With the growing number of sequenced genomes, automatic prediction of protein function is one of the central problems in computational biology. Traditional methods employ transfer of functional annotation on the basis of sequence or structural similarity and are unable to effectively deal with today's noisy high-throughput biological data. Most of the approaches based on machine learning, on the other hand, break the problem up into a collection of binary classification problems, effectively asking the question “does this protein perform this particular function?”; such methods often produce a set of predictions that are inconsistent with each other.
In this work, we present GOstruct, a structured-output framework that answers the question “what function does this protein perform?” in the context of hierarchical multilabel classification. We show that GOstruct is able to effectively deal with a large number of disparate data sources from multiple species. Our empirical results demonstrate that the framework achieves state-of-the-art accuracy in two of the recent challenges in automatic function prediction: Mousefunc and CAFA.
|Commitee:||Anderson, Chuck, McConnell, Ross M., Wang, Haonan|
|School:||Colorado State University|
|School Location:||United States -- Colorado|
|Source:||DAI-B 73/04, Dissertation Abstracts International|
|Subjects:||Bioinformatics, Computer science|
|Keywords:||Computational biology, Gene sequencing, Machine learning, Protein function prediction|
Copyright in each Dissertation and Thesis is retained by the author. All Rights Reserved
The supplemental file or files you are about to download were provided to ProQuest by the author as part of a
dissertation or thesis. The supplemental files are provided "AS IS" without warranty. ProQuest is not responsible for the
content, format or impact on the supplemental file(s) on our system. in some cases, the file type may be unknown or
may be a .exe file. We recommend caution as you open such files.
Copyright of the original materials contained in the supplemental file is retained by the author and your access to the
supplemental files is subject to the ProQuest Terms and Conditions of use.
Depending on the size of the file(s) you are downloading, the system may take some time to download them. Please be