arXiv subjects

Ian Foster

Publications and source records attributed to Ian Foster.

At least 55 records · Page 3Linked to original sources

arXiv2025

Topology-Aware Knowledge Propagation in Decentralized Learning

Decentralized learning enables collaborative training of models across naturally distributed data without centralized coordination or maintenance of a global model. Instead, devices are organized in arbitrary communication topologies, in which they can only communicate with neighboring devices. Each device maintains its own local model by training on its local data and integrating new knowledge via model aggregation with neighbors. Therefore, knowledge is propagated across the topology via successive aggregation rounds. We study, in particular, the propagation of out-of-distribution (OOD) knowledge. We find that popular decentralized learning algorithms struggle to propagate OOD knowledge effectively to all devices. Further, we find that both the location of OOD data within a topology, and the topology itself, significantly impact OOD knowledge propagation. We then propose topology-aware aggregation strategies to accelerate (OOD) knowledge propagation across devices. These strategies improve OOD data accuracy, compared to topology-unaware baselines, by 123% on average across models in a topology.

cs.LG↗

arXiv2025

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights

The volume of scientific literature is growing exponentially, leading to underutilized discoveries, duplicated efforts, and limited cross-disciplinary collaboration. Retrieval Augmented Generation (RAG) offers a way to assist scientists by improving the factuality of Large Language Models (LLMs) in processing this influx of information. However, scaling RAG to handle millions of articles introduces significant challenges, including the high computational costs associated with parsing documents and embedding scientific knowledge, as well as the algorithmic complexity of aligning these representations with the nuanced semantics of scientific content. To address these issues, we introduce HiPerRAG, a RAG workflow powered by high performance computing (HPC) to index and retrieve knowledge from more than 3.6 million scientific articles. At its core are Oreo, a high-throughput model for multimodal document parsing, and ColTrast, a query-aware encoder fine-tuning algorithm that enhances retrieval accuracy by using contrastive learning and late-interaction techniques. HiPerRAG delivers robust performance on existing scientific question answering benchmarks and two new benchmarks introduced in this work, achieving 90% accuracy on SciQ and 76% on PubMedQA-outperforming both domain-specific models like PubMedGPT and commercial LLMs such as GPT-4. Scaling to thousands of GPUs on the Polaris, Sunspot, and Frontier supercomputers, HiPerRAG delivers million document-scale RAG workflows for unifying scientific knowledge and fostering interdisciplinary innovation.

cs.IR↗

arXiv2025

AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine

Language models for scientific tasks are trained on text from scientific publications, most distributed as PDFs that require parsing. PDF parsing approaches range from inexpensive heuristics (for simple documents) to computationally intensive ML-driven systems (for complex or degraded ones). The choice of the "best" parser for a particular document depends on its computational cost and the accuracy of its output. To address these issues, we introduce an Adaptive Parallel PDF Parsing and Resource Scaling Engine (AdaParse), a data-driven strategy for assigning an appropriate parser to each document. We enlist scientists to select preferred parser outputs and incorporate this information through direct preference optimization (DPO) into AdaParse, thereby aligning its selection process with human judgment. AdaParse then incorporates hardware requirements and predicted accuracy of each parser to orchestrate computational resources efficiently for large-scale parsing campaigns. We demonstrate that AdaParse, when compared to state-of-the-art parsers, improves throughput by $17\times$ while still achieving comparable accuracy (0.2 percent better) on a benchmark set of 1000 scientific documents. AdaParse's combination of high accuracy and parallel scalability makes it feasible to parse large-scale scientific document corpora to support the development of high-quality, trillion-token-scale text datasets. The implementation is available at https://github.com/7shoe/AdaParse/

cs.IR↗

arXiv2025

Globus Service Enhancements for Exascale Applications and Facilities

Many extreme-scale applications require the movement of large quantities of data to, from, and among leadership computing facilities, as well as other scientific facilities and the home institutions of facility users. These applications, particularly when leadership computing facilities are involved, can touch upon edge cases (e.g., terabyte files) that had not been a focus of previous Globus optimization work, which had emphasized rather the movement of many smaller (megabyte to gigabyte) files. We report here on how automated client-driven chunking can be used to accelerate both the movement of large files and the integrity checking operations that have proven to be essential for large data transfers. We present detailed performance studies that provide insights into the benefits of these modifications in a range of file transfer scenarios.

cs.NI↗

arXiv2025

WRATH: Workload Resilience Across Task Hierarchies in Task-based Parallel Programming Frameworks

Failures in Task-based Parallel Programming (TBPP) can severely degrade performance and result in incomplete or incorrect outcomes. Existing failure-handling approaches, including reactive, proactive, and resilient methods such as retry and checkpointing mechanisms, often apply uniform retry mechanisms regardless of the root cause of failures, failing to account for the unique characteristics of TBPP frameworks such as heterogeneous resource availability and task-level failures. To address these limitations, we propose WRATH, a novel systematic approach that categorizes failures based on the unique layered structure of TBPP frameworks and defines specific responses to address failures at different layers. WRATH combines a distributed monitoring system and a resilient module to collaboratively address different types of failures in real time. The monitoring system captures execution and resource information, reports failures, and profiles tasks across different layers of TBPP frameworks. The resilient module then categorizes failures and responds with appropriate actions, such as hierarchically retrying failed tasks on suitable resources. Evaluations demonstrate that WRATH significantly improves TBPP robustness, tripling the task success rate and maintaining an application success rate of over 90% for resolvable failures. Additionally, WRATH can reduce the time to failure by 20%-50%, allowing tasks that are destined to fail to be identified and fail more quickly.

cs.DC↗

arXiv2025

Deep Model Merging: The Sister of Neural Network Interpretability -- A Survey

We survey the model merging literature through the lens of loss landscape geometry to connect observations from empirical studies on model merging and loss landscape analysis to phenomena that govern neural network training and the emergence of their inner representations. We distill repeated empirical observations from the literature in these fields into descriptions of four major characteristics of loss landscape geometry: mode convexity, determinism, directedness, and connectivity. We argue that insights into the structure of learned representations from model merging have applications to model interpretability and robustness, subsequently we propose promising new research directions at the intersection of these fields.

cs.LG↗

arXiv2025

Optimizing Fine-Grained Parallelism Through Dynamic Load Balancing on Multi-Socket Many-Core Systems

Achieving efficient task parallelism on many-core architectures is an important challenge. The widely used GNU OpenMP implementation of the popular OpenMP parallel programming model incurs high overhead for fine-grained, short-running tasks due to time spent on runtime synchronization. In this work, we introduce and analyze three key advances that collectively achieve significant performance gains. First, we introduce XQueue, a lock-less concurrent queue implementation to replace GNU's priority task queue and remove the global task lock. Second, we develop a scalable, efficient, and hybrid lock-free/lock-less distributed tree barrier to address the high hardware synchronization overhead from GNU's centralized barrier. Third, we develop two lock-less and NUMA-aware load balancing strategies. We evaluate our implementation using Barcelona OpenMP Task Suite (BOTS) benchmarks. We show that the use of XQueue and the distributed tree barrier can improve performance by up to 1522.8$\times$ compared to the original GNU OpenMP. We further show that lock-less load balancing can improve performance by up to 4$\times$ compared to GNU OpenMP using XQueue.

cs.DC↗

arXiv2025

Causal Discovery over High-Dimensional Structured Hypothesis Spaces with Causal Graph Partitioning

The aim in many sciences is to understand the mechanisms that underlie the observed distribution of variables, starting from a set of initial hypotheses. Causal discovery allows us to infer mechanisms as sets of cause and effect relationships in a generalized way -- without necessarily tailoring to a specific domain. Causal discovery algorithms search over a structured hypothesis space, defined by the set of directed acyclic graphs, to find the graph that best explains the data. For high-dimensional problems, however, this search becomes intractable and scalable algorithms for causal discovery are needed to bridge the gap. In this paper, we define a novel causal graph partition that allows for divide-and-conquer causal discovery with theoretical guarantees. We leverage the idea of a superstructure -- a set of learned or existing candidate hypotheses -- to partition the search space. We prove under certain assumptions that learning with a causal graph partition always yields the Markov Equivalence Class of the true causal graph. We show our algorithm achieves comparable accuracy and a faster time to solution for biologically-tuned synthetic networks and networks up to ${10^4}$ variables. This makes our method applicable to gene regulatory network inference and other domains with high-dimensional structured hypothesis spaces.

cs.LG↗

arXiv2025

EAIRA: Establishing a Methodology for Evaluating AI Models as Scientific Research Assistants

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

cs.AI↗

arXiv2025

Connecting Large Language Model Agent to High Performance Computing Resource

The Large Language Model agent workflow enables the LLM to invoke tool functions to increase the performance on specific scientific domain questions. To tackle large scale of scientific research, it requires access to computing resource and parallel computing setup. In this work, we implemented Parsl to the LangChain/LangGraph tool call setup, to bridge the gap between the LLM agent to the computing resource. Two tool call implementations were set up and tested on both local workstation and HPC environment on Polaris/ALCF. The first implementation with Parsl-enabled LangChain tool node queues the tool functions concurrently to the Parsl workers for parallel execution. The second configuration is implemented by converting the tool functions into Parsl ensemble functions, and is more suitable for large task on super computer environment. The LLM agent workflow was prompted to run molecular dynamics simulations, with different protein structure and simulation conditions. These results showed the LLM agent tools were managed and executed concurrently by Parsl on the available computing resource.

cs.DC↗

arXiv2025

DrugImproverGPT: A Large Language Model for Drug Optimization with Fine-Tuning via Structured Policy Optimization

Finetuning a Large Language Model (LLM) is crucial for generating results towards specific objectives. This research delves into the realm of drug optimization and introduce a novel reinforcement learning algorithm to finetune a drug optimization LLM-based generative model, enhancing the original drug across target objectives, while retains the beneficial chemical properties of the original drug. This work is comprised of two primary components: (1) DrugImprover: A framework tailored for improving robustness and efficiency in drug optimization. It includes a LLM designed for drug optimization and a novel Structured Policy Optimization (SPO) algorithm, which is theoretically grounded. This algorithm offers a unique perspective for fine-tuning the LLM-based generative model by aligning the improvement of the generated molecule with the input molecule under desired objectives. (2) A dataset of 1 million compounds, each with OEDOCK docking scores on 5 human proteins associated with cancer cells and 24 binding sites from SARS-CoV-2 virus. We conduct a comprehensive evaluation of SPO and demonstrate its effectiveness in improving the original drug across target properties. Our code and dataset will be publicly available at: https://github.com/xuefeng-cs/DrugImproverGPT.

cs.LG↗

arXiv2025

MOFA: Discovering Materials for Carbon Capture with a GenAI- and Simulation-Based Workflow

We present MOFA, an open-source generative AI (GenAI) plus simulation workflow for high-throughput generation of metal-organic frameworks (MOFs) on large-scale high-performance computing (HPC) systems. MOFA addresses key challenges in integrating GPU-accelerated computing for GPU-intensive GenAI tasks, including distributed training and inference, alongside CPU- and GPU-optimized tasks for screening and filtering AI-generated MOFs using molecular dynamics, density functional theory, and Monte Carlo simulations. These heterogeneous tasks are unified within an online learning framework that optimizes the utilization of available CPU and GPU resources across HPC systems. Performance metrics from a 450-node (14,400 AMD Zen 3 CPUs + 1800 NVIDIA A100 GPUs) supercomputer run demonstrate that MOFA achieves high-throughput generation of novel MOF structures, with CO$_2$ adsorption capacities ranking among the top 10 in the hypothetical MOF (hMOF) dataset. Furthermore, the production of high-quality MOFs exhibits a linear relationship with the number of nodes utilized. The modular architecture of MOFA will facilitate its integration into other scientific applications that dynamically combine GenAI with large-scale simulations.

cs.DC↗

arXiv2025

Computational Grids

In this introductory chapter, we lay the groundwork for the rest of the book by providing a more detailed picture of the expected purpose, shape, and architecture of future grid systems. We structure the chapter in terms of six questions that we believe are central to this discussion: Why do we need computational grids? What types of applications will grids be used for? Who will use grids? How will grids be used? What is involved in building a grid? And, what problems must be solved to make grids commonplace? We provide an overview of each of these issues here, referring to subsequent chapters for more detailed discussion.

cs.DC↗

arXiv2024

Object Proxy Patterns for Accelerating Distributed Applications

Workflow and serverless frameworks have empowered new approaches to distributed application design by abstracting compute resources. However, their typically limited or one-size-fits-all support for advanced data flow patterns leaves optimization to the application programmer -- optimization that becomes more difficult as data become larger. The transparent object proxy, which provides wide-area references that can resolve to data regardless of location, has been demonstrated as an effective low-level building block in such situations. Here we propose three high-level proxy-based programming patterns -- distributed futures, streaming, and ownership -- that make the power of the proxy pattern usable for more complex and dynamic distributed program structures. We motivate these patterns via careful review of application requirements and describe implementations of each pattern. We evaluate our implementations through a suite of benchmarks and by applying them in three substantial scientific applications, in which we demonstrate substantial improvements in runtime, throughput, and memory usage.

cs.DC↗

arXiv2024

Foundation Models for the Electric Power Grid

Foundation models (FMs) currently dominate news headlines. They employ advanced deep learning architectures to extract structural information autonomously from vast datasets through self-supervision. The resulting rich representations of complex systems and dynamics can be applied to many downstream applications. Therefore, FMs can find uses in electric power grids, challenged by the energy transition and climate change. In this paper, we call for the development of, and state why we believe in, the potential of FMs for electric grids. We highlight their strengths and weaknesses amidst the challenges of a changing grid. We argue that an FM learning from diverse grid data and topologies could unlock transformative capabilities, pioneering a new approach in leveraging AI to redefine how we manage complexity and uncertainty in the electric grid. Finally, we discuss a power grid FM concept, namely GridFM, based on graph neural networks and show how different downstream tasks benefit.

cs.LG↗

arXiv2024

Scaling transformer neural networks for skillful and reliable medium-range weather forecasting

Weather forecasting is a fundamental problem for anticipating and mitigating the impacts of climate change. Recently, data-driven approaches for weather forecasting based on deep learning have shown great promise, achieving accuracies that are competitive with operational systems. However, those methods often employ complex, customized architectures without sufficient ablation analysis, making it difficult to understand what truly contributes to their success. Here we introduce Stormer, a simple transformer model that achieves state-of-the-art performance on weather forecasting with minimal changes to the standard transformer backbone. We identify the key components of Stormer through careful empirical analyses, including weather-specific embedding, randomized dynamics forecast, and pressure-weighted loss. At the core of Stormer is a randomized forecasting objective that trains the model to forecast the weather dynamics over varying time intervals. During inference, this allows us to produce multiple forecasts for a target lead time and combine them to obtain better forecast accuracy. On WeatherBench 2, Stormer performs competitively at short to medium-range forecasts and outperforms current methods beyond 7 days, while requiring orders-of-magnitude less training data and compute. Additionally, we demonstrate Stormer's favorable scaling properties, showing consistent improvements in forecast accuracy with increases in model size and training tokens. Code and checkpoints are available at https://github.com/tung-nd/stormer.

physics.ao-ph↗

arXiv2024

Accelerating Python Applications with Dask and ProxyStore

Applications are increasingly written as dynamic workflows underpinned by an execution framework that manages asynchronous computations across distributed hardware. However, execution frameworks typically offer one-size-fits-all solutions for data flow management, which can restrict performance and scalability. ProxyStore, a middleware layer that optimizes data flow via an advanced pass-by-reference paradigm, has shown to be an effective mechanism for addressing these limitations. Here, we investigate integrating ProxyStore with Dask Distributed, one of the most popular libraries for distributed computing in Python, with the goal of supporting scalable and portable scientific workflows. Dask provides an easy-to-use and flexible framework, but is less optimized for scaling certain data-intensive workflows. We investigate these limitations and detail the technical contributions necessary to develop a robust solution for distributed applications and demonstrate improved performance on synthetic benchmarks and real applications.

cs.DC↗

arXiv2024

Octopus: Experiences with a Hybrid Event-Driven Architecture for Distributed Scientific Computing

Scientific research increasingly relies on distributed computational resources, storage systems, networks, and instruments, ranging from HPC and cloud systems to edge devices. Event-driven architecture (EDA) benefits applications targeting distributed research infrastructures by enabling the organization, communication, processing, reliability, and security of events generated from many sources. To support the development of scientific EDA, we introduce Octopus, a hybrid, cloud-to-edge event fabric designed to link many local event producers and consumers with cloud-hosted brokers. Octopus can be scaled to meet demand, permits the deployment of highly available Triggers for automatic event processing, and enforces fine-grained access control. We identify requirements in self-driving laboratories, scientific data automation, online task scheduling, epidemic modeling, and dynamic workflow management use cases, and present results demonstrating Octopus' ability to meet those requirements. Octopus supports producing and consuming events at a rate of over 4.2 M and 9.6 M events per second, respectively, from distributed clients.

cs.DC↗