Related papers: Extreme-Scale De Novo Genome Assembly
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further…
While graph-based dynamic programming (DP) is a cornerstone of genomics and network analytics, its efficiency is hampered by fundamentally conflicting computational patterns. Matrix-centric DP drives regular, compute-bound network…
The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…
Crossbar-based PIM DNN accelerators can provide massively parallel in-situ operations. A specifically designed compiler is important to achieve high performance for a wide variety of DNN workloads. However, some key compilation issues such…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
One of the greatest efforts of computational scientists is to translate the mathematical model describing a class of physical phenomena into large and complex codes. Many of these codes face the difficulty of implementing the mathematical…
Multiple matching algorithms are used to locate the occurrences of patterns from a finite pattern set in a large input string. Aho-Corasick and Wu-Manber, two of the most well known algorithms for multiple matching require an increased…
HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand CPU-equipped nodes. It relies on sparse matrix computations…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker…
Hyper-parameter optimization is crucial for pushing the accuracy of a deep learning model to its limits. A hyper-parameter optimization job, referred to as a study, involves numerous trials of training a model using different training…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing…
Database-search algorithms, that deduce peptides from Mass Spectrometry (MS) data, have tried to improve the computational efficiency to accomplish larger, and more complex systems biology studies. Existing serial, and high-performance…
Deep neural networks have become increasingly large and sparse, allowing for the storage of large-scale neural networks with decreased costs of storage and computation. Storage of a neural network with as many connections as the human brain…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…