MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale

We introduce MedAgentGYM, the first publicly available training environment designed to enhance coding-based medical reasoning capabilities in large language model (LLM) agents. MedAgentGYM comprises 72,413 task instances across 129 categories derived from authentic real-world biomedical scenarios. Tasks are encapsulated within executable coding environments, each featuring detailed task descriptions, interactive feedback mechanisms, verifiable ground-truth annotations, and scalable training trajectory generation. Extensive benchmarking of over 30 LLMs reveals a notable performance disparity between commercial API-based models and open-source counterparts. Leveraging MedAgentGYM, Med-Copilot-7B achieves substantial performance gains through supervised fine-tuning (+36.44%) and continued reinforcement learning (+42.47%), emerging as an affordable and privacy-preserving alternative competitive with gpt-4o. By offering both a comprehensive benchmark and accessible, expandable training resources within unified execution environments, MedAgentGYM delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical research and practice.

MSQA: Benchmarking LLMs on Graduate-Level Materials Science Reasoning and Knowledge

Despite recent advances in large language models (LLMs) for materials science, there is a lack of benchmarks for evaluating their domain-specific knowledge and complex reasoning abilities. To bridge this gap, we introduce MSQA, a comprehensive evaluation benchmark of 1,757 graduate-level materials science questions in two formats: detailed explanatory responses and binary True/False assessments. MSQA distinctively challenges LLMs by requiring both precise factual knowledge and multi-step reasoning across seven materials science sub-fields, such as structure-property relationships, synthesis processes, and computational modeling. Through experiments with 10 state-of-the-art LLMs, we identify significant gaps in current LLM performance. While API-based proprietary LLMs achieve up to 84.5% accuracy, open-source (OSS) LLMs peak around 60.5%, and domain-specific LLMs often underperform significantly due to overfitting and distributional shifts. MSQA represents the first benchmark to jointly evaluate the factual and reasoning capabilities of LLMs crucial for LLMs in advanced materials science.

WorkForceAgent-R1: Incentivizing Reasoning Capability in LLM-based Web Agents via Reinforcement Learning

Large language models (LLMs)-empowered web agents enables automating complex, real-time web navigation tasks in enterprise environments. However, existing web agents relying on supervised fine-tuning (SFT) often struggle with generalization and robustness due to insufficient reasoning capabilities when handling the inherently dynamic nature of web interactions. In this study, we introduce WorkForceAgent-R1, an LLM-based web agent trained using a rule-based R1-style reinforcement learning framework designed explicitly to enhance single-step reasoning and planning for business-oriented web navigation tasks. We employ a structured reward function that evaluates both adherence to output formats and correctness of actions, enabling WorkForceAgent-R1 to implicitly learn robust intermediate reasoning without explicit annotations or extensive expert demonstrations. Extensive experiments on the WorkArena benchmark demonstrate that WorkForceAgent-R1 substantially outperforms SFT baselines by 10.26-16.59%, achieving competitive performance relative to proprietary LLM-based agents (gpt-4o) in workplace-oriented web navigation tasks.

Towards Better Instruction Following Retrieval Models

Modern information retrieval (IR) models, trained exclusively on standard <query, passage> pairs, struggle to effectively interpret and follow explicit user instructions. We introduce InF-IR, a large-scale, high-quality training corpus tailored for enhancing retrieval models in Instruction-Following IR. InF-IR expands traditional training pairs into over 38,000 expressive <instruction, query, passage> triplets as positive samples. In particular, for each positive triplet, we generate two additional hard negative examples by poisoning both instructions and queries, then rigorously validated by an advanced reasoning model (o3-mini) to ensure semantic plausibility while maintaining instructional incorrectness. Unlike existing corpora that primarily support computationally intensive reranking tasks for decoder-only language models, the highly contrastive positive-negative triplets in InF-IR further enable efficient representation learning for smaller encoder-only models, facilitating direct embedding-based retrieval. Using this corpus, we train InF-Embed, an instruction-aware Embedding model optimized through contrastive learning and instruction-query attention mechanisms to align retrieval outcomes precisely with user intents. Extensive experiments across five instruction-based retrieval benchmarks demonstrate that InF-Embed significantly surpasses competitive baselines by 8.1% in p-MRR, measuring the instruction-following capabilities.

AmorLIP: Efficient Language-Image Pretraining via Amortization

Contrastive Language-Image Pretraining (CLIP) has demonstrated strong zero-shot performance across diverse downstream text-image tasks. Existing CLIP methods typically optimize a contrastive objective using negative samples drawn from each minibatch. To achieve robust representation learning, these methods require extremely large batch sizes and escalate computational demands to hundreds or even thousands of GPUs. Prior approaches to mitigate this issue often compromise downstream performance, prolong training duration, or face scalability challenges with very large datasets. To overcome these limitations, we propose AmorLIP, an efficient CLIP pretraining framework that amortizes expensive computations involved in contrastive learning through lightweight neural networks, which substantially improves training efficiency and performance. Leveraging insights from a spectral factorization of energy-based models, we introduce novel amortization objectives along with practical techniques to improve training stability. Extensive experiments across 38 downstream tasks demonstrate the superior zero-shot classification and retrieval capabilities of AmorLIP, consistently outperforming standard CLIP baselines with substantial relative improvements of up to 12.24%.

MLE-Dojo: Interactive Environments for Empowering LLM Agents in Machine Learning Engineering

We introduce MLE-Dojo, a Gym-style framework for systematically reinforcement learning, evaluating, and improving autonomous large language model (LLM) agents in iterative machine learning engineering (MLE) workflows. Unlike existing benchmarks that primarily rely on static datasets or single-attempt evaluations, MLE-Dojo provides an interactive environment enabling agents to iteratively experiment, debug, and refine solutions through structured feedback loops. Built upon 200+ real-world Kaggle challenges, MLE-Dojo covers diverse, open-ended MLE tasks carefully curated to reflect realistic engineering scenarios such as data processing, architecture search, hyperparameter tuning, and code debugging. Its fully executable environment supports comprehensive agent training via both supervised fine-tuning and reinforcement learning, facilitating iterative experimentation, realistic data sampling, and real-time outcome verification. Extensive evaluations of eight frontier LLMs reveal that while current models achieve meaningful iterative improvements, they still exhibit significant limitations in autonomously generating long-horizon solutions and efficiently resolving complex errors. Furthermore, MLE-Dojo's flexible and extensible architecture seamlessly integrates diverse data sources, tools, and evaluation protocols, uniquely enabling model-based agent tuning and promoting interoperability, scalability, and reproducibility. We open-source our framework and benchmarks to foster community-driven innovation towards next-generation MLE agents.

Collab-RAG: Boosting Retrieval-Augmented Generation for Complex Question Answering via White-Box and Black-Box LLM Collaboration

Retrieval-Augmented Generation (RAG) systems often struggle to handle multi-hop question-answering tasks accurately due to irrelevant context retrieval and limited complex reasoning capabilities. We introduce Collab-RAG, a collaborative training framework that leverages mutual enhancement between a white-box small language model (SLM) and a blackbox large language model (LLM) for RAG. Specifically, the SLM decomposes complex queries into simpler sub-questions, thus enhancing the accuracy of the retrieval and facilitating more effective reasoning by the black-box LLM. Concurrently, the black-box LLM provides feedback signals to improve the SLM's decomposition capability. We observe that Collab-RAG relies solely on supervision from an affordable black-box LLM without additional distillation from frontier LLMs, yet demonstrates strong generalization across multiple black-box LLMs. Experimental evaluations across five multi-hop QA datasets demonstrate that Collab-RAG substantially outperforms existing black-box-only and SLM fine-tuning baselines by 1.8%-14.2% on average. In particular, our fine-tuned 3B SLM surpasses a frozen 32B LLM in question decomposition, highlighting the efficiency of Collab-RAG in improving reasoning and retrieval for complex questions. The code of Collab-RAG is available on https://github.com/ritaranx/Collab-RAG/.

Hephaestus: Improving Fundamental Agent Capabilities of Large Language Models through Continual Pre-Training

Due to the scarcity of agent-oriented pre-training data, LLM-based autonomous agents typically rely on complex prompting or extensive fine-tuning, which often fails to introduce new capabilities while preserving strong generalizability. We introduce Hephaestus-Forge, the first large-scale pre-training corpus designed to enhance the fundamental capabilities of LLM agents in API function calling, intrinsic reasoning and planning, and adapting to environmental feedback. Hephaestus-Forge comprises 103B agent-specific data encompassing 76,537 APIs, including both tool documentation to introduce knowledge of API functions and function calling trajectories to strengthen intrinsic reasoning. To explore effective training protocols, we investigate scaling laws to identify the optimal recipe in data mixing ratios. By continual pre-training on Hephaestus-Forge, Hephaestus outperforms small- to medium-scale open-source LLMs and rivals commercial LLMs on three agent benchmarks, demonstrating the effectiveness of our pre-training corpus in enhancing fundamental agentic capabilities and generalization of LLMs to new tasks or environments.

Matryoshka: Learning to Drive Black-Box LLMs with LLMs

Despite the impressive generative abilities of black-box large language models (LLMs), their inherent opacity hinders further advancements in capabilities such as reasoning, planning, and personalization. Existing works aim to enhance LLM capabilities via domain-specific adaptation or in-context learning, which require additional training on accessible model parameters, an infeasible option for black-box LLMs. To address this challenge, we introduce Matryoshika, a lightweight white-box LLM controller that guides a large-scale black-box LLM generator by decomposing complex tasks into a series of intermediate outputs. Specifically, we consider the black-box LLM as an environment, with Matryoshika serving as a policy to provide intermediate guidance through prompts for driving the black-box LLM. Matryoshika is trained to pivot the outputs of the black-box LLM aligning with preferences during iterative interaction, which enables controllable multi-turn generation and self-improvement in optimizing intermediate guidance. Empirical evaluations on three diverse tasks demonstrate that Matryoshika effectively enhances the capabilities of black-box LLMs in complex, long-horizon tasks, including reasoning, planning, and personalization. By leveraging this pioneering controller-generator framework to mitigate dependence on model parameters, Matryoshika provides a transparent and practical solution for improving black-box LLMs through controllable multi-turn generation using white-box LLMs.

Efficient Evolutionary Search Over Chemical Space with Large Language Models

Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations. Our code is available at http://github.com/zoom-wang112358/MOLLEO