DNA comparisons in genomics: a reference-based perspective

Genomics is a field devoted to understanding the differences in genetics between populations, individuals, and even within individuals. By constantly comparing and contrasting data from diverse sources, genomics can refine our understanding of life and identify new ways to improve our lives. However, this often presents technical and biological...

Applications of Quantum Computation and Algorithmic Information: for Causal Modeling in Genomics and Reinforcement Learning

Efforts to realize a sufficiently large controllable quantum processor are actively being pursued globally. These quantum devices are programmed by specifying the manipulation of quantum information via quantum algorithms. This doctoral research provides an application perspective to the design requirements of a quantum accelerator architecture....

High-Performance Cluster-Scalable Computational Methods for Genomics Applications

The ever increasing pace of advancements in sequencing technologies has enabled rapid DNA/genome sequencing to become much more accessible. In particular, next (second) and third generation sequencing technologies offer high throughput, massively parallel and cost effective sequencing solutions. Individual sample sequencing data volumes as well...

Algorithms for Efficient Inference in Convolutional Neural Networks

In recent years, the accuracy of Deep Neural Networks (DNNs) has improved significantly because of three main factors: the availability of massive amounts training data, the introduction of powerful low-cost computational resources, and the development of complex deep learning models. The cloud can provide powerful computational resources to...

Methods for Efficient Integration of FPGA Accelerators with Big Data Systems

Because of fundamental limitations of CMOS technology, computing researchers and the computing industry are focusing on using transistors in integrated circuits more efficiently towards obtaining a computational goal. At the architectural level, this has led to an era of heterogeneous computing, where various types of computational components...

High Performance Seed-and-Extend Algorithms for Genomics

Recent advances in DNA sequencing technology have opened new doors for scientists to use genomic data analysis in a variety of applications that directly affect human lives. However, the analysis of unprecedented volumes of sequencing data being produced represents a formidable computational challenge. The conventional CPU-only computing...

Database Acceleration on FPGAs

Though field-programmable gate arrays (FPGAs) have been used to accelerate database systems, they have not been widely adopted for the following reasons. As databases have transitioned to higher bandwidth technology such as in-memory and NVMe, the communication overhead associated with accelerators has become more of a burden. Also, FPGAs are...

On Hardware-Accelerated Maximally-Efficient Systolic Arrays: Acceleration and Optimization of Genomics Pipelines Through Hardware/Software Co-Design

Developments in sequencing technology have drastically reduced the cost of DNA sequencing. The raw sequencing data being generated requires processing through computationally demanding suites of bioinformatics algorithms called genomics pipelines. The greatly decreased cost of sequencing has resulted in its widespread adoption, and the amount of...

Accelerating DNA Variant Calling Algorithms on High Performance Computing Systems

Next generation sequencing (NGS) technologies have transformed the landscape of genomic research. With the significant advances in NGS technologies, DNA sequencing is more affordable and accessible than ever before. Meanwhile, many DNA sequence analysis tools have been developed to derive useful information from the raw sequencing data produced...

Low power IC design characterization techniques under process variations

To overcome the increasing sensitivity to variability in nanoscale integrated circuits, operation parameters (e.g., supply voltage) are adapted in a customized way exclusively to each chip. AVS is a standard industrial technique which has been adopted widely to compensate for process, voltage, and temperature variations as well as power...