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Geoffrey Fox

Publications and source records attributed to Geoffrey Fox.

At least 19 recordsLinked to original sources

OpRAG: A Resource-Deterministic Runtime for GPU-Backed Multi-Stage RAG Workflows

Agentic retrieval-augmented generation (RAG) systems combine preprocessing, embedding, retrieval, memory access, context construction, generation, and vector-index updates. Although LLM decoding is GPU-bound, the surrounding orchestration layer can still limit end-to-end performance through serialization overhead, fragmented scheduling, inefficient batching, and CPU--GPU pipeline stalls. Existing frameworks provide flexible control flow, while distributed runtimes provide scalable task parallelism, but neither exposes RAG stages as resource-aware operators with deterministic execution semantics. We present OpRAG, a resource-deterministic distributed runtime for GPU-backed multi-stage RAG workflows. OpRAG models embedding, retrieval, reasoning, memory, and upsert as first-class operators and lowers them into communication-aware execution graphs. It combines an Arrow zero-copy data plane, persistent workers, bounded queues, CPU tokenizer prefetching, batched GPU embedding, and overlapped retrieval/generation execution to reduce non-model overhead around LLM inference. We evaluate OpRAG using Llama3-8B and Mistral-7B with FlashAttention~2, BF16 execution, and 32K RAG chunks. In end-to-end GPU pipeline experiments, OpRAG improves over the nearest competitor by 16.16% for Llama3-8B and 15.66% for Mistral-7B, and over RayScalableRAG by 20.57% and 20.71%, respectively. Against LangChain, LangGraph, CrewAI, and AutoGen, OpRAG is 17.77% and 17.48% faster than the best framework baseline. In Higress-style query serving, OpRAG reduces hybrid retrieval latency by 59.20--59.62% and generation-scenario latency by 52.48--53.55%, while preserving 100% Recall@5. These results show that optimizing the distributed orchestration layer can substantially improve GPU-backed multi-stage RAG without modifying the LLM decoding kernel.

cs.DC

Lantern: Conflict-Aware Gradient Blending for Physics-Guided Diffusion Models in Calorimeter Simulation

Monte Carlo simulation of calorimeter showers is a principal bottleneck for the High-Luminosity LHC, and diffusion models have emerged as fast, high-fidelity surrogates. Their denoising objective is purely statistical, however: a model can minimize it while placing the physics wrong. Existing physics-informed generative methods cannot close this gap, because they assume a closed-form law, a governing PDE residual or a hard per-sample constraint, that a shower does not supply: no per-sample PDE governs a stochastic cascade, and energy conservation fixes only one scalar per shower. Standard metrics ignore the correlation structure across calorimeter layers and voxels, comparing showers only in a physics feature space. We address both gaps. We introduce the Correlation Frobenius Distance (CFD), a single normalized score for correlation fidelity at layer-wise and voxel-wise scales. We then encode the soft per-sample structure available in a shower as two physics-aware auxiliary losses: a variance-stabilized voxel residual loss grounded in counting statistics, and a graph Laplacian loss over the detector geometry. We combine both with denoising through GradBlend, which anchors the step magnitude to the denoising gradient while letting the auxiliary steer its direction, yielding Lantern, a physics-guided diffusion surrogate. On CaloChallenge Dataset 2, injecting the physics losses through task-symmetric rules such as PCGrad, GradNorm, IMTL-G, and ConFIG inflates FPD by 2-100x relative to denoising alone, whereas GradBlend admits the same signal without regression and, with the Laplacian loss, Lantern improves both FPD and CFD. Our ablation on the auxiliary loss scheduler shows that the voxel residual loss, whose gradient conflicts with denoising, requires a terminal denoising-only phase to preserve shower fidelity, whereas the non-conflicting Laplacian loss is insensitive to the schedule.

cs.LG

Agentic Service-Oriented Computing: A Manifesto for the Next Frontier of Service-Oriented Computing

The rapid emergence of LLM-powered autonomous and semi-autonomous agents is reshaping software systems from static, request-response components into goal-directed, adaptive, and tool-using computational actors. As these agents move from isolated cognitive prototypes into complex distributed workflows, they confront challenges that the Service-Oriented Computing community has studied for more than two decades: composition, interoperability, quality of service, lifecycle management, governance, security, and trust. Yet much of today's agentic AI ecosystem is developing these foundations ad hoc, without the engineering rigour required for dependable enterprise and societal deployment. This paper introduces Agentic Service-Oriented Computing (ASOC) as a new research and practice area concerned with engineering agents as services, orchestrating services through autonomous and semi-autonomous agents, and governing ecosystems of agents and services under constraints of trust, cybersecurity, compliance, performance, and accountability. We articulate six foundational principles of ASOC (harness-ability, composability, lifecycle engineering, trustworthiness by design, goal-driven orchestration, and observability/accountability) and organise a five-dimensional research agenda spanning: (i) agentic services foundations and lifecycle engineering; (ii) composition, orchestration, and interoperability; (iii) governance, observability, and accountability; (iv) security, trust, and risk management; and (v) evaluation, certification, and Agentic QoS. We argue that the Services Computing community is especially well positioned to provide the conceptual and engineering spine for this emerging field, transforming agentic AI from fragmented demonstrations into dependable, service-based systems worthy of human and organisational trust.

cs.AI

[AAFLOW+] Stateful Operator Abstraction with Zero-Copy Distributed KV Cache Orchestration for Multi-Agent Workflows

Multi-agent LLM systems increasingly integrate retrieval, planning, and reasoning, but remain fundamentally text-centric, requiring agents to repeatedly recompute shared context through expensive prefill. Although single-request inference is known to be accelerated by KV-cache management, it is usually restricted to local serving scopes. We introduce AAFLOW+, a stateful extension of agentic workflow operators that makes KV cache a first-class distributed systems object. AAFLOW+ builds processes into communication-aware graphs that concurrently optimize data, prompts, and reusable model state. It also provides operators for KV materialization, transfer, fork, composition, and eviction. Its runtime enables zero-copy, transfer-aware execution, allowing agents to reuse long context without recomputation. AAFLOW+ reduces TTFT by up to 50.2x, achieves up to 7.63x reduced multi-agent compute cost at 16-agent scale, reduces KV memory by 1.72-6.10x, and increases throughput by more than 7.74x, based on an analytical cost model parameterized by empirical hardware microbenchmarks. The results demonstrate that KV transmission outperforms recomputation on networks with moderate to high bandwidth, making sure KV-state sharing greatly increases efficiency in multi-agent LLM systems by replacing text passing.

cs.DC

Experiments in Agentic AI for Science

This paper details two novel frameworks for developing autonomous, agentic AI in scientific workflows. Both systems leverage a hybrid Local Body, Remote Brain architecture via Google Colab, utilizing Python-based local orchestrators to invoke large language model (LLM) cloud backends. The first agent, DeepTS/DeepCollector, automates the large-scale curation, extraction, and deduplication of time-series datasets. The second, DeepScribe, is an autonomous presentation analyzer that converts visually dense, mathematically complex physics lectures into structured scientific reports. Through practical systems engineering-such as granular attribute extraction (Cellular RAG), remote data inspection, and distributed concurrency controls-we demonstrate how agentic AI can overcome the context and reasoning limitations of current state-of-the-art systems to rigorously support scientific workflows. Finally, we outline a generalization of DeepTS to support deep knowledge graphs and discuss the application of this conceptual approach to high-energy physics (DeepQCD).

cs.AI

Diagnosing Training Inference Mismatch in LLM Reinforcement Learning

Modern LLM RL systems separate rollout generation from policy optimization. These two stages are expected to produce token probabilities that match exactly. However, implementation differences can make them assign different values to the same sequence under the same model weights, inducing Training-Inference Mismatch (TIM). TIM is difficult to inspect because it is entangled with off-policy drift and common stabilization mechanisms. In this work, we isolate TIM in a zero-mismatch diagnostic setting (VeXact), and show that small token-level numerical disagreements can independently cause training collapse. We further show that TIM changes the effective optimization problem, and identify a set of remedies that could mitigate TIM. Our results suggest that TIM is not benign numerical noise, but a systems-level perturbation that should be treated as a first-order factor in analyzing LLM RL stability.

cs.LG

AAFLOW: Scalable Patterns for Agentic AI Workflows

Agentic workflows in large language model systems integrate retrieval, reasoning, and memory, but existing frameworks suffer from scalability and reproducibility limitations due to fragmented data orchestration, serialization overhead, and non-deterministic execution. Although these frameworks increase flexibility, they don't have a formal execution model that adheres to the principles of high-performance computing. We introduce AAFLOW, a unified distributed runtime that creates communication-efficient execution plans by modeling agentic workflows as an operator abstraction. Using Apache Arrow and Cylon, AAFLOW creates a zero-copy data plane that allows direct interoperability between preprocessing, embedding, and vector retrieval without the need for serialization overhead. To lower coordination costs, it uses resource-deterministic scheduling and asynchronous batching. While retaining comparable LLM generation throughput, experimental results demonstrate up to 4.64 times pipeline speedup and 2.8 times gains in embedding and upsert phases. Rather than LLM inference acceleration, these advantages result from enhanced data flow, batching, and communication efficiency.

cs.DC

IDOBE: Infectious Disease Outbreak forecasting Benchmark Ecosystem

Epidemic forecasting has become an integral part of real-time infectious disease outbreak response. While collaborative ensembles composed of statistical and machine learning models have become the norm for real-time forecasting, standardized benchmark datasets for evaluating such methods are lacking. Further, there is limited understanding on performance of these methods for novel outbreaks with limited historical data. In this paper, we propose IDOBE, a curated collection of epidemiological time series focused on outbreak forecasting. IDOBE compiles from multiple data repositories spanning over a century of surveillance and across U.S. states and global locations. We perform derivative-based segmentation to generate over 10,000 outbreaks covering multiple outcomes such as cases and hospitalizations for 13 diseases. We consider a variety of information-theoretic and distributional measures to quantify the epidemiological diversity of the dataset. Finally, we perform multi-horizon short-term forecasting (1- to 4-week-ahead) through the progression of the outbreak using 11 baseline models and report on their performance. In addition to standard metrics such as NMSE and MAPE for point forecasts, we include probabilistic scoring rules such as Normalized Weighted Interval Score (NWIS) to quantify the performance. We find that MLP-based methods have the most robust performance, with statistical methods having a slight edge during the pre-peak phase. IDOBE dataset along with baselines are released publicly on https://github.com/NSSAC/IDOBE to enable standardized, reproducible benchmarking of outbreak forecasting methods.

cs.LG

Exceedance Probabilities for Large Earthquakes From DIY Local Earthquake Ensemble Nowcasting and Forecasting

This paper focuses on the problem of anticipating the local occurrence of future large earthquakes. "Local" is defined as the probability of a large earthquake occurring with a defined circle of arbitrary radius surrounding a point of interest. The main (and for that matter, the only) assumption for all these works is that the Gutenberg-Richter (GR) magnitude-frequency relation holds. Here we describe a method for computing calendar time forecasts in a local area for large earthquakes of a target magnitude MT using a count small earthquakes MS < MT in the area. Using the idea that the GR relation is valid throughout the surrounding region, we define an ensemble of earthquakes in larger surrounding regions to be used in computing the forecast. What follows is simple data mining. The method has significant skill, as defined by the Receiver Operating Characteristic (ROC) test, which improves as time since the last major earthquake increases. The probability is conditioned on the number of small earthquakes n(t) that have occurred since the last large earthquake. The probability is computed directly as the Positive Predictive Value (PPV) associated with the ROC curve. The method is validated by comparison to the UCERF3 forecasts for the UCERF3-defined geographic boxes centered on Los Angeles and San Francisco. The method is then applied to a 125-KM radius circular area around Los Angeles, California, following the January 17, 1994 magnitude M6.7 Northridge earthquake, and short term forecasts (1 year and 5 year ) are computed.

physics.geo-ph

ScatterPrism: convergence for generative simulation and inverse problems in particle and nuclear physics

High-fidelity simulations and complex inverse problems, such as detector modeling and unfolding, are computationally intensive bottlenecks across subatomic physics, yet essential for accurate physical interpretation. While Conditional Flow Matching (CFM) offers a robust acceleration approach, we demonstrate its standard training loss is fundamentally misleading. Specifically, utilizing a Jefferson Lab Nuclear Physics (NP) kinematic dataset ($\gamma p \to \rho^0 p \to \pi^+\pi^- p$), we expose that CFM loss plateaus prematurely, obscuring ongoing physical refinement. To verify this disconnect is a dataset-agnostic pathology, we introduce ScatterPrism, an efficient generative surrogate evaluated against both the NP data and synthetic stress tests modeling challenging 1D distribution topologies. Coupling these benchmarks, we establish that physics-informed metrics continue improving long after standard loss converges. Consequently, we propose a multi-metric diagnostic protocol to ensure true kinematic fidelity without data memorization. Driven by NP challenges relevant to the forthcoming Electron-Ion Collider (EIC), this unified machinery has strong potential to extend to High-Energy Physics (HEP) applications, such as jet modeling. Furthermore, the framework holds promise for broader domains requiring rigorous generative reliability, including medical imaging, astrophysics, and quantitative finance.

cs.LG

Combining Serverless and High-Performance Computing Paradigms to support ML Data-Intensive Applications

Data is found everywhere, from health and human infrastructure to the surge of sensors and the proliferation of internet-connected devices. To meet this challenge, the data engineering field has expanded significantly in recent years in both research and industry. Traditionally, data engineering, Machine Learning, and AI workloads have been run on large clusters within data center environments, requiring substantial investment in hardware and maintenance. With the rise of the public cloud, it is now possible to run large applications across nodes without owning or maintaining hardware. Serverless functions such as AWS Lambda provide horizontal scaling and precise billing without the hassle of managing traditional cloud infrastructure. However, when processing large datasets, users often rely on external storage options that are significantly slower than direct communication typical of HPC clusters. We introduce Cylon, a high-performance distributed data frame solution that has shown promising results for data processing using Python. We describe how we took inspiration from the FMI library and designed a serverless communicator to tackle communication and performance issues associated with serverless functions. With our design, we demonstrate that the scaling efficiency of AWS Lambda achieves within 6.5% of serverful AWS (EC2) at 64 nodes, based on implementing direct communication via NAT Traversal TCP Hole Punching.

cs.DC

Leveraging Exogenous Signals for Hydrology Time Series Forecasting

Recent advances in time series research facilitate the development of foundation models. While many state-of-the-art time series foundation models have been introduced, few studies examine their effectiveness in specific downstream applications in physical science. This work investigates the role of integrating domain knowledge into time series models for hydrological rainfall-runoff modeling. Using the CAMELS-US dataset, which includes rainfall and runoff data from 671 locations with six time series streams and 30 static features, we compare baseline and foundation models. Results demonstrate that models incorporating comprehensive known exogenous inputs outperform more limited approaches, including foundation models. Notably, incorporating natural annual periodic time series contribute the most significant improvements.

cs.LG

An MLCommons Scientific Benchmarks Ontology

Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical scientific use-cases more fragmented and less clear in pathways to impact. This paper introduces an ontology for scientific benchmarking developed through a unified, community-driven effort that extends the MLCommons ecosystem to cover physics, chemistry, materials science, biology, climate science, and more. Building on prior initiatives such as XAI-BENCH, FastML Science Benchmarks, PDEBench, and the SciMLBench framework, our effort consolidates a large set of disparate benchmarks and frameworks into a single taxonomy of scientific, application, and system-level benchmarks. New benchmarks can be added through an open submission workflow coordinated by the MLCommons Science Working Group and evaluated against a six-category rating rubric that promotes and identifies high-quality benchmarks, enabling stakeholders to select benchmarks that meet their specific needs. The architecture is extensible, supporting future scientific and AI/ML motifs, and we discuss methods for identifying emerging computing patterns for unique scientific workloads. The MLCommons Science Benchmarks Ontology provides a standardized, scalable foundation for reproducible, cross-domain benchmarking in scientific machine learning. A companion webpage for this work has also been developed as the effort evolves: https://mlcommons-science.github.io/benchmark/

cs.LG

From Local Earthquake Nowcasting to Natural Time Forecasting: A Simple Do-It-Yourself (DIY) Method

Previous papers have outlined nowcasting methods to track the current state of earthquake hazard using only observed seismic catalogs. The basis for one of these methods, the "counting method", is the Gutenberg-Richter (GR) magnitude-frequency relation. The GR relation states that for every large earthquake of magnitude greater than MT , there are on average NGR small earthquakes of magnitude MS. In this paper we use this basic relation, combined with the Receiver Operating Characteristic (ROC) formalism from machine learning, to compute the probability of a large earthquake. The probability is conditioned on the number of small earthquakes n(t) that have occurred since the last large earthquake. We work in natural time, which is defined as the count of small earthquakes between large earthquakes. We do not need to assume a probability model, which is a major advantage. Instead, the probability is computed as the Positive Predictive Value (PPV) associated with the ROC curve. We find that the PPV following the last large earthquake initially decreases as more small earthquakes occur, indicating the property of temporal clustering of large earthquakes as is observed. As the number of small earthquakes continues to accumulate, the PPV subsequently begins to increase. Eventually a point is reached beyond which the rate of increase becomes much larger and more dramatic. Here we describe and illustrate the method by applying it to a local region around Los Angeles, California, following the January 17, 1994 magnitude M6.7 Northridge earthquake.

physics.geo-ph

IrrMap: A Large-Scale Comprehensive Dataset for Irrigation Method Mapping

We introduce IrrMap, the first large-scale dataset (1.1 million patches) for irrigation method mapping across regions. IrrMap consists of multi-resolution satellite imagery from LandSat and Sentinel, along with key auxiliary data such as crop type, land use, and vegetation indices. The dataset spans 1,687,899 farms and 14,117,330 acres across multiple western U.S. states from 2013 to 2023, providing a rich and diverse foundation for irrigation analysis and ensuring geospatial alignment and quality control. The dataset is ML-ready, with standardized 224x224 GeoTIFF patches, the multiple input modalities, carefully chosen train-test-split data, and accompanying dataloaders for seamless deep learning model training andbenchmarking in irrigation mapping. The dataset is also accompanied by a complete pipeline for dataset generation, enabling researchers to extend IrrMap to new regions for irrigation data collection or adapt it with minimal effort for other similar applications in agricultural and geospatial analysis. We also analyze the irrigation method distribution across crop groups, spatial irrigation patterns (using Shannon diversity indices), and irrigated area variations for both LandSat and Sentinel, providing insights into regional and resolution-based differences. To promote further exploration, we openly release IrrMap, along with the derived datasets, benchmark models, and pipeline code, through a GitHub repository: https://github.com/Nibir088/IrrMap and Data repository: https://huggingface.co/Nibir/IrrMap, providing comprehensive documentation and implementation details.

cs.CV

Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 590 times compared to CPM code execution. Over multiple recursive evaluations, our model effectively captures the emergent behaviors demonstrated by the original Cellular-Potts model of such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM of biological processes at greater spatial and temporal scales.

cs.LG

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

q-bio.QM

Building Machine Learning Challenges for Anomaly Detection in Science

Scientific discoveries are often made by finding a pattern or object that was not predicted by the known rules of science. Oftentimes, these anomalous events or objects that do not conform to the norms are an indication that the rules of science governing the data are incomplete, and something new needs to be present to explain these unexpected outliers. The challenge of finding anomalies can be confounding since it requires codifying a complete knowledge of the known scientific behaviors and then projecting these known behaviors on the data to look for deviations. When utilizing machine learning, this presents a particular challenge since we require that the model not only understands scientific data perfectly but also recognizes when the data is inconsistent and out of the scope of its trained behavior. In this paper, we present three datasets aimed at developing machine learning-based anomaly detection for disparate scientific domains covering astrophysics, genomics, and polar science. We present the different datasets along with a scheme to make machine learning challenges around the three datasets findable, accessible, interoperable, and reusable (FAIR). Furthermore, we present an approach that generalizes to future machine learning challenges, enabling the possibility of large, more compute-intensive challenges that can ultimately lead to scientific discovery.

cs.LG