From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective optimization in protein design. Yet whether RL can push PLMs beyond their pretraining priors to uncover latent sequence-structure-function rules remains unclear. We address this by pairing RL with PLMs across four domains: antimicrobial peptide design, kinase variant optimization, antibody engineering, and inverse folding. Using diverse RL algorithms and model classes, we ask if RL improves sampling efficiency and, more importantly, if it reveals capabilities not captured by supervised learning. Across benchmarks, RL consistently boosts success rates and sample efficiency. Performance follows a three-factor interaction: task headroom, reward fidelity, and policy capacity jointly determine gains. When rewards are accurate and informative, policies have sufficient capacity, and tasks leave room beyond supervised baselines, improvements scale; when rewards are noisy or capacity is constrained, gains saturate despite exploration. This view yields practical guidance for RL in protein design: prioritize reward modeling and calibration before scaling policy size, match algorithm and regularization strength to task difficulty, and allocate capacity where marginal gains are largest. Implementation is available at https://github.com/chq1155/RL-PLM.

Agent KB: Leveraging Cross-Domain Experience for Agentic Problem Solving

As language agents tackle increasingly complex tasks, they struggle with effective error correction and experience reuse across domains. We introduce Agent KB, a hierarchical experience framework that enables complex agentic problem solving via a novel Reason-Retrieve-Refine pipeline. Agent KB addresses a core limitation: agents traditionally cannot learn from each other's experiences. By capturing both high-level strategies and detailed execution logs, Agent KB creates a shared knowledge base that enables cross-agent knowledge transfer. Evaluated on the GAIA benchmark, Agent KB improves success rates by up to 16.28 percentage points. On the most challenging tasks, Claude-3 improves from 38.46% to 57.69%, while GPT-4 improves from 53.49% to 73.26% on intermediate tasks. On SWE-bench code repair, Agent KB enables Claude-3 to improve from 41.33% to 53.33%. Our results suggest that Agent KB provides a modular, framework-agnostic infrastructure for enabling agents to learn from past experiences and generalize successful strategies to new tasks.

When to Trust Context: Self-Reflective Debates for Context Reliability

Large language models frequently encounter conflicts between their parametric knowledge and contextual input, often resulting in factual inconsistencies or hallucinations. We propose Self-Reflective Debate for Contextual Reliability (SR-DCR), a lightweight framework that integrates token-level self-confidence with an asymmetric multi-agent debate to adjudicate such conflicts. A critic, deprived of context, challenges a defender who argues from the given passage; a judge model evaluates the debate and determines the context's reliability. The final answer is selected by combining the verdict with model confidence. Experiments on the ClashEval benchmark demonstrate that SR-DCR consistently enhances robustness to misleading context while maintaining accuracy on trustworthy inputs, outperforming both classical debate and confidence-only baselines with minimal computational overhead. The code is available at https://github.com/smiles724/Self-Reflective-Debates.

Large Language Models are Good Relational Learners

Large language models (LLMs) have demonstrated remarkable capabilities across various domains, yet their application to relational deep learning (RDL) remains underexplored. Existing approaches adapt LLMs by traversing relational links between entities in a database and converting the structured data into flat text documents. Still, this text-based serialization disregards critical relational structures, introduces redundancy, and often exceeds standard LLM context lengths. We introduce Rel-LLM, a novel architecture that utilizes a graph neural network (GNN)- based encoder to generate structured relational prompts for LLMs within a retrieval-augmented generation (RAG) framework. Unlike traditional text-based serialization approaches, our method preserves the inherent relational structure of databases while enabling LLMs to effectively process and reason over complex entity relationships. Specifically, the GNN encoder extracts a local subgraph around an entity to build feature representations that contain relevant entity relationships and temporal dependencies. These representations are transformed into structured prompts using a denormalization process, effectively allowing the LLM to reason over relational structures. Through extensive experiments, we demonstrate that Rel-LLM outperforms existing methods on key RDL tasks, offering a scalable and efficient approach to integrating LLMs with structured data sources. Code is available at https://github.com/smiles724/Rel-LLM.

AnchorAttention: Difference-Aware Sparse Attention with Stripe Granularity

Large Language Models (LLMs) with extended context lengths face significant computational challenges during the pre-filling phase, primarily due to the quadratic complexity of self-attention. Existing methods typically employ dynamic pattern matching and block-sparse low-level implementations. However, their reliance on local information for pattern identification fails to capture global contexts, and the coarse granularity of blocks leads to persistent internal sparsity, resulting in suboptimal accuracy and efficiency. To address these limitations, we propose \textbf{AnchorAttention}, a difference-aware, dynamic sparse attention mechanism that efficiently identifies critical attention regions at a finer stripe granularity while adapting to global contextual information, achieving superior speed and accuracy. AnchorAttention comprises three key components: (1) \textbf{Pattern-based Anchor Computation}, leveraging the commonalities present across all inputs to rapidly compute a set of near-maximum scores as the anchor; (2) \textbf{Difference-aware Stripe Sparsity Identification}, performing difference-aware comparisons with the anchor to quickly obtain discrete coordinates of significant regions in a stripe-like sparsity pattern; (3) \textbf{Fine-grained Sparse Computation}, replacing the traditional contiguous KV block loading approach with simultaneous discrete KV position loading to maximize sparsity rates while preserving full hardware computational potential. With its finer-grained sparsity strategy, \textbf{AnchorAttention} achieves higher sparsity rates at the same recall level, significantly reducing computation time. Compared to previous state-of-the-art methods, at a text length of 128k, it achieves a speedup of 1.44$\times$ while maintaining higher recall rates.

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.

LocAgent: Graph-Guided LLM Agents for Code Localization

Code localization--identifying precisely where in a codebase changes need to be made--is a fundamental yet challenging task in software maintenance. Existing approaches struggle to efficiently navigate complex codebases when identifying relevant code sections. The challenge lies in bridging natural language problem descriptions with the appropriate code elements, often requiring reasoning across hierarchical structures and multiple dependencies. We introduce LocAgent, a framework that addresses code localization through graph-based representation. By parsing codebases into directed heterogeneous graphs, LocAgent creates a lightweight representation that captures code structures (files, classes, functions) and their dependencies (imports, invocations, inheritance), enabling LLM agents to effectively search and locate relevant entities through powerful multi-hop reasoning. Experimental results on real-world benchmarks demonstrate that our approach significantly enhances accuracy in code localization. Notably, our method with the fine-tuned Qwen-2.5-Coder-Instruct-32B model achieves comparable results to SOTA proprietary models at greatly reduced cost (approximately 86% reduction), reaching up to 92.7% accuracy on file-level localization while improving downstream GitHub issue resolution success rates by 12% for multiple attempts (Pass@10). Our code is available at https://github.com/gersteinlab/LocAgent.

MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. While modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains under-explored. In this paper, we follow the guidance of the central dogma to redesign both the data and model pipeline and offer a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions of both coding and non-coding regions with masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive Experiments show that Life-Code achieves state-of-the-art performance on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

Retrieval-Reasoning Large Language Model-based Synthetic Clinical Trial Generation

Machine learning (ML) exhibits promise in the clinical domain. However, it is constrained by data scarcity and ethical considerations, as the generation of clinical trials presents significant challenges due to stringent privacy regulations, high costs, and the extended duration required for conducting studies with human participants. Despite the advancements of large language models (LLMs) in general generation tasks, their potential in facilitating the generation of synthetic clinical trials is under-explored. To address this gap, we introduce a novel Retrieval-Reasoning few-shot framework that leverages LLMs to generate artificial yet realistic and diverse clinical trials with binary success/failure labels. Experiments conducted on real clinical trials from the \url{ClinicalTrials.gov} database demonstrate that our synthetic data can effectively augment real datasets. Furthermore, by fine-tuning a pre-trained model as a binary classifier on synthetic clinical trial datasets, we demonstrate that this augmentation enhances model training for downstream tasks such as trial outcome prediction. Our findings suggest that LLMs for synthetic clinical trial generation hold promise for accelerating clinical research and upholding ethical standards for patient privacy. The code is publicly available at https://anonymous.4open.science/r/Retrieval_Reasoning_Clinical_Trial_Generation-3EC4.