4000 NFE. Code: https://github.com/1202kbs/DMCMC

  • 2 authors
·
Sep 29, 2022

M-RewardBench: Evaluating Reward Models in Multilingual Settings

Reward models (RMs) have driven the state-of-the-art performance of LLMs today by enabling the integration of human feedback into the language modeling process. However, RMs are primarily trained and evaluated in English, and their capabilities in multilingual settings remain largely understudied. In this work, we conduct a systematic evaluation of several reward models in multilingual settings. We first construct the first-of-its-kind multilingual RM evaluation benchmark, M-RewardBench, consisting of 2.87k preference instances for 23 typologically diverse languages, that tests the chat, safety, reasoning, and translation capabilities of RMs. We then rigorously evaluate a wide range of reward models on M-RewardBench, offering fresh insights into their performance across diverse languages. We identify a significant gap in RMs' performances between English and non-English languages and show that RM preferences can change substantially from one language to another. We also present several findings on how different multilingual aspects impact RM performance. Specifically, we show that the performance of RMs is improved with improved translation quality. Similarly, we demonstrate that the models exhibit better performance for high-resource languages. We release M-RewardBench dataset and the codebase in this study to facilitate a better understanding of RM evaluation in multilingual settings.

  • 10 authors
·
Oct 20, 2024 3

PPI2Text: Captioning Protein-Protein Interactions with Coordinate-Aligned Pair-Map Decoding

Protein-protein interaction (PPI) modeling has been widely studied as a binary or multi-label classification task. While emerging multimodal large language models (LLMs) can now describe single proteins, they remain unable to generate free-form descriptions of interactions between protein pairs. Moving beyond controlled vocabulary annotations, we propose to model PPI using free-text description, enabling richer expressiveness, improved interpretability, and better integration with literature knowledge base. We present PPI2Text, a multimodal LLM for free-form PPI captioning from amino acid sequences, that encodes each protein using ESM3 encoder, constructs a pair map from the two representations to capture interactions across all residue pairs, and autoregressively generates descriptions using a Qwen3 language decoder. We further introduce PaCo-RoPE, a coordinate-aligned positional encoding that aligns each axis of the pair grid with the residue positions of the corresponding protein. In addition, we release PPI2Text-Dataset, a 351k-pair corpus of free-form PPI descriptions aggregated from ten curated biological databases and further synthesized with Gemini under evidence-tiered prompting. PPI2Text consistently outperforms strong baselines across multiple ablation settings and evaluation protocols. It not only achieves higher scores on linguistic metrics against synthesized references, but also excels on factuality metrics, where an LLM-based judge evaluates outputs against raw biological evidence.

  • 7 authors
·
May 8

From Features to Actions: Explainability in Traditional and Agentic AI Systems

Over the last decade, explainable AI has primarily focused on interpreting individual model predictions, producing post-hoc explanations that relate inputs to outputs under a fixed decision structure. Recent advances in large language models (LLMs) have enabled agentic AI systems whose behaviour unfolds over multi-step trajectories. In these settings, success and failure are determined by sequences of decisions rather than a single output. While useful, it remains unclear how explanation approaches designed for static predictions translate to agentic settings where behaviour emerges over time. In this work, we bridge the gap between static and agentic explainability by comparing attribution-based explanations with trace-based diagnostics across both settings. To make this distinction explicit, we empirically compare attribution-based explanations used in static classification tasks with trace-based diagnostics used in agentic benchmarks (TAU-bench Airline and AssistantBench). Our results show that while attribution methods achieve stable feature rankings in static settings (Spearman ρ= 0.86), they cannot be applied reliably to diagnose execution-level failures in agentic trajectories. In contrast, trace-grounded rubric evaluation for agentic settings consistently localizes behaviour breakdowns and reveals that state tracking inconsistency is 2.7times more prevalent in failed runs and reduces success probability by 49\%. These findings motivate a shift towards trajectory-level explainability for agentic systems when evaluating and diagnosing autonomous AI behaviour. Resources: https://github.com/VectorInstitute/unified-xai-evaluation-framework https://vectorinstitute.github.io/unified-xai-evaluation-framework

Vulnerability Detection with Code Language Models: How Far Are We?

In the context of the rising interest in code language models (code LMs) and vulnerability detection, we study the effectiveness of code LMs for detecting vulnerabilities. Our analysis reveals significant shortcomings in existing vulnerability datasets, including poor data quality, low label accuracy, and high duplication rates, leading to unreliable model performance in realistic vulnerability detection scenarios. Additionally, the evaluation methods used with these datasets are not representative of real-world vulnerability detection. To address these challenges, we introduce PrimeVul, a new dataset for training and evaluating code LMs for vulnerability detection. PrimeVul incorporates a novel set of data labeling techniques that achieve comparable label accuracy to human-verified benchmarks while significantly expanding the dataset. It also implements a rigorous data de-duplication and chronological data splitting strategy to mitigate data leakage issues, alongside introducing more realistic evaluation metrics and settings. This comprehensive approach aims to provide a more accurate assessment of code LMs' performance in real-world conditions. Evaluating code LMs on PrimeVul reveals that existing benchmarks significantly overestimate the performance of these models. For instance, a state-of-the-art 7B model scored 68.26% F1 on BigVul but only 3.09% F1 on PrimeVul. Attempts to improve performance through advanced training techniques and larger models like GPT-3.5 and GPT-4 were unsuccessful, with results akin to random guessing in the most stringent settings. These findings underscore the considerable gap between current capabilities and the practical requirements for deploying code LMs in security roles, highlighting the need for more innovative research in this domain.

  • 9 authors
·
Mar 27, 2024

Evaluation of Language Models in the Medical Context Under Resource-Constrained Settings

Since the emergence of the Transformer architecture, language model development has increased, driven by their promising potential. However, releasing these models into production requires properly understanding their behavior, particularly in sensitive domains such as medicine. Despite this need, the medical literature still lacks technical assessments of pre-trained language models, which are especially valuable in resource-constrained settings in terms of computational power or limited budget. To address this gap, we provide a comprehensive survey of language models in the medical domain. In addition, we selected a subset of these models for thorough evaluation, focusing on classification and text generation tasks. Our subset encompasses 53 models, ranging from 110 million to 13 billion parameters, spanning the three families of Transformer-based models and from diverse knowledge domains. This study employs a series of approaches for text classification together with zero-shot prompting instead of model training or fine-tuning, which closely resembles the limited resource setting in which many users of language models find themselves. Encouragingly, our findings reveal remarkable performance across various tasks and datasets, underscoring the latent potential of certain models to contain medical knowledge, even without domain specialization. Consequently, our study advocates for further exploration of model applications in medical contexts, particularly in resource-constrained settings. The code is available on https://github.com/anpoc/Language-models-in-medicine.

  • 4 authors
·
Jun 24, 2024

Towards Realistic Evaluation of Commit Message Generation by Matching Online and Offline Settings

Commit message generation (CMG) is a crucial task in software engineering that is challenging to evaluate correctly. When a CMG system is integrated into the IDEs and other products at JetBrains, we perform online evaluation based on user acceptance of the generated messages. However, performing online experiments with every change to a CMG system is troublesome, as each iteration affects users and requires time to collect enough statistics. On the other hand, offline evaluation, a prevalent approach in the research literature, facilitates fast experiments but employs automatic metrics that are not guaranteed to represent the preferences of real users. In this work, we describe a novel way we employed to deal with this problem at JetBrains, by leveraging an online metric - the number of edits users introduce before committing the generated messages to the VCS - to select metrics for offline experiments. To support this new type of evaluation, we develop a novel markup collection tool mimicking the real workflow with a CMG system, collect a dataset with 57 pairs consisting of commit messages generated by GPT-4 and their counterparts edited by human experts, and design and verify a way to synthetically extend such a dataset. Then, we use the final dataset of 656 pairs to study how the widely used similarity metrics correlate with the online metric reflecting the real users' experience. Our results indicate that edit distance exhibits the highest correlation, whereas commonly used similarity metrics such as BLEU and METEOR demonstrate low correlation. This contradicts the previous studies on similarity metrics for CMG, suggesting that user interactions with a CMG system in real-world settings differ significantly from the responses by human labelers operating within controlled research environments. We release all the code and the dataset for researchers: https://jb.gg/cmg-evaluation.

  • 7 authors
·
Oct 15, 2024

Exposing Blindspots: Cultural Bias Evaluation in Generative Image Models

Generative image models produce striking visuals yet often misrepresent culture. Prior work has examined cultural bias mainly in text-to-image (T2I) systems, leaving image-to-image (I2I) editors underexplored. We bridge this gap with a unified evaluation across six countries, an 8-category/36-subcategory schema, and era-aware prompts, auditing both T2I generation and I2I editing under a standardized protocol that yields comparable diagnostics. Using open models with fixed settings, we derive cross-country, cross-era, and cross-category evaluations. Our framework combines standard automatic metrics, a culture-aware retrieval-augmented VQA, and expert human judgments collected from native reviewers. To enable reproducibility, we release the complete image corpus, prompts, and configurations. Our study reveals three findings: (1) under country-agnostic prompts, models default to Global-North, modern-leaning depictions that flatten cross-country distinctions; (2) iterative I2I editing erodes cultural fidelity even when conventional metrics remain flat or improve; and (3) I2I models apply superficial cues (palette shifts, generic props) rather than era-consistent, context-aware changes, often retaining source identity for Global-South targets. These results highlight that culture-sensitive edits remain unreliable in current systems. By releasing standardized data, prompts, and human evaluation protocols, we provide a reproducible, culture-centered benchmark for diagnosing and tracking cultural bias in generative image models.

  • 11 authors
·
Oct 22, 2025

Evaluation of GPT-3.5 and GPT-4 for supporting real-world information needs in healthcare delivery

Despite growing interest in using large language models (LLMs) in healthcare, current explorations do not assess the real-world utility and safety of LLMs in clinical settings. Our objective was to determine whether two LLMs can serve information needs submitted by physicians as questions to an informatics consultation service in a safe and concordant manner. Sixty six questions from an informatics consult service were submitted to GPT-3.5 and GPT-4 via simple prompts. 12 physicians assessed the LLM responses' possibility of patient harm and concordance with existing reports from an informatics consultation service. Physician assessments were summarized based on majority vote. For no questions did a majority of physicians deem either LLM response as harmful. For GPT-3.5, responses to 8 questions were concordant with the informatics consult report, 20 discordant, and 9 were unable to be assessed. There were 29 responses with no majority on "Agree", "Disagree", and "Unable to assess". For GPT-4, responses to 13 questions were concordant, 15 discordant, and 3 were unable to be assessed. There were 35 responses with no majority. Responses from both LLMs were largely devoid of overt harm, but less than 20% of the responses agreed with an answer from an informatics consultation service, responses contained hallucinated references, and physicians were divided on what constitutes harm. These results suggest that while general purpose LLMs are able to provide safe and credible responses, they often do not meet the specific information need of a given question. A definitive evaluation of the usefulness of LLMs in healthcare settings will likely require additional research on prompt engineering, calibration, and custom-tailoring of general purpose models.

  • 18 authors
·
Apr 26, 2023

Dual-Metric Evaluation of Social Bias in Large Language Models: Evidence from an Underrepresented Nepali Cultural Context

Large language models (LLMs) increasingly influence global digital ecosystems, yet their potential to perpetuate social and cultural biases remains poorly understood in underrepresented contexts. This study presents a systematic analysis of representational biases in seven state-of-the-art LLMs: GPT-4o-mini, Claude-3-Sonnet, Claude-4-Sonnet, Gemini-2.0-Flash, Gemini-2.0-Lite, Llama-3-70B, and Mistral-Nemo in the Nepali cultural context. Using Croissant-compliant dataset of 2400+ stereotypical and anti-stereotypical sentence pairs on gender roles across social domains, we implement an evaluation framework, Dual-Metric Bias Assessment (DMBA), combining two metrics: (1) agreement with biased statements and (2) stereotypical completion tendencies. Results show models exhibit measurable explicit agreement bias, with mean bias agreement ranging from 0.36 to 0.43 across decoding configurations, and an implicit completion bias rate of 0.740-0.755. Importantly, implicit completion bias follows a non-linear, U-shaped relationship with temperature, peaking at moderate stochasticity (T=0.3) and declining slightly at higher temperatures. Correlation analysis under different decoding settings revealed that explicit agreement strongly aligns with stereotypical sentence agreement but is a weak and often negative predictor of implicit completion bias, indicating generative bias is poorly captured by agreement metrics. Sensitivity analysis shows increasing top-p amplifies explicit bias, while implicit generative bias remains largely stable. Domain-level analysis shows implicit bias is strongest for race and sociocultural stereotypes, while explicit agreement bias is similar across gender and sociocultural categories, with race showing the lowest explicit agreement. These findings highlight the need for culturally grounded datasets and debiasing strategies for LLMs in underrepresented societies.

  • 2 authors
·
Mar 7

When F1 Fails: Granularity-Aware Evaluation for Dialogue Topic Segmentation

Dialogue topic segmentation supports summarization, retrieval, memory management, and conversational continuity. Despite decades of prior work, evaluation practice in dialogue topic segmentation remains dominated by strict boundary matching and F1-based metrics, even as modern LLM-based conversational systems increasingly rely on segmentation to manage conversation history beyond the model's fixed context window, where unstructured context accumulation degrades efficiency and coherence. This paper introduces an evaluation objective for dialogue topic segmentation that treats boundary density and segment coherence as primary criteria, alongside window-tolerant F1 (W-F1). Through extensive cross-dataset empirical evaluation, we show that reported performance differences across dialogue segmentation benchmarks are driven not by model quality, but by annotation granularity mismatches and sparse boundary labels. This indicates that many reported improvements arise from evaluation artifacts rather than improved boundary detection. We evaluated multiple, structurally distinct dialogue segmentation strategies across eight dialogue datasets spanning task-oriented, open-domain, meeting-style, and synthetic interactions. Across these settings, we observe high segment coherence combined with extreme oversegmentation relative to sparse labels, producing misleadingly low exact-match F1 scores. We show that topic segmentation is best understood as selecting an appropriate granularity rather than predicting a single correct boundary set. We operationalize this view by explicitly separating boundary scoring from boundary selection.

  • 1 authors
·
Dec 18, 2025

Benchmarks for Trajectory Safety Evaluation and Diagnosis in OpenClaw and Codex: ATBench-Claw and ATBench-CodeX

As agent systems move into increasingly diverse execution settings, trajectory-level safety evaluation and diagnosis require benchmarks that evolve with them. ATBench is a diverse and realistic agent trajectory benchmark for safety evaluation and diagnosis. This report presents ATBench-Claw and ATBench-CodeX, two domain-customized extensions that carry ATBench into the OpenClaw and OpenAI Codex / Codex-runtime settings. The key adaptation mechanism is to analyze each new setting, customize the three-dimensional Safety Taxonomy over risk source, failure mode, and real-world harm, and then use that customized taxonomy to define the benchmark specification consumed by the shared ATBench construction pipeline. This extensibility matters because agent frameworks remain relatively stable at the architectural level even as their concrete execution settings, tool ecosystems, and product capabilities evolve quickly. Concretely, ATBench-Claw targets OpenClaw-sensitive execution chains over tools, skills, sessions, and external actions, while ATBench-CodeX targets trajectories in the OpenAI Codex / Codex-runtime setting over repositories, shells, patches, dependencies, approvals, and runtime policy boundaries. Our emphasis therefore falls on taxonomy customization, domain-specific risk coverage, and benchmark design under a shared ATBench generation framework.

  • 9 authors
·
Apr 15