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Apr 17

Programmable Locking Cells (PLC) for Modular Robots with High Stiffness Tunability and Morphological Adaptability

Robotic systems operating in unstructured environments require the ability to switch between compliant and rigid states to perform diverse tasks such as adaptive grasping, high-force manipulation, shape holding, and navigation in constrained spaces, among others. However, many existing variable stiffness solutions rely on complex actuation schemes, continuous input power, or monolithic designs, limiting their modularity and scalability. This paper presents the Programmable Locking Cell (PLC)-a modular, tendon-driven unit that achieves discrete stiffness modulation through mechanically interlocked joints actuated by cable tension. Each unit transitions between compliant and firm states via structural engagement, and the assembled system exhibits high stiffness variation-up to 950% per unit-without susceptibility to damage under high payload in the firm state. Multiple PLC units can be assembled into reconfigurable robotic structures with spatially programmable stiffness. We validate the design through two functional prototypes: (1) a variable-stiffness gripper capable of adaptive grasping, firm holding, and in-hand manipulation; and (2) a pipe-traversing robot composed of serial PLC units that achieves shape adaptability and stiffness control in confined environments. These results demonstrate the PLC as a scalable, structure-centric mechanism for programmable stiffness and motion, enabling robotic systems with reconfigurable morphology and task-adaptive interaction.

  • 6 authors
·
Sep 9, 2025

Finch: Benchmarking Finance & Accounting across Spreadsheet-Centric Enterprise Workflows

We introduce a finance & accounting benchmark (Finch) for evaluating AI agents on real-world, enterprise-grade professional workflows -- interleaving data entry, structuring, formatting, web search, cross-file retrieval, calculation, modeling, validation, translation, visualization, and reporting. Finch is sourced from authentic enterprise workspaces at Enron (15,000 spreadsheets and 500,000 emails from 150 employees) and other financial institutions, preserving in-the-wild messiness across multimodal artifacts (text, tables, formulas, charts, code, and images) and spanning diverse domains such as budgeting, trading, and asset management. We propose a workflow construction process that combines LLM-assisted discovery with expert annotation: (1) LLM-assisted, expert-verified derivation of workflows from real-world email threads and version histories of spreadsheet files, and (2) meticulous expert annotation for workflows, requiring over 700 hours of domain-expert effort. This yields 172 composite workflows with 384 tasks, involving 1,710 spreadsheets with 27 million cells, along with PDFs and other artifacts, capturing the intrinsically messy, long-horizon, knowledge-intensive, and collaborative nature of real-world enterprise work. We conduct both human and automated evaluations of frontier AI systems including GPT 5.1, Claude Sonnet 4.5, Gemini 3 Pro, Grok 4, and Qwen 3 Max, and GPT 5.1 Pro spends 16.8 minutes per workflow yet passes only 38.4% of workflows, while Claude Sonnet 4.5 passes just 25.0%. Comprehensive case studies further surface the challenges that real-world enterprise workflows pose for AI agents.

Nonequilibrium Phenomena in Driven and Active Coulomb Field Theories

The classical Coulomb gas model has served as one of the most versatile frameworks in statistical physics, connecting a vast range of phenomena across many different areas. Nonequilibrium generalisations of this model have so far been studied much more scarcely. With the abundance of contemporary research into active and driven systems, one would naturally expect that such generalisations of systems with long-ranged Coulomb-like interactions will form a fertile playground for interesting developments. Here, we present two examples of novel macroscopic behaviour that arise from nonequilibrium fluctuations in long-range interacting systems, namely (1) unscreened long-ranged correlations in strong electrolytes driven by an external electric field and the associated fluctuation-induced forces in the confined Casimir geometry, and (2) out-of-equilibrium critical behaviour in self-chemotactic models that incorporate the particle polarity in the chemotactic response of the cells. Both of these systems have nonlocal Coulomb-like interactions among their constituent particles, namely, the electrostatic interactions in the case of the driven electrolyte, and the chemotactic forces mediated by fast-diffusing signals in the case of self-chemotactic systems. The results presented here hint to the rich phenomenology of nonequilibrium effects that can arise from strong fluctuations in Coulomb interacting systems, and a rich variety of potential future directions, which are discussed.

  • 2 authors
·
Jul 1, 2022

A Homogeneous Graph Neural Network for Precoding and Power Allocation in Scalable Wireless Networks

Deep learning is widely used in wireless communications but struggles with fixed neural network sizes, which limit their adaptability in environments where the number of users and antennas varies. To overcome this, this paper introduced a generalization strategy for precoding and power allocation in scalable wireless networks. Initially, we employ an innovative approach to abstract the wireless network into a homogeneous graph. This primarily focuses on bypassing the heterogeneous features between transmitter (TX) and user entities to construct a virtual homogeneous graph serving optimization objectives, thereby enabling all nodes in the virtual graph to share the same neural network. This "TX entity" is known as a base station (BS) in cellular networks and an access point (AP) in cell-free networks. Subsequently, we design a universal graph neural network, termed the information carrying graph neural network (ICGNN), to capture and integrate information from this graph, maintaining permutation invariance. Lastly, using ICGNN as the core algorithm, we tailor the neural network's input and output for specific problem requirements and validate its performance in two scenarios: 1) in cellular networks, we develop a matrix-inverse-free multi-user multi-input multi-output (MU-MIMO) precoding scheme using the conjugate gradient (CG) method, adaptable to varying user and antenna numbers; 2) in a cell-free network, facing dynamic variations in the number of users served by APs, the number of APs serving each user, and the number of antennas per AP, we propose a universal power allocation scheme. Simulations demonstrate that the proposed approach not only significantly reduces computational complexity but also achieves, and potentially exceeds, the spectral efficiency (SE) of conventional algorithms.

  • 6 authors
·
Aug 30, 2024

MANSA: Learning Fast and Slow in Multi-Agent Systems

In multi-agent reinforcement learning (MARL), independent learning (IL) often shows remarkable performance and easily scales with the number of agents. Yet, using IL can be inefficient and runs the risk of failing to successfully train, particularly in scenarios that require agents to coordinate their actions. Using centralised learning (CL) enables MARL agents to quickly learn how to coordinate their behaviour but employing CL everywhere is often prohibitively expensive in real-world applications. Besides, using CL in value-based methods often needs strong representational constraints (e.g. individual-global-max condition) that can lead to poor performance if violated. In this paper, we introduce a novel plug & play IL framework named Multi-Agent Network Selection Algorithm (MANSA) which selectively employs CL only at states that require coordination. At its core, MANSA has an additional agent that uses switching controls to quickly learn the best states to activate CL during training, using CL only where necessary and vastly reducing the computational burden of CL. Our theory proves MANSA preserves cooperative MARL convergence properties, boosts IL performance and can optimally make use of a fixed budget on the number CL calls. We show empirically in Level-based Foraging (LBF) and StarCraft Multi-agent Challenge (SMAC) that MANSA achieves fast, superior and more reliable performance while making 40% fewer CL calls in SMAC and using CL at only 1% CL calls in LBF.

  • 10 authors
·
Feb 12, 2023

Taskmaster-1: Toward a Realistic and Diverse Dialog Dataset

A significant barrier to progress in data-driven approaches to building dialog systems is the lack of high quality, goal-oriented conversational data. To help satisfy this elementary requirement, we introduce the initial release of the Taskmaster-1 dataset which includes 13,215 task-based dialogs comprising six domains. Two procedures were used to create this collection, each with unique advantages. The first involves a two-person, spoken "Wizard of Oz" (WOz) approach in which trained agents and crowdsourced workers interact to complete the task while the second is "self-dialog" in which crowdsourced workers write the entire dialog themselves. We do not restrict the workers to detailed scripts or to a small knowledge base and hence we observe that our dataset contains more realistic and diverse conversations in comparison to existing datasets. We offer several baseline models including state of the art neural seq2seq architectures with benchmark performance as well as qualitative human evaluations. Dialogs are labeled with API calls and arguments, a simple and cost effective approach which avoids the requirement of complex annotation schema. The layer of abstraction between the dialog model and the service provider API allows for a given model to interact with multiple services that provide similar functionally. Finally, the dataset will evoke interest in written vs. spoken language, discourse patterns, error handling and other linguistic phenomena related to dialog system research, development and design.

  • 10 authors
·
Sep 1, 2019

RedDino: A foundation model for red blood cell analysis

Red blood cells (RBCs) are essential to human health, and their precise morphological analysis is important for diagnosing hematological disorders. Despite the promise of foundation models in medical diagnostics, comprehensive AI solutions for RBC analysis remain scarce. We present RedDino, a self-supervised foundation model designed for RBC image analysis. RedDino uses an RBC-specific adaptation of the DINOv2 self-supervised learning framework and is trained on a curated dataset of 1.25 million RBC images from diverse acquisition modalities and sources. Extensive evaluations show that RedDino outperforms existing state-of-the-art models on RBC shape classification. Through assessments including linear probing and nearest neighbor classification, we confirm its strong feature representations and generalization ability. Our main contributions are: (1) a foundation model tailored for RBC analysis, (2) ablation studies exploring DINOv2 configurations for RBC modeling, and (3) a detailed evaluation of generalization performance. RedDino addresses key challenges in computational hematology by capturing nuanced morphological features, advancing the development of reliable diagnostic tools. The source code and pretrained models for RedDino are available at https://github.com/Snarci/RedDino, and the pretrained models can be downloaded from our Hugging Face collection at https://huggingface.co/collections/Snarcy/reddino-689a13e29241d2e5690202fc

  • 4 authors
·
Aug 11, 2025 2

Comprehensive Benchmarking of YOLOv11 Architectures for Scalable and Granular Peripheral Blood Cell Detection

Manual peripheral blood smear (PBS) analysis is labor intensive and subjective. While deep learning offers a promising alternative, a systematic evaluation of state of the art models such as YOLOv11 for fine grained PBS detection is still lacking. In this work, we make two key contributions. First, we curate a large scale annotated dataset for blood cell detection and classification, comprising 16,891 images across 12 peripheral blood cell (PBC) classes, along with the red blood cell class, all carefully re annotated for object detection tasks. In total, the dataset contains 298,850 annotated cells. Second, we leverage this dataset to conduct a comprehensive evaluation of five YOLOv11 variants (ranging from Nano to XLarge). These models are rigorously benchmarked under two data splitting strategies (70:20:10 and 80:10:10) and systematically assessed using multiple performance criteria, including mean Average Precision (mAP), precision, recall, F1 score, and computational efficiency. Our experiments show that the YOLOv11 Medium variant achieves the best trade off, reaching a mAP@0.5 of 0.934 under the 8:1:1 split. Larger models (Large and XLarge) provide only marginal accuracy gains at substantially higher computational cost. Moreover, the 8:1:1 split consistently outperforms the 7:2:1 split across all models. These findings highlight YOLOv11, particularly the Medium variant, as a highly effective framework for automated, fine grained PBS detection. Beyond benchmarking, our publicly released dataset (github.com/Mohamad-AbouAli/OI-PBC-Dataset) offers a valuable resource to advance research on blood cell detection and classification in hematology.

  • 7 authors
·
Sep 29, 2025

LoopTool: Closing the Data-Training Loop for Robust LLM Tool Calls

Augmenting Large Language Models (LLMs) with external tools enables them to execute complex, multi-step tasks. However, tool learning is hampered by the static synthetic data pipelines where data generation and model training are executed as two separate, non-interactive processes. This approach fails to adaptively focus on a model's specific weaknesses and allows noisy labels to persist, degrading training efficiency. We introduce LoopTool, a fully automated, model-aware data evolution framework that closes this loop by tightly integrating data synthesis and model training. LoopTool iteratively refines both the data and the model through three synergistic modules: (1) Greedy Capability Probing (GCP) diagnoses the model's mastered and failed capabilities; (2) Judgement-Guided Label Verification (JGLV) uses an open-source judge model to find and correct annotation errors, progressively purifying the dataset; and (3) Error-Driven Data Expansion (EDDE) generates new, challenging samples based on identified failures. This closed-loop process operates within a cost-effective, open-source ecosystem, eliminating dependence on expensive closed-source APIs. Experiments show that our 8B model trained with LoopTool significantly surpasses its 32B data generator and achieves new state-of-the-art results on the BFCL-v3 and ACEBench benchmarks for its scale. Our work demonstrates that closed-loop, self-refining data pipelines can dramatically enhance the tool-use capabilities of LLMs.

ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

  • 13 authors
·
Nov 4, 2024

BigCodeBench: Benchmarking Code Generation with Diverse Function Calls and Complex Instructions

Automated software engineering has been greatly empowered by the recent advances in Large Language Models (LLMs) for programming. While current benchmarks have shown that LLMs can perform various software engineering tasks like human developers, the majority of their evaluations are limited to short and self-contained algorithmic tasks. Solving challenging and practical programming tasks requires the capability of utilizing diverse function calls as tools to efficiently implement functionalities like data analysis and web development. In addition, using multiple tools to solve a task needs compositional reasoning by accurately understanding complex instructions. Fulfilling both of these characteristics can pose a great challenge for LLMs. To assess how well LLMs can solve challenging and practical programming tasks, we introduce Bench, a benchmark that challenges LLMs to invoke multiple function calls as tools from 139 libraries and 7 domains for 1,140 fine-grained programming tasks. To evaluate LLMs rigorously, each programming task encompasses 5.6 test cases with an average branch coverage of 99%. In addition, we propose a natural-language-oriented variant of Bench, Benchi, that automatically transforms the original docstrings into short instructions only with essential information. Our extensive evaluation of 60 LLMs shows that LLMs are not yet capable of following complex instructions to use function calls precisely, with scores up to 60%, significantly lower than the human performance of 97%. The results underscore the need for further advancements in this area.

bigcode BigCode
·
Jun 22, 2024 8

SWE-Bench++: A Framework for the Scalable Generation of Software Engineering Benchmarks from Open-Source Repositories

Benchmarks like SWE-bench have standardized the evaluation of Large Language Models (LLMs) on repository-level software engineering tasks. However, these efforts remain limited by manual curation, static datasets, and a focus on Python-based bug fixes. We introduce SWE-Bench++, an automated framework that generates repository-level coding tasks from open-source GitHub projects. Unlike synthetic approaches, our pipeline harvests live pull requests to cover both bug fixes and feature requests across 11 languages. SWE-Bench++ turns GitHub pull requests (PRs) into reproducible, execution-based tasks via four stages: programmatic sourcing, environment synthesis, test oracle extraction, and quality assurance. A final hint-guided trajectory synthesis step converts instances that strong models fail on into training trajectories. Our initial benchmark consists of 11,133 instances from 3,971 repositories across 11 languages. On a subset of 1,782 instances of this benchmark, today's strongest models perform as follows: claude-sonnet-4.5 achieves 36.20% pass@10, gpt-5-2025-08-07 34.57%, gemini/gemini-2.5-pro 24.92%, and gpt-4o 16.89%. We further demonstrate the utility of our dataset by showing that fine-tuning on SWE-Bench++ instances yields measurable improvements on the SWE-bench Multilingual benchmark. SWE-Bench++ provides a scalable, multilingual benchmark for evaluating and improving repository-level code generation.

TuringEnterprises Turing Inc.
·
Dec 19, 2025 2

Gaia Data Release 3: Summary of the content and survey properties

We present the third data release of the European Space Agency's Gaia mission, GDR3. The GDR3 catalogue is the outcome of the processing of raw data collected with the Gaia instruments during the first 34 months of the mission by the Gaia Data Processing and Analysis Consortium. The GDR3 catalogue contains the same source list, celestial positions, proper motions, parallaxes, and broad band photometry in the G, G_{BP}, and G_{RP} pass-bands already present in the Early Third Data Release. GDR3 introduces an impressive wealth of new data products. More than 33 million objects in the ranges G_{rvs} < 14 and 3100 <T_{eff} <14500 , have new determinations of their mean radial velocities based on data collected by Gaia. We provide G_{rvs} magnitudes for most sources with radial velocities, and a line broadening parameter is listed for a subset of these. Mean Gaia spectra are made available to the community. The GDR3 catalogue includes about 1 million mean spectra from the radial velocity spectrometer, and about 220 million low-resolution blue and red prism photometer BPRP mean spectra. The results of the analysis of epoch photometry are provided for some 10 million sources across 24 variability types. GDR3 includes astrophysical parameters and source class probabilities for about 470 million and 1500 million sources, respectively, including stars, galaxies, and quasars. Orbital elements and trend parameters are provided for some 800,000 astrometric, spectroscopic and eclipsing binaries. More than 150,000 Solar System objects, including new discoveries, with preliminary orbital solutions and individual epoch observations are part of this release. Reflectance spectra derived from the epoch BPRP spectral data are published for about 60\,000 asteroids. Finally, an additional data set is provided, namely the Gaia Andromeda Photometric Survey (abridged)

  • 456 authors
·
Jul 30, 2022

WorldBench: Disambiguating Physics for Diagnostic Evaluation of World Models

Recent advances in generative foundational models, often termed "world models," have propelled interest in applying them to critical tasks like robotic planning and autonomous system training. For reliable deployment, these models must exhibit high physical fidelity, accurately simulating real-world dynamics. Existing physics-based video benchmarks, however, suffer from entanglement, where a single test simultaneously evaluates multiple physical laws and concepts, fundamentally limiting their diagnostic capability. We introduce WorldBench, a novel video-based benchmark specifically designed for concept-specific, disentangled evaluation, allowing us to rigorously isolate and assess understanding of a single physical concept or law at a time. To make WorldBench comprehensive, we design benchmarks at two different levels: 1) an evaluation of intuitive physical understanding with concepts such as object permanence or scale/perspective, and 2) an evaluation of low-level physical constants and material properties such as friction coefficients or fluid viscosity. When SOTA video-based world models are evaluated on WorldBench, we find specific patterns of failure in particular physics concepts, with all tested models lacking the physical consistency required to generate reliable real-world interactions. Through its concept-specific evaluation, WorldBench offers a more nuanced and scalable framework for rigorously evaluating the physical reasoning capabilities of video generation and world models, paving the way for more robust and generalizable world-model-driven learning.

  • 10 authors
·
Jan 29 2

AgentCgroup: Understanding and Controlling OS Resources of AI Agents

AI agents are increasingly deployed in multi-tenant cloud environments, where they execute diverse tool calls within sandboxed containers, each call with distinct resource demands and rapid fluctuations. We present a systematic characterization of OS-level resource dynamics in sandboxed AI coding agents, analyzing 144 software engineering tasks from the SWE-rebench benchmark across two LLM models. Our measurements reveal that (1) OS-level execution (tool calls, container and agent initialization) accounts for 56-74% of end-to-end task latency; (2) memory, not CPU, is the concurrency bottleneck; (3) memory spikes are tool-call-driven with a up to 15.4x peak-to-average ratio; and (4) resource demands are highly unpredictable across tasks, runs, and models. Comparing these characteristics against serverless, microservice, and batch workloads, we identify three mismatches in existing resource controls: a granularity mismatch (container-level policies vs. tool-call-level dynamics), a responsiveness mismatch (user-space reaction vs. sub-second unpredictable bursts), and an adaptability mismatch (history-based prediction vs. non-deterministic stateful execution). We propose AgentCgroup, an intent-driven eBPF-based resource controller that exploits agents ability to declare resource needs and reconstruct execution strategies, using hierarchical cgroup structures aligned with tool-call boundaries, in-kernel enforcement via sched_ext and memcg_bpf_ops, and runtime-adaptive policies. Preliminary evaluation demonstrates improved multi-tenant isolation and reduced resource waste. AgentCgroup is open-source at https://github.com/eunomia-bpf/agentcgroup

  • 6 authors
·
Feb 9

ATCO2 corpus: A Large-Scale Dataset for Research on Automatic Speech Recognition and Natural Language Understanding of Air Traffic Control Communications

Personal assistants, automatic speech recognizers and dialogue understanding systems are becoming more critical in our interconnected digital world. A clear example is air traffic control (ATC) communications. ATC aims at guiding aircraft and controlling the airspace in a safe and optimal manner. These voice-based dialogues are carried between an air traffic controller (ATCO) and pilots via very-high frequency radio channels. In order to incorporate these novel technologies into ATC (low-resource domain), large-scale annotated datasets are required to develop the data-driven AI systems. Two examples are automatic speech recognition (ASR) and natural language understanding (NLU). In this paper, we introduce the ATCO2 corpus, a dataset that aims at fostering research on the challenging ATC field, which has lagged behind due to lack of annotated data. The ATCO2 corpus covers 1) data collection and pre-processing, 2) pseudo-annotations of speech data, and 3) extraction of ATC-related named entities. The ATCO2 corpus is split into three subsets. 1) ATCO2-test-set corpus contains 4 hours of ATC speech with manual transcripts and a subset with gold annotations for named-entity recognition (callsign, command, value). 2) The ATCO2-PL-set corpus consists of 5281 hours of unlabeled ATC data enriched with automatic transcripts from an in-domain speech recognizer, contextual information, speaker turn information, signal-to-noise ratio estimate and English language detection score per sample. Both available for purchase through ELDA at http://catalog.elra.info/en-us/repository/browse/ELRA-S0484. 3) The ATCO2-test-set-1h corpus is a one-hour subset from the original test set corpus, that we are offering for free at https://www.atco2.org/data. We expect the ATCO2 corpus will foster research on robust ASR and NLU not only in the field of ATC communications but also in the general research community.

  • 14 authors
·
Nov 8, 2022

AgencyBench: Benchmarking the Frontiers of Autonomous Agents in 1M-Token Real-World Contexts

Large Language Models (LLMs) based autonomous agents demonstrate multifaceted capabilities to contribute substantially to economic production. However, existing benchmarks remain focused on single agentic capability, failing to capture long-horizon real-world scenarios. Moreover, the reliance on human-in-the-loop feedback for realistic tasks creates a scalability bottleneck, hindering automated rollout collection and evaluation. To bridge this gap, we introduce AgencyBench, a comprehensive benchmark derived from daily AI usage, evaluating 6 core agentic capabilities across 32 real-world scenarios, comprising 138 tasks with specific queries, deliverables, and rubrics. These scenarios require an average of 90 tool calls, 1 million tokens, and hours of execution time to resolve. To enable automated evaluation, we employ a user simulation agent to provide iterative feedback, and a Docker sandbox to conduct visual and functional rubric-based assessment. Experiments reveal that closed-source models significantly outperform open-source models (48.4% vs 32.1%). Further analysis reveals significant disparities across models in resource efficiency, feedback-driven self-correction, and specific tool-use preferences. Finally, we investigate the impact of agentic scaffolds, observing that proprietary models demonstrate superior performance within their native ecosystems (e.g., Claude-4.5-Opus via Claude-Agent-SDK), while open-source models exhibit distinct performance peaks, suggesting potential optimization for specific execution frameworks. AgencyBench serves as a critical testbed for next-generation agents, highlighting the necessity of co-optimizing model architecture with agentic frameworks. We believe this work sheds light on the future direction of autonomous agents, and we release the full benchmark and evaluation toolkit at https://github.com/GAIR-NLP/AgencyBench.

GAIR SII - GAIR
·
Jan 16 3

DSGym: A Holistic Framework for Evaluating and Training Data Science Agents

Data science agents promise to accelerate discovery and insight-generation by turning data into executable analyses and findings. Yet existing data science benchmarks fall short due to fragmented evaluation interfaces that make cross-benchmark comparison difficult, narrow task coverage and a lack of rigorous data grounding. In particular, we show that a substantial portion of tasks in current benchmarks can be solved without using the actual data. To address these limitations, we introduce DSGym, a standardized framework for evaluating and training data science agents in self-contained execution environments. Unlike static benchmarks, DSGym provides a modular architecture that makes it easy to add tasks, agent scaffolds, and tools, positioning it as a live, extensible testbed. We curate DSGym-Tasks, a holistic task suite that standardizes and refines existing benchmarks via quality and shortcut solvability filtering. We further expand coverage with (1) DSBio: expert-derived bioinformatics tasks grounded in literature and (2) DSPredict: challenging prediction tasks spanning domains such as computer vision, molecular prediction, and single-cell perturbation. Beyond evaluation, DSGym enables agent training via execution-verified data synthesis pipeline. As a case study, we build a 2,000-example training set and trained a 4B model in DSGym that outperforms GPT-4o on standardized analysis benchmarks. Overall, DSGym enables rigorous end-to-end measurement of whether agents can plan, implement, and validate data analyses in realistic scientific context.

  • 9 authors
·
Jan 22 2

HiddenTables & PyQTax: A Cooperative Game and Dataset For TableQA to Ensure Scale and Data Privacy Across a Myriad of Taxonomies

A myriad of different Large Language Models (LLMs) face a common challenge in contextually analyzing table question-answering tasks. These challenges are engendered from (1) finite context windows for large tables, (2) multi-faceted discrepancies amongst tokenization patterns against cell boundaries, and (3) various limitations stemming from data confidentiality in the process of using external models such as gpt-3.5-turbo. We propose a cooperative game dubbed "HiddenTables" as a potential resolution to this challenge. In essence, "HiddenTables" is played between the code-generating LLM "Solver" and the "Oracle" which evaluates the ability of the LLM agents to solve Table QA tasks. This game is based on natural language schemas and importantly, ensures the security of the underlying data. We provide evidential experiments on a diverse set of tables that demonstrate an LLM's collective inability to generalize and perform on complex queries, handle compositional dependencies, and align natural language to programmatic commands when concrete table schemas are provided. Unlike encoder-based models, we have pushed the boundaries of "HiddenTables" to not be limited by the number of rows - therefore we exhibit improved efficiency in prompt and completion tokens. Our infrastructure has spawned a new dataset "PyQTax" that spans across 116,671 question-table-answer triplets and provides additional fine-grained breakdowns & labels for varying question taxonomies. Therefore, in tandem with our academic contributions regarding LLMs' deficiency in TableQA tasks, "HiddenTables" is a tactile manifestation of how LLMs can interact with massive datasets while ensuring data security and minimizing generation costs.

  • 4 authors
·
Jun 16, 2024 1

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.

  • 4 authors
·
Apr 19, 2023

MMAT-1M: A Large Reasoning Dataset for Multimodal Agent Tuning

Large Language Models (LLMs), enhanced through agent tuning, have demonstrated remarkable capabilities in Chain-of-Thought (CoT) and tool utilization, significantly surpassing the performance of standalone models. However, the multimodal domain still lacks a large-scale, high-quality agent tuning dataset to unlock the full potential of multimodal large language models. To bridge this gap, we introduce MMAT-1M, the first million-scale multimodal agent tuning dataset designed to support CoT, reflection, and dynamic tool usage. Our dataset is constructed through a novel four-stage data engine: 1) We first curate publicly available multimodal datasets containing question-answer pairs; 2) Then, leveraging GPT-4o, we generate rationales for the original question-answer pairs and dynamically integrate API calls and Retrieval Augmented Generation (RAG) information through a multi-turn paradigm; 3) Furthermore, we refine the rationales through reflection to ensure logical consistency and accuracy, creating a multi-turn dialogue dataset with both Rationale and Reflection (RR); 4) Finally, to enhance efficiency, we optionally compress multi-turn dialogues into a One-turn Rationale and Reflection (ORR) format. By fine-tuning open-source multimodal models on the MMAT-1M, we observe significant performance gains. For instance, the InternVL2.5-8B-RR model achieves an average improvement of 2.7% across eight public benchmarks and 8.8% on the RAG benchmark Dyn-VQA, demonstrating the dataset's effectiveness in enhancing multimodal reasoning and tool-based capabilities. The dataset is publicly available at https://github.com/VIS-MPU-Agent/MMAT-1M.

  • 6 authors
·
Jul 29, 2025

Deep Synoptic Array Science: Searching for Long Duration Radio Transients with the DSA-110

We describe the design and commissioning tests for the DSA-110 Not-So-Fast Radio Burst (NSFRB) search pipeline, a 1.4 GHz image-plane single-pulse search sensitive to 134 ms-160.8 s radio bursts. Extending the pulse width range of the Fast Radio Burst (FRB) search by 3 orders of magnitude, the NSFRB search is sensitive to the recently-discovered Galactic Long Period Radio Transients (LPRTs). The NSFRB search operates in real-time, utilizing a custom GPU-accelerated search code, cerberus, implemented in Python with JAX. We summarize successful commissioning sensitivity tests with continuum sources and pulsar B0329+54, estimating the 6sigma flux (fluence) threshold to be ~290 mJy (~40 Jy ms). Future tests of recovery of longer timescale transients, e.g. CHIME J1634+44, are planned to supplement injection testing and B0329+54 observations. An offline DSA-110 NSFRB Galactic Plane Survey was conducted to search for LPRTs, covering -3.5^circ<b<5.7^circ and 141^circ<l<225^circ (~770 square degrees) in Galactic coordinates. We estimate an upper limit Poissonian burst rate ~1 hr^{-1} per square degree (~7 hr^{-1} per 3^circtimes3^circ survey grid cell) maximized across the inner |b|<0.25^circ of the surveyed region. By imposing the ~290 mJy flux limit on two representative models (the magnetar plastic flow model and the White Dwarf-M Dwarf binary model), we reject with 95% confidence the presence of White Dwarf-M Dwarf binary LPRTs with periods between ~10-70s within ~95% of the surveyed region. Combined with the prevalence of LPRTs in the Galactic Plane, our results motivate further consideration of both White Dwarf-M Dwarf binary models and isolated magnetar models. We will continue to explore novel LPRT search strategies during real-time operations, such as triggered periodicity searches and additional targeted surveys.

  • 13 authors
·
Oct 20, 2025

Training-Free Multimodal Large Language Model Orchestration

Different Multimodal Large Language Models (MLLMs) cannot be integrated into a unified multimodal input-output system directly. In previous work, training has been considered as an inevitable component due to challenges in modal alignment, Text-to-Speech efficiency and other integration issues. In this paper, we introduce Multimodal Large Language Model Orchestration, an effective approach for creating interactive multimodal AI systems without additional training. MLLM Orchestration leverages the inherent reasoning capabilities of large language models to coordinate specialized models through explicit workflows, enabling natural multimodal interactions while maintaining modularity, improving interpretability, and significantly enhancing computational efficiency. Our orchestration framework is built upon three key innovations: (1) a central controller LLM that analyzes user inputs and dynamically routes tasks to appropriate specialized models through carefully designed agents; (2) a parallel Text-to-Speech architecture that enables true full-duplex interaction with seamless interruption handling and natural conversational flow; and (3) a cross-modal memory integration system that maintains coherent context across modalities through intelligent information synthesis and retrieval, selectively avoiding unnecessary modality calls in certain scenarios to improve response speed. Extensive evaluations demonstrate that MLLM Orchestration achieves comprehensive multimodal capabilities without additional training, performance improvements of up to 7.8% over traditional jointly-trained approaches on standard benchmarks, reduced latency by 10.3%, and significantly enhanced interpretability through explicit orchestration processes.

  • 5 authors
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Aug 6, 2025

Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

  • 5 authors
·
Aug 9, 2019

SHANKS: Simultaneous Hearing and Thinking for Spoken Language Models

Current large language models (LLMs) and spoken language models (SLMs) begin thinking and taking actions only after the user has finished their turn. This prevents the model from interacting during the user's turn and can lead to high response latency while it waits to think. Consequently, thinking after receiving the full input is not suitable for speech-to-speech interaction, where real-time, low-latency exchange is important. We address this by noting that humans naturally "think while listening." In this paper, we propose SHANKS, a general inference framework that enables SLMs to generate unspoken chain-of-thought reasoning while listening to the user input. SHANKS streams the input speech in fixed-duration chunks and, as soon as a chunk is received, generates unspoken reasoning based on all previous speech and reasoning, while the user continues speaking. SHANKS uses this unspoken reasoning to decide whether to interrupt the user and to make tool calls to complete the task. We demonstrate that SHANKS enhances real-time user-SLM interaction in two scenarios: (1) when the user is presenting a step-by-step solution to a math problem, SHANKS can listen, reason, and interrupt when the user makes a mistake, achieving 37.1% higher interruption accuracy than a baseline that interrupts without thinking; and (2) in a tool-augmented dialogue, SHANKS can complete 56.9% of the tool calls before the user finishes their turn. Overall, SHANKS moves toward models that keep thinking throughout the conversation, not only after a turn ends. Animated illustrations of Shanks can be found at https://d223302.github.io/SHANKS/

  • 10 authors
·
Oct 8, 2025 2

Efficient Multi-Hop Question Answering over Knowledge Graphs via LLM Planning and Embedding-Guided Search

Multi-hop question answering over knowledge graphs remains computationally challenging due to the combinatorial explosion of possible reasoning paths. Recent approaches rely on expensive Large Language Model (LLM) inference for both entity linking and path ranking, limiting their practical deployment. Additionally, LLM-generated answers often lack verifiable grounding in structured knowledge. We present two complementary hybrid algorithms that address both efficiency and verifiability: (1) LLM-Guided Planning that uses a single LLM call to predict relation sequences executed via breadth-first search, achieving near-perfect accuracy (micro-F1 > 0.90) while ensuring all answers are grounded in the knowledge graph, and (2) Embedding-Guided Neural Search that eliminates LLM calls entirely by fusing text and graph embeddings through a lightweight 6.7M-parameter edge scorer, achieving over 100 times speedup with competitive accuracy. Through knowledge distillation, we compress planning capability into a 4B-parameter model that matches large-model performance at zero API cost. Evaluation on MetaQA demonstrates that grounded reasoning consistently outperforms ungrounded generation, with structured planning proving more transferable than direct answer generation. Our results show that verifiable multi-hop reasoning does not require massive models at inference time, but rather the right architectural inductive biases combining symbolic structure with learned representations.

  • 2 authors
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Nov 24, 2025

UltraCUA: A Foundation Model for Computer Use Agents with Hybrid Action

Multimodal agents for computer use rely exclusively on primitive actions (click, type, scroll) that require accurate visual grounding and lengthy execution chains, leading to cascading failures and performance bottlenecks. While other agents leverage rich programmatic interfaces (APIs, MCP servers, tools), computer-use agents (CUAs) remain isolated from these capabilities. We present UltraCUA, a foundation model that bridges this gap through hybrid action -- seamlessly integrating GUI primitives with high-level programmatic tool calls. To achieve this, our approach comprises four key components: (1) an automated pipeline that scales programmatic tools from software documentation, open-source repositories, and code generation; (2) a synthetic data engine producing over 17,000 verifiable tasks spanning real-world computer-use scenarios; (3) a large-scale high-quality hybrid action trajectory collection with both low-level GUI actions and high-level programmatic tool calls; and (4) a two-stage training pipeline combining supervised fine-tuning with online reinforcement learning, enabling strategic alternation between low-level and high-level actions. Experiments with our 7B and 32B models demonstrate substantial improvements over state-of-the-art agents. On OSWorld, UltraCUA models achieve an average 22% relative improvement over base models, while being 11% faster in terms of steps. Out-of-domain evaluation on WindowsAgentArena shows our model reaches 21.7% success rate, outperforming baselines trained on Windows data. The hybrid action mechanism proves critical, reducing error propagation while maintaining execution efficiency.

apple Apple
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Oct 20, 2025 3

AEGIS: No Tool Call Left Unchecked -- A Pre-Execution Firewall and Audit Layer for AI Agents

AI agents increasingly act through external tools: they query databases, execute shell commands, read and write files, and send network requests. Yet in most current agent stacks, model-generated tool calls are handed to the execution layer with no framework-agnostic control point in between. Post-execution observability can record these actions, but it cannot stop them before side effects occur. We present AEGIS, a pre-execution firewall and audit layer for AI agents. AEGIS interposes on the tool-execution path and applies a three-stage pipeline: (i) deep string extraction from tool arguments, (ii) content-first risk scanning, and (iii) composable policy validation. High-risk calls can be held for human approval, and all decisions are recorded in a tamper-evident audit trail based on Ed25519 signatures and SHA-256 hash chaining. In the current implementation, AEGIS supports 14 agent frameworks across Python, JavaScript, and Go with lightweight integration. On a curated suite of 48 attackinstances, AEGIS blocks all attacks in the suite before execution; on 500 benign tool calls, it yields a 1.2% false positive rate; and across 1,000 consecutive interceptions, it adds 8.3 ms median latency. The live demo will show end-to-end interception of benign, malicious, and human-escalated tool calls, allowing attendees to observe real-time blocking, approval workflows, and audit-trail generation. These results suggest that pre-execution mediation for AI agents can be practical, low-overhead, and directly deployable.

  • 3 authors
·
Mar 12

ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics

Spatial transcriptomics (ST) provides high-resolution pathological images and whole-transcriptomic expression profiles at individual spots across whole-slide scales. This setting makes it an ideal data source to develop multimodal foundation models. Although recent studies attempted to fine-tune visual encoders with trainable gene encoders based on spot-level, the absence of a wider slide perspective and spatial intrinsic relationships limits their ability to capture ST-specific insights effectively. Here, we introduce ST-Align, the first foundation model designed for ST that deeply aligns image-gene pairs by incorporating spatial context, effectively bridging pathological imaging with genomic features. We design a novel pretraining framework with a three-target alignment strategy for ST-Align, enabling (1) multi-scale alignment across image-gene pairs, capturing both spot- and niche-level contexts for a comprehensive perspective, and (2) cross-level alignment of multimodal insights, connecting localized cellular characteristics and broader tissue architecture. Additionally, ST-Align employs specialized encoders tailored to distinct ST contexts, followed by an Attention-Based Fusion Network (ABFN) for enhanced multimodal fusion, effectively merging domain-shared knowledge with ST-specific insights from both pathological and genomic data. We pre-trained ST-Align on 1.3 million spot-niche pairs and evaluated its performance through two downstream tasks across six datasets, demonstrating superior zero-shot and few-shot capabilities. ST-Align highlights the potential for reducing the cost of ST and providing valuable insights into the distinction of critical compositions within human tissue.

  • 8 authors
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Nov 25, 2024