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Many scientific computing problems can be reduced to Matrix-Matrix Multiplications (MMM), making the General Matrix Multiply (GEMM) kernels in the Basic Linear Algebra Subroutine (BLAS) of interest to the high-performance computing…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…
We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…
Generalized linear mixed-effects models (GLMMs) are widely used to analyze grouped and hierarchical data. In a GLMM, each response is assumed to follow an exponential-family distribution where the natural parameter is given by a linear…
The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However,…
Quantized neural networks typically require smaller memory footprints and lower computation complexity, which is crucial for efficient deployment. However, quantization inevitably leads to a distribution divergence from the original…
Recently, Deep Neural Networks (DNNs) have recorded great success in handling medical and other complex classification tasks. However, as the sizes of a DNN model and the available dataset increase, the training process becomes more complex…
Weakly supervised learning generally faces challenges in applicability to various scenarios with diverse weak supervision and in scalability due to the complexity of existing algorithms, thereby hindering the practical deployment. This…
Combining data from several case-control genome-wide association (GWA) studies can yield greater efficiency for detecting associations of disease with single nucleotide polymorphisms (SNPs) than separate analyses of the component studies.…
Gaussian Mixture Models (GMMs) range among the most frequently used models in machine learning. However, training large, general GMMs becomes computationally prohibitive for datasets that have many data points $N$ of high-dimensionality…
This paper considers parallel Gr\"obner bases algorithms on distributed memory parallel computers with multi-core compute nodes. We summarize three different Gr\"obner bases implementations: shared memory parallel, pure distributed memory…
Supporting multiple partial computations efficiently at each of the workers is a keystone in distributed coded computing in order to speed up computations and to fully exploit the resources of heterogeneous workers in terms of…
Genome-wide association studies (GWA studies or GWAS) investigate the relationships between genetic variants such as single-nucleotide polymorphisms (SNPs) and individual traits. Recently, incorporating biological priors together with…
General-purpose optical accelerators (GOAs) have emerged as a promising platform to accelerate deep neural networks (DNNs) due to their low latency and energy consumption. Such an accelerator is usually composed of a given number of…
Transcriptome-wide association studies (TWAS) link genetic variation to complex traits by leveraging expression quantitative trait loci (eQTL) data. However, most implementations are typically limited to local (cis-acting) effects and fail…
One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association…
Generative Adversarial Networks (GANs) are formulated as minimax game problems, whereby generators attempt to approach real data distributions by virtue of adversarial learning against discriminators. The intrinsic problem complexity poses…
Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…
General-purpose processor vendors have integrated customized accelerator in their products due to the widespread use of General Matrix-Matrix Multiplication (GEMM) kernels. However, it remains a challenge to further improve the…
The generalized winding number (GWN) is a scalar field that supports robust containment queries on curved geometry, including non-watertight, overlapping, and nested boundary representations. While queries can be easily parallelized over…