Xiangru Tang

Xiangru Tang, Anni Zou, Zhuosheng Zhang et al.

Large language models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare. This field faces unique challenges such as domain-specific terminologies and reasoning over specialized knowledge. To address these issues, we propose MedAgents, a novel multi-disciplinary collaboration framework for the medical domain. MedAgents leverages LLM-based agents in a role-playing setting that participate in a collaborative multi-round discussion, thereby enhancing LLM proficiency and reasoning capabilities. This training-free framework encompasses five critical steps: gathering domain experts, proposing individual analyses, summarising these analyses into a report, iterating over discussions until a consensus is reached, and ultimately making a decision. Our work focuses on the zero-shot setting, which is applicable in real-world scenarios. Experimental results on nine datasets (MedQA, MedMCQA, PubMedQA, and six subtasks from MMLU) establish that our proposed MedAgents framework excels at mining and harnessing the medical expertise within LLMs, as well as extending its reasoning abilities. Our code can be found at https://github.com/gersteinlab/MedAgents.

Zhuosheng Zhang, Yao Yao, Aston Zhang et al.

Large language models (LLMs) have dramatically enhanced the field of language intelligence, as demonstrably evidenced by their formidable empirical performance across a spectrum of complex reasoning tasks. Additionally, theoretical proofs have illuminated their emergent reasoning capabilities, providing a compelling showcase of their advanced cognitive abilities in linguistic contexts. Critical to their remarkable efficacy in handling complex reasoning tasks, LLMs leverage the intriguing chain-of-thought (CoT) reasoning techniques, obliging them to formulate intermediate steps en route to deriving an answer. The CoT reasoning approach has not only exhibited proficiency in amplifying reasoning performance but also in enhancing interpretability, controllability, and flexibility. In light of these merits, recent research endeavors have extended CoT reasoning methodologies to nurture the development of autonomous language agents, which adeptly adhere to language instructions and execute actions within varied environments. This survey paper orchestrates a thorough discourse, penetrating vital research dimensions, encompassing: (i) the foundational mechanics of CoT techniques, with a focus on elucidating the circumstances and justification behind its efficacy; (ii) the paradigm shift in CoT; and (iii) the burgeoning of language agents fortified by CoT approaches. Prospective research avenues envelop explorations into generalization, efficiency, customization, scaling, and safety. This paper caters to a wide audience, including beginners seeking comprehensive knowledge of CoT reasoning and language agents, as well as experienced researchers interested in foundational mechanics and engaging in cutting-edge discussions on these topics. A repository for the related papers is available at https://github.com/Zoeyyao27/CoT-Igniting-Agent.

Cunxiang Wang, Xiaoze Liu, Yuanhao Yue et al. · pku

This survey addresses the crucial issue of factuality in Large Language Models (LLMs). As LLMs find applications across diverse domains, the reliability and accuracy of their outputs become vital. We define the Factuality Issue as the probability of LLMs to produce content inconsistent with established facts. We first delve into the implications of these inaccuracies, highlighting the potential consequences and challenges posed by factual errors in LLM outputs. Subsequently, we analyze the mechanisms through which LLMs store and process facts, seeking the primary causes of factual errors. Our discussion then transitions to methodologies for evaluating LLM factuality, emphasizing key metrics, benchmarks, and studies. We further explore strategies for enhancing LLM factuality, including approaches tailored for specific domains. We focus two primary LLM configurations standalone LLMs and Retrieval-Augmented LLMs that utilizes external data, we detail their unique challenges and potential enhancements. Our survey offers a structured guide for researchers aiming to fortify the factual reliability of LLMs.

Yilun Zhao, Yitao Long, Hongjun Liu et al.

Recent LLMs have demonstrated remarkable performance in solving exam-like math word problems. However, the degree to which these numerical reasoning skills are effective in real-world scenarios, particularly in expert domains, is still largely unexplored. This paper introduces DocMath-Eval, a comprehensive benchmark specifically designed to evaluate the numerical reasoning capabilities of LLMs in the context of understanding and analyzing specialized documents containing both text and tables. We conduct an extensive evaluation of 48 LLMs with Chain-of-Thought and Program-of-Thought prompting methods, aiming to comprehensively assess the capabilities and limitations of existing LLMs in DocMath-Eval. We found that even the current best-performing system (i.e., GPT-4o) still significantly lags behind human experts in solving complex numerical reasoning problems grounded in long contexts. We believe that DocMath-Eval can serve as a valuable benchmark for evaluating LLMs' capabilities in solving challenging numerical reasoning problems within expert domains.

Sirui Hong, Yizhang Lin, Bang Liu et al. · tencent-ai, tsinghua

Large Language Model (LLM)-based agents have shown effectiveness across many applications. However, their use in data science scenarios requiring solving long-term interconnected tasks, dynamic data adjustments and domain expertise remains challenging. Previous approaches primarily focus on individual tasks, making it difficult to assess the complete data science workflow. Moreover, they struggle to handle real-time changes in intermediate data and fail to adapt dynamically to evolving task dependencies inherent to data science problems. In this paper, we present Data Interpreter, an LLM-based agent designed to automatically solve various data science problems end-to-end. Our Data Interpreter incorporates two key modules: 1) Hierarchical Graph Modeling, which breaks down complex problems into manageable subproblems, enabling dynamic node generation and graph optimization; and 2) Programmable Node Generation, a technique that refines and verifies each subproblem to iteratively improve code generation results and robustness. Extensive experiments consistently demonstrate the superiority of Data Interpreter. On InfiAgent-DABench, it achieves a 25% performance boost, raising accuracy from 75.9% to 94.9%. For machine learning and open-ended tasks, it improves performance from 88% to 95%, and from 60% to 97%, respectively. Moreover, on the MATH dataset, Data Interpreter achieves remarkable performance with a 26% improvement compared to state-of-the-art baselines. The code is available at https://github.com/geekan/MetaGPT.

Stella Biderman, Hailey Schoelkopf, Lintang Sutawika et al. · cmu

Effective evaluation of language models remains an open challenge in NLP. Researchers and engineers face methodological issues such as the sensitivity of models to evaluation setup, difficulty of proper comparisons across methods, and the lack of reproducibility and transparency. In this paper we draw on three years of experience in evaluating large language models to provide guidance and lessons for researchers. First, we provide an overview of common challenges faced in language model evaluation. Second, we delineate best practices for addressing or lessening the impact of these challenges on research. Third, we present the Language Model Evaluation Harness (lm-eval): an open source library for independent, reproducible, and extensible evaluation of language models that seeks to address these issues. We describe the features of the library as well as case studies in which the library has been used to alleviate these methodological concerns.

Weizhen Li, Jianbo Lin, Zhuosong Jiang et al.

Recent advances in large language models (LLMs) and multi-agent systems have demonstrated remarkable capabilities in complex problem-solving tasks such as deep research, vibe coding, and mathematical reasoning. However, most existing multi-agent systems are built upon manual prompt/workflow engineering with sophisticated agent frameworks, making them computationally inefficient, less capable, and can not benefit from data-centric learning. In this work, we introduce Chain-of-Agents (CoA), a novel paradigm of LLM reasoning that enables native end-to-end complex problem-solving in the same way as a multi-agent system (i.e., multi-turn problem solving with multiple tools and multiple agents) within one model. In chain-of-agents problem-solving, the model dynamically activates different tool agents and role-playing agents to simulate multi-agent collaboration in an end-to-end fashion. To elicit end-to-end chain-of-agents problem-solving abilities in LLMs, we introduce a multi-agent distillation framework to distill state-of-the-art multi-agent systems into chain-of-agents trajectories for agentic supervised fine-tuning. We then use agentic reinforcement learning on verifiable agentic tasks to further improve the models' capabilities on chain-of-agents problem solving. We call the resulting models Agent Foundation Models (AFMs). Our empirical studies demonstrate that AFM establishes new state-of-the-art performance across diverse benchmarks in both web agent and code agent settings. We make the entire research, including the model weights, code for training and evaluation, and the training data, fully open-sourced, which offers a solid starting point for future research on agent models and agentic RL.

Xiangru Tang, Zhuoyun Yu, Jiapeng Chen et al.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Yutong Bian, Xianhao Lin, Yupeng Xie et al.

Large Language Models (LLMs) and code agents in software development are rapidly evolving from generating isolated code snippets to producing full-fledged software applications with graphical interfaces, interactive logic, and dynamic behaviors. However, current benchmarks fall short in evaluating such production-ready software, as they often rely on static checks or binary pass/fail scripts, failing to capture the interactive behaviors and runtime dynamics that define real-world usability - qualities that only emerge when an application is actively used. This is the blind spot of current evaluation: you don't know if an app works until you click through it, interact with it, and observe how it responds. To bridge this gap, we introduce RealDevWorld, a novel evaluation framework for automated end-to-end assessment of LLMs' ability to generate production-ready repositories from scratch. It features two key components: (1) RealDevBench, a diverse collection of 194 open-ended software engineering tasks across multiple domains, incorporating multimodal elements to reflect real-world complexity; and (2) AppEvalPilot, a new agent-as-a-judge evaluation system that simulates realistic, GUI-based user interactions to automatically and holistically assess software functional correctness, visual fidelity, and runtime behavior. The framework delivers fine-grained, task-specific diagnostic feedback, supporting nuanced evaluation beyond simple success/failure judgments. Empirical results show that RealDevWorld delivers effective, automatic, and human-aligned evaluations, achieving an accuracy of 0.92 and a correlation of 0.85 with expert human assessments, while significantly reducing the reliance on manual review. This enables scalable, human-aligned assessment of production-level software generated by LLMs. Our code is available on GitHub.

Ran Xu, Yuchen Zhuang, Yishan Zhong et al. · gatech

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.

Xiangru Tang, Qiao Jin, Kunlun Zhu et al.

AI scientists powered by large language models have demonstrated substantial promise in autonomously conducting experiments and facilitating scientific discoveries across various disciplines. While their capabilities are promising, these agents also introduce novel vulnerabilities that require careful consideration for safety. However, there has been limited comprehensive exploration of these vulnerabilities. This perspective examines vulnerabilities in AI scientists, shedding light on potential risks associated with their misuse, and emphasizing the need for safety measures. We begin by providing an overview of the potential risks inherent to AI scientists, taking into account user intent, the specific scientific domain, and their potential impact on the external environment. Then, we explore the underlying causes of these vulnerabilities and provide a scoping review of the limited existing works. Based on our analysis, we propose a triadic framework involving human regulation, agent alignment, and an understanding of environmental feedback (agent regulation) to mitigate these identified risks. Furthermore, we highlight the limitations and challenges associated with safeguarding AI scientists and advocate for the development of improved models, robust benchmarks, and comprehensive regulations.

Tiannan Wang, Jiamin Chen, Qingrui Jia et al.

This work introduces Weaver, our first family of large language models (LLMs) dedicated to content creation. Weaver is pre-trained on a carefully selected corpus that focuses on improving the writing capabilities of large language models. We then fine-tune Weaver for creative and professional writing purposes and align it to the preference of professional writers using a suit of novel methods for instruction data synthesis and LLM alignment, making it able to produce more human-like texts and follow more diverse instructions for content creation. The Weaver family consists of models of Weaver Mini (1.8B), Weaver Base (6B), Weaver Pro (14B), and Weaver Ultra (34B) sizes, suitable for different applications and can be dynamically dispatched by a routing agent according to query complexity to balance response quality and computation cost. Evaluation on a carefully curated benchmark for assessing the writing capabilities of LLMs shows Weaver models of all sizes outperform generalist LLMs several times larger than them. Notably, our most-capable Weaver Ultra model surpasses GPT-4, a state-of-the-art generalist LLM, on various writing scenarios, demonstrating the advantage of training specialized LLMs for writing purposes. Moreover, Weaver natively supports retrieval-augmented generation (RAG) and function calling (tool usage). We present various use cases of these abilities for improving AI-assisted writing systems, including integration of external knowledge bases, tools, or APIs, and providing personalized writing assistance. Furthermore, we discuss and summarize a guideline and best practices for pre-training and fine-tuning domain-specific LLMs.

Jiajun Shi, Jian Yang, Jiaheng Liu et al.

Recent advancements in large language models (LLMs) underscore the need for more comprehensive evaluation methods to accurately assess their reasoning capabilities. Existing benchmarks are often domain-specific and thus cannot fully capture an LLM's general reasoning potential. To address this limitation, we introduce the Knowledge Orthogonal Reasoning Gymnasium (KORGym), a dynamic evaluation platform inspired by KOR-Bench and Gymnasium. KORGym offers over fifty games in either textual or visual formats and supports interactive, multi-turn assessments with reinforcement learning scenarios. Using KORGym, we conduct extensive experiments on 19 LLMs and 8 VLMs, revealing consistent reasoning patterns within model families and demonstrating the superior performance of closed-source models. Further analysis examines the effects of modality, reasoning strategies, reinforcement learning techniques, and response length on model performance. We expect KORGym to become a valuable resource for advancing LLM reasoning research and developing evaluation methodologies suited to complex, interactive environments.

Chunyuan Deng, Yilun Zhao, Yuzhao Heng et al.

Data contamination has garnered increased attention in the era of large language models (LLMs) due to the reliance on extensive internet-derived training corpora. The issue of training corpus overlap with evaluation benchmarks--referred to as contamination--has been the focus of significant recent research. This body of work aims to identify contamination, understand its impacts, and explore mitigation strategies from diverse perspectives. However, comprehensive studies that provide a clear pathway from foundational concepts to advanced insights are lacking in this nascent field. Therefore, we present a comprehensive survey in the field of data contamination, laying out the key issues, methodologies, and findings to date, and highlighting areas in need of further research and development. In particular, we begin by examining the effects of data contamination across various stages and forms. We then provide a detailed analysis of current contamination detection methods, categorizing them to highlight their focus, assumptions, strengths, and limitations. We also discuss mitigation strategies, offering a clear guide for future research. This survey serves as a succinct overview of the most recent advancements in data contamination research, providing a straightforward guide for the benefit of future research endeavors.

Bo Peng, Eric Alcaide, Quentin Anthony et al.

Transformers have revolutionized almost all natural language processing (NLP) tasks but suffer from memory and computational complexity that scales quadratically with sequence length. In contrast, recurrent neural networks (RNNs) exhibit linear scaling in memory and computational requirements but struggle to match the same performance as Transformers due to limitations in parallelization and scalability. We propose a novel model architecture, Receptance Weighted Key Value (RWKV), that combines the efficient parallelizable training of transformers with the efficient inference of RNNs. Our approach leverages a linear attention mechanism and allows us to formulate the model as either a Transformer or an RNN, thus parallelizing computations during training and maintains constant computational and memory complexity during inference. We scale our models as large as 14 billion parameters, by far the largest dense RNN ever trained, and find RWKV performs on par with similarly sized Transformers, suggesting future work can leverage this architecture to create more efficient models. This work presents a significant step towards reconciling trade-offs between computational efficiency and model performance in sequence processing tasks.