BACKGROUND: Transcriptomic profiling technologies have advanced the analysis of biological and toxicological responses. However, substantial differences in probe design, dynamic range, gene coverage, and preprocessing pipelines across platforms introduce artifacts that limit cross-study integration and hinder the reuse of historical datasets. We aim to develop computational methods for accurate cross-platform translation to maximize the value of legacy resources. RESULTS: We present TransPlatformer a deep learning framework for translating gene expression profiles across heterogeneous toxicogenomics platforms. TransPlatformer employs a novel attention-based architecture to map high-dimensional fold-change vectors from legacy microarray technologies to current platforms. Models are trained and evaluated using DrugMatrix, spanning three technological generations. We investigate mixed-tissue, single-tissue, and cross-tissue training paradigms and benchmark performance against multilayer perceptron and matrix-completion baselines. In mixed-tissue training, TransPlatformer achieves a greater than 50% reduction in mean absolute error (0.043 vs. 0.09) and nearly doubles Pearson correlation (≈ 0.71 vs. 0.37) relative to baseline methods. Importantly, TransPlatformer preserves rare but biologically meaningful over- and under-expressed signals, with mean absolute error below 0.22. Single-tissue models yield further improvements for well-represented organs, such as a 10% reduction in liver mean absolute error, while underscoring the need for data augmentation strategies in low-sample tissues.ra CONCLUSIONS: TransPlatformer provides an effective and scalable computational solution for cross-platform transcriptomic translation. By enabling biologically faithful harmonization of gene expression data, the proposed approach facilitates the reuse of legacy toxicogenomics datasets, enhances downstream biomarker discovery, and supports more reproducible predictive modeling in toxicology.

We are motivated by newly proposed methods for mining large-scale corpora of scholarly publications (e.g., full biomedical literature), which consists of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover relationships among concepts. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as an all-pairs shortest paths (APSP) and validate connective paths against curated biomedical knowledge graphs (e.g., Spoke). In this context, we present Coast (Exascale Communication-Optimized All-Pairs Shortest Path) and demonstrate 1.004 EF/s on 9,200 Frontier nodes (73,600 GCDs). We develop hyperbolic performance models (HYPERMOD), which guide optimizations and parametric tuning. The proposed Coast algorithm achieved the memory constant parallel efficiency of 99% in the single-precision tropical semiring. Looking forward, Coast will enable the integration of scholarly corpora like PubMed into the Spoke biomedical knowledge graph.

This study aims to effectively analyze and visualize the concept to concept network derived from the COVID-19 Open Research Dataset (CORD-19) dataset, where we have more than 48,000 concepts with more than 300,000 relationships between concepts. In analyzing networks, we focus on finding relationship patterns between the coronavirus disease 2019 (COVID-19) concepts and other concepts. Given the node and edge datasets, we construct directional graphs and calculate all pair shortest paths based on multiple edge weight schemes. However, statistical metrics are not sufficient to identify specific relationships represented in the network. Therefore, we also propose a visual analytics approach to effectively understand the knowledge graph. Our highly interactive visual analytics allows users to effectively analyze the evolving graphs and (COVID-19) concept nodes and other nodes related to the COVID-19 nodes. We envision that this study will pave the path to develop strategies to provide more accurate and scalable predictive analysis on knowledge graphs related to CORD19 and other biomedical knowledge graphs.

Though robustness and resilience are commonly quoted as features of neuromorphic computing systems, the expected performance of neuromorphic systems in the face of hardware failures is not clear. In this work, we study the effect of failures on the performance of four different training algorithms for spiking neural networks on neuromorphic systems: two back-propagation-based training approaches (Whetstone and SLAYER), a liquid state machine or reservoir computing approach, and an evolutionary optimization-based approach (EONS). We show that these four different approaches have very different resilience characteristics with respect to simulated hardware failures. We then analyze an approach for training more resilient spiking neural networks using the evolutionary optimization approach. We show how this approach produces more resilient networks and discuss how it can be extended to other spiking neural network training approaches as well.

Designing spiking neural networks for neuromorphic deployment is a non-trivial task. It is further complicated when there are resource constraints for the neuromorphic implementation, such as size or power constraints, that may be present in edge applications. In this work, we utilize a previously presented approach, EONS, to design spiking neural networks for a memristive neuromorphic implementation for scientific data applications. We specifically use a multi-objective approach in EONS to maximize network accuracy on the scientific data application task, but also to minimize network size and energy. We illustrate that EONS determines both the network structure and the parameters, removing the burden from the user on determining the appropriate spiking neural network structure, and we show that the resulting networks are very different from the layered structure of typical neural networks. Finally, we show that the multi-objective approach produces smaller, more energy efficient networks than the original EONS approach and produces comparable accuracy to a back-propagation style training approach.

We are motivated by newly proposed methods for data mining large-scale corpora of scholarly publications, such as the full biomedical literature, which may consist of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover how concepts relate to one another. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as one of computing all-pairs shortest paths (APSP), which becomes a significant bottleneck. In this context, we present a new high-performance algorithm and implementation of the Floyd-Warshall algorithm for distributed-memory parallel computers accelerated by GPUs, which we call DSNAPSHOT (Distributed Accelerated Semiring All-Pairs Shortest Path). For our largest experiments, we ran DSNAPSHOT on a connected input graph with millions of vertices using 4, 096nodes (24,576GPUs) of the Oak Ridge National Laboratory's Summit supercomputer system. We find DSNAPSHOT achieves a sustained performance of $136\times 10^{15}$ floating-point operations per second (136petaflop/s) at a parallel efficiency of 90% under weak scaling and, in absolute speed, 70% of the best possible performance given our computation (in the single-precision tropical semiring or “min-plus” algebra). Looking forward, we believe this novel capability will enable the mining of scholarly knowledge corpora when embedded and integrated into artificial intelligence-driven natural language processing workflows at scale.

Deep learning is actively used in a wide range of fields for scientific discovery. To effectively apply deep learning to a particular problem, it is important to select an appropriate network architecture and other hyper-parameters (at each layer). Evolving architectures and hyper-parameters using a genetic algorithm is one current approach to search the huge space of all possible configurations to find those more optimal for the problem. However, examining an evolutionary process and tuning the genetic algorithm are challenging, pushing most users to treat the process as a black box. To address this challenge, we propose a visualization system for evolutionary neural networks for deep learning. The key feature of our visualization system is to provide a visual analytics environment for evaluating a genetic algorithm in order to improve the underlying operations to reduce time to find good solutions. Our system is able to not only visualize how a genetic algorithm traverses its search space but also allows users to examine evolving networks in-depth to get insights to improve performance through interactive visualization components.

Designing a neuromorphic computing system involves selection of several hyperparameters that not only affect the accuracy of the framework, but also the energy efficiency and speed of inference and training. These hyperparameters might be inherent to the training of the spiking neural network (SNN), the input/output encoding of the real-world data to spikes, or the underlying neuromorphic hardware. In this work, we present a Bayesian-based hyperparameter optimization approach for spiking neuromorphic systems, and we show how this optimization framework can lead to significant improvement in designing accurate neuromorphic computing systems. In particular, we show that this hyperparameter optimization approach can discover the same optimal hyperparameter set for input encoding as a grid search, but with far fewer evaluations and far less time. We also show the impact of hardware-specific hyperparameters on the performance of the system, and we demonstrate that by optimizing these hyperparameters, we can achieve significantly better application performance.

Deep learning, through the use of neural networks, has demonstrated remarkable ability to automate many routine tasks when presented with sufficient data for training. The neural network architecture (e.g. number of layers, types of layers, connections between layers, etc.) plays a critical role in determining what, if anything, the neural network is able to learn from the training data. The trend for neural network architectures, especially those trained on ImageNet, has been to grow ever deeper and more complex. The result has been ever increasing accuracy on benchmark datasets with the cost of increased computational demands. In this paper we demonstrate that neural network architectures can be automatically generated, tailored for a specific application, with dual objectives: accuracy of prediction and speed of prediction. Using MENNDL- an HPC-enabled software stack for neural architecture search-we generate a neural network with comparable accuracy to state-of-the-art networks on a cancer pathology dataset that is also 16× faster at inference. The speedup in inference is necessary because of the volume and velocity of cancer pathology data; specifically, the previous state-of-the-art networks are too slow for individual researchers without access to HPC systems to keep pace with the rate of data generation. Our new model enables researchers with modest computational resources to analyze newly generated data faster than it is collected.

As deep neural networks have been deployed in more and more applications over the past half decade and are finding their way into an ever increasing number of operational systems, their energy consumption becomes a concern whether running in the datacenter or on edge devices. Hyperparameter optimization and automated network design for deep learning is a quickly growing field, but much of the focus has remained only on optimizing for the performance of the machine learning task. In this work, we demonstrate that the best performing networks created through this automated network design process have radically different computational characteristics (e.g. energy usage, model size, inference time), presenting the opportunity to utilize this optimization process to make deep learning networks more energy efficient and deployable to smaller devices. Optimizing for these computational characteristics is critical as the number of applications of deep learning continues to expand.

Current deep learning approaches have been very successful using convolutional neural networks trained on large graphical-processing-unit-based computers. Three limitations of this approach are that (1) they are based on a simple layered network topology, i.e., highly connected layers, without intra-layer connections; (2) the networks are manually configured to achieve optimal results, and (3) the implementation of the network model is expensive in both cost and power. In this article, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing to automatically determine network topology, and neuromorphic computing for a low-power hardware implementation. We use the MNIST dataset for our experiment, due to input size limitations of current quantum computers. Our results show the feasibility of using the three architectures in tandem to address the above deep learning limitations. We show that a quantum computer can find high quality values of intra-layer connection weights in a tractable time as the complexity of the network increases, a high performance computer can find optimal layer-based topologies, and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware.

Deep learning offers new tools to improve our understanding of many important scientific problems. Neutrinos are the most abundant particles in existence and are hypothesized to explain the matter-antimatter asymmetry that dominates our universe. Definitive tests of this conjecture require a detailed understanding of neutrino interactions with a variety of nuclei. Many measurements of interest depend on vertex reconstruction — finding the origin of a neutrino interaction using data from the detector, which can be represented as images. Traditionally, this has been accomplished by utilizing methods that identify the tracks coming from the interaction. However, these methods are not ideal for interactions where an abundance of tracks and cascades occlude the vertex region. Manual algorithm engineering to handle these challenges is complicated and error prone. Deep learning extracts rich, semantic features directly from raw data, making it a promising solution to this problem. In this work, deep learning models are presented that classify the vertex location in regions meaningful to the domain scientists improving their ability to explore more complex interactions.

No abstract available.

Diabetic retinopathy (DR) is a leading cause of blindness and common complication of diabetes. Many diabetic patients take antihypertensive drugs to prevent cardiovascular problems, but these drugs may have unintended consequences on eyesight. Six common classes of antihypertensive drug are angiotensin converting enzyme (ACE) inhibitors, alpha blockers, angiotensin receptor blockers (ARBs), β-blockers, calcium channel blockers, and diuretics. Analysis of medical history data might indicate which of these drugs provide safe blood pressure control, and a literature review is often used to guide such analyses. Beyond manual reading of relevant publications, we sought to identify quantitative trends in literature from the biomedical database PubMed to compare with quantitative trends in the clinical data. By recording and analyzing PubMed search results, we found wide variation in the prevalence of each antihypertensive drug in DR literature. Drug classes developed more recently such as ACE inhibitors and ARBs were most prevalent. We also identified instances of change-over-time in publication patterns. We then compared these literature trends to a dataset of 500 diabetic patients from the UT Hamilton Eye Institute. Data for each patient included class of antihypertensive drug, presence and severity of DR. Graphical comparison revealed that older drug classes such as diuretics, calcium channel blockers, and β-blockers were much more prevalent in the clinical data than in the DR and antihypertensive literature. Finally, quantitative analysis of the dataset revealed that patients taking β-blockers were statistically more likely to have DR than patients taking other medications, controlling for presence of hypertension and year of diabetes onset. This finding was concerning given the prevalence of β-blockers in the clinical data. We determined that clinical use of β-blockers should be minimized in diabetic patients to prevent retinal damage.

In a world where large-scale text collections are not only becoming ubiquitous but also are growing at increasing rates, near duplicate documents are becoming a growing concern that has the potential to hinder many different information filtering tasks. While others have tried to address this problem, prior techniques have only been used on limited collection sizes and static cases. We will briefly describe the problem in the context of Open Source analysis along with our additional constraints for performance. In this work we propose two variations on Multi-dimensional Spectral Hash (MDSH) tailored for working on extremely large, growing sets of text documents. We analyze the memory and runtime characteristics of our techniques and provide an informal analysis of the quality of the near-duplicate clusters produced by our techniques.

Enterprise networks are comprised of thousands of interconnected computer hosts, each of which is capable of creating, removing, and exchanging data according to the needs of their users. Thus, the distribution of high-value, sensitive, and proprietary information across enterprise networks is poorly managed and understood. A significant technology gap in information security is the inability to automatically quantify the value of the information contained on each host in a network. Such insight would allow an enterprise to scale its defenses, react intelligently to an intrusion, manage its configuration audits, and understand the leak potential in the event that a host is compromised. This paper outlines a novel approach to the automated determination of the value of the information contained on a host computer. It involves the classification of each text document on the host machine using the frequency of the document's terms and phrases. A host information value is computed using an enterprise-defined weighting schema and applying it to a host's document distribution. The method is adaptable to specific organizational information needs, requires manual intervention only during schema creation, and is repeatable and consistent regardless of changes in information on the host machines.

Abstract—Most commercial intrusion detections systems (IDS) can produce a very high volume of alerts, and are typically plagued by a high false positive rate. The approach described here uses Splunk to aggregate IDS alerts. The aggregated IDS alerts are retrieved from Splunk programmatically and are then clustered using text analysis and visualized using a sunburst diagram to provide an additional understanding of the data. The equivalent of what the cluster analysis and visualization provides would require numerous detailed queries using Splunk and considerable manual effort. Keywords-hierarchical clustering, sunburst visualization, IDS analysis, vector space model I.

Assessing the potential property and social impacts of an event, such as tornado or wildfire, continues to be a challenging research area. From financial markets to disaster management to epidemiology, the importance of understanding the impacts that events create cannot be understated. Our work describes an approach to fuse information from multiple sources, then to analyze the information cycles to identify prior temporal patterns related to the impact of an event. This approach is then applied to the analysis of news reports from multiple news sources pertaining to several different natural disasters. Results show that our approach can project the severity of the impacts of certain natural disasters, such as heat waves on droughts and wild fires. In addition, results show that specific types of disaster consistently produce similar impacts when each time they occur.

There exists an enormous amount of information available via the Internet. Much of this data is in the form of text-based documents. These documents cover a variety of topics that are vitally important to the scientific, business, and defense/security communities. Currently, there are a many techniques for processing and analyzing such data. However, the ability to quickly characterize a large set of documents still proves challenging. Previous work has successfully demonstrated the use of a genetic algorithm for providing a representative subset for text documents via adaptive sampling. In this work, we further expand and explore this approach on much larger data sets using a parallel Genetic Algorithm (GA) with adaptive parameter control. Experimental results are presented and discussed.