Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

MATEX: A Distributed Framework for Transient Simulation of Power Distribution Networks

We proposed MATEX, a distributed framework for transient simulation of power distribution networks (PDNs). MATEX utilizes matrix exponential kernel with Krylov subspace approximations to solve differential equations of linear circuit. First, the whole simulation task is divided into subtasks based on decompositions of current sources, in order to reduce the computational overheads. Then these subtasks are distributed to different computing nodes and processed in parallel. Within each node, after the matrix factorization at the beginning of simulation, the adaptive time stepping solver is performed without extra matrix re-factorizations. MATEX overcomes the stiff-ness hinder of previous matrix exponential-based circuit simulator by rational Krylov subspace method, which leads to larger step sizes with smaller dimensions of Krylov subspace bases and highly accelerates the whole computation. MATEX outperforms both traditional fixed and adaptive time stepping methods, e.g., achieving around 13X over the trapezoidal framework with fixed time step for the IBM power grid benchmarks.Comment: ACM/IEEE DAC 2014. arXiv admin note: substantial text overlap with arXiv:1505.0669

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues