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Sep 9

CRAFT: Customizing LLMs by Creating and Retrieving from Specialized Toolsets

Large language models (LLMs) are often augmented with tools to solve complex tasks. By generating code snippets and executing them through task-specific Application Programming Interfaces (APIs), they can offload certain functions to dedicated external modules, such as image encoding and performing calculations. However, most existing approaches to augment LLMs with tools are constrained by general-purpose APIs and lack the flexibility for tailoring them to specific tasks. In this work, we present CRAFT, a general tool creation and retrieval framework for LLMs. It creates toolsets specifically curated for the tasks and equips LLMs with a component that retrieves tools from these sets to enhance their capability to solve complex tasks. For each task, we collect specific code solutions by prompting GPT-4 to solve the training examples. Following a validation step ensuring the correctness, these solutions are abstracted into code snippets to enhance reusability, and deduplicated for higher quality. At inference time, the language model retrieves snippets from the toolsets and then executes them or generates the output conditioning on the retrieved snippets. Our method is designed to be flexible and offers a plug-and-play approach to adapt off-the-shelf LLMs to unseen domains and modalities, without any finetuning. Experiments on vision-language, tabular processing, and mathematical reasoning tasks show that our approach achieves substantial improvements compared to strong baselines. In addition, our in-depth analysis reveals that: (1) consistent performance improvement can be achieved by scaling up the number of tools and the capability of the backbone models; (2) each component of our approach contributes to the performance gains; (3) the created tools are well-structured and reliable with low complexity and atomicity. The code is available at https://github.com/lifan-yuan/CRAFT.

NESTLE: a No-Code Tool for Statistical Analysis of Legal Corpus

The statistical analysis of large scale legal corpus can provide valuable legal insights. For such analysis one needs to (1) select a subset of the corpus using document retrieval tools, (2) structuralize text using information extraction (IE) systems, and (3) visualize the data for the statistical analysis. Each process demands either specialized tools or programming skills whereas no comprehensive unified "no-code" tools have been available. Especially for IE, if the target information is not predefined in the ontology of the IE system, one needs to build their own system. Here we provide NESTLE, a no code tool for large-scale statistical analysis of legal corpus. With NESTLE, users can search target documents, extract information, and visualize the structured data all via the chat interface with accompanying auxiliary GUI for the fine-level control. NESTLE consists of three main components: a search engine, an end-to-end IE system, and a Large Language Model (LLM) that glues the whole components together and provides the chat interface. Powered by LLM and the end-to-end IE system, NESTLE can extract any type of information that has not been predefined in the IE system opening up the possibility of unlimited customizable statistical analysis of the corpus without writing a single line of code. The use of the custom end-to-end IE system also enables faster and low-cost IE on large scale corpus. We validate our system on 15 Korean precedent IE tasks and 3 legal text classification tasks from LEXGLUE. The comprehensive experiments reveal NESTLE can achieve GPT-4 comparable performance by training the internal IE module with 4 human-labeled, and 192 LLM-labeled examples. The detailed analysis provides the insight on the trade-off between accuracy, time, and cost in building such system.

SonicMaster: Towards Controllable All-in-One Music Restoration and Mastering

Music recordings often suffer from audio quality issues such as excessive reverberation, distortion, clipping, tonal imbalances, and a narrowed stereo image, especially when created in non-professional settings without specialized equipment or expertise. These problems are typically corrected using separate specialized tools and manual adjustments. In this paper, we introduce SonicMaster, the first unified generative model for music restoration and mastering that addresses a broad spectrum of audio artifacts with text-based control. SonicMaster is conditioned on natural language instructions to apply targeted enhancements, or can operate in an automatic mode for general restoration. To train this model, we construct the SonicMaster dataset, a large dataset of paired degraded and high-quality tracks by simulating common degradation types with nineteen degradation functions belonging to five enhancements groups: equalization, dynamics, reverb, amplitude, and stereo. Our approach leverages a flow-matching generative training paradigm to learn an audio transformation that maps degraded inputs to their cleaned, mastered versions guided by text prompts. Objective audio quality metrics demonstrate that SonicMaster significantly improves sound quality across all artifact categories. Furthermore, subjective listening tests confirm that listeners prefer SonicMaster's enhanced outputs over the original degraded audio, highlighting the effectiveness of our unified approach.

Class-Level Code Generation from Natural Language Using Iterative, Tool-Enhanced Reasoning over Repository

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

EvoAgentX: An Automated Framework for Evolving Agentic Workflows

Multi-agent systems (MAS) have emerged as a powerful paradigm for orchestrating large language models (LLMs) and specialized tools to collaboratively address complex tasks. However, existing MAS frameworks often require manual workflow configuration and lack native support for dynamic evolution and performance optimization. In addition, many MAS optimization algorithms are not integrated into a unified framework. In this paper, we present EvoAgentX, an open-source platform that automates the generation, execution, and evolutionary optimization of multi-agent workflows. EvoAgentX employs a modular architecture consisting of five core layers: the basic components, agent, workflow, evolving, and evaluation layers. Specifically, within the evolving layer, EvoAgentX integrates three MAS optimization algorithms, TextGrad, AFlow, and MIPRO, to iteratively refine agent prompts, tool configurations, and workflow topologies. We evaluate EvoAgentX on HotPotQA, MBPP, and MATH for multi-hop reasoning, code generation, and mathematical problem solving, respectively, and further assess it on real-world tasks using GAIA. Experimental results show that EvoAgentX consistently achieves significant performance improvements, including a 7.44% increase in HotPotQA F1, a 10.00% improvement in MBPP pass@1, a 10.00% gain in MATH solve accuracy, and an overall accuracy improvement of up to 20.00% on GAIA. The source code is available at: https://github.com/EvoAgentX/EvoAgentX

An Agentic System for Rare Disease Diagnosis with Traceable Reasoning

Rare diseases collectively affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains a pervasive challenge. This is largely due to their clinical heterogeneity, low individual prevalence, and the limited familiarity most clinicians have with rare conditions. Here, we introduce DeepRare, the first rare disease diagnosis agentic system powered by a large language model (LLM), capable of processing heterogeneous clinical inputs. The system generates ranked diagnostic hypotheses for rare diseases, each accompanied by a transparent chain of reasoning that links intermediate analytic steps to verifiable medical evidence. DeepRare comprises three key components: a central host with a long-term memory module; specialized agent servers responsible for domain-specific analytical tasks integrating over 40 specialized tools and web-scale, up-to-date medical knowledge sources, ensuring access to the most current clinical information. This modular and scalable design enables complex diagnostic reasoning while maintaining traceability and adaptability. We evaluate DeepRare on eight datasets. The system demonstrates exceptional diagnostic performance among 2,919 diseases, achieving 100% accuracy for 1013 diseases. In HPO-based evaluations, DeepRare significantly outperforms other 15 methods, like traditional bioinformatics diagnostic tools, LLMs, and other agentic systems, achieving an average Recall@1 score of 57.18% and surpassing the second-best method (Reasoning LLM) by a substantial margin of 23.79 percentage points. For multi-modal input scenarios, DeepRare achieves 70.60% at Recall@1 compared to Exomiser's 53.20% in 109 cases. Manual verification of reasoning chains by clinical experts achieves 95.40% agreements. Furthermore, the DeepRare system has been implemented as a user-friendly web application http://raredx.cn/doctor.

SridBench: Benchmark of Scientific Research Illustration Drawing of Image Generation Model

Recent years have seen rapid advances in AI-driven image generation. Early diffusion models emphasized perceptual quality, while newer multimodal models like GPT-4o-image integrate high-level reasoning, improving semantic understanding and structural composition. Scientific illustration generation exemplifies this evolution: unlike general image synthesis, it demands accurate interpretation of technical content and transformation of abstract ideas into clear, standardized visuals. This task is significantly more knowledge-intensive and laborious, often requiring hours of manual work and specialized tools. Automating it in a controllable, intelligent manner would provide substantial practical value. Yet, no benchmark currently exists to evaluate AI on this front. To fill this gap, we introduce SridBench, the first benchmark for scientific figure generation. It comprises 1,120 instances curated from leading scientific papers across 13 natural and computer science disciplines, collected via human experts and MLLMs. Each sample is evaluated along six dimensions, including semantic fidelity and structural accuracy. Experimental results reveal that even top-tier models like GPT-4o-image lag behind human performance, with common issues in text/visual clarity and scientific correctness. These findings highlight the need for more advanced reasoning-driven visual generation capabilities.

Tool Learning with Foundation Models

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.

The Digital Cybersecurity Expert: How Far Have We Come?

The increasing deployment of large language models (LLMs) in the cybersecurity domain underscores the need for effective model selection and evaluation. However, traditional evaluation methods often overlook specific cybersecurity knowledge gaps that contribute to performance limitations. To address this, we develop CSEBenchmark, a fine-grained cybersecurity evaluation framework based on 345 knowledge points expected of cybersecurity experts. Drawing from cognitive science, these points are categorized into factual, conceptual, and procedural types, enabling the design of 11,050 tailored multiple-choice questions. We evaluate 12 popular LLMs on CSEBenchmark and find that even the best-performing model achieves only 85.42% overall accuracy, with particular knowledge gaps in the use of specialized tools and uncommon commands. Different LLMs have unique knowledge gaps. Even large models from the same family may perform poorly on knowledge points where smaller models excel. By identifying and addressing specific knowledge gaps in each LLM, we achieve up to an 84% improvement in correcting previously incorrect predictions across three existing benchmarks for two cybersecurity tasks. Furthermore, our assessment of each LLM's knowledge alignment with specific cybersecurity roles reveals that different models align better with different roles, such as GPT-4o for the Google Senior Intelligence Analyst and Deepseek-V3 for the Amazon Privacy Engineer. These findings underscore the importance of aligning LLM selection with the specific knowledge requirements of different cybersecurity roles for optimal performance.

ChemCrow: Augmenting large-language models with chemistry tools

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.

Perception Tokens Enhance Visual Reasoning in Multimodal Language Models

Multimodal language models (MLMs) still face challenges in fundamental visual perception tasks where specialized models excel. Tasks requiring reasoning about 3D structures benefit from depth estimation, and reasoning about 2D object instances benefits from object detection. Yet, MLMs can not produce intermediate depth or boxes to reason over. Finetuning MLMs on relevant data doesn't generalize well and outsourcing computation to specialized vision tools is too compute-intensive and memory-inefficient. To address this, we introduce Perception Tokens, intrinsic image representations designed to assist reasoning tasks where language is insufficient. Perception tokens act as auxiliary reasoning tokens, akin to chain-of-thought prompts in language models. For example, in a depth-related task, an MLM augmented with perception tokens can reason by generating a depth map as tokens, enabling it to solve the problem effectively. We propose AURORA, a training method that augments MLMs with perception tokens for improved reasoning over visual inputs. AURORA leverages a VQVAE to transform intermediate image representations, such as depth maps into a tokenized format and bounding box tokens, which is then used in a multi-task training framework. AURORA achieves notable improvements across counting benchmarks: +10.8% on BLINK, +11.3% on CVBench, and +8.3% on SEED-Bench, outperforming finetuning approaches in generalization across datasets. It also improves on relative depth: over +6% on BLINK. With perception tokens, AURORA expands the scope of MLMs beyond language-based reasoning, paving the way for more effective visual reasoning capabilities.

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

Galaxy Spectra neural Networks (GaSNets). I. Searching for strong lens candidates in eBOSS spectra using Deep Learning

With the advent of new spectroscopic surveys from ground and space, observing up to hundreds of millions of galaxies, spectra classification will become overwhelming for standard analysis techniques. To prepare for this challenge, we introduce a family of deep learning tools to classify features in one-dimensional spectra. As the first application of these Galaxy Spectra neural Networks (GaSNets), we focus on tools specialized at identifying emission lines from strongly lensed star-forming galaxies in the eBOSS spectra. We first discuss the training and testing of these networks and define a threshold probability, PL, of 95% for the high quality event detection. Then, using a previous set of spectroscopically selected strong lenses from eBOSS, confirmed with HST, we estimate a completeness of ~80% as the fraction of lenses recovered above the adopted PL. We finally apply the GaSNets to ~1.3M spectra to collect a first list of ~430 new high quality candidates identified with deep learning applied to spectroscopy and visually graded as highly probable real events. A preliminary check against ground-based observations tentatively shows that this sample has a confirmation rate of 38%, in line with previous samples selected with standard (no deep learning) classification tools and follow-up by Hubble Space Telescope. This first test shows that machine learning can be efficiently extended to feature recognition in the wavelength space, which will be crucial for future surveys like 4MOST, DESI, Euclid, and the Chinese Space Station Telescope (CSST).

Intelligent System for Automated Molecular Patent Infringement Assessment

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.

MedReseacher-R1: Expert-Level Medical Deep Researcher via A Knowledge-Informed Trajectory Synthesis Framework

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and synthesis tasks. While general-purpose deep research agents have shown impressive capabilities, they struggle significantly with medical domain challenges, as evidenced by leading proprietary systems achieving limited accuracy on complex medical benchmarks. The key limitations are: (1) the model lacks sufficient dense medical knowledge for clinical reasoning, and (2) the framework is constrained by the absence of specialized retrieval tools tailored for medical contexts.We present a medical deep research agent that addresses these challenges through two core innovations. First, we develop a novel data synthesis framework using medical knowledge graphs, extracting the longest chains from subgraphs around rare medical entities to generate complex multi-hop question-answer pairs. Second, we integrate a custom-built private medical retrieval engine alongside general-purpose tools, enabling accurate medical information synthesis. Our approach generates 2100+ diverse trajectories across 12 medical specialties, each averaging 4.2 tool interactions.Through a two-stage training paradigm combining supervised fine-tuning and online reinforcement learning with composite rewards, our MedResearcher-R1-32B model demonstrates exceptional performance, establishing new state-of-the-art results on medical benchmarks while maintaining competitive performance on general deep research tasks. Our work demonstrates that strategic domain-specific innovations in architecture, tool design, and training data construction can enable smaller open-source models to outperform much larger proprietary systems in specialized domains.

Reinforcing Spatial Reasoning in Vision-Language Models with Interwoven Thinking and Visual Drawing

As textual reasoning with large language models (LLMs) has advanced significantly, there has been growing interest in enhancing the multimodal reasoning capabilities of large vision-language models (LVLMs). However, existing methods primarily approach multimodal reasoning in a straightforward, text-centric manner, where both reasoning and answer derivation are conducted purely through text, with the only difference being the presence of multimodal input. As a result, these methods often encounter fundamental limitations in spatial reasoning tasks that demand precise geometric understanding and continuous spatial tracking-capabilities that humans achieve through mental visualization and manipulation. To address the limitations, we propose drawing to reason in space, a novel paradigm that enables LVLMs to reason through elementary drawing operations in the visual space. By equipping models with basic drawing operations, including annotating bounding boxes and drawing auxiliary lines, we empower them to express and analyze spatial relationships through direct visual manipulation, meanwhile avoiding the performance ceiling imposed by specialized perception tools in previous tool-integrated reasoning approaches. To cultivate this capability, we develop a three-stage training framework: cold-start training with synthetic data to establish basic drawing abilities, reflective rejection sampling to enhance self-reflection behaviors, and reinforcement learning to directly optimize for target rewards. Extensive experiments demonstrate that our model, named VILASR, consistently outperforms existing methods across diverse spatial reasoning benchmarks, involving maze navigation, static spatial reasoning, video-based reasoning, and multi-view-based reasoning tasks, with an average improvement of 18.4%.

FinRobot: An Open-Source AI Agent Platform for Financial Applications using Large Language Models

As financial institutions and professionals increasingly incorporate Large Language Models (LLMs) into their workflows, substantial barriers, including proprietary data and specialized knowledge, persist between the finance sector and the AI community. These challenges impede the AI community's ability to enhance financial tasks effectively. Acknowledging financial analysis's critical role, we aim to devise financial-specialized LLM-based toolchains and democratize access to them through open-source initiatives, promoting wider AI adoption in financial decision-making. In this paper, we introduce FinRobot, a novel open-source AI agent platform supporting multiple financially specialized AI agents, each powered by LLM. Specifically, the platform consists of four major layers: 1) the Financial AI Agents layer that formulates Financial Chain-of-Thought (CoT) by breaking sophisticated financial problems down into logical sequences; 2) the Financial LLM Algorithms layer dynamically configures appropriate model application strategies for specific tasks; 3) the LLMOps and DataOps layer produces accurate models by applying training/fine-tuning techniques and using task-relevant data; 4) the Multi-source LLM Foundation Models layer that integrates various LLMs and enables the above layers to access them directly. Finally, FinRobot provides hands-on for both professional-grade analysts and laypersons to utilize powerful AI techniques for advanced financial analysis. We open-source FinRobot at https://github.com/AI4Finance-Foundation/FinRobot.

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

Visual Program Distillation: Distilling Tools and Programmatic Reasoning into Vision-Language Models

Solving complex visual tasks such as "Who invented the musical instrument on the right?" involves a composition of skills: understanding space, recognizing instruments, and also retrieving prior knowledge. Recent work shows promise by decomposing such tasks using a large language model (LLM) into an executable program that invokes specialized vision models. However, generated programs are error-prone: they omit necessary steps, include spurious ones, and are unable to recover when the specialized models give incorrect outputs. Moreover, they require loading multiple models, incurring high latency and computation costs. We propose Visual Program Distillation (VPD), an instruction tuning framework that produces a vision-language model (VLM) capable of solving complex visual tasks with a single forward pass. VPD distills the reasoning ability of LLMs by using them to sample multiple candidate programs, which are then executed and verified to identify a correct one. It translates each correct program into a language description of the reasoning steps, which are then distilled into a VLM. Extensive experiments show that VPD improves the VLM's ability to count, understand spatial relations, and reason compositionally. Our VPD-trained PaLI-X outperforms all prior VLMs, achieving state-of-the-art performance across complex vision tasks, including MMBench, OK-VQA, A-OKVQA, TallyQA, POPE, and Hateful Memes. An evaluation with human annotators also confirms that VPD improves model response factuality and consistency. Finally, experiments on content moderation demonstrate that VPD is also helpful for adaptation to real-world applications with limited data.

A Review on Large Language Models for Visual Analytics

This paper provides a comprehensive review of the integration of Large Language Models (LLMs) with visual analytics, addressing their foundational concepts, capabilities, and wide-ranging applications. It begins by outlining the theoretical underpinnings of visual analytics and the transformative potential of LLMs, specifically focusing on their roles in natural language understanding, natural language generation, dialogue systems, and text-to-media transformations. The review further investigates how the synergy between LLMs and visual analytics enhances data interpretation, visualization techniques, and interactive exploration capabilities. Key tools and platforms including LIDA, Chat2VIS, Julius AI, and Zoho Analytics, along with specialized multimodal models such as ChartLlama and CharXIV, are critically evaluated. The paper discusses their functionalities, strengths, and limitations in supporting data exploration, visualization enhancement, automated reporting, and insight extraction. The taxonomy of LLM tasks, ranging from natural language understanding (NLU), natural language generation (NLG), to dialogue systems and text-to-media transformations, is systematically explored. This review provides a SWOT analysis of integrating Large Language Models (LLMs) with visual analytics, highlighting strengths like accessibility and flexibility, weaknesses such as computational demands and biases, opportunities in multimodal integration and user collaboration, and threats including privacy concerns and skill degradation. It emphasizes addressing ethical considerations and methodological improvements for effective integration.

Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

MeNTi: Bridging Medical Calculator and LLM Agent with Nested Tool Calling

Integrating tools into Large Language Models (LLMs) has facilitated the widespread application. Despite this, in specialized downstream task contexts, reliance solely on tools is insufficient to fully address the complexities of the real world. This particularly restricts the effective deployment of LLMs in fields such as medicine. In this paper, we focus on the downstream tasks of medical calculators, which use standardized tests to assess an individual's health status. We introduce MeNTi, a universal agent architecture for LLMs. MeNTi integrates a specialized medical toolkit and employs meta-tool and nested calling mechanisms to enhance LLM tool utilization. Specifically, it achieves flexible tool selection and nested tool calling to address practical issues faced in intricate medical scenarios, including calculator selection, slot filling, and unit conversion. To assess the capabilities of LLMs for quantitative assessment throughout the clinical process of calculator scenarios, we introduce CalcQA. This benchmark requires LLMs to use medical calculators to perform calculations and assess patient health status. CalcQA is constructed by professional physicians and includes 100 case-calculator pairs, complemented by a toolkit of 281 medical tools. The experimental results demonstrate significant performance improvements with our framework. This research paves new directions for applying LLMs in demanding scenarios of medicine.

DoraemonGPT: Toward Understanding Dynamic Scenes with Large Language Models

Recent LLM-driven visual agents mainly focus on solving image-based tasks, which limits their ability to understand dynamic scenes, making it far from real-life applications like guiding students in laboratory experiments and identifying their mistakes. Considering the video modality better reflects the ever-changing nature of real-world scenarios, we devise DoraemonGPT, a comprehensive and conceptually elegant system driven by LLMs to handle dynamic video tasks. Given a video with a question/task, DoraemonGPT begins by converting the input video into a symbolic memory that stores task-related attributes. This structured representation allows for spatial-temporal querying and reasoning by well-designed sub-task tools, resulting in concise intermediate results. Recognizing that LLMs have limited internal knowledge when it comes to specialized domains (e.g., analyzing the scientific principles underlying experiments), we incorporate plug-and-play tools to assess external knowledge and address tasks across different domains. Moreover, a novel LLM-driven planner based on Monte Carlo Tree Search is introduced to explore the large planning space for scheduling various tools. The planner iteratively finds feasible solutions by backpropagating the result's reward, and multiple solutions can be summarized into an improved final answer. We extensively evaluate DoraemonGPT's effectiveness on three benchmarks and challenging in-the-wild scenarios. Code will be released at: https://github.com/z-x-yang/DoraemonGPT.

Surface-based parcellation and vertex-wise analysis of ultra high-resolution ex vivo 7 tesla MRI in Alzheimer's disease and related dementias

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

HDFlow: Enhancing LLM Complex Problem-Solving with Hybrid Thinking and Dynamic Workflows

Despite recent advancements in large language models (LLMs), their performance on complex reasoning problems requiring multi-step thinking and combining various skills is still limited. To address this, we propose a novel framework HDFlow for complex reasoning with LLMs that combines fast and slow thinking modes in an adaptive manner. Our approach consists of two key components: 1) a new approach for slow, deliberate reasoning called Dynamic Workflow, which automatically decomposes complex problems into more manageable sub-tasks and dynamically designs a workflow to assemble specialized LLM or symbolic reasoning tools to solve sub-tasks; 2) Hybrid Thinking, a general framework that dynamically combines fast and slow thinking based on problem complexity. Finally, we propose an easy-to-scale method for automatically synthesizing a large-scale dataset of 27K challenging reasoning problems for complex reasoning and a hybrid thinking tuning method that trains smaller LLMs on this dataset to internalize the fast/slow hybrid reasoning strategies. Experiments on four reasoning benchmark datasets demonstrate that our slow thinking with dynamic workflows significantly outperforms Chain-of-Thought, and hybrid thinking achieves the highest accuracy while providing an effective balance between computational efficiency and performance. Fine-tuning using our hybrid thinking approach also significantly boosts the complex reasoning capabilities of open-source language models. The results showcase the promise of slow thinking, dynamic workflows, and hybrid thinking in expanding the frontier of complex problem-solving with LLMsCode and data will be released at \url{https://github.com/wenlinyao/HDFlow.}.

FailureSensorIQ: A Multi-Choice QA Dataset for Understanding Sensor Relationships and Failure Modes

We introduce FailureSensorIQ, a novel Multi-Choice Question-Answering (MCQA) benchmarking system designed to assess the ability of Large Language Models (LLMs) to reason and understand complex, domain-specific scenarios in Industry 4.0. Unlike traditional QA benchmarks, our system focuses on multiple aspects of reasoning through failure modes, sensor data, and the relationships between them across various industrial assets. Through this work, we envision a paradigm shift where modeling decisions are not only data-driven using statistical tools like correlation analysis and significance tests, but also domain-driven by specialized LLMs which can reason about the key contributors and useful patterns that can be captured with feature engineering. We evaluate the Industrial knowledge of over a dozen LLMs-including GPT-4, Llama, and Mistral-on FailureSensorIQ from different lens using Perturbation-Uncertainty-Complexity analysis, Expert Evaluation study, Asset-Specific Knowledge Gap analysis, ReAct agent using external knowledge-bases. Even though closed-source models with strong reasoning capabilities approach expert-level performance, the comprehensive benchmark reveals a significant drop in performance that is fragile to perturbations, distractions, and inherent knowledge gaps in the models. We also provide a real-world case study of how LLMs can drive the modeling decisions on 3 different failure prediction datasets related to various assets. We release: (a) expert-curated MCQA for various industrial assets, (b) FailureSensorIQ benchmark and Hugging Face leaderboard based on MCQA built from non-textual data found in ISO documents, and (c) LLMFeatureSelector, an LLM-based feature selection scikit-learn pipeline. The software is available at https://github.com/IBM/FailureSensorIQ.

Aime: Towards Fully-Autonomous Multi-Agent Framework

Multi-Agent Systems (MAS) powered by Large Language Models (LLMs) are emerging as a powerful paradigm for solving complex, multifaceted problems. However, the potential of these systems is often constrained by the prevalent plan-and-execute framework, which suffers from critical limitations: rigid plan execution, static agent capabilities, and inefficient communication. These weaknesses hinder their adaptability and robustness in dynamic environments. This paper introduces Aime, a novel multi-agent framework designed to overcome these challenges through dynamic, reactive planning and execution. Aime replaces the conventional static workflow with a fluid and adaptive architecture. Its core innovations include: (1) a Dynamic Planner that continuously refines the overall strategy based on real-time execution feedback; (2) an Actor Factory that implements Dynamic Actor instantiation, assembling specialized agents on-demand with tailored tools and knowledge; and (3) a centralized Progress Management Module that serves as a single source of truth for coherent, system-wide state awareness. We empirically evaluated Aime on a diverse suite of benchmarks spanning general reasoning (GAIA), software engineering (SWE-bench Verified), and live web navigation (WebVoyager). The results demonstrate that Aime consistently outperforms even highly specialized state-of-the-art agents in their respective domains. Its superior adaptability and task success rate establish Aime as a more resilient and effective foundation for multi-agent collaboration.

Phikon-v2, A large and public feature extractor for biomarker prediction

Gathering histopathology slides from over 100 publicly available cohorts, we compile a diverse dataset of 460 million pathology tiles covering more than 30 cancer sites. Using this dataset, we train a large self-supervised vision transformer using DINOv2 and publicly release one iteration of this model for further experimentation, coined Phikon-v2. While trained on publicly available histology slides, Phikon-v2 surpasses our previously released model (Phikon) and performs on par with other histopathology foundation models (FM) trained on proprietary data. Our benchmarks include eight slide-level tasks with results reported on external validation cohorts avoiding any data contamination between pre-training and evaluation datasets. Our downstream training procedure follows a simple yet robust ensembling strategy yielding a +1.75 AUC increase across tasks and models compared to one-shot retraining (p<0.001). We compare Phikon (ViT-B) and Phikon-v2 (ViT-L) against 14 different histology feature extractors, making our evaluation the most comprehensive to date. Our result support evidences that DINOv2 handles joint model and data scaling better than iBOT. Also, we show that recent scaling efforts are overall beneficial to downstream performance in the context of biomarker prediction with GigaPath and H-Optimus-0 (two ViT-g with 1.1B parameters each) standing out. However, the statistical margins between the latest top-performing FMs remain mostly non-significant; some even underperform on specific indications or tasks such as MSI prediction - deposed by a 13x smaller model developed internally. While latest foundation models may exhibit limitations for clinical deployment, they nonetheless offer excellent grounds for the development of more specialized and cost-efficient histology encoders fueling AI-guided diagnostic tools.

Interactive Natural Language Processing

Interactive Natural Language Processing (iNLP) has emerged as a novel paradigm within the field of NLP, aimed at addressing limitations in existing frameworks while aligning with the ultimate goals of artificial intelligence. This paradigm considers language models as agents capable of observing, acting, and receiving feedback iteratively from external entities. Specifically, language models in this context can: (1) interact with humans for better understanding and addressing user needs, personalizing responses, aligning with human values, and improving the overall user experience; (2) interact with knowledge bases for enriching language representations with factual knowledge, enhancing the contextual relevance of responses, and dynamically leveraging external information to generate more accurate and informed responses; (3) interact with models and tools for effectively decomposing and addressing complex tasks, leveraging specialized expertise for specific subtasks, and fostering the simulation of social behaviors; and (4) interact with environments for learning grounded representations of language, and effectively tackling embodied tasks such as reasoning, planning, and decision-making in response to environmental observations. This paper offers a comprehensive survey of iNLP, starting by proposing a unified definition and framework of the concept. We then provide a systematic classification of iNLP, dissecting its various components, including interactive objects, interaction interfaces, and interaction methods. We proceed to delve into the evaluation methodologies used in the field, explore its diverse applications, scrutinize its ethical and safety issues, and discuss prospective research directions. This survey serves as an entry point for researchers who are interested in this rapidly evolving area and offers a broad view of the current landscape and future trajectory of iNLP.

VideoAgent2: Enhancing the LLM-Based Agent System for Long-Form Video Understanding by Uncertainty-Aware CoT

Long video understanding has emerged as an increasingly important yet challenging task in computer vision. Agent-based approaches are gaining popularity for processing long videos, as they can handle extended sequences and integrate various tools to capture fine-grained information. However, existing methods still face several challenges: (1) they often rely solely on the reasoning ability of large language models (LLMs) without dedicated mechanisms to enhance reasoning in long video scenarios; and (2) they remain vulnerable to errors or noise from external tools. To address these issues, we propose a specialized chain-of-thought (CoT) process tailored for long video analysis. Our proposed CoT with plan-adjust mode enables the LLM to incrementally plan and adapt its information-gathering strategy. We further incorporate heuristic uncertainty estimation of both the LLM and external tools to guide the CoT process. This allows the LLM to assess the reliability of newly collected information, refine its collection strategy, and make more robust decisions when synthesizing final answers. Empirical experiments show that our uncertainty-aware CoT effectively mitigates noise from external tools, leading to more reliable outputs. We implement our approach in a system called VideoAgent2, which also includes additional modules such as general context acquisition and specialized tool design. Evaluation on three dedicated long video benchmarks (and their subsets) demonstrates that VideoAgent2 outperforms the previous state-of-the-art agent-based method, VideoAgent, by an average of 13.1% and achieves leading performance among all zero-shot approaches

Efficient and Scalable Estimation of Tool Representations in Vector Space

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

Toolshed: Scale Tool-Equipped Agents with Advanced RAG-Tool Fusion and Tool Knowledge Bases

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).

MetaTool Benchmark for Large Language Models: Deciding Whether to Use Tools and Which to Use

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.

Surgical tool classification and localization: results and methods from the MICCAI 2022 SurgToolLoc challenge

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.