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DOE OSTI2025

Emerging Tools to Support DILI Assessment in Clinical Trials with Abnormal Baseline Serum Liver Tests or Pre-existing Liver Diseases

Abstract Based on the late Dr. Hyman Zimmerman’s observation that hepatocellular drug-induced liver injury (DILI) leading to jaundice carries a ≥ 10% fatality risk (coined as Hy’s law by others), evaluation of Drug-Induced Serious Hepatotoxicity (eDISH) continues to play a central role in the assessment of a study drug’s liability for acute hepatocellular DILI. The eDISH identifies drugs in clinical trials with DILI fatality (death or transplant) risk that may be unacceptable in a post-market setting. As a two-dimensional graph that plots peak total bilirubin (TB) versus peak serum aminotransferase levels for each patient during study drug or comparator treatment, eDISH identifies potential cases of acute, modest, and serious hepatocellular DILI for in-depth analysis of liver tests (LT) and clinical course so that the likelihood of causal association with the study drug can be determined. Unfortunately, the generalizable utility of this tool only pertains to trials enrolling patients with normal or near normal (NNN) baseline (BL) serum LTs. The eDISH does not necessarily apply to trials of patients with abnormal baseline (ABN-BL) LTs that often coincide with underlying liver disorders. Because drug development programs being reviewed by the FDA increasingly target liver disorders, we are often challenged to evaluate DILI risk in trials of patients with ABN-BL LTs. Also, the high background prevalence of metabolic dysfunction associated steatotic liver disease (MASLD) means patients with LTs above NNN may need to be enrolled in trials treating non-liver disorders to reflect the target population. Such study populations create challenges for industry and regulators because eDISH may not reliably categorize or identify potential cases of DILI for further analysis, as it so efficiently does in NNN-BL trials. We describe the main functionalities of eDISH in NNN-BL trials to understand what should be emulated by new tools or eDISH modifications. We then discuss non-eDISH–based plots that may be useful in ABN-BL trials.

Amirzadegan, Jasmine↗

DOE OSTI2022

Detecting anomalous sequences in electronic health records using higher-order tensor networks

Detecting anomalous sequences is an integral part of building and protecting modern large-scale health information technology (HIT) systems. These HIT systems generate a large volume of records of patients’ state and significant events, which provide a valuable resource to help improve clinical decisions, patient care processes, and other issues. However, detecting anomalous sequences in electronic health records (EHR) remains a challenge in healthcare applications for several reasons, including imbalances in the data, complexity of relationships between events in the sequence, and the curse of dimensionality. Conventional anomaly detection methods use the finite sequence of events to discriminate sequences. They fail to incorporate salient event details under variable higher-order dependencies (e.g., duration between events) that can provide better discrimination of sequences in their models. To address this problem, we propose event sequence and subsequence anomaly detection algorithms that (1) use network-based representations of interactions in the data, (2) account for variable higher-order dependencies in the data, and (3) incorporate events duration for adequate discrimination of the data. The proposed approach identifies anomalies by monitoring the change in the graph after the test sequence is removed from the network. The change is quantified using graph distance metrics so that dramatic changes in the network can be attributed to the removed sequence. Furthermore, the proposed subsequence algorithm recommends plausible paths and salient information for the detected anomalous subsequences. Our results show that the proposed event sequence anomaly detection algorithm outperforms the baseline methods for both synthetic data and real-world EHR data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

An automated workflow that generates atom mappings for large‐scale metabolic models and its application to Arabidopsis thaliana

SUMMARY Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large‐scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large‐scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana . We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating 15 N isotope enrichment and identifying nitrogen (N)‐containing metabolites which show enrichment patterns that are informative for flux estimation in future 15 N‐MFA studies of A. thaliana . The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph‐theoretic structural analyses with large‐scale metabolic networks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry: Are we getting the same answer?

Since the first detailed compositional analysis of dissolved organic matter (DOM) in 1995, high resolution mass spectrometry (HRMS) has become a vital tool for DOM characterization. While the upward trend in HRMS for molecular level analysis of DOM continues, so do the challenges of data comparison and interpretation between laboratories operating instruments of differing performance and user operating conditions. It is therefore essential that the community establishes whether data and trends can be compared robustly between research groups. To this end, 4 identically prepared DOM samples were each studied by 16 laboratories, representing 17 commercially-purchased instruments located across 8 countries, using positive- and negative-mode electrospray ionization (ESI) HRMS analysis. Despite the widely reported sensitivity of ESI experiments to sample matrix, preparation, ion source operation and instrument tuning parameters, the instruments used in this study showed relatively low variability between results for the same samples, particularly H/C and AI metrics. The variation in O/C and m/z metrics was relatively higher, although z-score graphs and %BCD demonstrated that the relative difference in general chemical composition between samples was the same for each instrument included in the study. As such, these metrics can be used for fingerprinting of DOM samples and as a benchmark for quality control in participating laboratories, with future strides in environmental science building upon these efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

Reanalysis of Rodent Data from Spacelab Life Sciences-1

The space bioscience field has long been plagued by the challenge of spaceflight with effects of radiation and microgravity. Having multiple and repeated spaceflight experiments for model organisms to solve these space stressors is costly and time consuming. Therefore, reusing and reanalyzing legacy experiments is one way that scientists can draw new conclusions in a timely manner and without using too many resources. Moreover, advances in general biological knowledge allows legacy experiments to be placed into more complete context.Here we aim to analyze all data and metadata taken from rats flown on the SLS-1 mission to create a comprehensive biological model that can be supplemented with current data to allow new discoveries in how space flown organisms adapt to the space environment. Our approach begins with the identification of all the data and metadata, including graphs and tables, for SLS-1 in NASA archives and other sources. Then, each piece of data and metadata will be digitized, reformatted and analyzed. Lastly, a previously developed astronaut model will be used to create the data framework and a comprehensive biological rodent model. The datasets we are using is from the 1991 SpaceLab Life Science 1 (SLS-1) NASA Mission. This was the first designated spacelab mission flown. All 29 rodents were tested for nine days in two different habitats: Research Animal Holding Facility (RAHF) and Animal Enclosure Module (AEM). The rodents were prepared for a live return and compared to a ground control. A total of 30 rodent experiments were accepted as flight studies on the mission. By digitization and reorganizing SLS-1 rat data we will both directly generate new insights and indirectly enable other scientists to by providing the data and metadata in a digitized form.

Space Biology↗

NASA NTRSDate not supplied

Reanalysis of Rodent Data from Spacelab Life Science-1

Space Biology↗

DOE OSTI2019

XScan: An Integrated Tool for Understanding Open Source Community-Based Scientific Code

Many scientific communities have adopted community-based models that integrate multiple components to simulate whole system dynamics. The community software projects’ complexity, stems from the integration of multiple individual software components that were developed under different application requirements and various machine architectures, has become a challenge for effective software system understanding and continuous software development. The paper presents an integrated software toolkit called X-ray Software Scanner (in abbreviation, XScan) for a better understanding of large-scale community-based scientific codes. Our software tool provides support to quickly summarize the overall information of scientific codes, including the number of lines of code, programming languages, external library dependencies, as well as architecture-dependent parallel software features. The XScan toolkit also realizes a static software analysis component to collect detailed structural information and provides an interactive visualization and analysis of the functions. We use a large-scale community-based Earth System Model to demonstrate the workflow, functions and visualization of the toolkit. We also discuss the application of advanced graph analytics techniques to assist software modular design and component refactoring.

Zheng, Weijian↗

DOE OSTI2022

CPES-QSM: A Quantitative Method Towards the Secure Operation of Cyber-Physical Energy Systems

Power systems are evolving into cyber-physical energy systems (CPES) mainly due to the integration of modern communication and Internet-of-Things (IoT) devices. CPES security evaluation is challenging since the physical and cyber layers are often not considered holistically. Existing literature focuses on only optimizing the operation of either the physical or cyber layer while ignoring the interactions between them. This paper proposes a metric, the Cyber-Physical Energy System Quantitative Security Metric (CPES-QSM), that quantifies the interaction between the cyber and physical layers across three domains: electrical, cyber-risk, and network topology. A method for incorporating the proposed cyber-metric into operational decisions is also proposed by formulating a cyber-constrained AC optimal power flow (C-ACOPF) that considers the status of all the CPES layers. The C-ACOPF considers the vulnerabilities of physical and cyber networks by incorporating factors such as voltage stability, contingencies, graph-theory, and IoT cyber risks, while using a multi-criteria decision-making technique. We note that simulation studies are conducted using standard IEEE test systems to evaluate the effectiveness of the proposed metric and the C-ACOPF formulation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

ORCHA: A performance portability system for extreme heterogeneity

Heterogeneity is the prevalent trend in the rapidly evolving high-performance computing (HPC) landscape in both hardware and application software. The diversity in hardware platforms, currently comprising various accelerators and a future possibility of specializable chiplets, poses a significant challenge for scientific software developers aiming to harness optimal performance across different computing platforms while maintaining the quality of solutions when their applications are simultaneously growing more complex. Code synthesis and code generation can provide mechanisms to mitigate this challenge. We have developed a divide and conquer approach where different aspects of performance are handled by different stand-alone tools that are interfaced with the application through generated code. This portability system, ORCHA, enables users to configure and orchestrate their computations among available resources on a platform by specifying a high-level recipe, thereby permitting a many-to-many paradigm where each recipe results in a different variant of the application. The core design goal is to let users decide the application’s hardware mapping and orchestration by editing only the high-level recipe—without modifying the maintained source code or binding the application to a particular runtime system. Tools in ORCHA distribution are: CG-Kit for translating the recipe into an execution graph; Milhoja to execute the graph by orchestrating data and task movement among hardware resources; and Macroprocessor that enables users to define their own code-shorthand for higher composability and easier management of code variants. Additionally, the design of ORCHA permits tools to work in a plug-and-play mode where the application can build and run without CG-Kit and Milhoja, and either tool can be swapped out for other tools with similar capabilities by modifying the code generation portion of ORCHA. In this paper, we describe the design of ORCHA and the role that code-generation plays in isolating applications from tools. We demonstrate the breadth of configurations ORCHA enables with a case study in which an application configuration is realized on three distinct hardware mappings—a GPU-centric, a CPU/GPU balanced, and a CPU/GPU concurrent layouts by using different recipes.

Lee, Youngjun↗

DOE OSTI2021

Neuromorphic Graph Algorithms

Graph algorithms enable myriad large-scale applications including cybersecurity, social network analysis, resource allocation, and routing. The scalability of current graph algorithm implementations on conventional computing architectures are hampered by the demise of Moore’s law. We present a theoretical framework for designing and assessing the performance of graph algorithms executing in networks of spiking artificial neurons. Although spiking neural networks (SNNs) are capable of general-purpose computation, few algorithmic results with rigorous asymptotic performance analysis are known. SNNs are exceptionally well-motivated practically, as neuromorphic computing systems with 100 million spiking neurons are available, and systems with a billion neurons are anticipated in the next few years. Beyond massive parallelism and scalability, neuromorphic computing systems offer energy consumption orders of magnitude lower than conventional high-performance computing systems. We employ our framework to design and analyze new spiking algorithms for shortest path and dynamic programming problems. Our neuromorphic algorithms are message-passing algorithms relying critically on data movement for computation. For fair and rigorous comparison with conventional algorithms and architectures, which is challenging but paramount, we develop new models of data-movement in conventional computing architectures. This allows us to prove polynomial-factor advantages, even when we assume a SNN consisting of a simple grid-like network of neurons. To the best of our knowledge, this is one of the first examples of a rigorous asymptotic computational advantage for neuromorphic computing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Improving Variational Autoencoders for New Physics Detection at the LHC With Normalizing Flows

We investigate how to improve new physics detection strategies exploiting variational autoencoders and normalizing flows for anomaly detection at the Large Hadron Collider. As a working example, we consider the DarkMachines challenge dataset. We show how different design choices (e.g., event representations, anomaly score definitions, network architectures) affect the result on specific benchmark new physics models. Once a baseline is established, we discuss how to improve the anomaly detection accuracy by exploiting normalizing flow layers in the latent space of the variational autoencoder.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

yProv4ML: Effortless provenance tracking for machine learning systems

The rapid growth in interest in deep learning and foundation models (FMs) in particular, has attracted the attention of a diverse range of researchers thanks to their generalization ability. However, the advent of these techniques has also brought to light the lack of transparency and rigor in the way development is pursued. In particular, the inability to determine the number of epochs and other hyperparameters in advance presents challenges in identifying the best model. To address this challenge, machine learning frameworks such as MLFlow can automate the collection of this type of information. However, these tools capture data using proprietary formats and pose little attention to lineage. This paper proposes yProv4ML, a framework that captures provenance information generated during machine learning processes in PROV-JSON format, with minimal code modification.

Machine learning↗

DOE OSTI2024

Theoretical guarantees for permutation-equivariant quantum neural networks

Despite the great promise of quantum machine learning models, there are several challenges one must overcome before unlocking their full potential. For instance, models based on quantum neural networks (QNNs) can suffer from excessive local minima and barren plateaus in their training landscapes. Recently, the nascent field of geometric quantum machine learning (GQML) has emerged as a potential solution to some of those issues. The key insight of GQML is that one should design architectures, such as equivariant QNNs, encoding the symmetries of the problem at hand. Here, we focus on problems with permutation symmetry (i.e., symmetry group $S_n$), and show how to build $S_n$-equivariant QNNs We provide an analytical study of their performance, proving that they do not suffer from barren plateaus, quickly reach overparametrization, and generalize well from small amounts of data. To verify our results, we perform numerical simulations for a graph state classification task. Our work provides theoretical guarantees for equivariant QNNs, thus indicating the power and potential of GQML.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Scaling Wind Power Innovation Assessment for Rapid Energy Transition with Artificial Intelligence

Planning for energy system decarbonization requires new insights into the potential of renewable technologies, deployed at unprecedented scale, to meet urgent sustainability goals. However, limited scalability of current wind energy research tools restricts characterization of innovation impacts to isolated reference sites, challenging investment and decision making under rapid growth. We demonstrate the transformative potential of artificial intelligence (AI) to inform future technology advancement and energy systems design by leveraging a state-of-the-art surrogate model to conduct a series of fleet-wide wind plant layout optimizations for greater than 6,800 projected U.S. onshore buildout locations. We show how innovative wake steering technology can address an array of barriers to large-scale deployment and integration of wind power. Specifically, wake steering reduces required plant area by an average of 18% and could preserve upwards of 13,000 km2 for future greenfield deployment, potentially easing siting challenges associated with wind energy infrastructure. Further, by enabling reduced turbine spacing and increased energy production, flexible operations of wake steering improve levelized cost of energy, particularly for large plants and in land-constrained settings. Finally, optimizations that consider dynamic energy prices can deliver increased power production and revenue capture during high-value (often low-wind) periods, further bolstering plant economics. Our computationally efficient approach offers a pathway to accelerate nationwide geographic evaluation of innovative technologies.

graph neural networks↗

DOE OSTI2018

Structural Correlations and Percolation in Twisted Perylene Diimides Using a Simple Anisotropic Coarse-Grained Model

Large, twisted, and fused conjugated molecular architectures have begun to appear more prominently in the organic semiconductor literature. From a modeling perspective, such structures present a challenge to conventional simulation techniques; atomistic resolutions are computationally inefficient, while traditional isotropic coarse-grained models do not capture the inherent anisotropies of the molecules. In this work, we develop a simple coarse-grained model that explicitly incorporates the anisotropy of these molecular architectures, thereby providing a route toward analyzing pi-stacking, and thus qualitative electronic structure, at a computationally efficient coarse-grained resolution. Our simple coarse-grained model maintains relative orientations of conjugated rings, as well as inter-ring dihedrals, that are critical for understanding electronic and excitonic transport in bulk systems. We apply this model to understand structural correlations in several recently synthesized perylene diimide (PDI)-based organic semiconductors. Twisted and nonplanar molecular architectures are found to promote amorphous morphologies while maintaining local pi-stacking. In conclusion, a graph theoretical network analysis demonstrates that these twisted molecules are more likely to form percolating three-dimensional pathways for charge motion than strictly planar molecules, which show connectivity in only one dimension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

First-principles treatment of Mott insulators: linearized QSGW+DMFT approach

The theoretical understanding of emergent phenomena in quantum materials is one of the greatest challenges in condensed matter physics. In contrast to simple materials such as noble metals and semiconductors, macroscopic properties of quantum materials cannot be predicted by the properties of individual electrons. One of the examples of scientific importance is strongly correlated electron system. Neither localized nor itinerant behaviors of electrons in partially filled 3d, 4f, and 5f orbitals give rise to rich physics such as Mott insulators, high-temperature superconductors, and superior thermoelectricity, but hinder quantitative understanding of low-lying excitation spectrum. Here we present a new first-principles approach to strongly correlated solids. It is based on a combination of the quasiparticle self-consistent GW approximation and the dynamical mean-field theory. The sole input in this method is the projector to the set of correlated orbitals for which all local Feynman graphs are being evaluated. For that purpose, we choose very localized quasiatomic orbitals spanning large energy window, which contains most strongly hybridized bands, as well as upper and lower Hubbard bands. The self-consistency is carried out on the Matsubara axis. This method enables the first-principles study of Mott insulators in both their paramagnetic and antiferromagnetic phases. We illustrate the method on the archetypical charge transfer correlated insulators La 2 CuO 4 and NiO, and obtain spectral properties and magnetic moments in good agreement with experiments.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Coherency-Constrained Spectral Clustering for Power Network Reduction

This paper presents a methodology for reducing the complexity of large-scale power network models using spectral clustering, aggregation of electrical components, and cost function approximation. Two approaches are explored using unconstrained and constrained spectral clustering to determine areas for effective system reduction. Once the system areas are determined, both loads and generators by type are aggregated, and their new cost function is approximated through polynomial curve-fitting or statistical methods. The performance of reduced networks is evaluated in terms of their ability to follow the true daily cost of the original system over a 24-hour period considering a set of several days. Two test systems are taken as test beds. Application of the methodology to a modified version of the IEEE 39-bus system reduces it from 17 generators to a 4-bus system and 9 generators with about 93% of accuracy. Similarly, the IEEE 118-bus system is reduced from 19 generators to a 3-bus system with three aggregated units achieving over 99% of accuracy. These findings address scalability challenges and enhance accuracy for high and mid-loading level conditions, and by aggregating thermal units with similar cost functions.

42 ENGINEERING↗

DOE OSTI2024

HDBind: encoding of molecular structure with hyperdimensional binary representations

Traditional methods for identifying “hit” molecules from a large collection of potential drug-like candidates rely on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have a significant limitation in that they require exceptional computing capabilities for even relatively small collections of molecules. Increasingly large and complex state-of-the-art deep learning approaches have gained popularity with the promise to improve the productivity of drug design, notorious for its numerous failures. However, as deep learning models increase in their size and complexity, their acceleration at the hardware level becomes more challenging. Hyperdimensional Computing (HDC) has recently gained attention in the computer hardware community due to its algorithmic simplicity relative to deep learning approaches. The HDC learning paradigm, which represents data with high-dimension binary vectors, allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas (computer vision, bioinformatics, mass spectrometery, remote sensing, edge devices, etc.). To the best of our knowledge, our work is the first to consider HDC for the task of fast and efficient screening of modern drug-like compound libraries. We also propose the first HDC graph-based encoding methods for molecular data, demonstrating consistent and substantial improvement over previous work. We compare our approaches to alternative approaches on the well-studied MoleculeNet dataset and the recently proposed LIT-PCBA dataset derived from high quality PubChem assays. We demonstrate our methods on multiple target hardware platforms, including Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs), showing at least an order of magnitude improvement in energy efficiency versus even our smallest neural network baseline model with a single hidden layer. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools. We make our code publicly available at https://github.com/LLNL/hdbind.

59 BASIC BIOLOGICAL SCIENCES↗