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Testing of synchronous reactive systems is challenging because long input sequences are often needed to drive them into a state at which a desired feature can be tested. This is particularly problematic in on-target testing, where a system…
The HPC community is actively researching and evaluating tools to support execution of scientific applications in cloud-based environments. Among the various technologies, containers have recently gained importance as they have…
Data analyses in the life sciences are moving from tools run on a personal computer to services run on large computing platforms. This creates a need to package tools and dependencies for easy installation, configuration and deployment on…
Containers offer an array of advantages that benefit research reproducibility and portability across groups and systems. As container tools mature, container security improves, and High-performance computing (HPC) and cloud system tools…
Studies show that neural networks, not unlike traditional programs, are subject to bugs, e.g., adversarial samples that cause classification errors and discriminatory instances that demonstrate the lack of fairness. Given that neural…
The Liquid Argon Time Projection Chamber (LArTPC) technology plays an essential role in many current and future neutrino experiments. Accurate and fast simulation is critical to developing efficient analysis algorithms and precise physics…
Exascale computers will offer transformative capabilities to combine data-driven and learning-based approaches with traditional simulation applications to accelerate scientific discovery and insight. These software combinations and…
This system paper documents the technical foundations for the extension of the Topology ToolKit (TTK) to distributed-memory parallelism with the Message Passing Interface (MPI). While several recent papers introduced topology-based…
Cycle-accurate software simulation of multicores with complex microarchitectures is often excruciatingly slow. People use simplified core models to gain simulation speed. However, a persistent question is to what extent the results derived…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…
The explosive growth of multimodal data - spanning text, image, video, spatial, and relational modalities, coupled with the need for real-time semantic search and retrieval over these data - has outpaced the capabilities of existing…
We propose Chunks and Tasks, a parallel programming model built on abstractions for both data and work. The application programmer specifies how data and work can be split into smaller pieces, chunks and tasks, respectively. The Chunks and…
This note provides a description of a procedure that is designed to efficiently optimize expensive black-box functions. It uses the response surface methodology by incorporating radial basis functions as the response model. A simple method…
In today's world data is being generated at a high rate due to which it has become inevitable to analyze and quickly get results from this data. Most of the relational databases primarily support SQL querying with a limited support for…
The purpose of this paper is to show how existing scientific software can be parallelized using a separate thin layer of Python code where all parallel communication is implemented. We provide specific examples on such layers of code, and…
This article describes SimEngine, an open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments. Several R packages exist for structuring…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
We extended our simulation tool Ntccrt for probabilistic ntcc (pntcc) models. In addition, we developed a verification tool for pntcc models. Using this tool we can prove properties such as the system will go to a successful state with…
This paper presents the outcome of a research collaboration between academia and industry to implement and utilize the capabilities of constrained interaction testing for an open-source tool for industrial-scale application. The project…