arXiv subjects

Renan Souza

Publications and source records attributed to Renan Souza.

At least 19 recordsLinked to original sources

arXiv2026

Exploring the Genesis Platform Capabilities to Accelerate Scientific Discovery in OPAL

Autonomous, cross-facility science requires capabilities that no individual project should have to build for itself: managed execution for long-lived services, versioned distribution of models to remote compute systems, governed access to large language models, a shared substrate for experimental data, and end-to-end provenance. The U.S. Department of Energy Genesis Mission platform, delivered through the American Science Cloud, provides these as reusable services. This paper reports how the Genesis platform enables cross-facility experiments and accelerates scientific discovery. We explore the plant phenotyping workflow of the Orchestrated Platform for Autonomous Laboratories as the exemplar: it couples Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory with the Frontier supercomputer. In a 40-day nickel-treatment campaign, the resulting workflow replaced roughly twelve hours of manual analysis with interactive queries returning in seconds to minutes.

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arXiv2026

Workflow Cards: Structured Summaries of Workflow Executions Using Provenance Data

Model Cards and Data Cards have demonstrated the value of structured, human-readable documentation for machine learning artifacts, capturing their context, parameters, limitations, and intended use. However, these practices remain focused on static artifacts (the datasets and trained models themselves) while overlooking the workflow executions that produce, transform, and evaluate them. Such executions hold critical details about data preparation, parameter choice, runtime behavior, resource use, and intermediate transformations, precisely where bias, performance variation, and reproducibility gaps tend to originate. To close this gap, we introduce Workflow Cards: structured summaries that condense the machine-readable provenance data of a workflow execution into a form both humans and large language models (LLMs) can read and analyze. This paper has two main parts. First, it defines a Workflow Card template informed by a representative set of provenance questions that surface from the execution-level data missing from Model and Data Cards. Second, it evaluates how effectively LLMs use Workflow Cards to understand workflow executions compared with querying provenance databases through a schema-based interface. Results show that Workflow Cards provide execution-level information absent from existing card types, such as Model Cards and Data Cards, thereby filling an important documentation gap; and that Workflow Cards nearly double answer quality compared with schema-based querying, consistently across LLM-as-a-Judge and human assessments.

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arXiv2026

Automated Data Readiness for Scientific AI

Leadership computing facilities steward large-scale scientific datasets that routinely require substantial transformation before serving as AI training data. However, no existing framework fully unifies automated transformation, readiness assessment, provenance tracking, and agent-native deployment. We present REDI, an open-source framework that addresses this gap through a unified five-stage pipeline (ingest, preprocess, transform, structure, and output) with per-stage instrumentation for reproducibility and deployment as an agent-callable skill; companion tool SetGo automates FAIR compliance and catalog publication. Evaluated across climate, proteomics, materials science, and nuclear fusion, REDI transforms all datasets from raw to AI-ready, with outputs validated against domain-expert references, and preliminary results show near-ideal parallel scaling to 100 nodes on Frontier for the climate case. Provenance-instrumented profiling reveals file I/O as the dominant pipeline cost, with format selection a first-order optimization lever. These results establish REDI as a cross-domain platform providing automated data readiness for scientific AI, transforming data preparation bottlenecks into reproducible, reusable community assets.

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arXiv2026

An Agentic AI Framework to Accelerate Scientific Discovery in Plant Phenotyping

High-throughput plant phenotyping now generates image derived datasets far faster than scientists can analyze them. At Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory (APPL), automated stations image hundreds of plants daily across multiple remote sensing modalities; yet, trait extraction and interpretation remain manual, expert-bound, and strictly post-hoc, making analysis, not acquisition, the binding constraint on discovery. We present an end-to-end agentic AI framework that turns the facility from a data factory into an interactive autonomous, discovery platform, where scientists partner with AI agents to accelerate time to insight. A conversational Co-Scientist Agent translates a scientist's natural-language question into a structured analysis plan, and a headless Compute Agent dispatches Vision Transformer segmentation and trait extraction on the Frontier exascale supercomputer. The two agents run in separate security and resource domains and communicate over a secure, token-authenticated streaming channel, a design that accounts for the federation, data-movement, and provenance realities cloud-native agentic frameworks ignore, ensuring end-to-end provenance is captured for every interaction. The framework turns a days- to weeks-long analysis process into an interactive loop where agents reason over results, recommend next analyses, and respond to follow-up questions in seconds.

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arXiv2025

LLM Agents for Interactive Workflow Provenance: Reference Architecture and Evaluation Methodology

Modern scientific discovery increasingly relies on workflows that process data across the Edge, Cloud, and High Performance Computing (HPC) continuum. Comprehensive and in-depth analyses of these data are critical for hypothesis validation, anomaly detection, reproducibility, and impactful findings. Although workflow provenance techniques support such analyses, at large scale, the provenance data become complex and difficult to analyze. Existing systems depend on custom scripts, structured queries, or static dashboards, limiting data interaction. In this work, we introduce an evaluation methodology, reference architecture, and open-source implementation that leverages interactive Large Language Model (LLM) agents for runtime data analysis. Our approach uses a lightweight, metadata-driven design that translates natural language into structured provenance queries. Evaluations across LLaMA, GPT, Gemini, and Claude, covering diverse query classes and a real-world chemistry workflow, show that modular design, prompt tuning, and Retrieval-Augmented Generation (RAG) enable accurate and insightful LLM agent responses beyond recorded provenance.

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arXiv2025

The (R)evolution of Scientific Workflows in the Agentic AI Era: Towards Autonomous Science

Modern scientific discovery increasingly requires coordinating distributed facilities and heterogeneous resources, forcing researchers to act as manual workflow coordinators rather than scientists. Advances in AI leading to AI agents show exciting new opportunities that can accelerate scientific discovery by providing intelligence as a component in the ecosystem. However, it is unclear how this new capability would materialize and integrate in the real world. To address this, we propose a conceptual framework where workflows evolve along two dimensions which are intelligence (from static to intelligent) and composition (from single to swarm) to chart an evolutionary path from current workflow management systems to fully autonomous, distributed scientific laboratories. With these trajectories in mind, we present an architectural blueprint that can help the community take the next steps towards harnessing the opportunities in autonomous science with the potential for 100x discovery acceleration and transformational scientific workflows.

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arXiv2025

PROV-AGENT: Unified Provenance for Tracking AI Agent Interactions in Agentic Workflows

Large Language Models (LLMs) and other foundation models are increasingly used as the core of AI agents. In agentic workflows, these agents plan tasks, interact with humans and peers, and influence scientific outcomes across federated and heterogeneous environments. However, agents can hallucinate or reason incorrectly, propagating errors when one agent's output becomes another's input. Thus, assuring that agents' actions are transparent, traceable, reproducible, and reliable is critical to assess hallucination risks and mitigate their workflow impacts. While provenance techniques have long supported these principles, existing methods fail to capture and relate agent-centric metadata such as prompts, responses, and decisions with the broader workflow context and downstream outcomes. In this paper, we introduce PROV-AGENT, a provenance model that extends W3C PROV and leverages the Model Context Protocol (MCP) and data observability to integrate agent interactions into end-to-end workflow provenance. Our contributions include: (1) a provenance model tailored for agentic workflows, (2) a near real-time, open-source system for capturing agentic provenance, and (3) a cross-facility evaluation spanning edge, cloud, and HPC environments, demonstrating support for critical provenance queries and agent reliability analysis.

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arXiv2024

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.

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arXiv2023

Towards Lightweight Data Integration using Multi-workflow Provenance and Data Observability

Modern large-scale scientific discovery requires multidisciplinary collaboration across diverse computing facilities, including High Performance Computing (HPC) machines and the Edge-to-Cloud continuum. Integrated data analysis plays a crucial role in scientific discovery, especially in the current AI era, by enabling Responsible AI development, FAIR, Reproducibility, and User Steering. However, the heterogeneous nature of science poses challenges such as dealing with multiple supporting tools, cross-facility environments, and efficient HPC execution. Building on data observability, adapter system design, and provenance, we propose MIDA: an approach for lightweight runtime Multi-workflow Integrated Data Analysis. MIDA defines data observability strategies and adaptability methods for various parallel systems and machine learning tools. With observability, it intercepts the dataflows in the background without requiring instrumentation while integrating domain, provenance, and telemetry data at runtime into a unified database ready for user steering queries. We conduct experiments showing end-to-end multi-workflow analysis integrating data from Dask and MLFlow in a real distributed deep learning use case for materials science that runs on multiple environments with up to 276 GPUs in parallel. We show near-zero overhead running up to 100,000 tasks on 1,680 CPU cores on the Summit supercomputer.

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arXiv2023

ProvLight: Efficient Workflow Provenance Capture on the Edge-to-Cloud Continuum

Modern scientific workflows require hybrid infrastructures combining numerous decentralized resources on the IoT/Edge interconnected to Cloud/HPC systems (aka the Computing Continuum) to enable their optimized execution. Understanding and optimizing the performance of such complex Edge-to-Cloud workflows is challenging. Capturing the provenance of key performance indicators, with their related data and processes, may assist in understanding and optimizing workflow executions. However, the capture overhead can be prohibitive, particularly in resource-constrained devices, such as the ones on the IoT/Edge.To address this challenge, based on a performance analysis of existing systems, we propose ProvLight, a tool to enable efficient provenance capture on the IoT/Edge. We leverage simplified data models, data compression and grouping, and lightweight transmission protocols to reduce overheads. We further integrate ProvLight into the E2Clab framework to enable workflow provenance capture across the Edge-to-Cloud Continuum. This integration makes E2Clab a promising platform for the performance optimization of applications through reproducible experiments.We validate ProvLight at a large scale with synthetic workloads on 64 real-life IoT/Edge devices in the FIT IoT LAB testbed. Evaluations show that ProvLight outperforms state-of-the-art systems like ProvLake and DfAnalyzer in resource-constrained devices. ProvLight is 26 -- 37x faster to capture and transmit provenance data; uses 5 -- 7x less CPU; 2x less memory; transmits 2x less data; and consumes 2 -- 2.5x less energy. ProvLight and E2Clab are available as open-source tools.

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arXiv2023

Workflows Community Summit 2022: A Roadmap Revolution

Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from execution of a cloud-based data preprocessing pipeline to multi-facility instrument-to-edge-to-HPC computational workflows. Given the changing landscape of scientific computing and the evolving needs of emerging scientific applications, it is paramount that the development of novel scientific workflows and system functionalities seek to increase the efficiency, resilience, and pervasiveness of existing systems and applications. Specifically, the proliferation of machine learning/artificial intelligence (ML/AI) workflows, need for processing large scale datasets produced by instruments at the edge, intensification of near real-time data processing, support for long-term experiment campaigns, and emergence of quantum computing as an adjunct to HPC, have significantly changed the functional and operational requirements of workflow systems. Workflow systems now need to, for example, support data streams from the edge-to-cloud-to-HPC enable the management of many small-sized files, allow data reduction while ensuring high accuracy, orchestrate distributed services (workflows, instruments, data movement, provenance, publication, etc.) across computing and user facilities, among others. Further, to accelerate science, it is also necessary that these systems implement specifications/standards and APIs for seamless (horizontal and vertical) integration between systems and applications, as well as enabling the publication of workflows and their associated products according to the FAIR principles. This document reports on discussions and findings from the 2022 international edition of the Workflows Community Summit that took place on November 29 and 30, 2022.

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arXiv2021

Workflow Provenance in the Lifecycle of Scientific Machine Learning

Machine Learning (ML) has already fundamentally changed several businesses. More recently, it has also been profoundly impacting the computational science and engineering domains, like geoscience, climate science, and health science. In these domains, users need to perform comprehensive data analyses combining scientific data and ML models to provide for critical requirements, such as reproducibility, model explainability, and experiment data understanding. However, scientific ML is multidisciplinary, heterogeneous, and affected by the physical constraints of the domain, making such analyses even more challenging. In this work, we leverage workflow provenance techniques to build a holistic view to support the lifecycle of scientific ML. We contribute with (i) characterization of the lifecycle and taxonomy for data analyses; (ii) design principles to build this view, with a W3C PROV compliant data representation and a reference system architecture; and (iii) lessons learned after an evaluation in an Oil & Gas case using an HPC cluster with 393 nodes and 946 GPUs. The experiments show that the principles enable queries that integrate domain semantics with ML models while keeping low overhead (<1%), high scalability, and an order of magnitude of query acceleration under certain workloads against without our representation.

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arXiv2021

Context-aware Execution Migration Tool for Data Science Jupyter Notebooks on Hybrid Clouds

Interactive computing notebooks, such as Jupyter notebooks, have become a popular tool for developing and improving data-driven models. Such notebooks tend to be executed either in the user's own machine or in a cloud environment, having drawbacks and benefits in both approaches. This paper presents a solution developed as a Jupyter extension that automatically selects which cells, as well as in which scenarios, such cells should be migrated to a more suitable platform for execution. We describe how we reduce the execution state of the notebook to decrease migration time and we explore the knowledge of user interactivity patterns with the notebook to determine which blocks of cells should be migrated. Using notebooks from Earth science (remote sensing), image recognition, and hand written digit identification (machine learning), our experiments show notebook state reductions of up to 55x and migration decisions leading to performance gains of up to 3.25x when the user interactivity with the notebook is taken into consideration.

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arXiv2021

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale HPC platforms. Workflows will play a crucial role in the data-oriented and post-Moore's computing landscape as they democratize the application of cutting-edge research techniques, computationally intensive methods, and use of new computing platforms. As workflows continue to be adopted by scientific projects and user communities, they are becoming more complex. Workflows are increasingly composed of tasks that perform computations such as short machine learning inference, multi-node simulations, long-running machine learning model training, amongst others, and thus increasingly rely on heterogeneous architectures that include CPUs but also GPUs and accelerators. The workflow management system (WMS) technology landscape is currently segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. Another fundamental problem is that there are conflicting theoretical bases and abstractions for a WMS. Systems that use the same underlying abstractions can likely be translated between, which is not the case for systems that use different abstractions. More information: https://workflowsri.org/summits/technical

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arXiv2021

Distributed In-memory Data Management for Workflow Executions

Complex scientific experiments from various domains are typically modeled as workflows and executed on large-scale machines using a Parallel Workflow Management System (WMS). Since such executions usually last for hours or days, some WMSs provide user steering support, i.e., they allow users to run data analyses and, depending on the results, adapt the workflows at runtime. A challenge in the parallel execution control design is to manage workflow data for efficient executions while enabling user steering support. Data access for high scalability is typically transaction-oriented, while for data analysis, it is online analytical-oriented so that managing such hybrid workloads makes the challenge even harder. In this work, we present SchalaDB, an architecture with a set of design principles and techniques based on distributed in-memory data management for efficient workflow execution control and user steering. We propose a distributed data design for scalable workflow task scheduling and high availability driven by a parallel and distributed in-memory DBMS. To evaluate our proposal, we develop d-Chiron, a WMS designed according to SchalaDB's principles. We carry out an extensive experimental evaluation on an HPC cluster with up to 960 computing cores. Among other analyses, we show that even when running data analyses for user steering, SchalaDB's overhead is negligible for workloads composed of hundreds of concurrent tasks on shared data. Our results encourage workflow engine developers to follow a parallel and distributed data-oriented approach not only for scheduling and monitoring but also for user steering.

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arXiv2020

Managing Data Lineage of O&G Machine Learning Models: The Sweet Spot for Shale Use Case

Machine Learning (ML) has increased its role, becoming essential in several industries. However, questions around training data lineage, such as "where has the dataset used to train this model come from?"; the introduction of several new data protection legislation; and, the need for data governance requirements, have hindered the adoption of ML models in the real world. In this paper, we discuss how data lineage can be leveraged to benefit the ML lifecycle to build ML models to discover sweet-spots for shale oil and gas production, a major application in the Oil and Gas O&G Industry.

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arXiv2019

Provenance Data in the Machine Learning Lifecycle in Computational Science and Engineering

Machine Learning (ML) has become essential in several industries. In Computational Science and Engineering (CSE), the complexity of the ML lifecycle comes from the large variety of data, scientists' expertise, tools, and workflows. If data are not tracked properly during the lifecycle, it becomes unfeasible to recreate a ML model from scratch or to explain to stakeholders how it was created. The main limitation of provenance tracking solutions is that they cannot cope with provenance capture and integration of domain and ML data processed in the multiple workflows in the lifecycle while keeping the provenance capture overhead low. To handle this problem, in this paper we contribute with a detailed characterization of provenance data in the ML lifecycle in CSE; a new provenance data representation, called PROV-ML, built on top of W3C PROV and ML Schema; and extensions to a system that tracks provenance from multiple workflows to address the characteristics of ML and CSE, and to allow for provenance queries with a standard vocabulary. We show a practical use in a real case in the Oil and Gas industry, along with its evaluation using 48 GPUs in parallel.

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arXiv2019

Keeping Track of User Steering Actions in Dynamic Workflows

In long-lasting scientific workflow executions in HPC machines, computational scientists (the users in this work) often need to fine-tune several workflow parameters. These tunings are done through user steering actions that may significantly improve performance (e.g., reduce execution time) or improve the overall results. However, in executions that last for weeks, users can lose track of what has been adapted if the tunings are not properly registered. In this work, we build on provenance data management to address the problem of tracking online parameter fine-tuning in dynamic workflows steered by users. We propose a lightweight solution to capture and manage provenance of the steering actions online with negligible overhead. The resulting provenance database relates tuning data with data for domain, dataflow provenance, execution, and performance, and is available for analysis at runtime. We show how users may get a detailed view of the execution, providing insights to determine when and how to tune. We discuss the applicability of our solution in different domains and validate its ability to allow for online capture and analyses of parameter fine-tunings in a real workflow in the Oil and Gas industry. In this experiment, the user could determine which tuned parameters influenced simulation accuracy and performance. The observed overhead for keeping track of user steering actions at runtime is less than 1% of total execution time.

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