SearcharxivSearch

arXiv subjects

Ian T. Foster

Publications and source records attributed to Ian T. Foster.

At least 19 recordsLinked to original sources

Wrong but Useful: Trajectory Value Beyond Answer Correctness in Multi-Agent Messages

Multi-agent reasoning systems often use agreement, confidence, or automated scores to decide which messages should shape a final answer. Such filtering assumes that a message likely to be correct is also worth keeping. Yet a wrong answer can contain a useful decomposition, constraint, or scientific principle. We test this distinction with Diverse Hypothesis Deliberation (DHD), a controlled measurement protocol that caches five independently generated messages and replays the same downstream solver, called the integrator, with each message available or hidden. The replay comparison measures a message's trajectory value: whether making the message available helps or harms subsequent reasoning. Across five mathematics and science benchmarks and two openly available model families, gpt-oss-120b and gemma-4-31B-it, wrong-helpful messages appear in every benchmark-model combination. Among wrong-answer messages that change final correctness, more than four in ten changes are helpful in each model. Controlled repeats show that the number of repeatable message effects is unlikely to arise from replay variation alone (p=0.0002). A focused intervention on repeatable wrong-helpful messages finds that the complete message works best, while retaining its reasoning preserves more success than retaining only its answer; the source of the complete-message advantage remains open. Within the same problem, repeated trajectory-value evidence also identifies a better keep-or-remove choice than answer correctness alone. Answer correctness is therefore informative but does not determine trajectory value. DHD measures this missing property and produces reusable labels for learning when agents should listen.

cs.AI

Harnessing X-ray Absorption Spectroscopy Data through Multimodal Mining of Battery Literature

X-ray absorption spectroscopy (XAS) is central to understanding the local electronic and atomic structure of materials, yet most published spectra remain inaccessible to data-driven analysis because they are embedded in figures and described through fragmented textual context in the literature. Here, we use multimodal (image and text) literature mining to transform this dispersed knowledge into an AI-ready experimental data resource. We developed a scalable spectroscopy data digitization pipeline that identifies XAS figures in full-text articles, digitizes spectral curves, and links each spectrum to accompanying metadata on the measured edge and material. Applying this pipeline to the battery literature produced an open dataset of 13,740 XAS spectra, spanning 66 absorbing elements and diverse battery chemistries, with expert validation confirming accurate extraction of spectral and metadata information. By converting literature-embedded spectra into structured numerical data, this dataset provides a foundation for large-scale XAS analysis, cross-laboratory comparison, high-throughput characterization, and autonomous discovery of advanced materials.

cond-mat.mtrl-sci

Precise but Uncoupled: Reviewer Precision Does Not Guarantee Critique Uptake in Multi-Agent Math Reasoning

Many math- and science-oriented agent systems use hierarchical designs with specialized reviewer roles, assuming that a dedicated review stage should help turn wrong candidates into correct ones. We test this assumption on 4,181 verifier-grounded Omni-MATH problems using matched gpt-oss-120b actors. Collaboration adds little on the easiest tiers, but from tier 4 onward the gains open sharply; in this harder regime, broadcast-style peer discussion reaches higher final accuracy than a planner-executor-reviewer pipeline (PER). We ask whether this gap is explained by reviewer quality or by whether critique changes the next answer the protocol carries forward. It is not explained by reviewer precision alone: PER's reviewer is more precise than broadcast's (0.861 vs. 0.644), yet evaluator-verified useful critique is much less likely to change the next candidate and produces lower reviewer-guided repair. These results show that reviewer detection quality and critique uptake are empirically separable. Within matched PER interventions, forcing explicit acknowledgment lowers final accuracy, while embedding reviewer guidance directly in the solver's working context partially improves follow-through without closing the gap. Overall, reviewer-centric evaluation can overstate system quality: a protocol may spot errors well yet still fail to solve more problems if it does not act on those critiques.

cs.AI

BioAlchemy: Distilling Biological Literature into Reasoning-Ready Reinforcement Learning Training Data

Despite the large corpus of biology training text, the impact of reasoning models on biological research generally lags behind math and coding. In this work, we show that biology questions from current large-scale reasoning datasets do not align well with modern research topic distributions in biology, and that this topic imbalance may negatively affect performance. In addition, we find that methods for extracting challenging and verifiable research problems from biology research text are a critical yet underdeveloped ingredient in applying reinforcement learning for better performance on biology research tasks. We introduce BioAlchemy, a pipeline for sourcing a diverse set of verifiable question-and-answer pairs from a scientific corpus of biology research text. We curate BioAlchemy-345K, a training dataset containing over 345K scientific reasoning problems in biology. Then, we demonstrate how aligning our dataset to the topic distribution of modern scientific biology can be used with reinforcement learning to improve reasoning performance. Finally, we present BioAlchemist-8B, which improves over its base reasoning model by 9.12% on biology benchmarks. These results demonstrate the efficacy of our approach for developing stronger scientific reasoning capabilities in biology. The BioAlchemist-8B model is available at: https://huggingface.co/BioAlchemy.

cs.AI

Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) represent crucial therapeutic targets due to their significant role in disease -- approximately 80\% of cancer-related proteins contain long disordered regions -- but their lack of stable secondary/tertiary structures makes them "undruggable". While recent computational advances, such as diffusion models, can design high-affinity IDP binders, translating these to practical drug discovery requires autonomous systems capable of reasoning across complex conformational ensembles and orchestrating diverse computational tools at scale.To address this challenge, we designed and implemented StructBioReasoner, a scalable multi-agent system for designing biologics that can be used to target IDPs. StructBioReasoner employs a novel tournament-based reasoning framework where specialized agents compete to generate and refine therapeutic hypotheses, naturally distributing computational load for efficient exploration of the vast design space. Agents integrate domain knowledge with access to literature synthesis, AI-structure prediction, molecular simulations, and stability analysis, coordinating their execution on HPC infrastructure via an extensible federated agentic middleware, Academy. We benchmark StructBioReasoner across Der f 21 and NMNAT-2 and demonstrate that over 50\% of 787 designed and validated candidates for Der f 21 outperformed the human-designed reference binders from literature, in terms of improved binding free energy. For the more challenging NMNAT-2 protein, we identified three binding modes from 97,066 binders, including the well-studied NMNAT2:p53 interface. Thus, StructBioReasoner lays the groundwork for agentic reasoning systems for IDP therapeutic discovery on Exascale platforms.

q-bio.QM

Who Gets the Reward & Who Gets the Blame? Evaluation-Aligned Training Signals for Multi-LLM Agents

Large Language Models (LLMs) in multi-agent systems (MAS) have shown promise for complex tasks, yet current training methods lack principled ways to connect system-level evaluation with agent- and message-level learning. We propose a theoretical framework that unifies cooperative game-theoretic attribution with process reward modeling to transform system evaluation to agent credit to response-level signals. Unlike prior approaches that rely only on attribution (Shapley) or step-level labels (PRM), our method produces local, signed, and credit-conserving signals. In success cases, Shapley-based credit assignment fairly allocates outcomes across agents and is refined into per-message rewards that promote cooperation while discouraging redundancy or sabotage; in failure cases, first-error localization yields repair-aware preferences that penalize harmful steps while rewarding corrective attempts. The resulting signals are bounded, cooperative, and directly compatible with reinforcement- or preference-based post-training, providing a unified and auditable pathway from global evaluation to local supervision in LLM multi-agent training. Our contribution is conceptual: we present a theoretical foundation and training signals, leaving empirical validation for future work.

cs.MA

Agentic Discovery: Closing the Loop with Cooperative Agents

As data-driven methods, artificial intelligence (AI), and automated workflows accelerate scientific tasks, we see the rate of discovery increasingly limited by human decision-making tasks such as setting objectives, generating hypotheses, and designing experiments. We postulate that cooperative agents are needed to augment the role of humans and enable autonomous discovery. Realizing such agents will require progress in both AI and infrastructure.

cs.MA

Automated MCQA Benchmarking at Scale: Evaluating Reasoning Traces as Retrieval Sources for Domain Adaptation of Small Language Models

As scientific knowledge grows at an unprecedented pace, evaluation benchmarks must evolve to reflect new discoveries and ensure language models are tested on current, diverse literature. We propose a scalable, modular framework for generating multiple-choice question-answering (MCQA) benchmarks directly from large corpora of scientific papers. Our pipeline automates every stage of MCQA creation, including PDF parsing, semantic chunking, question generation, and model evaluation. As a case study, we generate more than 16,000 MCQs from 22,000 open-access articles in radiation and cancer biology. We then evaluate a suite of small language models (1.1B-14B parameters) on these questions, comparing baseline accuracy with retrieval-augmented generation (RAG) from paper-derived semantic chunks and from reasoning traces distilled from GPT-4.1. We find that reasoning-trace retrieval consistently improves performance on both synthetic and expert-annotated benchmarks, enabling several small models to surpass GPT-4 on the 2023 Astro Radiation and Cancer Biology exam.

cs.CL

Understanding the Landscape of Ampere GPU Memory Errors

Graphics Processing Units (GPUs) have become a de facto solution for accelerating high-performance computing (HPC) applications. Understanding their memory error behavior is an essential step toward achieving efficient and reliable HPC systems. In this work, we present a large-scale cross-supercomputer study to characterize GPU memory reliability, covering three supercomputers - Delta, Polaris, and Perlmutter - all equipped with NVIDIA A100 GPUs. We examine error logs spanning 67.77 million GPU device-hours across 10,693 GPUs. We compare error rates and mean-time-between-errors (MTBE) and highlight both shared and distinct error characteristics among these three systems. Based on these observations and analyses, we discuss the implications and lessons learned, focusing on the reliable operation of supercomputers, the choice of checkpointing interval, and the comparison of reliability characteristics with those of previous-generation GPUs. Our characterization study provides valuable insights into fault-tolerant HPC system design and operation, enabling more efficient execution of HPC applications.

cs.DC

RADAR-Radio Afterglow Detection and AI-driven Response: A Federated Framework for Gravitational Wave Event Follow-Up

The landmark detection of both gravitational waves (GWs) and electromagnetic (EM) radiation from the binary neutron star merger GW170817 has spurred efforts to streamline the follow-up of GW alerts in current and future observing runs of ground-based GW detectors. Within this context, the radio band of the EM spectrum presents unique challenges. Sensitive radio facilities capable of detecting the faint radio afterglow seen in GW170817, and with sufficient angular resolution, have small fields of view compared to typical GW localization areas. Additionally, theoretical models predict that the radio emission from binary neutron star mergers can evolve over weeks to years, necessitating long-term monitoring to probe the physics of the various post-merger ejecta components. These constraints, combined with limited radio observing resources, make the development of more coordinated follow-up strategies essential -- especially as the next generation of GW detectors promise a dramatic increase in detection rates. Here, we present RADAR, a framework designed to address these challenges by promoting community-driven information sharing, federated data analysis, and system resilience, while integrating AI methods for both GW signal identification and radio data aggregation. We show that it is possible to preserve data rights while sharing models that can help design and/or update follow-up strategies. We demonstrate our approach through a case study of GW170817, and discuss future directions for refinement and broader application.

astro-ph.HE

A Grassroots Network and Community Roadmap for Interconnected Autonomous Science Laboratories for Accelerated Discovery

Scientific discovery is being revolutionized by AI and autonomous systems, yet current autonomous laboratories remain isolated islands unable to collaborate across institutions. We present the Autonomous Interconnected Science Lab Ecosystem (AISLE), a grassroots network transforming fragmented capabilities into a unified system that shorten the path from ideation to innovation to impact and accelerates discovery from decades to months. AISLE addresses five critical dimensions: (1) cross-institutional equipment orchestration, (2) intelligent data management with FAIR compliance, (3) AI-agent driven orchestration grounded in scientific principles, (4) interoperable agent communication interfaces, and (5) AI/ML-integrated scientific education. By connecting autonomous agents across institutional boundaries, autonomous science can unlock research spaces inaccessible to traditional approaches while democratizing cutting-edge technologies. This paradigm shift toward collaborative autonomous science promises breakthroughs in sustainable energy, materials development, and public health.

cs.CY

Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows

The Workflows Community Summit gathered 111 participants from 18 countries to discuss emerging trends and challenges in scientific workflows, focusing on six key areas: time-sensitive workflows, AI-HPC convergence, multi-facility workflows, heterogeneous HPC environments, user experience, and FAIR computational workflows. The integration of AI and exascale computing has revolutionized scientific workflows, enabling higher-fidelity models and complex, time-sensitive processes, while introducing challenges in managing heterogeneous environments and multi-facility data dependencies. The rise of large language models is driving computational demands to zettaflop scales, necessitating modular, adaptable systems and cloud-service models to optimize resource utilization and ensure reproducibility. Multi-facility workflows present challenges in data movement, curation, and overcoming institutional silos, while diverse hardware architectures require integrating workflow considerations into early system design and developing standardized resource management tools. The summit emphasized improving user experience in workflow systems and ensuring FAIR workflows to enhance collaboration and accelerate scientific discovery. Key recommendations include developing standardized metrics for time-sensitive workflows, creating frameworks for cloud-HPC integration, implementing distributed-by-design workflow modeling, establishing multi-facility authentication protocols, and accelerating AI integration in HPC workflow management. The summit also called for comprehensive workflow benchmarks, workflow-specific UX principles, and a FAIR workflow maturity model, highlighting the need for continued collaboration in addressing the complex challenges posed by the convergence of AI, HPC, and multi-facility research environments.

cs.DC

Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges in life sciences, including therapeutic design, protein engineering, enzyme optimization, and elucidating biological mechanisms. Much work has been devoted to predicting binding affinity over the past decades. Here, we review recent significant works, with a focus on methods, evaluation strategies, and benchmark datasets. We note growing use of both traditional machine learning and deep learning models for predicting binding affinity, accompanied by an increasing amount of data on proteins and small drug-like molecules. With improved predictive performance and the FDA's phasing out of animal testing, AI-driven in silico models, such as AI virtual cells (AIVCs), are poised to advance binding affinity prediction; reciprocally, progress in building binding affinity predictors can refine AIVCs. Future efforts in binding affinity prediction and AI-driven in silico models can enhance the simulation of temporal dynamics, cell-type specificity, and multi-omics integration to support more accurate and personalized outcomes.

q-bio.QM

Sustainable Data Democratization: A Multifaceted Investment for an Equitable Future

The urgent need for data democratization in scientific research was the focal point of a panel discussion at SC23 in Denver, Colorado, from November 12 to 17, 2023. This article summarizes the outcomes of that discussion and subsequent conversations. We advocate for strategic investments in financial, human, and technological resources for sustainable data democratization. Emphasizing that data is central to scientific discovery and AI deployment, we highlight barriers such as limited access, inadequate financial incentives for cross-domain collaboration, and a shortage of workforce development initiatives. Our recommendations aim to guide decision-makers in fostering an inclusive research community, breaking down research silos, and developing a skilled workforce to advance scientific discovery.

cs.DB

Automated, Reliable, and Efficient Continental-Scale Replication of 7.3 Petabytes of Climate Simulation Data: A Case Study

We report on our experiences replicating 7.3 petabytes (PB) of Earth System Grid Federation (ESGF) climate simulation data from Lawrence Livermore National Laboratory (LLNL) in California to Argonne National Laboratory (ANL) in Illinois and Oak Ridge National Laboratory (ORNL) in Tennessee. This movement of some 29 million files, twice, undertaken in order to establish new ESGF nodes at ANL and ORNL, was performed largely automatically by a simple replication tool, a script that invoked Globus to transfer large bundles of files while tracking progress in a database. Under the covers, Globus organized transfers to make efficient use of the high-speed Energy Sciences network (ESnet) and the data transfer nodes deployed at participating sites, and also addressed security, integrity checking, and recovery from a variety of transient failures. This success demonstrates the considerable benefits that can accrue from the adoption of performant data replication infrastructure.

cs.DC

Steering a Fleet: Adaptation for Large-Scale, Workflow-Based Experiments

Experimental science is increasingly driven by instruments that produce vast volumes of data and thus a need to manage, compute, describe, and index this data. High performance and distributed computing provide the means of addressing the computing needs; however, in practice, the variety of actions required and the distributed set of resources involved, requires sophisticated "flows" defining the steps to be performed on data. As each scan or measurement is performed by an instrument, a new instance of the flow is initiated resulting in a "fleet" of concurrently running flows, with the overall goal to process all the data collected during a potentially long-running experiment. During the course of the experiment, each flow may need to adapt its execution due to changes in the environment, such as computational or storage resource availability, or based on the progress of the fleet as a whole such as completion or discovery of an intermediate result leading to a change in subsequent flow's behavior. We introduce a cloud-based decision engine, Braid, which flows consult during execution to query their run-time environment and coordinate with other flows within their fleet. Braid accepts streams of measurements taken from the run-time environment or from within flow runs which can then be statistically aggregated and compared to other streams to determine a strategy to guide flow execution. For example, queue lengths in execution environments can be used to direct a flow to run computations in one environment or another, or experiment progress as measured by individual flows can be aggregated to determine the progress and subsequent direction of the flows within a fleet. We describe Braid, its interface, implementation and performance characteristics. We further show through examples and experience modifying an existing scientific flow how Braid is used to make adaptable flows.

cs.DC

Rapid detection of rare events from in situ X-ray diffraction data using machine learning

High-energy X-ray diffraction methods can non-destructively map the 3D microstructure and associated attributes of metallic polycrystalline engineering materials in their bulk form. These methods are often combined with external stimuli such as thermo-mechanical loading to take snapshots over time of the evolving microstructure and attributes. However, the extreme data volumes and the high costs of traditional data acquisition and reduction approaches pose a barrier to quickly extracting actionable insights and improving the temporal resolution of these snapshots. Here we present a fully automated technique capable of rapidly detecting the onset of plasticity in high-energy X-ray microscopy data. Our technique is computationally faster by at least 50 times than the traditional approaches and works for data sets that are up to 9 times sparser than a full data set. This new technique leverages self-supervised image representation learning and clustering to transform massive data into compact, semantic-rich representations of visually salient characteristics (e.g., peak shapes). These characteristics can be a rapid indicator of anomalous events such as changes in diffraction peak shapes. We anticipate that this technique will provide just-in-time actionable information to drive smarter experiments that effectively deploy multi-modal X-ray diffraction methods that span many decades of length scales.

cs.LG

What is missing in autonomous discovery: Open challenges for the community

Self-driving labs (SDLs) leverage combinations of artificial intelligence, automation, and advanced computing to accelerate scientific discovery. The promise of this field has given rise to a rich community of passionate scientists, engineers, and social scientists, as evidenced by the development of the Acceleration Consortium and recent Accelerate Conference. Despite its strengths, this rapidly developing field presents numerous opportunities for growth, challenges to overcome, and potential risks of which to remain aware. This community perspective builds on a discourse instantiated during the first Accelerate Conference, and looks to the future of self-driving labs with a tempered optimism. Incorporating input from academia, government, and industry, we briefly describe the current status of self-driving labs, then turn our attention to barriers, opportunities, and a vision for what is possible. Our field is delivering solutions in technology and infrastructure, artificial intelligence and knowledge generation, and education and workforce development. In the spirit of community, we intend for this work to foster discussion and drive best practices as our field grows.

cond-mat.mtrl-sci