arXiv subjects

Michela Taufer

Publications and source records attributed to Michela Taufer.

At least 19 recordsLinked to original sources

arXiv2026

Toward Trustworthy Autonomous Science: A Two-Year Community Roadmap

One year ago, the AISLE roadmap argued that autonomous laboratories operated as isolated islands and proposed a grassroots network organized around five critical dimensions. The field has since moved faster than anticipated. Multi-agent systems have produced experimentally validated hypotheses, self-driving laboratories have grown more interoperable and orchestrated, reasoning-trained and domain foundation models have raised the capability ceiling, and the Genesis Mission has placed autonomous experimentation at the center of U.S. federal science strategy, with industry emerging as a primary actor. Progress has met a sobering counter-current, including a corrected flagship discovery result, benchmarks showing that agents which rival experts on closed-ended questions still complete only a fraction of open-ended research, and fabricated citations surfacing at leading venues. We read this as the defining tension of the field. Producing a candidate discovery is no longer the hard part, but verifying it is, and this asymmetry now limits autonomous science more than raw model capability. We update the roadmap around seven dimensions, revisiting the original five and elevating two former cross-cutting concerns, trust, verification, and reproducibility, and safety, security, and governance, to first-class status. We assess the original milestones (M1 through M14) as achieved, partially achieved, reframed, or open, add four new milestones (M15 through M18), and scope the path forward to a two-year horizon. The first year concentrates on interfaces, protocol adoption, and the scaffolding of verification, and the second targets federation, zero-trust coordination, and governance. Throughout, we position the grassroots network as the interoperability fabric that lets national programs, international initiatives, and commercial platforms connect rather than re-silo.

cs.DC↗

arXiv2026

Large Data Acquisition and Analytics at Synchrotron Radiation Facilities

Synchrotron facilities like the Cornell High Energy Synchrotron Source (CHESS) generate massive data volumes from complex beamline experiments, but face challenges such as limited access time, the need for on-site experiment monitoring, and managing terabytes of data per user group. We present the design, deployment, and evaluation of a framework that addresses CHESS's data acquisition and management issues. Deployed on a secure CHESS server, our system provides real time, web-based tools for remote experiment monitoring and data quality assessment, improving operational efficiency. Implemented across three beamlines (ID3A, ID3B, ID4B), the framework managed 50-100 TB of data and over 10 million files in late 2024. Testing with 43 research groups and 86 dashboards showed reduced overhead, improved accessibility, and streamlined data workflows. Our paper highlights the development, deployment, and evaluation of our framework and its transformative impact on synchrotron data acquisition.

cs.HC↗

arXiv2025

Exascale Implicit Kinetic Plasma Simulations on El~Capitan for Solving the Micro-Macro Coupling in Magnetospheric Physics

Our fully kinetic, implicit Particle-in-Cell (PIC) simulations of global magnetospheres on up to 32,768 of El Capitan's AMD Instinct MI300A Accelerated Processing Units (APUs) represent an unprecedented computational capability that addresses a fundamental challenge in space physics: resolving the multi-scale coupling between microscopic (electron-scale) and macroscopic (global-scale) dynamics in planetary magnetospheres. The implicit scheme of iPIC3D supports time steps and grid spacing that are up to 10 times larger than those of explicit methods, without sacrificing physical accuracy. This enables the simulation of magnetospheres while preserving fine-scale electron physics, which is critical for key processes such as magnetic reconnection and plasma turbulence. Our algorithmic and technological innovations include GPU-optimized kernels, particle control, and physics-aware data compression using Gaussian Mixture Models. With simulation domains spanning 100-1,000 ion skin depths, we reach the global scale of small-to-medium planetary magnetospheres, such as those of Mercury and Ganymede, which supports fully kinetic treatment of global-scale dynamics in systems previously out of reach for fully kinetic PIC codes.

cs.CE↗

arXiv2025

The Making of a Community Dark Matter Dataset with the National Science Data Fabric

Dark matter is believed to constitute approximately 85 percent of the universes matter, yet its fundamental nature remains elusive. Direct detection experiments, though globally deployed, generate data that is often locked within custom formats and non-reproducible software stacks, limiting interdisciplinary analysis and innovation. This paper presents a collaboration between the National Science Data Fabric (NSDF) and dark matter researchers to improve accessibility, usability, and scientific value of a calibration dataset collected with Cryogenic Dark Matter Search (CDMS) detectors at the University of Minnesota. We describe how NSDF services were used to convert data from a proprietary format into an open, multi-resolution IDX structure; develop a web-based dashboard for easily viewing signals; and release a Python-compatible CLI to support scalable workflows and machine learning applications. These contributions enable broader use of high-value dark matter datasets, lower the barrier to entry for new collaborators, and support reproducible, cross-disciplinary research.

hep-ex↗

arXiv2025

Scalable Climate Data Analysis: Balancing Petascale Fidelity and Computational Cost

The growing resolution and volume of climate data from remote sensing and simulations pose significant storage, processing, and computational challenges. Traditional compression or subsampling methods often compromise data fidelity, limiting scientific insights. We introduce a scalable ecosystem that integrates hierarchical multiresolution data management, intelligent transmission, and ML-assisted reconstruction to balance accuracy and efficiency. Our approach reduces storage and computational costs by 99\%, lowering expenses from \$100,000 to \$24 while maintaining a Root Mean Square (RMS) error of 1.46 degrees Celsius. Our experimental results confirm that even with significant data reduction, essential features required for accurate climate analysis are preserved. Validated on petascale NASA climate datasets, this solution enables cost-effective, high-fidelity climate analysis for research and decision-making.

physics.ao-ph↗

arXiv2025

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↗

arXiv2025

Now More Than Ever, Foundational AI Research and Infrastructure Depends on the Federal Government

Leadership in the field of AI is vital for our nation's economy and security. Maintaining this leadership requires investments by the federal government. The federal investment in foundation AI research is essential for U.S. leadership in the field. Providing accessible AI infrastructure will benefit everyone. Now is the time to increase the federal support, which will be complementary to, and help drive, the nation's high-tech industry investments.

cs.CY↗

arXiv2024

Design Concerns for Integrated Scripting and Interactive Visualization in Notebook Environments

Interactive visualization can support fluid exploration but is often limited to predetermined tasks. Scripting can support a vast range of queries but may be more cumbersome for free-form exploration. Embedding interactive visualization in scripting environments, such as computational notebooks, provides an opportunity to leverage the strengths of both direct manipulation and scripting. We investigate interactive visualization design methodology, choices, and strategies under this paradigm through a design study of calling context trees used in performance analysis, a field which exemplifies typical exploratory data analysis workflows with Big Data and hard to define problems. We first produce a formal task analysis assigning tasks to graphical or scripting contexts based on their specificity, frequency, and suitability. We then design a notebook-embedded interactive visualization and validate it with intended users. In a follow-up study, we present participants with multiple graphical and scripting interaction modes to elicit feedback about notebook-embedded visualization design, finding consensus in support of the interaction model. We report and reflect on observations regarding the process and design implications for combining visualization and scripting in notebooks.

cs.HC↗

arXiv2024

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↗

arXiv2024

Reproducing the results for NICER observation of PSR J0030+0451

NASA's Neutron Star Interior Composition Explorer (NICER) observed X-ray emission from the pulsar PSR J0030+0451 in 2018. Riley et al. reported Bayesian parameter measurements of the mass and the star's radius using pulse-profile modeling of the X-ray data. This paper reproduces their result using the open-source software X-PSI and publicly available data within expected statistical errors. We note the challenges we faced in reproducing the results and demonstrate that the analysis can be reproduced and reused in future works by changing the prior distribution for the radius and the sampler configuration. We find no significant change in the measurement of the mass and radius, demonstrating that the original result is robust to these changes. Finally, we provide a containerized working environment that facilitates third-party reproduction of the measurements of mass and radius of PSR J0030+0451 using the NICER observations.

astro-ph.HE↗

arXiv2022

Co-scheduling Ensembles of In Situ Workflows

Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging, even with modern supercomputers. To overcome the timescale limitation, the simulation of a long MD trajectory is replaced by multiple short-range simulations that are executed simultaneously in an ensemble of simulations. Analyses are usually co-scheduled with these simulations to efficiently process large volumes of data generated by the simulations at runtime, thanks to in situ techniques. Executing a workflow ensemble of simulations and their in situ analyses requires efficient co-scheduling strategies and sophisticated management of computational resources so that they are not slowing down each other. In this paper, we propose an efficient method to co-schedule simulations and in situ analyses such that the makespan of the workflow ensemble is minimized. We present a novel approach to allocate resources for a workflow ensemble under resource constraints by using a theoretical framework modeling the workflow ensemble's execution. We evaluate the proposed approach using an accurate simulator based on the WRENCH simulation framework on various workflow ensemble configurations. Results demonstrate the significance of co-scheduling simulations and in situ analyses that couple data together to benefit from data locality, in which inefficient scheduling decisions can lead up to a factor 30 slowdown in makespan.

cs.DC↗

arXiv2022

Reproducibility of the First Image of a Black Hole in the Galaxy M87 from the Event Horizon Telescope (EHT) Collaboration

This paper presents an interdisciplinary effort aiming to develop and share sustainable knowledge necessary to analyze, understand, and use published scientific results to advance reproducibility in multi-messenger astrophysics. Specifically, we target the breakthrough work associated with the generation of the first image of a black hole, called M87. The image was computed by the Event Horizon Telescope Collaboration. Based on the artifacts made available by EHT, we deliver documentation, code, and a computational environment to reproduce the first image of a black hole. Our deliverables support new discovery in multi-messenger astrophysics by providing all the necessary tools for generalizing methods and findings from the EHT use case. Challenges encountered during the reproducibility of EHT results are reported. The result of our effort is an open-source, containerized software package that enables the public to reproduce the first image of a black hole in the galaxy M87.

astro-ph.IM↗

arXiv2021

PEng4NN: An Accurate Performance Estimation Engine for Efficient Automated Neural Network Architecture Search

Neural network (NN) models are increasingly used in scientific simulations, AI, and other high performance computing (HPC) fields to extract knowledge from datasets. Each dataset requires tailored NN model architecture, but designing structures by hand is a time-consuming and error-prone process. Neural architecture search (NAS) automates the design of NN architectures. NAS attempts to find well-performing NN models for specialized datsets, where performance is measured by key metrics that capture the NN capabilities (e.g., accuracy of classification of samples in a dataset). Existing NAS methods are resource intensive, especially when searching for highly accurate models for larger and larger datasets. To address this problem, we propose a performance estimation strategy that reduces the resources for training NNs and increases NAS throughput without jeopardizing accuracy. We implement our strategy via an engine called PEng4NN that plugs into existing NAS methods; in doing so, PEng4NN predicts the final accuracy of NNs early in the training process, informs the NAS of NN performance, and thus enables the NAS to terminate training NNs early. We assess our engine on three diverse datasets (i.e., CIFAR-100, Fashion MNIST, and SVHN). By reducing the training epochs needed, our engine achieves substantial throughput gain; on average, our engine saves 61% to 82% of training epochs, increasing throughput by a factor of 2.5 to 5 compared to a state-of-the-art NAS method. We achieve this gain without compromising accuracy, as we demonstrate with two key outcomes. First, across all our tests, between 74% and 97% of the ground truth best models lie in our set of predicted best models. Second, the accuracy distributions of the ground truth best models and our predicted best models are comparable, with the mean accuracy values differing by at most .7 percentage points across all tests.

cs.LG↗

arXiv2021

Cybercosm: New Foundations for a Converged Science Data Ecosystem

Scientific communities naturally tend to organize around data ecosystems created by the combination of their observational devices, their data repositories, and the workflows essential to carry their research from observation to discovery. However, these legacy data ecosystems are now breaking down under the pressure of the exponential growth in the volume and velocity of these workflows, which are further complicated by the need to integrate the highly data intensive methods of the Artificial Intelligence revolution. Enabling ground breaking science that makes full use of this new, data saturated research environment will require distributed systems that support dramatically improved resource sharing, workflow portability and composability, and data ecosystem convergence. The Cybercosm vision presented in this white paper describes a radically different approach to the architecture of distributed systems for data-intensive science and its application workflows. As opposed to traditional models that restrict interoperability by hiving off storage, networking, and computing resources in separate technology silos, Cybercosm defines a minimally sufficient hypervisor as a spanning layer for its data plane that virtualizes and converges the local resources of the system's nodes in a fully interoperable manner. By building on a common, universal interface into which the problems that infect today's data-intensive workflows can be decomposed and attacked, Cybercosm aims to support scalable, portable and composable workflows that span and merge the distributed data ecosystems that characterize leading edge research communities today.

cs.NI↗

arXiv2021

Reproducing GW150914: the first observation of gravitational waves from a binary black hole merger

In 2016, LIGO and Virgo announced the first observation of gravitational waves from a binary black hole merger, known as GW150914. To establish the confidence of this detection, large-scale scientific workflows were used to measure the event's statistical significance. They used code written by the LIGO/Virgo and were executed on the LIGO Data Grid. The codes are publicly available, but there has not yet been an attempt to directly reproduce the results, although several analyses have replicated the analysis, confirming the detection. We attempt to reproduce the result presented in the GW150914 discovery paper using publicly available code on the Open Science Grid. We show that we can reproduce the main result but we cannot exactly reproduce the LIGO analysis as the original data set used is not public. We discuss the challenges we encountered and make recommendations for scientists who wish to make their work reproducible.

cs.DC↗

arXiv2021

VPIC 2.0: Next Generation Particle-in-Cell Simulations

VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large numbers of particles. VPIC's capacity in both fidelity and scale makes it particularly well-suited for plasma research on pre-exascale and exascale platforms. In this paper we demonstrate the unique challenges involved in preparing the VPIC code for operation at exascale, outlining important optimizations to make VPIC efficient on accelerators. Specifically, we show the work undertaken in adapting VPIC to exploit the portability-enabling framework Kokkos and highlight the enhancements to VPIC's modeling capabilities to achieve performance at exascale. We assess the achieved performance-portability trade-off through a suite of studies on nine different varieties of modern pre-exascale hardware. Our performance-portability study includes weak-scaling runs on three of the top ten TOP500 supercomputers, as well as a comparison of low-level system performance of hardware from four different vendors.

cs.DC↗

arXiv2020

Building Containerized Environments for Reproducibility and Traceability of Scientific Workflows

Scientists rely on simulations to study natural phenomena. Trusting the simulation results is vital to develop sciences in any field. One approach to build trust is to ensure the reproducibility and traceability of the simulations through the annotation of executions at the system-level; by the generation of record trails of data moving through the simulation workflow. In this work, we present a system-level solution that leverages the intrinsic characteristics of containers (i.e., portability, isolation, encapsulation, and unique identifiers). Our solution consists of a containerized environment capable to annotate workflows, capture provenance metadata, and build record trails. We assess our environment on four different workflows and measure containerization costs in terms of time and space. Our solution, built with a tolerable time and space overhead, enables transparent and automatic provenance metadata collection and access, an easy-to-read record trail, and tight connections between data and metadata.

cs.DC↗

arXiv2019

SOMOSPIE: A modular SOil MOisture SPatial Inference Engine based on data driven decisions

The current availability of soil moisture data over large areas comes from satellite remote sensing technologies (i.e., radar-based systems), but these data have coarse resolution and often exhibit large spatial information gaps. Where data are too coarse or sparse for a given need (e.g., precision agriculture), one can leverage machine-learning techniques coupled with other sources of environmental information (e.g., topography) to generate gap-free information and at a finer spatial resolution (i.e., increased granularity). To this end, we develop a spatial inference engine consisting of modular stages for processing spatial environmental data, generating predictions with machine-learning techniques, and analyzing these predictions. We demonstrate the functionality of this approach and the effects of data processing choices via multiple prediction maps over a United States ecological region with a highly diverse soil moisture profile (i.e., the Middle Atlantic Coastal Plains). The relevance of our work derives from a pressing need to improve the spatial representation of soil moisture for applications in environmental sciences (e.g., ecological niche modeling, carbon monitoring systems, and other Earth system models) and precision agriculture (e.g., optimizing irrigation practices and other land management decisions).

cs.LG↗