We describe a series of novel computational models, CERENKOV (Computational Elucidation of the REgulatory NonKOding Variome) and its successors CERENKOV2, CERENKOV3, and Convolutional CERENKOV3, for discriminating regulatory single nucleotide polymorphisms (rSNPs) from non-regulatory SNPs within non-coding genetic loci. The CERENKOV models are designed for recognizing rSNPs in the context of...
With the development of technologies in genome sequencing and variant detection, a huge number of variants are detected. To further analyze the variants, it requires an efficient tool to annotate the functional effect of variants. This project managed to develop an efficient program to annotate the functional effect of variants...
An important impact of the genome technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer and the selection of cancer treatment. Integrated with current well-studied massive knowledge and findings about the role of protein-coding mutations in cancer, demystifying the functional...
A project is described wherein a source code browser was implemented based upon tasks performed by software engineers looking for source code modules with only UNIX utilities. These tasks were discovered by observing the actions of software engineers looking for code modules in a library, The success of the implementation...
Causal inference is an important analytical tool to bridge the gap between prediction and decision-making. However, learning a causal network solely from data is a challenging task. In this work, various techniques have been explored for a better and improved causal network learning from data. Firstly, the problem of learning...
Ph.D. candidate Qi Wei's thesis consists of two projects: Chemotherapy Project: a study based on the research paper "Predicting chemotherapy response of various cancer types using a variational auto-encoder approach" submitted to the bioRxiv preprint archive and accepted by the BMC bioinformatics; and Wound Monitor Project: implementing and assessing analytics...
Historically, coding theory has dealt with binary
codes correcting symmetric errors, in which errors are
made in both 0 and 1 bits with equal likelihood.
Within the past ten years, some study has been made of
asymmetric codes, under the assumption that the only
errors which occur are errors in...
A radix 2n non-restoring division algorithm is described. The
algorithm is designed to be compatible with hardware multiprecision
multiplication methods currectly used in high speed digital computers.
This enables the use of the same hardware, with only changes in
control logic, to be used to implement both multiplication and
division....
The practice of literate programming is not widespread because existing literate programming systems have some undesirable characteristics such as programming language and text processor dependence and lack of flexible tools for viewing and manipulation of the source file. This dissertation describes the literate programming system AOPS (Abstraction Oriented Programming System)...
Understanding of techniques that can be used to develop software for various parallel machines has not fully matched the dramatic progress in hardware in recent years. Most parallel programming techniques have been closely tied to specific hardware. Different machines have different primitives and architectures. Programming and porting an application with...