A Computational Framework for Learning from Complex Data: Formulations, Algorithms, and Applications

<p>Many real-world processes are dynamically changing over time. As a consequence, the observed complex data generated by these processes also evolve smoothly. For example, in computational biology, the expression data matrices are evolving, since gene expression controls are deployed sequentially during development in many biological processes. Investigations into the spatial and temporal gene expression dynamics are essential for understanding the regulatory biology governing development. In this dissertation, I mainly focus on two types of complex data: genome-wide spatial gene expression patterns in the model organism fruit fly and Allen Brain Atlas mouse brain data. I provide a framework to explore spatiotemporal regulation of gene expression during development. I develop evolutionary co-clustering formulation to identify co-expressed domains and the associated genes simultaneously over different temporal stages using a mesh-generation pipeline. I also propose to employ the deep convolutional neural networks as a multi-layer feature extractor to generate generic representations for gene expression pattern in situ hybridization (ISH) images. Furthermore, I employ the multi-task learning method to fine-tune the pre-trained models with labeled ISH images. My proposed computational methods are evaluated using synthetic data sets and real biological data sets including the gene expression data from the fruit fly BDGP data sets and Allen Developing Mouse Brain Atlas in comparison with baseline existing methods. Experimental results indicate that the proposed representations, formulations, and methods are efficient and effective in annotating and analyzing the large-scale biological data sets.</p>

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Computer Science

Year dc:date.available

2016

Author dc:creator

• Zhang, Wenlu

Contributors dc:contributor

• Shuiwang Ji
• Andrey Chernikov
• Nikos Chrisochoides
• Christopher Osgood

• Clustering
• Deep learning
• Image analysis
• Transfer learning
• Bioinformatics
• Computer Sciences

Statement dc:rights

• <p>In Copyright. URI: <a href="http://rightsstatements.org/vocab/InC/1.0/">http://rightsstatements.org/vocab/InC/1.0/</a> This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).</p>

Identifier

9781369183627

OAI identifier oai:identifier

oai:digitalcommons.odu.edu:computerscience_etds-1018