Daily Papers

Large language models (LLMs) struggle to effectively utilize a growing number of external tools, such as those defined by the Model Context Protocol (MCP)IntroducingMCP, due to prompt bloat and selection complexity. We introduce RAG-MCP, a Retrieval-Augmented Generation framework that overcomes this challenge by offloading tool discovery. RAG-MCP uses semantic retrieval to identify the most relevant MCP(s) for a given query from an external index before engaging the LLM. Only the selected tool descriptions are passed to the model, drastically reducing prompt size and simplifying decision-making. Experiments, including an MCP stress test, demonstrate RAG-MCP significantly cuts prompt tokens (e.g., by over 50%) and more than triples tool selection accuracy (43.13% vs 13.62% baseline) on benchmark tasks. RAG-MCP enables scalable and accurate tool integration for LLMs.

As Large Language Models (LLMs) evolve from passive text generators to active reasoning agents capable of tool interaction, the Model Context Protocol (MCP) has emerged as a standardized framework for dynamic tool discovery and orchestration. Despite widespread industry adoption, existing evaluation methodologies fail to adequately assess tool utilization capabilities within this new paradigm. This paper introduces MCP-RADAR, the first comprehensive benchmark specifically designed to evaluate LLM performance in the MCP framework through a novel five-dimensional approach measuring: answer accuracy, tool selection efficiency, computational resource efficiency, parameter construction accuracy, and execution speed. Unlike conventional benchmarks that rely on subjective human evaluations or binary success metrics, MCP-RADAR employs objective, quantifiable measurements across multiple task domains including software engineering, mathematical reasoning, and general problem-solving. Our evaluations of leading commercial and open-source LLMs reveal distinctive capability profiles with significant trade-offs between accuracy, efficiency, and speed, challenging traditional single-metric performance rankings. Besides, we provide valuable guidance for developers to optimize their tools for maximum model compatibility and effectiveness. While focused on MCP due to its standardized approach, our methodology remains applicable across all LLM agent tool integration frameworks, providing valuable insights for both LLM developers and tool creators to optimize the entire LLM-tool interaction ecosystem. The implementation, configurations, and datasets used in our evaluation are publicly available at https://anonymous.4open.science/r/MCPRadar-B143.

Large reasoning models have demonstrated strong problem-solving abilities, yet real-world tasks often require external tools and long-horizon interactions. Existing agent frameworks typically follow predefined workflows, which limit autonomous and global task completion. In this paper, we introduce DeepAgent, an end-to-end deep reasoning agent that performs autonomous thinking, tool discovery, and action execution within a single, coherent reasoning process. To address the challenges of long-horizon interactions, particularly the context length explosion from multiple tool calls and the accumulation of interaction history, we introduce an autonomous memory folding mechanism that compresses past interactions into structured episodic, working, and tool memories, reducing error accumulation while preserving critical information. To teach general-purpose tool use efficiently and stably, we develop an end-to-end reinforcement learning strategy, namely ToolPO, that leverages LLM-simulated APIs and applies tool-call advantage attribution to assign fine-grained credit to the tool invocation tokens. Extensive experiments on eight benchmarks, including general tool-use tasks (ToolBench, API-Bank, TMDB, Spotify, ToolHop) and downstream applications (ALFWorld, WebShop, GAIA, HLE), demonstrate that DeepAgent consistently outperforms baselines across both labeled-tool and open-set tool retrieval scenarios. This work takes a step toward more general and capable agents for real-world applications. The code and demo are available at https://github.com/RUC-NLPIR/DeepAgent.

AlphaEvolve is a generic evolutionary coding agent that combines the generative capabilities of LLMs with automated evaluation in an iterative evolutionary framework that proposes, tests, and refines algorithmic solutions to challenging scientific and practical problems. In this paper we showcase AlphaEvolve as a tool for autonomously discovering novel mathematical constructions and advancing our understanding of long-standing open problems. To demonstrate its breadth, we considered a list of 67 problems spanning mathematical analysis, combinatorics, geometry, and number theory. The system rediscovered the best known solutions in most of the cases and discovered improved solutions in several. In some instances, AlphaEvolve is also able to generalize results for a finite number of input values into a formula valid for all input values. Furthermore, we are able to combine this methodology with Deep Think and AlphaProof in a broader framework where the additional proof-assistants and reasoning systems provide automated proof generation and further mathematical insights. These results demonstrate that large language model-guided evolutionary search can autonomously discover mathematical constructions that complement human intuition, at times matching or even improving the best known results, highlighting the potential for significant new ways of interaction between mathematicians and AI systems. We present AlphaEvolve as a powerful new tool for mathematical discovery, capable of exploring vast search spaces to solve complex optimization problems at scale, often with significantly reduced requirements on preparation and computation time.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

Ligand strain energy, the energy difference between the bound and unbound conformations of a ligand, is an important component of structure-based small molecule drug design. A large majority of observed ligands in protein-small molecule co-crystal structures bind in low-strain conformations, making strain energy a useful filter for structure-based drug design. In this work we present a tool for calculating ligand strain with a high accuracy. StrainRelief uses a MACE Neural Network Potential (NNP), trained on a large database of Density Functional Theory (DFT) calculations to estimate ligand strain of neutral molecules with quantum accuracy. We show that this tool estimates strain energy differences relative to DFT to within 1.4 kcal/mol, more accurately than alternative NNPs. These results highlight the utility of NNPs in drug discovery, and provide a useful tool for drug discovery teams.

Identifying recurring patterns and rare events in large-scale signals is a fundamental challenge in fields such as astronomy, physical simulations, and biomedical science. Convolutional Dictionary Learning (CDL) offers a powerful framework for modeling local structures in signals, but its use for detecting rare or anomalous events remains largely unexplored. In particular, CDL faces two key challenges in this setting: high computational cost and sensitivity to artifacts and outliers. In this paper, we introduce RoseCDL, a scalable and robust CDL algorithm designed for unsupervised rare event detection in long signals. RoseCDL combines stochastic windowing for efficient training on large datasets with inline outlier detection to enhance robustness and isolate anomalous patterns. This reframes CDL as a practical tool for event discovery and characterization in real-world signals, extending its role beyond traditional tasks like compression or denoising.

Designing effective agentic systems requires the seamless composition and integration of agents, tools, and models within dynamic and uncertain environments. Most existing methods rely on static, semantic retrieval approaches for tool or agent discovery. However, effective reuse and composition of existing components remain challenging due to incomplete capability descriptions and the limitations of retrieval methods. Component selection suffers because the decisions are not based on capability, cost, and real-time utility. To address these challenges, we introduce a structured, automated framework for agentic system composition that is inspired by the knapsack problem. Our framework enables a composer agent to systematically identify, select, and assemble an optimal set of agentic components by jointly considering performance, budget constraints, and compatibility. By dynamically testing candidate components and modeling their utility in real-time, our approach streamlines the assembly of agentic systems and facilitates scalable reuse of resources. Empirical evaluation with Claude 3.5 Sonnet across five benchmarking datasets shows that our online-knapsack-based composer consistently lies on the Pareto frontier, achieving higher success rates at significantly lower component costs compared to our baselines. In the single-agent setup, the online knapsack composer shows a success rate improvement of up to 31.6% in comparison to the retrieval baselines. In multi-agent systems, the online knapsack composer increases success rate from 37% to 87% when agents are selected from an agent inventory of 100+ agents. The substantial performance gap confirms the robust adaptability of our method across diverse domains and budget constraints.

This project investigates the efficacy of Large Language Models (LLMs) in understanding and extracting scientific knowledge across specific domains and to create a deep learning framework: Knowledge AI. As a part of this framework, we employ pre-trained models and fine-tune them on datasets in the scientific domain. The models are adapted for four key Natural Language Processing (NLP) tasks: summarization, text generation, question answering, and named entity recognition. Our results indicate that domain-specific fine-tuning significantly enhances model performance in each of these tasks, thereby improving their applicability for scientific contexts. This adaptation enables non-experts to efficiently query and extract information within targeted scientific fields, demonstrating the potential of fine-tuned LLMs as a tool for knowledge discovery in the sciences.

Long-form video understanding presents significant challenges due to extensive temporal-spatial complexity and the difficulty of question answering under such extended contexts. While Large Language Models (LLMs) have demonstrated considerable advancements in video analysis capabilities and long context handling, they continue to exhibit limitations when processing information-dense hour-long videos. To overcome such limitations, we propose the Deep Video Discovery agent to leverage an agentic search strategy over segmented video clips. Different from previous video agents manually designing a rigid workflow, our approach emphasizes the autonomous nature of agents. By providing a set of search-centric tools on multi-granular video database, our DVD agent leverages the advanced reasoning capability of LLM to plan on its current observation state, strategically selects tools, formulates appropriate parameters for actions, and iteratively refines its internal reasoning in light of the gathered information. We perform comprehensive evaluation on multiple long video understanding benchmarks that demonstrates the advantage of the entire system design. Our DVD agent achieves SOTA performance, significantly surpassing prior works by a large margin on the challenging LVBench dataset. Comprehensive ablation studies and in-depth tool analyses are also provided, yielding insights to further advance intelligent agents tailored for long-form video understanding tasks. The code will be released later.

This paper describes the KnowledgeHub tool, a scientific literature Information Extraction (IE) and Question Answering (QA) pipeline. This is achieved by supporting the ingestion of PDF documents that are converted to text and structured representations. An ontology can then be constructed where a user defines the types of entities and relationships they want to capture. A browser-based annotation tool enables annotating the contents of the PDF documents according to the ontology. Named Entity Recognition (NER) and Relation Classification (RC) models can be trained on the resulting annotations and can be used to annotate the unannotated portion of the documents. A knowledge graph is constructed from these entity and relation triples which can be queried to obtain insights from the data. Furthermore, we integrate a suite of Large Language Models (LLMs) that can be used for QA and summarisation that is grounded in the included documents via a retrieval component. KnowledgeHub is a unique tool that supports annotation, IE and QA, which gives the user full insight into the knowledge discovery pipeline.

We present the discovery of 118 new ultracool dwarf candidates, discovered using a new machine learning tool, named SMDET, applied to time series images from the Wide-field Infrared Survey Explorer. We gathered photometric and astrometric data to estimate each candidate's spectral type, distance, and tangential velocity. This sample has a photometrically estimated spectral class distribution of 28 M dwarfs, 64 L dwarfs, and 18 T dwarfs. We also identify a T subdwarf candidate, two extreme T subdwarf candidates, and two candidate young ultracool dwarfs. Five objects did not have enough photometric data for any estimations to be made. To validate our estimated spectral types, spectra were collected for 2 objects, yielding confirmed spectral types of T5 (estimated T5) and T3 (estimated T4). Demonstrating the effectiveness of machine learning tools as a new large-scale discovery technique.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose a new DL algorithm, Iterative Codebook Feature Learning~(ICFL), and combine it with a pre-processing step that uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

In this work, we propose MetaAgent, an agentic paradigm inspired by the principle of learning-by-doing, where expertise is developed through hands-on practice and continual self-improvement. MetaAgent starts with a minimal workflow, equipped only with basic reasoning and adaptive help-seeking abilities. When a knowledge gap is encountered, MetaAgent generates natural language help requests, which are routed to the most suitable external tool by a dedicated tool router. As MetaAgent solves tasks, it continually conducts self-reflection and answer verification, distilling actionable experience into concise texts that are dynamically incorporated into future task contexts. Besides, MetaAgent autonomously builds in-house tools and a persistent knowledge base by organizing its tool-use history, further enhancing its ability to retrieve and integrate relevant information We term this continual, data-driven process as meta tool learning, through which MetaAgent incrementally refines its reasoning and tool-use strategies, without changing model parameters or requiring further post-training. Evaluated on challenging knowledge discovery benchmarks, including GAIA, WebWalkerQA, and BrowseCamp, MetaAgent consistently outperforms workflow-based baselines and matches or exceeds end-to-end trained agents, demonstrating the promise of self-evolving agentic systems for robust, general-purpose knowledge discovery. We provide our source codes in https://github.com/qhjqhj00/MetaAgent.

Large language models are emerging as powerful tools for scientific law discovery, a foundational challenge in AI-driven science. However, existing benchmarks for this task suffer from a fundamental methodological trilemma, forcing a trade-off between scientific relevance, scalability, and resistance to memorization. Furthermore, they oversimplify discovery as static function fitting, failing to capture the authentic scientific process of uncovering embedded laws through the interactive exploration of complex model systems. To address these critical gaps, we introduce NewtonBench, a benchmark comprising 324 scientific law discovery tasks across 12 physics domains. Our design mitigates the evaluation trilemma by using metaphysical shifts - systematic alterations of canonical laws - to generate a vast suite of problems that are scalable, scientifically relevant, and memorization-resistant. Moreover, we elevate the evaluation from static function fitting to interactive model discovery, requiring agents to experimentally probe simulated complex systems to uncover hidden principles. Our extensive experiment reveals a clear but fragile capability for discovery in frontier LLMs: this ability degrades precipitously with increasing system complexity and exhibits extreme sensitivity to observational noise. Notably, we uncover a paradoxical effect of tool assistance: providing a code interpreter can hinder more capable models by inducing a premature shift from exploration to exploitation, causing them to satisfice on suboptimal solutions. These results demonstrate that robust, generalizable discovery in complex, interactive environments remains the core challenge. By providing a scalable, robust, and scientifically authentic testbed, NewtonBench offers a crucial tool for measuring true progress and guiding the development of next-generation AI agents capable of genuine scientific discovery.

Complex networks can be used for modeling street meshes and urban agglomerates. With such a model, many aspects of a city can be investigated to promote a better quality of life to its citizens. Along these lines, this paper proposes a set of distance-based pattern-discovery algorithmic instruments to improve urban structures modeled as complex networks, detecting nodes that lack access from/to points of interest in a given city. Furthermore, we introduce a greedy algorithm that is able to recommend improvements to the structure of a city by suggesting where points of interest are to be placed. We contribute to a thorough process to deal with complex networks, including mathematical modeling and algorithmic innovation. The set of our contributions introduces a systematic manner to treat a recurrent problem of broad interest in cities.

Recent work in vision-and-language demonstrates that large-scale pretraining can learn generalizable models that are efficiently transferable to downstream tasks. While this may improve dataset-scale aggregate metrics, analyzing performance around hand-crafted subgroups targeting specific bias dimensions reveals systemic undesirable behaviors. However, this subgroup analysis is frequently stalled by annotation efforts, which require extensive time and resources to collect the necessary data. Prior art attempts to automatically discover subgroups to circumvent these constraints but typically leverages model behavior on existing task-specific annotations and rapidly degrades on more complex inputs beyond "tabular" data, none of which study vision-and-language models. This paper presents VLSlice, an interactive system enabling user-guided discovery of coherent representation-level subgroups with consistent visiolinguistic behavior, denoted as vision-and-language slices, from unlabeled image sets. We show that VLSlice enables users to quickly generate diverse high-coherency slices in a user study (n=22) and release the tool publicly.

Understanding and reasoning on the web-scale scientific literature is a crucial touchstone for large language model (LLM) based agents designed to support complex knowledge-intensive tasks. However, existing works are mainly restricted to tool-free tasks within isolated papers, largely due to the lack of a benchmark for cross-paper reasoning and multi-tool orchestration in real research scenarios. In this work, we propose PaperArena, an evaluation benchmark for agents to address real-world research questions that typically require integrating information across multiple papers with the assistance of external tools. Given a research question, agents should integrate diverse formats across multiple papers through reasoning and interacting with appropriate tools, thereby producing a well-grounded answer. To support standardized evaluation, we provide a modular and extensible platform for agent execution, offering tools such as multimodal parsing, context retrieval, and programmatic computation. Experimental results reveal that even the most advanced LLM powering a well-established agent system achieves merely 38.78% average accuracy. On the hard subset, accuracy drops to only 18.47%, highlighting great potential for improvement. We also present several empirical findings, including that all agents tested exhibit inefficient tool usage, often invoking more tools than necessary to solve a task. We invite the community to adopt PaperArena to develop and evaluate more capable agents for scientific discovery. Our code and data are available https://github.com/Melmaphother/PaperArena.

Large language models (LLMs) have shown remarkable potential in various domains, but they often lack the ability to access and reason over domain-specific knowledge and tools. In this paper, we introduced CACTUS (Chemistry Agent Connecting Tool-Usage to Science), an LLM-based agent that integrates cheminformatics tools to enable advanced reasoning and problem-solving in chemistry and molecular discovery. We evaluate the performance of CACTUS using a diverse set of open-source LLMs, including Gemma-7b, Falcon-7b, MPT-7b, Llama2-7b, and Mistral-7b, on a benchmark of thousands of chemistry questions. Our results demonstrate that CACTUS significantly outperforms baseline LLMs, with the Gemma-7b and Mistral-7b models achieving the highest accuracy regardless of the prompting strategy used. Moreover, we explore the impact of domain-specific prompting and hardware configurations on model performance, highlighting the importance of prompt engineering and the potential for deploying smaller models on consumer-grade hardware without significant loss in accuracy. By combining the cognitive capabilities of open-source LLMs with domain-specific tools, CACTUS can assist researchers in tasks such as molecular property prediction, similarity searching, and drug-likeness assessment. Furthermore, CACTUS represents a significant milestone in the field of cheminformatics, offering an adaptable tool for researchers engaged in chemistry and molecular discovery. By integrating the strengths of open-source LLMs with domain-specific tools, CACTUS has the potential to accelerate scientific advancement and unlock new frontiers in the exploration of novel, effective, and safe therapeutic candidates, catalysts, and materials. Moreover, CACTUS's ability to integrate with automated experimentation platforms and make data-driven decisions in real time opens up new possibilities for autonomous discovery.

While reasoning models (e.g., DeepSeek R1) trained with reinforcement learning (RL), excel in textual reasoning, they struggle in scenarios requiring structured problem-solving, such as geometric reasoning, concise computation, or complex equation solving-areas where computational tools like code interpreters (CI) demonstrate distinct advantages. To bridge this gap, we propose ReTool, which enhances long-form reasoning with tool-integrated learning, including two key features: (1) dynamic interleaving of real-time code execution within natural language reasoning processes, and (2) an automated RL paradigm that allows policy rollouts with multi-turn real-time code execution and teaches the model in learning when and how to invoke tools based on outcome feedback. ReTool employs a systematic training framework, beginning with synthetic cold-start data generation to produce code-augmented long-form reasoning traces for fine-tuning base models. Subsequent RL training leverages task outcomes as rewards to iteratively refine the model's tool use strategy, enabling autonomous discovery of optimal tool invocation patterns without human priors. Experiments on the challenging MATH Olympiad benchmark AIME demonstrate ReTool's superiority: Our 32B model achieves 67% accuracy with 400 training steps, outperforming text-based RL baseline (40% accuracy, 1080 steps) in efficiency and performance. Remarkably, ReTool-32B attains 72.5% accuracy in extended settings, surpassing OpenAI's o1-preview by 27.9%. Further analysis reveals emergent behaviors such as code self-correction, signaling an ''aha moment'' in which the model autonomously masters adaptive tool use. These findings highlight the promise of outcome-driven tool integration for advancing complex mathematical reasoning and offer new insights into hybrid neuro-symbolic systems.

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

Large language models (LLMs) have recently demonstrated promising capabilities in chemistry tasks while still facing challenges due to outdated pretraining knowledge and the difficulty of incorporating specialized chemical expertise. To address these issues, we propose an LLM-based agent that synergistically integrates 137 external chemical tools created ranging from basic information retrieval to complex reaction predictions, and a dataset curation pipeline to generate the dataset ChemToolBench that facilitates both effective tool selection and precise parameter filling during fine-tuning and evaluation. We introduce a Hierarchical Evolutionary Monte Carlo Tree Search (HE-MCTS) framework, enabling independent optimization of tool planning and execution. By leveraging self-generated data, our approach supports step-level fine-tuning (FT) of the policy model and training task-adaptive PRM and ORM that surpass GPT-4o. Experimental evaluations demonstrate that our approach significantly improves performance in Chemistry QA and discovery tasks, offering a robust solution to integrate specialized tools with LLMs for advanced chemical applications. All datasets and code are available at https://github.com/AI4Chem/ChemistryAgent .

The distribution of subpopulations is an important property hidden within a dataset. Uncovering and analyzing the subpopulation distribution within datasets provides a comprehensive understanding of the datasets, standing as a powerful tool beneficial to various downstream tasks, including Dataset Subpopulation Organization, Subpopulation Shift, and Slice Discovery. Despite its importance, there has been no work that systematically explores the subpopulation distribution of datasets to our knowledge. To address the limitation and solve all the mentioned tasks in a unified way, we introduce a novel concept of subpopulation structures to represent, analyze, and utilize subpopulation distributions within datasets. To characterize the structures in an interpretable manner, we propose the Subpopulation Structure Discovery with Large Language Models (SSD-LLM) framework, which employs world knowledge and instruction-following capabilities of Large Language Models (LLMs) to linguistically analyze informative image captions and summarize the structures. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery.

We tackle the challenging task of unsupervised object localization in this work. Recently, transformers trained with self-supervised learning have been shown to exhibit object localization properties without being trained for this task. In this work, we present Multiple Object localization with Self-supervised Transformers (MOST) that uses features of transformers trained using self-supervised learning to localize multiple objects in real world images. MOST analyzes the similarity maps of the features using box counting; a fractal analysis tool to identify tokens lying on foreground patches. The identified tokens are then clustered together, and tokens of each cluster are used to generate bounding boxes on foreground regions. Unlike recent state-of-the-art object localization methods, MOST can localize multiple objects per image and outperforms SOTA algorithms on several object localization and discovery benchmarks on PASCAL-VOC 07, 12 and COCO20k datasets. Additionally, we show that MOST can be used for self-supervised pre-training of object detectors, and yields consistent improvements on fully, semi-supervised object detection and unsupervised region proposal generation.

Automated discovery of physical laws from observational data in the real world is a grand challenge in AI. Current methods, relying on symbolic regression or LLMs, are limited to uni-modal data and overlook the rich, visual phenomenological representations of motion that are indispensable to physicists. This "sensory deprivation" severely weakens their ability to interpret the inherent spatio-temporal patterns within dynamic phenomena. To address this gap, we propose VIPER-R1, a multimodal model that performs Visual Induction for Physics-based Equation Reasoning to discover fundamental symbolic formulas. It integrates visual perception, trajectory data, and symbolic reasoning to emulate the scientific discovery process. The model is trained via a curriculum of Motion Structure Induction (MSI), using supervised fine-tuning to interpret kinematic phase portraits and to construct hypotheses guided by a Causal Chain of Thought (C-CoT), followed by Reward-Guided Symbolic Calibration (RGSC) to refine the formula structure with reinforcement learning. During inference, the trained VIPER-R1 acts as an agent: it first posits a high-confidence symbolic ansatz, then proactively invokes an external symbolic regression tool to perform Symbolic Residual Realignment (SR^2). This final step, analogous to a physicist's perturbation analysis, reconciles the theoretical model with empirical data. To support this research, we introduce PhysSymbol, a new 5,000-instance multimodal corpus. Experiments show that VIPER-R1 consistently outperforms state-of-the-art VLM baselines in accuracy and interpretability, enabling more precise discovery of physical laws. Project page: https://jiaaqiliu.github.io/VIPER-R1/

Identifying and predicting the factors that contribute to the success of interdisciplinary research is crucial for advancing scientific discovery. However, there is a lack of methods to quantify the integration of new ideas and technological advancements in astronomical research and how these new technologies drive further scientific breakthroughs. Large language models, with their ability to extract key concepts from vast literature beyond keyword searches, provide a new tool to quantify such processes. In this study, we extracted concepts in astronomical research from 297,807 publications between 1993 and 2024 using large language models, resulting in a set of 24,939 concepts. These concepts were then used to form a knowledge graph, where the link strength between any two concepts was determined by their relevance through the citation-reference relationships. By calculating this relevance across different time periods, we quantified the impact of numerical simulations and machine learning on astronomical research. The knowledge graph demonstrates two phases of development: a phase where the technology was integrated and another where the technology was explored in scientific discovery. The knowledge graph reveals that despite machine learning has made much inroad in astronomy, there is currently a lack of new concept development at the intersection of AI and Astronomy, which may be the current bottleneck preventing machine learning from further transforming the field of astronomy.

With the discovery of Wasserstein GANs, Optimal Transport (OT) has become a powerful tool for large-scale generative modeling tasks. In these tasks, OT cost is typically used as the loss for training GANs. In contrast to this approach, we show that the OT map itself can be used as a generative model, providing comparable performance. Previous analogous approaches consider OT maps as generative models only in the latent spaces due to their poor performance in the original high-dimensional ambient space. In contrast, we apply OT maps directly in the ambient space, e.g., a space of high-dimensional images. First, we derive a min-max optimization algorithm to efficiently compute OT maps for the quadratic cost (Wasserstein-2 distance). Next, we extend the approach to the case when the input and output distributions are located in the spaces of different dimensions and derive error bounds for the computed OT map. We evaluate the algorithm on image generation and unpaired image restoration tasks. In particular, we consider denoising, colorization, and inpainting, where the optimality of the restoration map is a desired attribute, since the output (restored) image is expected to be close to the input (degraded) one.

In Marius von Senden's Space and Sight, a newly sighted blind patient describes the experience of a corner as lemon-like, because corners "prick" sight like lemons prick the tongue. Prickliness, here, is a dimension in the feature space of sensory experience, an effect of the perceived on the perceiver that arises where the two interact. In the account of the newly sighted, an effect familiar from one interaction translates to a novel context. Perception serves as the vehicle for generalization, in that an effect shared across different experiences produces a concrete abstraction grounded in those experiences. Cezanne and the post-impressionists, fluent in the language of experience translation, realized that the way to paint a concrete form that best reflected reality was to paint not what they saw, but what it was like to see. We envision a future of creation using AI where what it is like to see is replicable, transferrable, manipulable - part of the artist's palette that is both grounded in a particular context, and generalizable beyond it. An active line of research maps human-interpretable features onto directions in GAN latent space. Supervised and self-supervised approaches that search for anticipated directions or use off-the-shelf classifiers to drive image manipulation in embedding space are limited in the variety of features they can uncover. Unsupervised approaches that discover useful new directions show that the space of perceptually meaningful directions is nowhere close to being fully mapped. As this space is broad and full of creative potential, we want tools for direction discovery that capture the richness and generalizability of human perception. Our approach puts creators in the discovery loop during real-time tool use, in order to identify directions that are perceptually meaningful to them, and generate interpretable image translations along those directions.

A multi-agent AI system (MAS) is composed of multiple autonomous agents that interact, exchange information, and make decisions based on internal generative models. Recent advances in large language models and tool-using agents have made MAS increasingly practical in areas like scientific discovery and collaborative automation. However, key questions remain: When are MAS more effective than single-agent systems? What new safety risks arise from agent interactions? And how should we evaluate their reliability and structure? This paper outlines a formal framework for analyzing MAS, focusing on two core aspects: effectiveness and safety. We explore whether MAS truly improve robustness, adaptability, and performance, or merely repackage known techniques like ensemble learning. We also study how inter-agent dynamics may amplify or suppress system vulnerabilities. While MAS are relatively new to the signal processing community, we envision them as a powerful abstraction that extends classical tools like distributed estimation and sensor fusion to higher-level, policy-driven inference. Through experiments on data science automation, we highlight the potential of MAS to reshape how signal processing systems are designed and trusted.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Inverse design of solid-state materials with desired properties represents a formidable challenge in materials science. Although recent generative models have demonstrated potential, their adoption has been hindered by limitations such as inefficiency, architectural constraints and restricted open-source availability. The representation of crystal structures using the SLICES (Simplified Line-Input Crystal-Encoding System) notation as a string of characters enables the use of state-of-the-art natural language processing models, such as Transformers, for crystal design. Drawing inspiration from the success of GPT models in generating coherent text, we trained a generative Transformer on the next-token prediction task to generate solid-state materials with targeted properties. We demonstrate MatterGPT's capability to generate de novo crystal structures with targeted single properties, including both lattice-insensitive (formation energy) and lattice-sensitive (band gap) properties. Furthermore, we extend MatterGPT to simultaneously target multiple properties, addressing the complex challenge of multi-objective inverse design of crystals. Our approach showcases high validity, uniqueness, and novelty in generated structures, as well as the ability to generate materials with properties beyond the training data distribution. This work represents a significant step forward in computational materials discovery, offering a powerful and open tool for designing materials with tailored properties for various applications in energy, electronics, and beyond.

Software is prone to security vulnerabilities. Program analysis tools to detect them have limited effectiveness in practice due to their reliance on human labeled specifications. Large language models (or LLMs) have shown impressive code generation capabilities but they cannot do complex reasoning over code to detect such vulnerabilities especially since this task requires whole-repository analysis. We propose IRIS, a neuro-symbolic approach that systematically combines LLMs with static analysis to perform whole-repository reasoning for security vulnerability detection. Specifically, IRIS leverages LLMs to infer taint specifications and perform contextual analysis, alleviating needs for human specifications and inspection. For evaluation, we curate a new dataset, CWE-Bench-Java, comprising 120 manually validated security vulnerabilities in real-world Java projects. A state-of-the-art static analysis tool CodeQL detects only 27 of these vulnerabilities whereas IRIS with GPT-4 detects 55 (+28) and improves upon CodeQL's average false discovery rate by 5% points. Furthermore, IRIS identifies 4 previously unknown vulnerabilities which cannot be found by existing tools. IRIS is available publicly at https://github.com/iris-sast/iris.

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

Biomedical image analysis is fundamental for biomedical discovery in cell biology, pathology, radiology, and many other biomedical domains. Holistic image analysis comprises interdependent subtasks such as segmentation, detection, and recognition of relevant objects. Here, we propose BiomedParse, a biomedical foundation model for imaging parsing that can jointly conduct segmentation, detection, and recognition for 82 object types across 9 imaging modalities. Through joint learning, we can improve accuracy for individual tasks and enable novel applications such as segmenting all relevant objects in an image through a text prompt, rather than requiring users to laboriously specify the bounding box for each object. We leveraged readily available natural-language labels or descriptions accompanying those datasets and use GPT-4 to harmonize the noisy, unstructured text information with established biomedical object ontologies. We created a large dataset comprising over six million triples of image, segmentation mask, and textual description. On image segmentation, we showed that BiomedParse is broadly applicable, outperforming state-of-the-art methods on 102,855 test image-mask-label triples across 9 imaging modalities (everything). On object detection, which aims to locate a specific object of interest, BiomedParse again attained state-of-the-art performance, especially on objects with irregular shapes (everywhere). On object recognition, which aims to identify all objects in a given image along with their semantic types, we showed that BiomedParse can simultaneously segment and label all biomedical objects in an image (all at once). In summary, BiomedParse is an all-in-one tool for biomedical image analysis by jointly solving segmentation, detection, and recognition for all major biomedical image modalities, paving the path for efficient and accurate image-based biomedical discovery.

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, molecules generated by artificial intelligence may unintentionally infringe on existing patents, posing legal and financial risks that impede the full automation of drug discovery pipelines. This paper introduces PatentFinder, a novel multi-agent and tool-enhanced intelligence system that can accurately and comprehensively evaluate small molecules for patent infringement. PatentFinder features five specialized agents that collaboratively analyze patent claims and molecular structures with heuristic and model-based tools, generating interpretable infringement reports. To support systematic evaluation, we curate MolPatent-240, a benchmark dataset tailored for patent infringement assessment algorithms. On this benchmark, PatentFinder outperforms baseline methods that rely solely on large language models or specialized chemical tools, achieving a 13.8% improvement in F1-score and a 12% increase in accuracy. Additionally, PatentFinder autonomously generates detailed and interpretable patent infringement reports, showcasing enhanced accuracy and improved interpretability. The high accuracy and interpretability of PatentFinder make it a valuable and reliable tool for automating patent infringement assessments, offering a practical solution for integrating patent protection analysis into the drug discovery pipeline.

Large language model powered autonomous agents demand robust, standardized protocols to integrate tools, share contextual data, and coordinate tasks across heterogeneous systems. Ad-hoc integrations are difficult to scale, secure, and generalize across domains. This survey examines four emerging agent communication protocols: Model Context Protocol (MCP), Agent Communication Protocol (ACP), Agent-to-Agent Protocol (A2A), and Agent Network Protocol (ANP), each addressing interoperability in deployment contexts. MCP provides a JSON-RPC client-server interface for secure tool invocation and typed data exchange. ACP defines a general-purpose communication protocol over RESTful HTTP, supporting MIME-typed multipart messages and synchronous and asynchronous interactions. Its lightweight and runtime-independent design enables scalable agent invocation, while features like session management, message routing, and integration with role-based and decentralized identifiers (DIDs). A2A enables peer-to-peer task delegation using capability-based Agent Cards, supporting secure and scalable collaboration across enterprise agent workflows. ANP supports open network agent discovery and secure collaboration using W3C decentralized identifiers DIDs and JSON-LD graphs. The protocols are compared across multiple dimensions, including interaction modes, discovery mechanisms, communication patterns, and security models. Based on the comparative analysis, a phased adoption roadmap is proposed: beginning with MCP for tool access, followed by ACP for structured, multimodal messaging session-aware interaction and both online and offline agent discovery across scalable, HTTP-based deployments A2A for collaborative task execution, and extending to ANP for decentralized agent marketplaces. This work provides a comprehensive foundation for designing secure, interoperable, and scalable ecosystems of LLM-powered agents.

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. However, the landscape remains fragmented and lacks a unified taxonomy or comprehensive survey. Therefore, we present a side-by-side comparison of benchmarks developed between 2019 and 2025 that evaluate these models and agents across multiple domains. In addition, we propose a taxonomy of approximately 60 benchmarks that cover general and academic knowledge reasoning, mathematical problem-solving, code generation and software engineering, factual grounding and retrieval, domain-specific evaluations, multimodal and embodied tasks, task orchestration, and interactive assessments. Furthermore, we review AI-agent frameworks introduced between 2023 and 2025 that integrate large language models with modular toolkits to enable autonomous decision-making and multi-step reasoning. Moreover, we present real-world applications of autonomous AI agents in materials science, biomedical research, academic ideation, software engineering, synthetic data generation, chemical reasoning, mathematical problem-solving, geographic information systems, multimedia, healthcare, and finance. We then survey key agent-to-agent collaboration protocols, namely the Agent Communication Protocol (ACP), the Model Context Protocol (MCP), and the Agent-to-Agent Protocol (A2A). Finally, we discuss recommendations for future research, focusing on advanced reasoning strategies, failure modes in multi-agent LLM systems, automated scientific discovery, dynamic tool integration via reinforcement learning, integrated search capabilities, and security vulnerabilities in agent protocols.

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

The ability to generate 3D multiphase microstructures on-demand with targeted attributes can greatly accelerate the design of advanced materials. Here, we present a conditional latent diffusion model (LDM) framework that rapidly synthesizes high-fidelity 3D multiphase microstructures tailored to user specifications. Using this approach, we generate diverse two-phase and three-phase microstructures at high resolution (volumes of 128 times 128 times 64 voxels, representing >10^6 voxels each) within seconds, overcoming the scalability and time limitations of traditional simulation-based methods. Key design features, such as desired volume fractions and tortuosities, are incorporated as controllable inputs to guide the generative process, ensuring that the output structures meet prescribed statistical and topological targets. Moreover, the framework predicts corresponding manufacturing (processing) parameters for each generated microstructure, helping to bridge the gap between digital microstructure design and experimental fabrication. While demonstrated on organic photovoltaic (OPV) active-layer morphologies, the flexible architecture of our approach makes it readily adaptable to other material systems and microstructure datasets. By combining computational efficiency, adaptability, and experimental relevance, this framework addresses major limitations of existing methods and offers a powerful tool for accelerated materials discovery.

Autonomous agents have recently achieved remarkable progress across diverse domains, yet most evaluations focus on short-horizon, fully observable tasks. In contrast, many critical real-world tasks, such as large-scale software development, commercial investment, and scientific discovery, unfold in long-horizon and partially observable scenarios where success hinges on sustained reasoning, planning, memory management, and tool use. Existing benchmarks rarely capture these long-horizon challenges, leaving a gap in systematic evaluation. To bridge this gap, we introduce UltraHorizon a novel benchmark that measures the foundational capabilities essential for complex real-world challenges. We use exploration as a unifying task across three distinct environments to validate these core competencies. Agents are designed in long-horizon discovery tasks where they must iteratively uncover hidden rules through sustained reasoning, planning, memory and tools management, and interaction with environments. Under the heaviest scale setting, trajectories average 200k+ tokens and 400+ tool calls, whereas in standard configurations they still exceed 35k tokens and involve more than 60 tool calls on average. Our extensive experiments reveal that LLM-agents consistently underperform in these settings, whereas human participants achieve higher scores, underscoring a persistent gap in agents' long-horizon abilities. We also observe that simple scaling fails in our task. To better illustrate the failure of agents, we conduct an in-depth analysis of collected trajectories. We identify eight types of errors and attribute them to two primary causes: in-context locking and functional fundamental capability gaps. https://github.com/StarDewXXX/UltraHorizon{Our code will be available here.}

Tool learning aims to enhance and expand large language models' (LLMs) capabilities with external tools, which has gained significant attention recently. Current methods have shown that LLMs can effectively handle a certain amount of tools through in-context learning or fine-tuning. However, in real-world scenarios, the number of tools is typically extensive and irregularly updated, emphasizing the necessity for a dedicated tool retrieval component. Tool retrieval is nontrivial due to the following challenges: 1) complex user instructions and tool descriptions; 2) misalignment between tool retrieval and tool usage models. To address the above issues, we propose to enhance tool retrieval with iterative feedback from the large language model. Specifically, we prompt the tool usage model, i.e., the LLM, to provide feedback for the tool retriever model in multi-round, which could progressively improve the tool retriever's understanding of instructions and tools and reduce the gap between the two standalone components. We build a unified and comprehensive benchmark to evaluate tool retrieval models. The extensive experiments indicate that our proposed approach achieves advanced performance in both in-domain evaluation and out-of-domain evaluation.

Humans possess an extraordinary ability to create and utilize tools, allowing them to overcome physical limitations and explore new frontiers. With the advent of foundation models, AI systems have the potential to be equally adept in tool use as humans. This paradigm, i.e., tool learning with foundation models, combines the strengths of specialized tools and foundation models to achieve enhanced accuracy, efficiency, and automation in problem-solving. Despite its immense potential, there is still a lack of a comprehensive understanding of key challenges, opportunities, and future endeavors in this field. To this end, we present a systematic investigation of tool learning in this paper. We first introduce the background of tool learning, including its cognitive origins, the paradigm shift of foundation models, and the complementary roles of tools and models. Then we recapitulate existing tool learning research into tool-augmented and tool-oriented learning. We formulate a general tool learning framework: starting from understanding the user instruction, models should learn to decompose a complex task into several subtasks, dynamically adjust their plan through reasoning, and effectively conquer each sub-task by selecting appropriate tools. We also discuss how to train models for improved tool-use capabilities and facilitate the generalization in tool learning. Considering the lack of a systematic tool learning evaluation in prior works, we experiment with 18 representative tools and show the potential of current foundation models in skillfully utilizing tools. Finally, we discuss several open problems that require further investigation for tool learning. In general, we hope this paper could inspire future research in integrating tools with foundation models.

Recent advancements in large language models (LLMs) integrated with external tools and APIs have successfully addressed complex tasks by using in-context learning or fine-tuning. Despite this progress, the vast scale of tool retrieval remains challenging due to stringent input length constraints. In response, we propose a pre-retrieval strategy from an extensive repository, effectively framing the problem as the massive tool retrieval (MTR) task. We introduce the MTRB (massive tool retrieval benchmark) to evaluate real-world tool-augmented LLM scenarios with a large number of tools. This benchmark is designed for low-resource scenarios and includes a diverse collection of tools with descriptions refined for consistency and clarity. It consists of three subsets, each containing 90 test samples and 10 training samples. To handle the low-resource MTR task, we raise a new query-tool alignment (QTA) framework leverages LLMs to enhance query-tool alignment by rewriting user queries through ranking functions and the direct preference optimization (DPO) method. This approach consistently outperforms existing state-of-the-art models in top-5 and top-10 retrieval tasks across the MTRB benchmark, with improvements up to 93.28% based on the metric Sufficiency@k, which measures the adequacy of tool retrieval within the first k results. Furthermore, ablation studies validate the efficacy of our framework, highlighting its capacity to optimize performance even with limited annotated samples. Specifically, our framework achieves up to 78.53% performance improvement in Sufficiency@k with just a single annotated sample. Additionally, QTA exhibits strong cross-dataset generalizability, emphasizing its potential for real-world applications.

Recent advancements in function calling and tool use have significantly enhanced the capabilities of large language models (LLMs) by enabling them to interact with external information sources and execute complex tasks. However, the limited context window of LLMs presents challenges when a large number of tools are available, necessitating efficient methods to manage prompt length and maintain accuracy. Existing approaches, such as fine-tuning LLMs or leveraging their reasoning capabilities, either require frequent retraining or incur significant latency overhead. A more efficient solution involves training smaller models to retrieve the most relevant tools for a given query, although this requires high quality, domain-specific data. To address those challenges, we present a novel framework for generating synthetic data for tool retrieval applications and an efficient data-driven tool retrieval strategy using small encoder models. Empowered by LLMs, we create ToolBank, a new tool retrieval dataset that reflects real human user usages. For tool retrieval methodologies, we propose novel approaches: (1) Tool2Vec: usage-driven tool embedding generation for tool retrieval, (2) ToolRefiner: a staged retrieval method that iteratively improves the quality of retrieved tools, and (3) MLC: framing tool retrieval as a multi-label classification problem. With these new methods, we achieve improvements of up to 27.28 in Recall@K on the ToolBench dataset and 30.5 in Recall@K on ToolBank. Additionally, we present further experimental results to rigorously validate our methods. Our code is available at https://github.com/SqueezeAILab/Tool2Vec

Tool learning aims to augment large language models (LLMs) with diverse tools, enabling them to act as agents for solving practical tasks. Due to the limited context length of tool-using LLMs, adopting information retrieval (IR) models to select useful tools from large toolsets is a critical initial step. However, the performance of IR models in tool retrieval tasks remains underexplored and unclear. Most tool-use benchmarks simplify this step by manually pre-annotating a small set of relevant tools for each task, which is far from the real-world scenarios. In this paper, we propose ToolRet, a heterogeneous tool retrieval benchmark comprising 7.6k diverse retrieval tasks, and a corpus of 43k tools, collected from existing datasets. We benchmark six types of models on ToolRet. Surprisingly, even the models with strong performance in conventional IR benchmarks, exhibit poor performance on ToolRet. This low retrieval quality degrades the task pass rate of tool-use LLMs. As a further step, we contribute a large-scale training dataset with over 200k instances, which substantially optimizes the tool retrieval ability of IR models.

Recent developments in retrieval-augmented generation (RAG) for selecting relevant tools from a tool knowledge base enable LLM agents to scale their complex tool calling capabilities to hundreds or thousands of external tools, APIs, or agents-as-tools. However, traditional RAG-based tool retrieval fails to capture structured dependencies between tools, limiting the retrieval accuracy of a retrieved tool's dependencies. For example, among a vector database of tools, a "get stock price" API requires a "stock ticker" parameter from a "get stock ticker" API, and both depend on OS-level internet connectivity tools. In this paper, we address this limitation by introducing Graph RAG-Tool Fusion, a novel plug-and-play approach that combines the strengths of vector-based retrieval with efficient graph traversal to capture all relevant tools (nodes) along with any nested dependencies (edges) within the predefined tool knowledge graph. We also present ToolLinkOS, a new tool selection benchmark of 573 fictional tools, spanning over 15 industries, each with an average of 6.3 tool dependencies. We demonstrate that Graph RAG-Tool Fusion achieves absolute improvements of 71.7% and 22.1% over na\"ive RAG on ToolLinkOS and ToolSandbox benchmarks, respectively (mAP@10). ToolLinkOS dataset is available at https://github.com/EliasLumer/Graph-RAG-Tool-Fusion-ToolLinkOS

The ability to use, understand, and create tools is a hallmark of human intelligence, enabling sophisticated interaction with the physical world. For any general-purpose intelligent agent to achieve true versatility, it must also master these fundamental skills. While modern Multimodal Large Language Models (MLLMs) leverage their extensive common knowledge for high-level planning in embodied AI and in downstream Vision-Language-Action (VLA) models, the extent of their true understanding of physical tools remains unquantified. To bridge this gap, we present PhysToolBench, the first benchmark dedicated to evaluating the comprehension of physical tools by MLLMs. Our benchmark is structured as a Visual Question Answering (VQA) dataset comprising over 1,000 image-text pairs. It assesses capabilities across three distinct difficulty levels: (1) Tool Recognition: Requiring the recognition of a tool's primary function. (2) Tool Understanding: Testing the ability to grasp the underlying principles of a tool's operation. (3) Tool Creation: Challenging the model to fashion a new tool from surrounding objects when conventional options are unavailable. Our comprehensive evaluation of 32 MLLMs-spanning proprietary, open-source, specialized embodied, and backbones in VLAs-reveals a significant deficiency in tool understanding. Furthermore, we provide an in-depth analysis and propose preliminary solutions. Code and dataset are publicly available.

Using tools by Large Language Models (LLMs) is a promising avenue to extend their reach beyond language or conversational settings. The number of tools can scale to thousands as they enable accessing sensory information, fetching updated factual knowledge, or taking actions in the real world. In such settings, in-context learning by providing a short list of relevant tools in the prompt is a viable approach. To retrieve relevant tools, various approaches have been suggested, ranging from simple frequency-based matching to dense embedding-based semantic retrieval. However, such approaches lack the contextual and common-sense understanding required to retrieve the right tools for complex user requests. Rather than increasing the complexity of the retrieval component itself, we propose leveraging LLM understanding to generate a retrieval query. Then, the generated query is embedded and used to find the most relevant tools via a nearest-neighbor search. We investigate three approaches for query generation: zero-shot prompting, supervised fine-tuning on tool descriptions, and alignment learning by iteratively optimizing a reward metric measuring retrieval performance. By conducting extensive experiments on a dataset covering complex and multi-tool scenarios, we show that leveraging LLMs for query generation improves the retrieval for in-domain (seen tools) and out-of-domain (unseen tools) settings.

Recent advances in large language models (LLMs) have enabled autonomous agents with complex reasoning and task-fulfillment capabilities using a wide range of tools. However, effectively identifying the most relevant tools for a given task becomes a key bottleneck as the toolset size grows, hindering reliable tool utilization. To address this, we introduce Re-Invoke, an unsupervised tool retrieval method designed to scale effectively to large toolsets without training. Specifically, we first generate a diverse set of synthetic queries that comprehensively cover different aspects of the query space associated with each tool document during the tool indexing phase. Second, we leverage LLM's query understanding capabilities to extract key tool-related context and underlying intents from user queries during the inference phase. Finally, we employ a novel multi-view similarity ranking strategy based on intents to pinpoint the most relevant tools for each query. Our evaluation demonstrates that Re-Invoke significantly outperforms state-of-the-art alternatives in both single-tool and multi-tool scenarios, all within a fully unsupervised setting. Notably, on the ToolE datasets, we achieve a 20% relative improvement in nDCG@5 for single-tool retrieval and a 39% improvement for multi-tool retrieval.

Large language models (LLMs) have garnered significant attention due to their impressive natural language processing (NLP) capabilities. Recently, many studies have focused on the tool utilization ability of LLMs. They primarily investigated how LLMs effectively collaborate with given specific tools. However, in scenarios where LLMs serve as intelligent agents, as seen in applications like AutoGPT and MetaGPT, LLMs are expected to engage in intricate decision-making processes that involve deciding whether to employ a tool and selecting the most suitable tool(s) from a collection of available tools to fulfill user requests. Therefore, in this paper, we introduce MetaTool, a benchmark designed to evaluate whether LLMs have tool usage awareness and can correctly choose tools. Specifically, we create a dataset called ToolE within the benchmark. This dataset contains various types of user queries in the form of prompts that trigger LLMs to use tools, including both single-tool and multi-tool scenarios. Subsequently, we set the tasks for both tool usage awareness and tool selection. We define four subtasks from different perspectives in tool selection, including tool selection with similar choices, tool selection in specific scenarios, tool selection with possible reliability issues, and multi-tool selection. We conduct experiments involving nine popular LLMs and find that the majority of them still struggle to effectively select tools, highlighting the existing gaps between LLMs and genuine intelligent agents. However, through the error analysis, we found there is still significant room for improvement. Finally, we conclude with insights for tool developers that follow ChatGPT to provide detailed descriptions that can enhance the tool selection performance of LLMs.

Augmenting large language models (LLMs) with external tools has emerged as a promising approach to extend their utility, empowering them to solve practical tasks. Existing work typically empowers LLMs as tool users with a manually designed workflow, where the LLM plans a series of tools in a step-by-step manner, and sequentially executes each tool to obtain intermediate results until deriving the final answer. However, they suffer from two challenges in realistic scenarios: (1) The handcrafted control flow is often ad-hoc and constraints the LLM to local planning; (2) The LLM is instructed to use only manually demonstrated tools or well-trained Python functions, which limits its generalization to new tools. In this work, we first propose Automatic Tool Chain (ATC), a framework that enables the LLM to act as a multi-tool user, which directly utilizes a chain of tools through programming. To scale up the scope of the tools, we next propose a black-box probing method. This further empowers the LLM as a tool learner that can actively discover and document tool usages, teaching themselves to properly master new tools. For a comprehensive evaluation, we build a challenging benchmark named ToolFlow, which diverges from previous benchmarks by its long-term planning scenarios and complex toolset. Experiments on both existing datasets and ToolFlow illustrate the superiority of our framework. Analysis on different settings also validates the effectiveness and the utility of our black-box probing algorithm.

Recent advancements in tool-equipped Agents (LLMs) have enabled complex tasks like secure database interactions and multi-agent code development. However, scaling tool capacity beyond agent reasoning or model limits remains a challenge. In this paper, we address these challenges by introducing Toolshed Knowledge Bases, a tool knowledge base (vector database) designed to store enhanced tool representations and optimize tool selection for large-scale tool-equipped Agents. Additionally, we propose Advanced RAG-Tool Fusion, a novel ensemble of tool-applied advanced retrieval-augmented generation (RAG) techniques across the pre-retrieval, intra-retrieval, and post-retrieval phases, without requiring model fine-tuning. During pre-retrieval, tool documents are enhanced with key information and stored in the Toolshed Knowledge Base. Intra-retrieval focuses on query planning and transformation to increase retrieval accuracy. Post-retrieval refines the retrieved tool documents and enables self-reflection. Furthermore, by varying both the total number of tools (tool-M) an Agent has access to and the tool selection threshold (top-k), we address trade-offs between retrieval accuracy, agent performance, and token cost. Our approach achieves 46%, 56%, and 47% absolute improvements on the ToolE single-tool, ToolE multi-tool and Seal-Tools benchmark datasets, respectively (Recall@5).

Tools serve as pivotal interfaces that enable humans to understand and reshape the world. With the advent of foundational models, AI systems can utilize tools to expand their capabilities and interact with the world. Existing tool learning methodologies, encompassing supervised fine-tuning and prompt engineering approaches, often induce language models to utilize tools indiscriminately, as complex problems often exceed their own competencies. However, introducing tools for simple tasks, which the models themselves can readily resolve, can inadvertently propagate errors rather than enhance performance. This leads to the research question: can we teach language models when and how to use tools? To meet this need, we propose Tool leaRning wIth exeCution fEedback (TRICE), a two-stage end-to-end framework that enables the model to continually learn through feedback derived from tool execution, thereby learning when and how to use tools effectively. Experimental results, backed by further analysis, show that TRICE can make the language model to selectively use tools by decreasing the model's dependency on tools while enhancing the performance. Code and datasets will be available in https://github.com/zjunlp/trice.

As large language models (LLMs) advance, their inability to autonomously execute tasks by directly interacting with external tools remains a critical limitation. Traditional methods rely on inputting tool descriptions as context, which is constrained by context length and requires separate, often inefficient, retrieval mechanisms. We introduce ToolGen, a paradigm shift that integrates tool knowledge directly into the LLM's parameters by representing each tool as a unique token. This enables the LLM to generate tool calls and arguments as part of its next token prediction capabilities, seamlessly blending tool invocation with language generation. Our framework allows the LLM to access and utilize a vast amount of tools with no additional retrieval step, significantly enhancing both performance and scalability. Experimental results with over 47,000 tools show that ToolGen not only achieves superior results in both tool retrieval and autonomous task completion but also sets the stage for a new era of AI agents that can adapt to tools across diverse domains. By fundamentally transforming tool retrieval into a generative process, ToolGen paves the way for more versatile, efficient, and autonomous AI systems. ToolGen enables end-to-end tool learning and opens opportunities for integration with other advanced techniques such as chain-of-thought and reinforcement learning, thereby expanding the practical capabilities of LLMs.

Since the introduction of the Model Context Protocol (MCP), the number of available tools for Large Language Models (LLMs) has increased significantly. These task-specific tool sets offer an alternative to general-purpose tools such as web browsers, while being easier to develop and maintain than GUIs. However, current general-purpose agents predominantly rely on web browsers for interacting with the environment. Here, we introduce TheMCPCompany, a benchmark for evaluating tool-calling agents on tasks that involve interacting with various real-world services. We use the REST APIs of these services to create MCP servers, which include over 18,000 tools. We also provide manually annotated ground-truth tools for each task. In our experiments, we use the ground truth tools to show the potential of tool-calling agents for both improving performance and reducing costs assuming perfect tool retrieval. Next, we explore agent performance using tool retrieval to study the real-world practicality of tool-based agents. While all models with tool retrieval perform similarly or better than browser-based agents, smaller models cannot take full advantage of the available tools through retrieval. On the other hand, GPT-5's performance with tool retrieval is very close to its performance with ground-truth tools. Overall, our work shows that the most advanced reasoning models are effective at discovering tools in simpler environments, but seriously struggle with navigating complex enterprise environments. TheMCPCompany reveals that navigating tens of thousands of tools and combining them in non-trivial ways to solve complex problems is still a challenging task for current models and requires both better reasoning and better retrieval models.

This paper presents a new tool learning dataset Seal-Tools, which contains self-instruct API-like tools. Seal-Tools not only offers a large number of tools, but also includes instances which demonstrate the practical application of tools. Seeking to generate data on a large scale while ensuring reliability, we propose a self-instruct method to generate tools and instances, allowing precise control over the process. Moreover, our Seal-Tools contains hard instances that call multiple tools to complete the job, among which some are nested tool callings. For precise and comprehensive evaluation, we use strict format control and design three metrics from different dimensions. Therefore, Seal-Tools can serve as a new benchmark to evaluate the tool-calling ability of LLMs. Finally, we evaluate several prevalent LLMs and our finetuned model on Seal-Tools. The results show that current systems are far from perfect. The code, data and experiment results are available at https://github.com/fairyshine/Seal-Tools .

Tool learning enables Large Language Models (LLMs) to interact with external environments by invoking tools, serving as an effective strategy to mitigate the limitations inherent in their pre-training data. In this process, tool documentation plays a crucial role by providing usage instructions for LLMs, thereby facilitating effective tool utilization. This paper concentrates on the critical challenge of bridging the comprehension gap between LLMs and external tools due to the inadequacies and inaccuracies inherent in existing human-centric tool documentation. We propose a novel framework, DRAFT, aimed at Dynamically Refining tool documentation through the Analysis of Feedback and Trails emanating from LLMs' interactions with external tools. This methodology pivots on an innovative trial-and-error approach, consisting of three distinct learning phases: experience gathering, learning from experience, and documentation rewriting, to iteratively enhance the tool documentation. This process is further optimized by implementing a diversity-promoting exploration strategy to ensure explorative diversity and a tool-adaptive termination mechanism to prevent overfitting while enhancing efficiency. Extensive experiments on multiple datasets demonstrate that DRAFT's iterative, feedback-based refinement significantly ameliorates documentation quality, fostering a deeper comprehension and more effective utilization of tools by LLMs. Notably, our analysis reveals that the tool documentation refined via our approach demonstrates robust cross-model generalization capabilities.

Tool learning, which enables large language models (LLMs) to utilize external tools effectively, has garnered increasing attention for its potential to revolutionize productivity across industries. Despite rapid development in tool learning, key challenges and opportunities remain understudied, limiting deeper insights and future advancements. In this paper, we investigate the tool learning ability of 41 prevalent LLMs by reproducing 33 benchmarks and enabling one-click evaluation for seven of them, forming a Tool Learning Platform named ToLeaP. We also collect 21 out of 33 potential training datasets to facilitate future exploration. After analyzing over 3,000 bad cases of 41 LLMs based on ToLeaP, we identify four main critical challenges: (1) benchmark limitations induce both the neglect and lack of (2) autonomous learning, (3) generalization, and (4) long-horizon task-solving capabilities of LLMs. To aid future advancements, we take a step further toward exploring potential directions, namely (1) real-world benchmark construction, (2) compatibility-aware autonomous learning, (3) rationale learning by thinking, and (4) identifying and recalling key clues. The preliminary experiments demonstrate their effectiveness, highlighting the need for further research and exploration.

The tool-using capability of large language models (LLMs) enables them to access up-to-date external information and handle complex tasks. Current approaches to enhancing this capability primarily rely on distilling advanced models by data synthesis. However, this method incurs significant costs associated with advanced model usage and often results in data compatibility issues, led by the high discrepancy in the knowledge scope between the advanced model and the target model. To address these challenges, we propose ToolACE-DEV, a self-improving framework for tool learning. First, we decompose the tool-learning objective into sub-tasks that enhance basic tool-making and tool-using abilities. Then, we introduce a self-evolving paradigm that allows lightweight models to self-improve, reducing reliance on advanced LLMs. Extensive experiments validate the effectiveness of our approach across models of varying scales and architectures.

Recent research shows the potential of enhancing the problem-solving ability of large language models (LLMs) through the use of external tools. However, prior work along this line depends on the availability of existing tools. In this work, we take an initial step towards removing this dependency by proposing a closed-loop framework, referred to as LLMs As Tool Makers (LATM), where LLMs create their own reusable tools for problem-solving. Our approach consists of two key phases: 1) tool making: an LLM acts as the tool maker that crafts tools for given tasks, where a tool is implemented as a Python utility function. 2) tool using: an LLM acts as the tool user, which applies the tool built by the tool maker for problem-solving. The tool user can be either the same or a different LLM from the tool maker. Tool-making enables an LLM to continually generate tools that can be applied to different requests so that future requests can call the corresponding APIs when beneficial for solving the tasks. Furthermore, the division of labor among LLMs for tool-making and tool-using phases introduces the opportunity to achieve cost effectiveness without degrading the quality of generated tools and problem solutions. For example, recognizing that tool-making demands more sophisticated capabilities than tool-using, we can apply a powerful yet resource-intensive model as the tool maker, and a lightweight while cost-effective model as the tool user. We validate the effectiveness of our approach across a variety of complex reasoning tasks, including Big-Bench tasks. With GPT-4 as the tool maker and GPT-3.5 as the tool user, LATM can achieve performance that is on par with using GPT-4 for both tool making and tool using, while the inference cost is significantly reduced.

Conventional recommender systems (RSs) face challenges in precisely capturing users' fine-grained preferences. Large language models (LLMs) have shown capabilities in commonsense reasoning and leveraging external tools that may help address these challenges. However, existing LLM-based RSs suffer from hallucinations, misalignment between the semantic space of items and the behavior space of users, or overly simplistic control strategies (e.g., whether to rank or directly present existing results). To bridge these gap, we introduce ToolRec, a framework for LLM-empowered recommendations via tool learning that uses LLMs as surrogate users, thereby guiding the recommendation process and invoking external tools to generate a recommendation list that aligns closely with users' nuanced preferences. We formulate the recommendation process as a process aimed at exploring user interests in attribute granularity. The process factors in the nuances of the context and user preferences. The LLM then invokes external tools based on a user's attribute instructions and probes different segments of the item pool. We consider two types of attribute-oriented tools: rank tools and retrieval tools. Through the integration of LLMs, ToolRec enables conventional recommender systems to become external tools with a natural language interface. Extensive experiments verify the effectiveness of ToolRec, particularly in scenarios that are rich in semantic content.

Tool-augmented large language models (LLMs) are attracting widespread attention when accessing up-to-date knowledge and alleviating hallucination issues. Nowadays, advanced closed-source LLMs (e.g., ChatGPT) have demonstrated surprising tool-usage capabilities through prompting and in-context learning techniques. To empower the capabilities of open-source LLMs (e.g., LLaMA) in manipulating tools, current efforts focus on either template-driven or token-triggered tool-usage. However, the former hampers LLMs' flexibility to address diverse user's queries due to constrained tool interactions, while the latter limits the generalizability when engaging with new tools, since tool-usage learning is based on task- and tool-specific datasets. To alleviate these concerns, in this paper, we propose a decision-aware and generalizable tool-usage framework (DEER). Specifically, we first construct the tool-usage samples with multiple decision branches via an automatic generation pipeline, thereby inspiring the decision-making awareness of LLMs under diverse scenarios. Meanwhile, we propose a novel tool sampling strategy to enhance the generalizability of LLMs over unseen tools. Extensive experiments demonstrate that our proposed DEER is effective and significantly outperforms baselines across various datasets.

Information-seeking is a core capability for AI agents, requiring them to gather and reason over tool-generated information across long trajectories. However, such multi-step information-seeking tasks remain challenging for agents backed by language models. While process reward models (PRMs) can guide agents by ranking candidate steps at test-time, existing PRMs, designed for short reasoning with binary judgment, cannot capture richer dimensions of information-seeking steps, such as tool interactions and reasoning over tool outputs, nor handle the rapidly growing context in long-horizon tasks. To address these limitations, we introduce PRInTS, a generative PRM trained with dual capabilities: (1) dense scoring based on the PRM's reasoning across multiple step quality dimensions (e.g., interpretation of tool outputs, tool call informativeness) and (2) trajectory summarization that compresses the growing context while preserving essential information for step evaluation. Extensive evaluations across FRAMES, GAIA (levels 1-3), and WebWalkerQA (easy-hard) benchmarks on multiple models, along with ablations, reveal that best-of-n sampling with PRInTS enhances information-seeking abilities of open-source models as well as specialized agents, matching or surpassing the performance of frontier models with a much smaller backbone agent and outperforming other strong reward modeling baselines.

Existing evaluations of tool learning primarily focus on validating the alignment of selected tools for large language models (LLMs) with expected outcomes. However, these approaches rely on a limited set of scenarios where answers can be pre-determined, diverging from genuine needs. Furthermore, a sole emphasis on outcomes disregards the intricate capabilities essential for LLMs to effectively utilize tools. To tackle this issue, we propose ToolEyes, a fine-grained system tailored for the evaluation of the LLMs' tool learning capabilities in authentic scenarios. The system meticulously examines seven real-world scenarios, analyzing five dimensions crucial to LLMs in tool learning: format alignment, intent comprehension, behavior planning, tool selection, and answer organization. Additionally, ToolEyes incorporates a tool library boasting approximately 600 tools, serving as an intermediary between LLMs and the physical world. Evaluations involving ten LLMs across three categories reveal a preference for specific scenarios and limited cognitive abilities in tool learning. Intriguingly, expanding the model size even exacerbates the hindrance to tool learning. These findings offer instructive insights aimed at advancing the field of tool learning. The data is available att https://github.com/Junjie-Ye/ToolEyes.

Recent research has demonstrated that Large Language Models (LLMs) can enhance their capabilities by utilizing external tools. However, three pivotal questions remain unanswered: (1) How effective are current LLMs in utilizing tools? (2) How can we enhance LLMs' ability to utilize tools? (3) What obstacles need to be overcome to leverage tools? To address these questions, we introduce API-Bank, a groundbreaking benchmark, specifically designed for tool-augmented LLMs. For the first question, we develop a runnable evaluation system consisting of 73 API tools. We annotate 314 tool-use dialogues with 753 API calls to assess the existing LLMs' capabilities in planning, retrieving, and calling APIs. For the second question, we construct a comprehensive training set containing 1,888 tool-use dialogues from 2,138 APIs spanning 1,000 distinct domains. Using this dataset, we train Lynx, a tool-augmented LLM initialized from Alpaca. Experimental results demonstrate that GPT-3.5 exhibits improved tool utilization compared to GPT-3, while GPT-4 excels in planning. However, there is still significant potential for further improvement. Moreover, Lynx surpasses Alpaca's tool utilization performance by more than 26 pts and approaches the effectiveness of GPT-3.5. Through error analysis, we highlight the key challenges for future research in this field to answer the third question.

Tool calling has become increasingly popular for Large Language Models (LLMs). However, for large tool sets, the resulting tokens would exceed the LLM's context window limit, making it impossible to include every tool. Hence, an external retriever is used to provide LLMs with the most relevant tools for a query. Existing retrieval models rank tools based on the similarity between a user query and a tool description (TD). This leads to suboptimal retrieval as user requests are often poorly aligned with the language of TD. To remedy the issue, we propose ToolDreamer, a framework to condition retriever models to fetch tools based on hypothetical (synthetic) TD generated using an LLM, i.e., description of tools that the LLM feels will be potentially useful for the query. The framework enables a more natural alignment between queries and tools within the language space of TD's. We apply ToolDreamer on the ToolRet dataset and show that our method improves the performance of sparse and dense retrievers with and without training, thus showcasing its flexibility. Through our proposed framework, our aim is to offload a portion of the reasoning burden to the retriever so that the LLM may effectively handle a large collection of tools without inundating its context window.

Language models (LMs) are powerful yet mostly for text generation tasks. Tools have substantially enhanced their performance for tasks that require complex skills. However, many works adopt the term "tool" in different ways, raising the question: What is a tool anyway? Subsequently, where and how do tools help LMs? In this survey, we provide a unified definition of tools as external programs used by LMs, and perform a systematic review of LM tooling scenarios and approaches. Grounded on this review, we empirically study the efficiency of various tooling methods by measuring their required compute and performance gains on various benchmarks, and highlight some challenges and potential future research in the field.

Can the rapid advances in code generation, function calling, and data analysis using large language models (LLMs) help automate the search and verification of hypotheses purely from a set of provided datasets? To evaluate this question, we present DiscoveryBench, the first comprehensive benchmark that formalizes the multi-step process of data-driven discovery. The benchmark is designed to systematically assess current model capabilities in discovery tasks and provide a useful resource for improving them. Our benchmark contains 264 tasks collected across 6 diverse domains, such as sociology and engineering, by manually deriving discovery workflows from published papers to approximate the real-world challenges faced by researchers, where each task is defined by a dataset, its metadata, and a discovery goal in natural language. We additionally provide 903 synthetic tasks to conduct controlled evaluations across task complexity. Furthermore, our structured formalism of data-driven discovery enables a facet-based evaluation that provides useful insights into different failure modes. We evaluate several popular LLM-based reasoning frameworks using both open and closed LLMs as baselines on DiscoveryBench and find that even the best system scores only 25%. Our benchmark, thus, illustrates the challenges in autonomous data-driven discovery and serves as a valuable resource for the community to make progress.

Tool learning can further broaden the usage scenarios of large language models (LLMs). However most of the existing methods either need to finetune that the model can only use tools seen in the training data, or add tool demonstrations into the prompt with lower efficiency. In this paper, we present a new Tool Learning method Chain-of-Tools. It makes full use of the powerful semantic representation capability of frozen LLMs to finish tool calling in CoT reasoning with a huge and flexible tool pool which may contain unseen tools. Especially, to validate the effectiveness of our approach in the massive unseen tool scenario, we construct a new dataset SimpleToolQuestions. We conduct experiments on two numerical reasoning benchmarks (GSM8K-XL and FuncQA) and two knowledge-based question answering benchmarks (KAMEL and SimpleToolQuestions). Experimental results show that our approach performs better than the baseline. We also identify dimensions of the model output that are critical in tool selection, enhancing the model interpretability. Our code and data are available at: https://github.com/fairyshine/Chain-of-Tools .

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analyses into a common ecosystem. In omics, unified ecosystems have transformed research by enabling interoperability, reuse, and community-driven development; AI scientists require comparable infrastructure. We present ToolUniverse, an ecosystem for building AI scientists from any language or reasoning model, whether open or closed. TOOLUNIVERSE standardizes how AI scientists identify and call tools, integrating more than 600 machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design. It automatically refines tool interfaces for correct use by AI scientists, creates new tools from natural language descriptions, iteratively optimizes tool specifications, and composes tools into agentic workflows. In a case study of hypercholesterolemia, ToolUniverse was used to create an AI scientist to identify a potent analog of a drug with favorable predicted properties. The open-source ToolUniverse is available at https://aiscientist.tools.

External tools help large language models succeed at tasks where they would otherwise typically fail. In existing frameworks, choosing tools at test time relies on naive greedy decoding, regardless of whether the model has been fine-tuned on tool-annotated data or prompted with in-context examples. In contrast, we find that gathering and choosing among a suitable set of candidate tools has greater potential to lead to an optimal selection. We present Tool selECTion via meta-reasONing (TECTON), a two-phase system that first reasons over a task and outputs candidate tools using a custom fine-tuned language modelling head. Then, with the custom head disabled, it meta-reasons (i.e., it reasons over the previous reasoning process) to make a final choice. We show that TECTON results in substantial gains--both in-distribution and out-of-distribution--on a range of math reasoning datasets.

Large language models (LLMs) have demonstrated exceptional reasoning capabilities, enabling them to solve various complex problems. Recently, this ability has been applied to the paradigm of tool learning. Tool learning involves providing examples of tool usage and their corresponding functions, allowing LLMs to formulate plans and demonstrate the process of invoking and executing each tool. LLMs can address tasks that they cannot complete independently, thereby enhancing their potential across different tasks. However, this approach faces two key challenges. First, redundant error correction leads to unstable planning and long execution time. Additionally, designing a correct plan among multiple tools is also a challenge in tool learning. To address these issues, we propose Tool-Planner, a task-processing framework based on toolkits. Tool-Planner groups tools based on the API functions with the same function into a toolkit and allows LLMs to implement planning across the various toolkits. When a tool error occurs, the language model can reselect and adjust tools based on the toolkit. Experiments show that our approach demonstrates a high pass and win rate across different datasets and optimizes the planning scheme for tool learning in models such as GPT-4 and Claude 3, showcasing the potential of our method.

Tool learning has emerged as a promising direction by extending Large Language Models' (LLMs) capabilities with external tools. Existing tool learning studies primarily focus on the general-purpose tool-use capability, which addresses explicit user requirements in instructions. However, they overlook the importance of personalized tool-use capability, leading to an inability to handle implicit user preferences. To address the limitation, we first formulate the task of personalized tool learning, which integrates user's interaction history towards personalized tool usage. To fill the gap of missing benchmarks, we construct PEToolBench, featuring diverse user preferences reflected in interaction history under three distinct personalized settings, and encompassing a wide range of tool-use scenarios. Moreover, we propose a framework PEToolLLaMA to adapt LLMs to the personalized tool learning task, which is trained through supervised fine-tuning and direct preference optimization. Extensive experiments on PEToolBench demonstrate the superiority of PEToolLLaMA over existing LLMs.

Recently, large language models (LLMs) have shown remarkable reasoning capabilities via large-scale reinforcement learning (RL). However, leveraging the RL algorithm to empower effective multi-tool collaborative reasoning in LLMs remains an open challenge. In this paper, we introduce Tool-Star, an RL-based framework designed to empower LLMs to autonomously invoke multiple external tools during stepwise reasoning. Tool-Star integrates six types of tools and incorporates systematic designs in both data synthesis and training. To address the scarcity of tool-use data, we propose a general tool-integrated reasoning data synthesis pipeline, which combines tool-integrated prompting with hint-based sampling to automatically and scalably generate tool-use trajectories. A subsequent quality normalization and difficulty-aware classification process filters out low-quality samples and organizes the dataset from easy to hard. Furthermore, we propose a two-stage training framework to enhance multi-tool collaborative reasoning by: (1) cold-start fine-tuning, which guides LLMs to explore reasoning patterns via tool-invocation feedback; and (2) a multi-tool self-critic RL algorithm with hierarchical reward design, which reinforces reward understanding and promotes effective tool collaboration. Experimental analyses on over 10 challenging reasoning benchmarks highlight the effectiveness and efficiency of Tool-Star. The code is available at https://github.com/dongguanting/Tool-Star.

Despite the advancements of open-source large language models (LLMs) and their variants, e.g., LLaMA and Vicuna, they remain significantly limited in performing higher-level tasks, such as following human instructions to use external tools (APIs). This is because current instruction tuning largely focuses on basic language tasks instead of the tool-use domain. This is in contrast to state-of-the-art (SOTA) LLMs, e.g., ChatGPT, which have demonstrated excellent tool-use capabilities but are unfortunately closed source. To facilitate tool-use capabilities within open-source LLMs, we introduce ToolLLM, a general tool-use framework of data construction, model training and evaluation. We first present ToolBench, an instruction-tuning dataset for tool use, which is created automatically using ChatGPT. Specifically, we collect 16,464 real-world RESTful APIs spanning 49 categories from RapidAPI Hub, then prompt ChatGPT to generate diverse human instructions involving these APIs, covering both single-tool and multi-tool scenarios. Finally, we use ChatGPT to search for a valid solution path (chain of API calls) for each instruction. To make the searching process more efficient, we develop a novel depth-first search-based decision tree (DFSDT), enabling LLMs to evaluate multiple reasoning traces and expand the search space. We show that DFSDT significantly enhances the planning and reasoning capabilities of LLMs. For efficient tool-use assessment, we develop an automatic evaluator: ToolEval. We fine-tune LLaMA on ToolBench and obtain ToolLLaMA. Our ToolEval reveals that ToolLLaMA demonstrates a remarkable ability to execute complex instructions and generalize to unseen APIs, and exhibits comparable performance to ChatGPT. To make the pipeline more practical, we devise a neural API retriever to recommend appropriate APIs for each instruction, negating the need for manual API selection.

Large language models (LLMs) have shown promising capabilities in using external tools to solve complex problems. However, existing approaches either involve fine-tuning on tool demonstrations, which do not generalize to new tools without additional training, or providing tool documentation in context, limiting the number of tools. Both approaches often generate syntactically invalid tool calls. In this paper, we propose ToolDec, a finite-state machine-guided decoding algorithm for tool-augmented LLMs. ToolDec eliminates tool-related errors for any tool-augmented LLMs by ensuring valid tool names and type-conforming arguments. Furthermore, ToolDec enables LLM to effectively select tools using only the information contained in their names, with no need for fine-tuning or in-context documentation. We evaluated multiple prior methods and their ToolDec-enhanced versions on a variety of tasks involving tools like math functions, knowledge graph relations, and complex real-world RESTful APIs. Our experiments show that ToolDec reduces syntactic errors to zero, consequently achieving significantly better performance and as much as a 2x speedup. We also show that ToolDec achieves superior generalization performance on unseen tools, performing up to 8x better than the baselines.

Integrating external tools into Large Foundation Models (LFMs) has emerged as a promising approach to enhance their problem-solving capabilities. While existing studies have demonstrated strong performance in tool-augmented Visual Question Answering (VQA), recent benchmarks reveal significant gaps in real-world tool-use proficiency, particularly in functionally diverse multimodal settings requiring multi-step reasoning. In this work, we introduce ToolVQA, a large-scale multimodal dataset comprising 23K instances, designed to bridge this gap. Unlike previous datasets that rely on synthetic scenarios and simplified queries, ToolVQA features real-world visual contexts and challenging implicit multi-step reasoning tasks, better aligning with real user interactions. To construct this dataset, we propose ToolEngine, a novel data generation pipeline that employs Depth-First Search (DFS) with a dynamic in-context example matching mechanism to simulate human-like tool-use reasoning. ToolVQA encompasses 10 multimodal tools across 7 diverse task domains, with an average inference length of 2.78 reasoning steps per instance. The fine-tuned 7B LFMs on ToolVQA not only achieve impressive performance on our test set but also surpass the large close-sourced model GPT-3.5-turbo on various out-of-distribution (OOD) datasets, demonstrating strong generalizability to real-world tool-use scenarios.

There is a growing need for Large Language Models (LLMs) to effectively use tools and external Application Programming Interfaces (APIs) to plan and complete tasks. As such, there is tremendous interest in methods that can acquire sufficient quantities of train and test data that involve calls to tools / APIs. Two lines of research have emerged as the predominant strategies for addressing this challenge. The first has focused on synthetic data generation techniques, while the second has involved curating task-adjacent datasets which can be transformed into API / Tool-based tasks. In this paper, we focus on the task of identifying, curating, and transforming existing datasets and, in turn, introduce API-BLEND, a large corpora for training and systematic testing of tool-augmented LLMs. The datasets mimic real-world scenarios involving API-tasks such as API / tool detection, slot filling, and sequencing of the detected APIs. We demonstrate the utility of the API-BLEND dataset for both training and benchmarking purposes.

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

Tool learning enables large language models (LLMs) to interact with external tools and APIs, greatly expanding the application scope of LLMs. However, due to the dynamic nature of external environments, these tools and APIs may become outdated over time, preventing LLMs from correctly invoking tools. Existing research primarily focuses on static environments and overlooks this issue, limiting the adaptability of LLMs in real-world applications. In this paper, we propose ToolEVO, a novel framework designed to enhance the adaptive and reflective capabilities of LLMs against tool variability. By leveraging Monte Carlo Tree Search, ToolEVO facilitates active exploration and interaction of LLMs within dynamic environments, allowing for autonomous self-reflection and self-updating of tool usage based on environmental feedback. Additionally, we introduce ToolQA-D, a benchmark specifically designed to evaluate the impact of tool variability. Extensive experiments demonstrate the effectiveness and stability of our approach, highlighting the importance of adaptability to tool variability for effective tool learning.

Recent studies on software tool manipulation with large language models (LLMs) mostly rely on closed model APIs. The industrial adoption of these models is substantially constrained due to the security and robustness risks in exposing information to closed LLM API services. In this paper, we ask can we enhance open-source LLMs to be competitive to leading closed LLM APIs in tool manipulation, with practical amount of human supervision. By analyzing common tool manipulation failures, we first demonstrate that open-source LLMs may require training with usage examples, in-context demonstration and generation style regulation to resolve failures. These insights motivate us to revisit classical methods in LLM literature, and demonstrate that we can adapt them as model alignment with programmatic data generation, system prompts and in-context demonstration retrievers to enhance open-source LLMs for tool manipulation. To evaluate these techniques, we create the ToolBench, a tool manipulation benchmark consisting of diverse software tools for real-world tasks. We demonstrate that our techniques can boost leading open-source LLMs by up to 90% success rate, showing capabilities competitive to OpenAI GPT-4 in 4 out of 8 ToolBench tasks. We show that such enhancement typically requires about one developer day to curate data for each tool, rendering a recipe with practical amount of human supervision.

Current tool-use large language models (LLMs) are trained on static datasets, enabling them to interact with external tools and perform multi-step, tool-integrated reasoning, which produces tool-call trajectories. However, these models imitate how a query is resolved in a generic tool-call routine, thereby failing to explore possible solutions and demonstrating limited performance in an evolved, dynamic tool-call environment. In this work, we propose PORTool, a reinforcement learning (RL) method that encourages a tool-use LLM to explore various trajectories yielding the correct answer. Specifically, this method starts with generating multiple rollouts for a given query, and some of them share the first few tool-call steps, thereby forming a tree-like structure. Next, we assign rewards to each step, based on its ability to produce a correct answer and make successful tool calls. A shared step across different trajectories receives the same reward, while different steps under the same fork receive different rewards. Finally, these step-wise rewards are used to calculate fork-relative advantages, blended with trajectory-relative advantages, to train the LLM for tool use. The experiments utilize 17 tools to address user queries, covering both time-sensitive and time-invariant topics. We conduct ablation studies to systematically justify the necessity and the design robustness of step-wise rewards. Furthermore, we compare the proposed PORTool with other training approaches and demonstrate significant improvements in final accuracy and the number of tool-call steps.

Recent advancements in LLM-based agents have demonstrated remarkable capabilities in handling complex, knowledge-intensive tasks by integrating external tools. Among diverse choices of tools, search tools play a pivotal role in accessing vast external knowledge. However, open-source agents still fall short of achieving expert-level Search Intelligence, the ability to resolve ambiguous queries, generate precise searches, analyze results, and conduct thorough exploration. Existing approaches fall short in scalability, efficiency, and data quality. For example, small turn limits in existing online RL methods, e.g. <=10, restrict complex strategy learning. This paper introduces ASearcher, an open-source project for large-scale RL training of search agents. Our key contributions include: (1) Scalable fully asynchronous RL training that enables long-horizon search while maintaining high training efficiency. (2) A prompt-based LLM agent that autonomously synthesizes high-quality and challenging QAs, creating a large-scale QA dataset. Through RL training, our prompt-based QwQ-32B agent achieves substantial improvements, with 46.7% and 20.8% Avg@4 gains on xBench and GAIA, respectively. Notably, our agent exhibits extreme long-horizon search, with tool calls exceeding 40 turns and output tokens exceeding 150k during training time. With a simple agent design and no external LLMs, ASearcher-Web-QwQ achieves Avg@4 scores of 42.1 on xBench and 52.8 on GAIA, surpassing existing open-source 32B agents. We open-source our models, training data, and codes in https://github.com/inclusionAI/ASearcher.

Large Language Models (LLMs) have demonstrated significant progress in utilizing external APIs as tools for various tasks. However, their tool-using ability is limited by the availability of suitable APIs and the instability of implicit reasoning, particularly when simultaneously engaging in reasoning about plans and actual calculations. To address these limitations, we propose CREATOR, a novel framework that empowers LLMs to create their own tools through documentation and code realization. CREATOR disentangles the LLM's ability into two distinct phases: abstract tool creation and concrete decision execution, which results in improved LLM performance. We evaluate CREATOR on two established benchmarks: MATH, which consists of challenging math competition problems, and TabMWP, which includes diverse tabular contents for problem-solving. Remarkably, CREATOR significantly outperforms existing chain-of-thought (CoT), program-of-thought (PoT), and tool-using baselines on these two benchmarks. Additionally, we present a new dataset, Creation Challenge, comprising 2K diverse questions, to highlight the necessity and benefits of LLMs' tool creation ability in effectively addressing these problems. Furthermore, our research reveals that leveraging LLMs as tool creators facilitates knowledge transfer, and LLMs exhibit varying levels of tool creation abilities, enabling them to flexibly tackle diverse situations. Our study represents a promising avenue for maximizing the potential of LLMs and advancing toward truly intelligent and adaptable AI systems.

Today, large language models (LLMs) are taught to use new tools by providing a few demonstrations of the tool's usage. Unfortunately, demonstrations are hard to acquire, and can result in undesirable biased usage if the wrong demonstration is chosen. Even in the rare scenario that demonstrations are readily available, there is no principled selection protocol to determine how many and which ones to provide. As tasks grow more complex, the selection search grows combinatorially and invariably becomes intractable. Our work provides an alternative to demonstrations: tool documentation. We advocate the use of tool documentation, descriptions for the individual tool usage, over demonstrations. We substantiate our claim through three main empirical findings on 6 tasks across both vision and language modalities. First, on existing benchmarks, zero-shot prompts with only tool documentation are sufficient for eliciting proper tool usage, achieving performance on par with few-shot prompts. Second, on a newly collected realistic tool-use dataset with hundreds of available tool APIs, we show that tool documentation is significantly more valuable than demonstrations, with zero-shot documentation significantly outperforming few-shot without documentation. Third, we highlight the benefits of tool documentations by tackling image generation and video tracking using just-released unseen state-of-the-art models as tools. Finally, we highlight the possibility of using tool documentation to automatically enable new applications: by using nothing more than the documentation of GroundingDino, Stable Diffusion, XMem, and SAM, LLMs can re-invent the functionalities of the just-released Grounded-SAM and Track Anything models.

Materials discovery and design are essential for advancing technology across various industries by enabling the development of application-specific materials. Recent research has leveraged Large Language Models (LLMs) to accelerate this process. We explore the potential of LLMs to generate viable hypotheses that, once validated, can expedite materials discovery. Collaborating with materials science experts, we curated a novel dataset from recent journal publications, featuring real-world goals, constraints, and methods for designing real-world applications. Using this dataset, we test LLM-based agents that generate hypotheses for achieving given goals under specific constraints. To assess the relevance and quality of these hypotheses, we propose a novel scalable evaluation metric that emulates the process a materials scientist would use to evaluate a hypothesis critically. Our curated dataset, proposed method, and evaluation framework aim to advance future research in accelerating materials discovery and design with LLMs.

Recent advancements in Large Language Models (LLMs) and the introduction of the Model Context Protocol (MCP) have significantly expanded LLM agents' capability to interact dynamically with external tools and APIs. However, existing tool selection frameworks do not integrate MCP servers, instead relying heavily on error-prone manual updates to monolithic local tool repositories, leading to duplication, inconsistencies, and inefficiencies. Additionally, current approaches abstract tool selection before the LLM agent is invoked, limiting its autonomy and hindering dynamic re-querying capabilities during multi-turn interactions. To address these issues, we introduce ScaleMCP, a novel tool selection approach that dynamically equips LLM agents with a MCP tool retriever, giving agents the autonomy to add tools into their memory, as well as an auto-synchronizing tool storage system pipeline through CRUD (create, read, update, delete) operations with MCP servers as the single source of truth. We also propose a novel embedding strategy, Tool Document Weighted Average (TDWA), designed to selectively emphasize critical components of tool documents (e.g. tool name or synthetic questions) during the embedding process. Comprehensive evaluations conducted on a created dataset of 5,000 financial metric MCP servers, across 10 LLM models, 5 embedding models, and 5 retriever types, demonstrate substantial improvements in tool retrieval and agent invocation performance, emphasizing ScaleMCP's effectiveness in scalable, dynamic tool selection and invocation.

While the recent developments in large language models (LLMs) have successfully enabled generative recommenders with natural language interactions, their recommendation behavior is limited, leaving other simpler yet crucial components such as metadata or attribute filtering underutilized in the system. We propose an LLM-based music recommendation system with tool calling to serve as a unified retrieval-reranking pipeline. Our system positions an LLM as an end-to-end recommendation system that interprets user intent, plans tool invocations, and orchestrates specialized components: boolean filters (SQL), sparse retrieval (BM25), dense retrieval (embedding similarity), and generative retrieval (semantic IDs). Through tool planning, the system predicts which types of tools to use, their execution order, and the arguments needed to find music matching user preferences, supporting diverse modalities while seamlessly integrating multiple database filtering methods. We demonstrate that this unified tool-calling framework achieves competitive performance across diverse recommendation scenarios by selectively employing appropriate retrieval methods based on user queries, envisioning a new paradigm for conversational music recommendation systems.

Recent advances in LLMs have made automated scientific research the next frontline in the path to artificial superintelligence. However, these systems are bound either to tasks of narrow scope or the limited creative capabilities of LLMs. We propose Spacer, a scientific discovery system that develops creative and factually grounded concepts without external intervention. Spacer attempts to achieve this via 'deliberate decontextualization,' an approach that disassembles information into atomic units - keywords - and draws creativity from unexplored connections between them. Spacer consists of (i) Nuri, an inspiration engine that builds keyword sets, and (ii) the Manifesting Pipeline that refines these sets into elaborate scientific statements. Nuri extracts novel, high-potential keyword sets from a keyword graph built with 180,000 academic publications in biological fields. The Manifesting Pipeline finds links between keywords, analyzes their logical structure, validates their plausibility, and ultimately drafts original scientific concepts. According to our experiments, the evaluation metric of Nuri accurately classifies high-impact publications with an AUROC score of 0.737. Our Manifesting Pipeline also successfully reconstructs core concepts from the latest top-journal articles solely from their keyword sets. An LLM-based scoring system estimates that this reconstruction was sound for over 85% of the cases. Finally, our embedding space analysis shows that outputs from Spacer are significantly more similar to leading publications compared with those from SOTA LLMs.

To address intricate real-world tasks, there has been a rising interest in tool utilization in applications of large language models (LLMs). To develop LLM-based agents, it usually requires LLMs to understand many tool functions from different tool documentation. But these documentations could be diverse, redundant or incomplete, which immensely affects the capability of LLMs in using tools. To solve this, we introduce EASYTOOL, a framework transforming diverse and lengthy tool documentation into a unified and concise tool instruction for easier tool usage. EasyTool purifies essential information from extensive tool documentation of different sources, and elaborates a unified interface (i.e., tool instruction) to offer standardized tool descriptions and functionalities for LLM-based agents. Extensive experiments on multiple different tasks demonstrate that EasyTool can significantly reduce token consumption and improve the performance of tool utilization in real-world scenarios. Our code will be available at https://github.com/microsoft/JARVIS/ in the future.

Tools enhance the reasoning capabilities of large language models (LLMs) in complex problem-solving tasks, but not all tasks have available tools. In the absence of predefined tools, prior works have explored instructing LLMs to generate tools on their own. However, such approaches rely heavily on the models' internal knowledge and would fail in domains beyond the LLMs' knowledge scope. To address this limitation, we propose RefTool, a reference-guided framework for automatic tool creation that leverages structured external materials such as textbooks. RefTool consists of two modules: (1) tool creation, where LLMs generate executable tools from reference content, validate them using illustrative examples, and organize them hierarchically into a toolbox; and (2) tool utilization, where LLMs navigate the toolbox structure to select and apply the appropriate tools to solve problems. Experiments on causality, physics, and chemistry benchmarks demonstrate that RefTool outperforms existing tool-creation and domain-specific reasoning methods by 11.3% on average accuracy, while being cost-efficient and broadly generalizable. Analyses reveal that grounding tool creation in references produces accurate and faithful tools, and that the hierarchical structure facilitates effective tool selection. RefTool enables LLMs to overcome knowledge limitations, demonstrating the value of grounding tool creation in external references for enhanced and generalizable reasoning.

Recent advancements in integrating large language models (LLMs) with tools have allowed the models to interact with real-world environments. However, these tool-augmented LLMs often encounter incomplete scenarios when users provide partial information or the necessary tools are unavailable. Recognizing and managing such scenarios is crucial for LLMs to ensure their reliability, but this exploration remains understudied. This study examines whether LLMs can identify incomplete conditions and appropriately determine when to refrain from using tools. To this end, we address a dataset by manipulating instances from two datasets by removing necessary tools or essential information for tool invocation. We confirm that most LLMs are challenged to identify the additional information required to utilize specific tools and the absence of appropriate tools. Our research can contribute to advancing reliable LLMs by addressing scenarios that commonly arise during interactions between humans and LLMs.

Recently, tool-augmented LLMs have gained increasing attention. Given an instruction, tool-augmented LLMs can interact with various external tools in multiple rounds and provide a final answer. However, previous LLMs were trained on overly detailed instructions, which included API names or parameters, while real users would not explicitly mention these API details. This leads to a gap between trained LLMs and real-world scenarios. In addition, most works ignore whether the interaction process follows the instruction. To address these issues, we constructed a training dataset called MGToolBench, which contains statement and category-level instructions to better reflect real-world scenarios. In addition, we propose ToolPlanner, a two-stage reinforcement learning framework that utilizes path planning and two feedback mechanisms to enhance the LLM's task completion and instruction-following capabilities. Experimental results show that ToolPlanner significantly improves the Match Rate, Pass Rate and Win Rate by 26.8%, 20.2%, and 5.6% compared to the SOTA model. Human evaluation verifies that the multi-granularity instructions can better align with users' usage habits. Our data and code will be released upon acceptance.

Despite recent advances in AI, the development of systems capable of executing complex, multi-step reasoning tasks involving multiple tools remains a significant challenge. Current benchmarks fall short in capturing the real-world complexity of tool-use reasoning, where verifying the correctness of not only the final answer but also the intermediate steps is important for evaluation, development, and identifying failures during inference time. To bridge this gap, we introduce ToolComp, a comprehensive benchmark designed to evaluate multi-step tool-use reasoning. ToolComp is developed through a collaboration between models and human annotators, featuring human-edited/verified prompts, final answers, and process supervision labels, allowing for the evaluation of both final outcomes and intermediate reasoning. Evaluation across six different model families demonstrates the challenging nature of our dataset, with the majority of models achieving less than 50% accuracy. Additionally, we generate synthetic training data to compare the performance of outcome-supervised reward models (ORMs) with process-supervised reward models (PRMs) to assess their ability to improve complex tool-use reasoning as evaluated by ToolComp. Our results show that PRMs generalize significantly better than ORMs, achieving a 19% and 11% improvement in rank@1 accuracy for ranking base and fine-tuned model trajectories, respectively. These findings highlight the critical role of process supervision in both the evaluation and training of AI models, paving the way for more robust and capable systems in complex, multi-step tool-use tasks.

Despite having powerful reasoning and inference capabilities, Large Language Models (LLMs) still need external tools to acquire real-time information retrieval or domain-specific expertise to solve complex tasks, which is referred to as tool learning. Existing tool learning methods primarily rely on tuning with expert trajectories, focusing on token-sequence learning from a linguistic perspective. However, there are several challenges: 1) imitating static trajectories limits their ability to generalize to new tasks. 2) even expert trajectories can be suboptimal, and better solution paths may exist. In this work, we introduce StepTool, a novel step-grained reinforcement learning framework to improve tool learning in LLMs. It consists of two components: Step-grained Reward Shaping, which assigns rewards at each tool interaction based on tool invocation success and its contribution to the task, and Step-grained Optimization, which uses policy gradient methods to optimize the model in a multi-step manner. Experimental results demonstrate that StepTool significantly outperforms existing methods in multi-step, tool-based tasks, providing a robust solution for complex task environments. Codes are available at https://github.com/yuyq18/StepTool.

Enabling large language models to utilize real-world tools effectively is crucial for achieving embodied intelligence. Existing approaches to tool learning have either primarily relied on extremely large language models, such as GPT-4, to attain generalized tool-use abilities in a zero-shot manner, or utilized supervised learning to train limited scopes of tools on compact models. However, it remains uncertain whether smaller language models can achieve generalized tool-use abilities without tool-specific training. To address this question, this paper introduces ToolAlpaca, a novel framework designed to automatically generate a diverse tool-use corpus and learn generalized tool-use abilities on compact language models with minimal human intervention. Specifically, ToolAlpaca first automatically creates a highly diversified tool-use corpus by building a multi-agent simulation environment. The corpus contains 3938 tool-use instances from more than 400 real-world tool APIs spanning 50 distinct categories. Subsequently, the constructed corpus is employed to fine-tune compact language models, resulting in two models, namely ToolAlpaca-7B and ToolAlpaca-13B, respectively. Finally, we evaluate the ability of these models to utilize previously unseen tools without specific training. Experimental results demonstrate that ToolAlpaca achieves effective generalized tool-use capabilities comparable to those of extremely large language models like GPT-3.5, demonstrating that learning generalized tool-use ability is feasible for compact language models.

Large language model (LLM)-based agents increasingly rely on tool use to complete real-world tasks. While existing works evaluate the LLMs' tool use capability, they largely focus on the final answers yet overlook the detailed tool usage trajectory, i.e., whether tools are selected, parameterized, and ordered correctly. We introduce TRAJECT-Bench, a trajectory-aware benchmark to comprehensively evaluate LLMs' tool use capability through diverse tasks with fine-grained evaluation metrics. TRAJECT-Bench pairs high-fidelity, executable tools across practical domains with tasks grounded in production-style APIs, and synthesizes trajectories that vary in breadth (parallel calls) and depth (interdependent chains). Besides final accuracy, TRAJECT-Bench also reports trajectory-level diagnostics, including tool selection and argument correctness, and dependency/order satisfaction. Analyses reveal failure modes such as similar tool confusion and parameter-blind selection, and scaling behavior with tool diversity and trajectory length where the bottleneck of transiting from short to mid-length trajectories is revealed, offering actionable guidance for LLMs' tool use.

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

Large language models (LLMs) can now access a wide range of external tools, thanks to the Model Context Protocol (MCP). This greatly expands their abilities as various agents. However, LLMs rely entirely on the text descriptions of tools to decide which ones to use--a process that is surprisingly fragile. In this work, we expose a vulnerability in prevalent tool/function-calling protocols by investigating a series of edits to tool descriptions, some of which can drastically increase a tool's usage from LLMs when competing with alternatives. Through controlled experiments, we show that tools with properly edited descriptions receive over 10 times more usage from GPT-4.1 and Qwen2.5-7B than tools with original descriptions. We further evaluate how various edits to tool descriptions perform when competing directly with one another and how these trends generalize or differ across a broader set of 10 different models. These phenomenons, while giving developers a powerful way to promote their tools, underscore the need for a more reliable foundation for agentic LLMs to select and utilize tools and resources.

Tool learning, which allows Large Language Models (LLMs) to leverage external tools for solving complex user tasks, has emerged as a promising avenue for extending model capabilities. However, current approaches primarily focus on data synthesis for fine-tuning LLMs to invoke tools effectively, largely ignoring how to fully stimulate the potential of the model. In this paper, we propose ToolACE-R, a novel method that introduces adaptive self-refinement for tool invocations. Our approach features a model-aware iterative training procedure that progressively incorporates more training samples based on the model's evolving capabilities. Additionally, it allows LLMs to iteratively refine their tool calls, optimizing performance without requiring external feedback. To further enhance computational efficiency, we integrate an adaptive mechanism when scaling the inference time, enabling the model to autonomously determine when to stop the refinement process. We conduct extensive experiments across several benchmark datasets, showing that ToolACE-R achieves competitive performance compared to advanced API-based models, even without any refinement. Furthermore, its performance can be further improved efficiently through adaptive self-refinement. Our results demonstrate the effectiveness of the proposed method, which is compatible with base models of various sizes, offering a promising direction for more efficient tool learning.

Large language models (LLMs) are increasingly employed for complex multi-step planning tasks, where the tool retrieval (TR) step is crucial for achieving successful outcomes. Two prevalent approaches for TR are single-step retrieval, which utilizes the complete query, and sequential retrieval using task decomposition (TD), where a full query is segmented into discrete atomic subtasks. While single-step retrieval lacks the flexibility to handle "inter-tool dependency," the TD approach necessitates maintaining "subtask-tool atomicity alignment," as the toolbox can evolve dynamically. To address these limitations, we introduce the Progressive Tool retrieval to Improve Planning (ProTIP) framework. ProTIP is a lightweight, contrastive learning-based framework that implicitly performs TD without the explicit requirement of subtask labels, while simultaneously maintaining subtask-tool atomicity. On the ToolBench dataset, ProTIP outperforms the ChatGPT task decomposition-based approach by a remarkable margin, achieving a 24% improvement in Recall@K=10 for TR and a 41% enhancement in tool accuracy for plan generation.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Effective evaluation of multi-hop tool use is critical for analyzing the understanding, reasoning, and function-calling capabilities of large language models (LLMs). However, progress has been hindered by a lack of reliable evaluation datasets. To address this, we present ToolHop, a dataset comprising 995 user queries and 3,912 associated tools, specifically designed for rigorous evaluation of multi-hop tool use. ToolHop ensures diverse queries, meaningful interdependencies, locally executable tools, detailed feedback, and verifiable answers through a novel query-driven data construction approach that includes tool creation, document refinement, and code generation. We evaluate 14 LLMs across five model families (i.e., LLaMA3.1, Qwen2.5, Gemini1.5, Claude3.5, and GPT), uncovering significant challenges in handling multi-hop tool-use scenarios. The leading model, GPT-4o, achieves an accuracy of 49.04%, underscoring substantial room for improvement. Further analysis reveals variations in tool-use strategies for various families, offering actionable insights to guide the development of more effective approaches. Code and data can be found in https://huggingface.co/bytedance-research/ToolHop.

Text-to-image models like stable diffusion and DALLE-3 still struggle with multi-turn image editing. We decompose such a task as an agentic workflow (path) of tool use that addresses a sequence of subtasks by AI tools of varying costs. Conventional search algorithms require expensive exploration to find tool paths. While large language models (LLMs) possess prior knowledge of subtask planning, they may lack accurate estimations of capabilities and costs of tools to determine which to apply in each subtask. Can we combine the strengths of both LLMs and graph search to find cost-efficient tool paths? We propose a three-stage approach "CoSTA*" that leverages LLMs to create a subtask tree, which helps prune a graph of AI tools for the given task, and then conducts A* search on the small subgraph to find a tool path. To better balance the total cost and quality, CoSTA* combines both metrics of each tool on every subtask to guide the A* search. Each subtask's output is then evaluated by a vision-language model (VLM), where a failure will trigger an update of the tool's cost and quality on the subtask. Hence, the A* search can recover from failures quickly to explore other paths. Moreover, CoSTA* can automatically switch between modalities across subtasks for a better cost-quality trade-off. We build a novel benchmark of challenging multi-turn image editing, on which CoSTA* outperforms state-of-the-art image-editing models or agents in terms of both cost and quality, and performs versatile trade-offs upon user preference.

Tool-integrated reasoning has emerged as a key focus for enabling agentic applications. Among these, DeepResearch Agents have gained significant attention for their strong performance on complex, open-ended information-seeking tasks. We introduce Fathom-DeepResearch, an agentic system composed of two specialized models. The first is Fathom-Search-4B, a DeepSearch model trained from Qwen3-4B and optimized for evidence-based investigation through live web search and targeted webpage querying. Its training combines three advances: (i) DUETQA, a 5K-sample dataset generated via multi-agent self-play that enforces strict web-search dependence and heterogeneous source grounding; (ii) RAPO, a zero-overhead extension of GRPO that stabilizes multi-turn Reinforcement Learning with Verifiable Rewards through curriculum pruning, reward-aware advantage scaling, and per-prompt replay buffers; and (iii) a steerable step-level reward that classifies each tool call by cognitive behavior and marginal utility, enabling explicit control over search trajectory breadth, depth, and horizon. These improvements enable reliable extension of tool-calling beyond 20 calls when warranted. The second is Fathom-Synthesizer-4B, trained from Qwen3-4B, which converts multi-turn DeepSearch traces into structured, citation-dense DeepResearch Reports for comprehensive synthesis. Evaluated on DeepSearch benchmarks (SimpleQA, FRAMES, WebWalker, Seal0, MuSiQue) and DeepResearch-Bench, the system achieves state-of-the-art performance in the open-weights category while demonstrating strong generalization to diverse reasoning tasks including HLE, AIME-25, GPQA-Diamond, and MedQA.

The ability of large language models (LLMs) to utilize external tools has enabled them to tackle an increasingly diverse range of tasks. However, as the tasks become more complex and long-horizon, the intricate tool utilization process may trigger various unexpected errors. Therefore, how to effectively handle such errors, including identifying, diagnosing, and recovering from them, has emerged as a key research direction for advancing tool learning. In this work, we first extensively analyze the types of errors encountered during the function-calling process on several competitive tool evaluation benchmarks. Based on it, we introduce CRITICTOOL, a comprehensive critique evaluation benchmark specialized for tool learning. Building upon a novel evolutionary strategy for dataset construction, CRITICTOOL holds diverse tool-use errors with varying complexities, which better reflects real-world scenarios. We conduct extensive experiments on CRITICTOOL, and validate the generalization and effectiveness of our constructed benchmark strategy. We also provide an in-depth analysis of the tool reflection ability on various LLMs, offering a new perspective on the field of tool learning in LLMs. The code is available at https://github.com/Shellorley0513/CriticTool{https://github.com/Shellorley0513/CriticTool}.

Large language models (LLMs) have the remarkable ability to solve new tasks with just a few examples, but they need access to the right tools. Retrieval Augmented Generation (RAG) addresses this problem by retrieving a list of relevant tools for a given task. However, RAG's tool retrieval step requires all the required information to be explicitly present in the query. This is a limitation, as semantic search, the widely adopted tool retrieval method, can fail when the query is incomplete or lacks context. To address this limitation, we propose Context Tuning for RAG, which employs a smart context retrieval system to fetch relevant information that improves both tool retrieval and plan generation. Our lightweight context retrieval model uses numerical, categorical, and habitual usage signals to retrieve and rank context items. Our empirical results demonstrate that context tuning significantly enhances semantic search, achieving a 3.5-fold and 1.5-fold improvement in Recall@K for context retrieval and tool retrieval tasks respectively, and resulting in an 11.6% increase in LLM-based planner accuracy. Additionally, we show that our proposed lightweight model using Reciprocal Rank Fusion (RRF) with LambdaMART outperforms GPT-4 based retrieval. Moreover, we observe context augmentation at plan generation, even after tool retrieval, reduces hallucination.

The recent trend of using Large Language Models (LLMs) as intelligent agents in real-world applications underscores the necessity for comprehensive evaluations of their capabilities, particularly in complex scenarios involving planning, creating, and using tools. However, existing benchmarks typically focus on simple synthesized queries that do not reflect real-world complexity, thereby offering limited perspectives in evaluating tool utilization. To address this issue, we present UltraTool, a novel benchmark designed to improve and evaluate LLMs' ability in tool utilization within real-world scenarios. UltraTool focuses on the entire process of using tools - from planning and creating to applying them in complex tasks. It emphasizes real-world complexities, demanding accurate, multi-step planning for effective problem-solving. A key feature of UltraTool is its independent evaluation of planning with natural language, which happens before tool usage and simplifies the task solving by mapping out the intermediate steps. Thus, unlike previous work, it eliminates the restriction of pre-defined toolset during planning. Through extensive experiments on various LLMs, we offer novel insights into the evaluation of capabilities of LLMs in tool utilization, thereby contributing a fresh perspective to this rapidly evolving field. The benchmark is publicly available at https://github.com/JoeYing1019/UltraTool.

Large language models (LLMs) have demonstrated strong capabilities in language understanding and reasoning, yet they remain limited when tackling real-world tasks that require up-to-date knowledge, precise operations, or specialized tool use. To address this, we propose Tool-R1, a reinforcement learning framework that enables LLMs to perform general, compositional, and multi-step tool use by generating executable Python code. Tool-R1 supports integration of user-defined tools and standard libraries, with variable sharing across steps to construct coherent workflows. An outcome-based reward function, combining LLM-based answer judgment and code execution success, guides policy optimization. To improve training efficiency, we maintain a dynamic sample queue to cache and reuse high-quality trajectories, reducing the overhead of costly online sampling. Experiments on the GAIA benchmark show that Tool-R1 substantially improves both accuracy and robustness, achieving about 10\% gain over strong baselines, with larger improvements on complex multi-step tasks. These results highlight the potential of Tool-R1 for enabling reliable and efficient tool-augmented reasoning in real-world applications. Our code will be available at https://github.com/YBYBZhang/Tool-R1.

With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery. They harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery broadly. We present the Generative Toolkit for Scientific Discovery (GT4SD). This extensible open-source library enables scientists, developers, and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on material design.

Large language models have demonstrated exceptional performance, yet struggle with complex tasks such as numerical reasoning, plan generation. Integrating external tools, such as calculators and databases, into large language models (LLMs) is crucial for enhancing problem-solving capabilities. Current methods assign a unique token to each tool, enabling LLMs to call tools through token prediction-similar to word generation. However, this approach fails to account for the relationship between tool and word tokens, limiting adaptability within pre-trained LLMs. To address this issue, we propose a novel token learning method that aligns tool tokens with the existing word embedding space from the perspective of initialization, thereby enhancing model performance. We begin by constructing prior token embeddings for each tool based on the tool's name or description, which are used to initialize and regularize the learnable tool token embeddings. This ensures the learned embeddings are well-aligned with the word token space, improving tool call accuracy. We evaluate the method on tasks such as numerical reasoning, knowledge-based question answering, and embodied plan generation using GSM8K-XL, FuncQA, KAMEL, and VirtualHome datasets. The results demonstrate clear improvements over recent baselines, including CoT, REACT, ICL, and ToolkenGPT, indicating that our approach effectively augments LLMs with tools through relevant tokens across diverse domains.

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers, hindering the applicability of LLM agents in domains which demand large numbers of highly specialised tools, like in life sciences and medicine. Motivated by the growing trend of scientific studies accompanied by public code repositories, we propose ToolMaker, a novel agentic framework that autonomously transforms papers with code into LLM-compatible tools. Given a short task description and a repository URL, ToolMaker autonomously installs required dependencies and generates code to perform the task, using a closed-loop self-correction mechanism to iteratively diagnose and rectify errors. To evaluate our approach, we introduce a benchmark comprising 15 diverse and complex computational tasks spanning both medical and non-medical domains with over 100 unit tests to objectively assess tool correctness and robustness. ToolMaker correctly implements 80% of the tasks, substantially outperforming current state-of-the-art software engineering agents. ToolMaker therefore is a step towards fully autonomous agent-based scientific workflows.

Large language models (LLMs) have displayed massive improvements in reason- ing and decision-making skills and can hold natural conversations with users. Many recent works seek to augment LLM-based assistants with external tools so they can access private or up-to-date information and carry out actions on behalf of users. To better measure the performance of these assistants, this paper introduces ToolTalk, a benchmark consisting of complex user intents re- quiring multi-step tool usage specified through dialogue. ToolTalk contains 28 tools grouped into 7 plugins, and includes a complete simulated implementa- tion of each tool, allowing for fully automated evaluation of assistants that rely on execution feedback. ToolTalk also emphasizes tools that externally affect the world rather than only tools for referencing or searching information. We evaluate GPT-3.5 and GPT-4 on ToolTalk resulting in success rates of 26% and 50% respectively. Our analysis of the errors reveals three major categories and suggests some future directions for improvement. We release ToolTalk at https://github.com/microsoft/ToolTalk.

Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require precise, domain-specific knowledge unavailable from the web. The emergence of the Model Context Protocol (MCP) now allows agents to interface with thousands of specialized tools, seemingly resolving this limitation. Yet it remains unclear whether agents can effectively leverage such tools -- and more importantly, whether they can integrate them with general-purpose search to solve complex tasks. Therefore, we introduce InfoMosaic-Bench, the first benchmark dedicated to multi-source information seeking in tool-augmented agents. Covering six representative domains (medicine, finance, maps, video, web, and multi-domain integration), InfoMosaic-Bench requires agents to combine general-purpose search with domain-specific tools. Tasks are synthesized with InfoMosaic-Flow, a scalable pipeline that grounds task conditions in verified tool outputs, enforces cross-source dependencies, and filters out shortcut cases solvable by trivial lookup. This design guarantees both reliability and non-triviality. Experiments with 14 state-of-the-art LLM agents reveal three findings: (i) web information alone is insufficient, with GPT-5 achieving only 38.2% accuracy and 67.5% pass rate; (ii) domain tools provide selective but inconsistent benefits, improving some domains while degrading others; and (iii) 22.4% of failures arise from incorrect tool usage or selection, highlighting that current LLMs still struggle with even basic tool handling.

Tools are essential for large language models (LLMs) to acquire up-to-date information and take consequential actions in external environments. Existing work on tool-augmented LLMs primarily focuses on the broad coverage of tools and the flexibility of adding new tools. However, a critical aspect that has surprisingly been understudied is simply how accurately an LLM uses tools for which it has been trained. We find that existing LLMs, including GPT-4 and open-source LLMs specifically fine-tuned for tool use, only reach a correctness rate in the range of 30% to 60%, far from reliable use in practice. We propose a biologically inspired method for tool-augmented LLMs, simulated trial and error (STE), that orchestrates three key mechanisms for successful tool use behaviors in the biological system: trial and error, imagination, and memory. Specifically, STE leverages an LLM's 'imagination' to simulate plausible scenarios for using a tool, after which the LLM interacts with the tool to learn from its execution feedback. Both short-term and long-term memory are employed to improve the depth and breadth of the exploration, respectively. Comprehensive experiments on ToolBench show that STE substantially improves tool learning for LLMs under both in-context learning and fine-tuning settings, bringing a boost of 46.7% to Mistral-Instruct-7B and enabling it to outperform GPT-4. We also show effective continual learning of tools via a simple experience replay strategy.

Tool-augmented large language models (LLMs) are rapidly being integrated into real-world applications. Due to the lack of benchmarks, the community still needs to fully understand the hallucination issues within these models. To address this challenge, we introduce a comprehensive diagnostic benchmark, ToolBH. Specifically, we assess the LLM's hallucinations through two perspectives: depth and breadth. In terms of depth, we propose a multi-level diagnostic process, including (1) solvability detection, (2) solution planning, and (3) missing-tool analysis. For breadth, we consider three scenarios based on the characteristics of the toolset: missing necessary tools, potential tools, and limited functionality tools. Furthermore, we developed seven tasks and collected 700 evaluation samples through multiple rounds of manual annotation. The results show the significant challenges presented by the ToolBH benchmark. The current advanced models Gemini-1.5-Pro and GPT-4o only achieve a total score of 45.3 and 37.0, respectively, on a scale of 100. In this benchmark, larger model parameters do not guarantee better performance; the training data and response strategies also play a crucial role in tool-enhanced LLM scenarios. Our diagnostic analysis indicates that the primary reason for model errors lies in assessing task solvability. Additionally, open-weight models suffer from performance drops with verbose replies, whereas proprietary models excel with longer reasoning.

Through the integration of external tools, large language models (LLMs) such as GPT-4o and Llama 3.1 significantly expand their functional capabilities, evolving from elementary conversational agents to general-purpose assistants. We argue that the primary drivers of these advancements are the quality and diversity of the training data. However, the existing LLMs with external tool integration provide only limited transparency regarding their datasets and data collection methods, which has led to the initiation of this research. Specifically, in this paper, our objective is to elucidate the detailed process involved in constructing datasets that empower LLMs to effectively learn how to utilize external tools and make this information available to the public through the introduction of ToolBridge. ToolBridge proposes to employ a collection of general open-access datasets as its raw dataset pool and applies a series of strategies to identify appropriate data entries from the pool for external tool API insertions. By supervised fine-tuning on these curated data entries, LLMs can invoke external tools in appropriate contexts to boost their predictive accuracy, particularly for basic functions including data processing, numerical computation, and factual retrieval. Our experiments rigorously isolates model architectures and training configurations, focusing exclusively on the role of data. The experimental results indicate that LLMs trained on ToolBridge demonstrate consistent performance improvements on both standard benchmarks and custom evaluation datasets. All the associated code and data will be open-source at https://github.com/CharlesPikachu/ToolBridge, promoting transparency and facilitating the broader community to explore approaches for equipping LLMs with external tools capabilities.