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Bremer, Peer-Timo

Publications and source records attributed to Bremer, Peer-Timo.

At least 19 records
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DOE OSTI2024

IEEE LDAV 2024 Preface

Join us here for the 14th IEEE Symposium on Large Data Analysis and Visualization (IEEE LDAV) on Sunday, October 13th 2024 collocated with IEEE VIS 2024 in St. Pete Beach, Florida, USA.

Beyer, Johanna↗
DOE OSTI2024

Generating Protein Structures for Pathway Discovery Using Deep Learning

Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The ECP ALPINE project: In situ and post hoc visualization infrastructure and analysis capabilities for exascale

A significant challenge on an exascale computer is the speed at which we compute results exceeds by many orders of magnitude the speed at which we save these results. Therefore the Exascale Computing Project (ECP) ALPINE project focuses on providing exascale-ready visualization solutions including in situ processing. In situ visualization and analysis runs as the simulation is run, on simulations results are they are generated avoiding the need to save entire simulations to storage for later analysis. The ALPINE project made post hoc visualization tools, ParaView and VisIt, exascale ready and developed in situ algorithms and infrastructures. The suite of ALPINE algorithms developed under ECP includes novel approaches to enable automated data analysis and visualization to focus on the most important aspects of the simulation. Many of the algorithms also provide data reduction benefits to meet the I/O challenges at exascale. ALPINE developed a new lightweight in situ infrastructure, Ascent.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Safety in Artificial Intelligence: Challenges and Opportunities for the U.S. National Labs and Beyond

This report discusses the importance of the critical and underexplored topic of artificial intelligence (AI) safety, as highlighted during the “Strategy Alignment on AI Safety” workshop convened at Lawrence Livermore National Laboratory (LLNL) in April 2024. Through a summary of keynote talks, panel discussions, and breakout sessions, world-leading AI safety experts from academic, industry, national labs, and government agencies clearly agree on the need for and importance of large-scale investments for research and capabilities in AI safety. With the field innovating at unprecedented rates, there is increasing urgency to develop novel evaluation methodologies that allow full considerations of risks/threats of AI technologies in different domains. Quantitative metrics and effective methodologies that can evaluate and audit the “safeness” of how a given AI technology is trained, deployed, or regulated are, at best, nascent for certain scenarios or, more commonly, nonexistent. This maturation gap presents the possibility of serious threats to national security, and further inaction may have serious consequences. Additionally, the gap between the public’s and research community’s perceptions of AI risks/rewards is significant. While numerous voices from the AI community have expressed concern that the risks could be so high that future AI systems could inflict extinction-level damage to humanity if deployed incorrectly, the public largely is aware only of risk in low-impact scenarios. This discrepancy highlights the crucial need for researchers to articulate to governmental bodies what, why, and when various AI risks matter as part of motivating funding requests. Thus, the call to action for this community is to pursue AI safety as a “Big Science” project on a scale comparable to the Manhattan Project. High risks and high payoffs are on the table, but safe AI is a fast-moving target, and large-scale investments are needed to guide development of this technology in a responsible way. We highlight the need for a multilayered solution combining the development of new methods and algorithmic approaches to mitigate threats with an active participation of the government(s) in setting high industry standards and regulations based on state-of-the-art technology. The U.S. Department of Energy (DOE) national laboratories have served as leading institutions for scientific innovation in the U.S. for more than 70 years. Drawing on their expertise in the AI community and their history of safeguarding critical and sensitive information, and as we look to the future, national labs are the best choice for evaluating and safeguarding AI technologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Preface IEEE LDAV 2023

Join us for the 13th IEEE Symposium on Large Data Analysis and Visualization (IEEE LDAV) on Monday, October 23rd 2023 collocated with IEEE VIS 2023 in Melbourne, Victoria, Australia.

Bremer, Peer-Timo↗
DOE OSTI2023

Universal image representation based on a multimodal graph

A system for classifying a target image with segments having attributes is provided. The system generates a graph for the target image that includes vertices representing segments of the image and edges representing relationships between the connected vertices. For each vertex, the system generates a subgraph that includes the vertex as a home vertex and neighboring vertices representing segments of the target image within a neighborhood of the segment represented by the home vertex. The system applies an autoencoder to each subgraph to generate latent variables to represent the subgraph. The system applies a machine learning algorithm to a feature vector comprising a universal image representation of the target image that is derived from the generated latent variables of the subgraphs to generate a classification for the target image.

Bremer, Peer-Timo↗
DOE OSTI2023

Autonomous MultiScale Library

AMSLib provides infrastructure to tightly couple multi-scale physics simulation code with ML surrogate model inference. It provides a wholistic runtime execution paradigm to supports uncertainty quantification, surrogate model inference, persistent data storing throughout the execution of a simulation.

Bhatia, Harsh↗
DOE OSTI2023

The confluence of machine learning and multiscale simulations

Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, have promoted advances in virtually every field of science and engineering and are revitalizing the traditional notions of multiscale modeling. Deep learning has found success in various approaches for distilling information from fine-scale models, such as building surrogate models and guiding the development of coarse-grained potentials. However, perhaps its most powerful use in multiscale modeling is in defining latent spaces that enable efficient exploration of conformational space. In conclusion, this confluence of machine learning and multiscale simulation with modern high-performance computing promises a new era of discovery and innovation in structural biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Visualization for Scientific Discovery, Decision-Making, and Communication

Visualization–the use of visual elements to explore data, form hypotheses, or convey conclusions–is an integral part of the scientific process. Starting from an initial exploration of new data to illustrating outcomes to the general public, visualization is one of the most intuitive and powerful modes of communication. With the explosion of new data sources and types, unprecedented volumes of data, and new technologies, such as virtual reality and AI, visualization has become increasingly essential but also ever more challenging. Department of Energy’s (DOE) Office of Advanced Scientific Computing Research (ASCR) sponsored a Basic Research Needs workshop in January 2022 to understand the major opportunities and grand challenges in visualization tools and technologies for scientific computing, with a special focus on DOE-relevant applications and goals. The workshop identified five priority research directions (PRDs) for visualization to support scientific discovery, decision-making, and communication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

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 the 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 (often referred to as a computing continuum) 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 enable the publication of workflows and their associated products according to the FAIR principles.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A Visual Comparison of Silent Error Propagation

High-performance computing (HPC) systems play a critical role in facilitating scientific discoveries. Their scale and complexity (e.g., the number of computational units and software stack) continue to grow as new systems are expected to process increasingly more data and reduce computing time. However, with more processing elements, the probability that these systems will experience a random bit-flip error that corrupts a program's output also increases, which is often recognized as silent data corruption. Analyzing the resiliency of HPC applications in extreme-scale computing to silent data corruption is crucial but difficult. An HPC application often contains a large number of computation units that need to be tested, and error propagation caused by error corruption is complex and difficult to interpret. Here, to accommodate this challenge, we propose an interactive visualization system that helps HPC researchers understand the resiliency of HPC applications and compare their error propagation. Our system models an application's error propagation to study a program's resiliency by constructing and visualizing its fault tolerance boundary. Coordinating with multiple interactive designs, our system enables domain experts to efficiently explore the complicated spatial and temporal correlation between error propagations. At the end, the system integrated a nonmonotonic error propagation analysis with an adjustable graph propagation visualization to help domain experts examine the details of error propagation and answer such questions as why an error is mitigated or amplified by program execution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Data-driven model for divertor plasma detachment prediction

We present a fast and accurate data-driven surrogate model for divertor plasma detachment prediction leveraging the latent feature space concept in machine learning research. Our approach involves constructing and training two neural networks: an autoencoder that finds a proper latent space representation (LSR) of plasma state by compressing the multi-modal diagnostic measurements and a forward model using multi-layer perception (MLP) that projects a set of plasma control parameters to its corresponding LSR. By combining the forward model and the decoder network from autoencoder, this new data-driven surrogate model is able to predict a consistent set of diagnostic measurements based on a few plasma control parameters. In order to ensure that the crucial detachment physics is correctly captured, highly efficient 1D UEDGE model is used to generate training and validation data in this study. The benchmark between the data-driven surrogate model and UEDGE simulations shows that our surrogate model is capable of providing accurate detachment prediction (usually within a few per cent relative error margin) but with at least four orders of magnitude speed-up, indicating that performance-wise, it has the potential to facilitate integrated tokamak design and plasma control. Comparing with the widely used two-point model and/or two-point model formatting, the new data-driven model features additional detachment front prediction and can be easily extended to incorporate richer physics. This study demonstrates that the complicated divertor and scrape-off-layer plasma state has a low-dimensional representation in latent space. Understanding plasma dynamics in latent space and utilising this knowledge could open a new path for plasma control in magnetic fusion energy research.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗