Daily Papers

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 .

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).

Tool retrieval determines which external tools are exposed to an LLM agent for a user query or task, making retrieval a critical pre-execution safety boundary. Unlike document retrieval, tool retrieval exposes executable actions: a tool that is useful for one task may be unnecessary or risky for another. However, existing tool-retrieval methods primarily optimize semantic relevance, and safety evaluations often focus on failures after tool execution rather than risks introduced during retrieval. We study risk-aware tool retrieval, where the goal is to retrieve useful tools while reducing exposure to higher-risk tools. We propose a lightweight reranking framework on top of a frozen first-stage retriever. The framework models query-conditioned relevance and tool-level exposure risk separately, combines them through an explicit parameter controlling the tradeoff between safety and utility, smooths scores over a ToolGraph, and optionally applies rule-based safety constraints. To support retrieval-time safety evaluation, we annotate 6,108 tools across UltraTool and Seal-Tools with five ordinal risk levels and define metrics that measure risky-tool exposure in the top-k results. Experiments on UltraTool and Seal-Tools show that our approach improves the relevance--safety tradeoff over relevance-only retrievers and reranking baselines, with the rule-filtered variant providing a conservative operating point for safety-critical deployments. These findings indicate that retrieval-stage filtering can reduce the candidate action space exposed to agents before execution, complementing downstream tool-use safeguards. The code and supplementary materials are available at: https://github.com/qli447/risk-aware-tool-retrieval-release.

The proliferation of AI-generated content and sophisticated video editing tools has made it both important and challenging to moderate digital platforms. Video watermarking addresses these challenges by embedding imperceptible signals into videos, allowing for identification. However, the rare open tools and methods often fall short on efficiency, robustness, and flexibility. To reduce these gaps, this paper introduces Video Seal, a comprehensive framework for neural video watermarking and a competitive open-sourced model. Our approach jointly trains an embedder and an extractor, while ensuring the watermark robustness by applying transformations in-between, e.g., video codecs. This training is multistage and includes image pre-training, hybrid post-training and extractor fine-tuning. We also introduce temporal watermark propagation, a technique to convert any image watermarking model to an efficient video watermarking model without the need to watermark every high-resolution frame. We present experimental results demonstrating the effectiveness of the approach in terms of speed, imperceptibility, and robustness. Video Seal achieves higher robustness compared to strong baselines especially under challenging distortions combining geometric transformations and video compression. Additionally, we provide new insights such as the impact of video compression during training, and how to compare methods operating on different payloads. Contributions in this work - including the codebase, models, and a public demo - are open-sourced under permissive licenses to foster further research and development in the field.

Verification and validation of autonomous driving (AD) systems and components is of increasing importance, as such technology increases in real-world prevalence. Safety-critical scenario generation is a key approach to robustify AD policies through closed-loop training. However, existing approaches for scenario generation rely on simplistic objectives, resulting in overly-aggressive or non-reactive adversarial behaviors. To generate diverse adversarial yet realistic scenarios, we propose SEAL, a scenario perturbation approach which leverages learned objective functions and adversarial, human-like skills. SEAL-perturbed scenarios are more realistic than SOTA baselines, leading to improved ego task success across real-world, in-distribution, and out-of-distribution scenarios, of more than 20%. To facilitate future research, we release our code and tools: https://github.com/cmubig/SEAL

Artificial intelligence (AI) agents are emerging as transformative tools in drug discovery, with the ability to autonomously reason, act, and learn through complicated research workflows. Building on large language models (LLMs) coupled with perception, computation, action, and memory tools, these agentic AI systems could integrate diverse biomedical data, execute tasks, carry out experiments via robotic platforms, and iteratively refine hypotheses in closed loops. We provide a conceptual and technical overview of agentic AI architectures, ranging from ReAct and Reflection to Supervisor and Swarm systems, and illustrate their applications across key stages of drug discovery, including literature synthesis, toxicity prediction, automated protocol generation, small-molecule synthesis, drug repurposing, and end-to-end decision-making. To our knowledge, this represents the first comprehensive work to present real-world implementations and quantifiable impacts of agentic AI systems deployed in operational drug discovery settings. Early implementations demonstrate substantial gains in speed, reproducibility, and scalability, compressing workflows that once took months into hours while maintaining scientific traceability. We discuss the current challenges related to data heterogeneity, system reliability, privacy, and benchmarking, and outline future directions towards technology in support of science and translation.

We introduce SealQA, a new challenge benchmark for evaluating SEarch-Augmented Language models on fact-seeking questions where web search yields conflicting, noisy, or unhelpful results. SealQA comes in three flavors: (1) Seal-0 (main) and (2) Seal-Hard, which assess factual accuracy and reasoning capabilities, with Seal-0 focusing on the most challenging questions where chat models (e.g., GPT-4.1) typically achieve near-zero accuracy; and (3) LongSeal, which extends SealQA to test long-context, multi-document reasoning in "needle-in-a-haystack" settings. Our evaluation reveals critical limitations in current models: Even frontier LLMs perform poorly across all SealQA flavors. On Seal-0, frontier agentic models equipped with tools like o3 and o4-mini achieve only 17.1% and 6.3% accuracy, respectively, at their best reasoning efforts. We find that advanced reasoning models such as DeepSeek-R1-671B and o3-mini are highly vulnerable to noisy search results. Notably, increasing test-time compute does not yield reliable gains across o3-mini, o4-mini, and o3, with performance often plateauing or even declining early. Additionally, while recent models are less affected by the "lost-in-the-middle" issue, they still fail to reliably identify relevant documents in LongSeal when faced with numerous distractors. To facilitate future work, we release SealQA at huggingface.co/datasets/vtllms/sealqa.

Long-horizon information-seeking agents often accumulate noisy or misleading context, causing early mistakes to persist and making recovery increasingly difficult. We introduce an autonomous search harness in which the agent manages its own search process through three states: Rubric, Answer, and Verify. The agent first defines criteria for a valid answer, searches under these criteria, and then independently verifies the result before deciding whether to terminate or continue searching. It is further equipped with a Seal Memory tool that enables active context management. Training this behavior with reinforcement learning, however, can induce Seal Collapse, resulting in unstable training and preventing the agent from reliably learning when and how to use its memory tools. We solve this with a simple strategy that trains only the final segment after context management. Our 35B model achieves 72.83 on BrowseComp, outperforming comparable open-source systems, and consistently improves over the base model across BrowseComp-ZH, xbench, DeepSearchQA, WideSearch, financial investigation, and product search. Ablations show that autonomous compression outperforms automatic compaction and validate our RL design.

With the advent of Transformers, large language models (LLMs) have saturated well-known NLP benchmarks and leaderboards with high aggregate performance. However, many times these models systematically fail on tail data or rare groups not obvious in aggregate evaluation. Identifying such problematic data groups is even more challenging when there are no explicit labels (e.g., ethnicity, gender, etc.) and further compounded for NLP datasets due to the lack of visual features to characterize failure modes (e.g., Asian males, animals indoors, waterbirds on land, etc.). This paper introduces an interactive Systematic Error Analysis and Labeling (\seal) tool that uses a two-step approach to first identify high error slices of data and then, in the second step, introduce methods to give human-understandable semantics to those underperforming slices. We explore a variety of methods for coming up with coherent semantics for the error groups using language models for semantic labeling and a text-to-image model for generating visual features. SEAL toolkit and demo screencast is available at https://huggingface.co/spaces/nazneen/seal.

Large language models (LLMs) have limitations in handling tasks that require real-time access to external APIs. While several benchmarks like ToolBench and APIGen have been developed to assess LLMs' API-use capabilities, they often suffer from issues such as lack of generalizability, limited multi-step reasoning coverage, and instability due to real-time API fluctuations. In this paper, we introduce SEAL, an end-to-end testbed designed to evaluate LLMs in real-world API usage. SEAL standardizes existing benchmarks, integrates an agent system for testing API retrieval and planning, and addresses the instability of real-time APIs by introducing a GPT-4-powered API simulator with caching for deterministic evaluations. Our testbed provides a comprehensive evaluation pipeline that covers API retrieval, API calls, and final responses, offering a reliable framework for structured performance comparison in diverse real-world scenarios. SEAL is publicly available, with ongoing updates for new benchmarks.

Large Language Model (LLM) agents are increasingly improved through interaction, yet most self-evolution methods adapt either the policy or the learning environment in isolation. We identify this structural gap as Agent-Environment Misalignment: the agent's capability frontier changes during training, while the environment that provides supervision remains static or only weakly coupled to the agent's revealed failures. We propose SEAL, a closed-loop co-evolution framework for interactive tool-use agents. SEAL collects on-policy trajectories under executable verification, diagnoses failed rollouts into turn-level failure labels, and uses these diagnoses as a shared signal for both environment-side adaptation and model-side policy optimization. The environment evolves its training-time learning interface by exposing clearer tool affordance cues, constraint information, and recovery-oriented feedback, while the policy is updated with diagnosis-guided advantage reweighting. Extensive experiments across in-distribution and out-of-distribution multi-turn tool-use evaluations show that SEAL improves low-resource agent learning: with only 400 training samples, it yields +8.25 to +26.25 average-point gains across three backbones and exhibits positive out-of-distribution transfer. These results demonstrate the value of jointly adapting the learner and its training-time learning substrate for robust self-improving LLM agents.

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

Circuit link prediction, which identifies missing component connections from incomplete netlists, is crucial in analog circuit design automation. However, existing methods face three main challenges: 1) Insufficient use of topological patterns in circuit graphs reduces prediction accuracy; 2) Data scarcity due to the complexity of annotations hinders model generalization; 3) Limited adaptability to various netlist formats restricts model flexibility. We propose Graph Neural Networks Based Analog Circuit Link Prediction (GNN-ACLP), a graph neural networks (GNNs) based method featuring three innovations to tackle these challenges. First, we introduce the SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction) framework and achieve port-level accuracy in circuit link prediction. Second, we propose Netlist Babel Fish, a netlist format conversion tool that leverages retrieval-augmented generation (RAG) with a large language model (LLM) to enhance the compatibility of netlist formats. Finally, we build a comprehensive dataset, SpiceNetlist, comprising 775 annotated circuits of 7 different types across 10 component classes. Experiments demonstrate accuracy improvements of 16.08% on SpiceNetlist, 11.38% on Image2Net, and 16.01% on Masala-CHAI compared to the baseline in intra-dataset evaluation, while maintaining accuracy from 92.05% to 99.07% in cross-dataset evaluation, demonstrating robust feature transfer capabilities. However, its linear computational complexity makes processing large-scale netlists challenging and requires future addressing.

Cloud-based large language models (LLMs) require users to disclose plaintext data to service providers, creating privacy risks in sensitive domains. Existing privacy-preserving approaches often trade utility for protection, incur substantial computational or communication overhead, remain vulnerable to reconstruction from intermediate representations, or protect only a subset of the training and inference pipeline. We introduce Client-Resolved Generation (CRG), a genera- tion interface that separates server-side generation from the lexical realization of input-derived content. The client transmits only pooled and noise-perturbed rep- resentations, while input-derived output content is represented using request-local positional references and resolved to its original strings only on the client. This interface protects private input and input-derived output content during both train- ing and inference while allowing the service provider to keep its proprietary model parameters hidden from the client. At the same time, exact lexical reuse remains possible without directly exposing the reused content on the provider-visible gen- eration path. We evaluate CRG on medical and document-grounded QA, sensi- tive identifier transfer, and tool calling, together with reconstruction and raw-logit leakage analyses. On SealTools, CRG improves complete-call exact match from 57.3% to 79.9% over the input-privacy framework PPFT, with larger gains as more required output content can be resolved through references. Together, these results show that CRG provides a practical interface for privacy-sensitive cloud LLMs by reducing plaintext exposure across both input and output pathways while preserv- ing task utility and server-side model confidentiality.