SH Muggleton
Learning Chomsky-like grammars for biological sequence families
Muggleton, SH; Bryant, CH; Srinivasan, A
Authors
Contributors
P Langley
Editor
Abstract
This paper presents a new method of measuring performance when positives are rare and investigates whether Chomsky-like grammar representations are useful for learning accurate comprehensible predictors of members of biological sequence families. The positive-only learning framework of the Inductive Logic Programming (ILP) system CProgol is used to generate a grammar for recognising a class of proteins known as human neuropeptide precursors (NPPs). As far as these authors are aware, this is both the first biological grammar learnt using ILP and the first real-world scientific application of the positive-only learning framework of CProgol. Performance is measured using both predictive accuracy and a new cost function, em Relative Advantage (RA). The RA results show that searching for NPPs by using our best NPP predictor as a filter is more than 100 times more efficient than randomly selecting proteins for synthesis and testing them for biological activity. The highest RA was achieved by a model which includes grammar-derived features. This RA is significantly higher than the best RA achieved without the use of the grammar-derived features.
Citation
Muggleton, S., Bryant, C., & Srinivasan, A. (2000). Learning Chomsky-like grammars for biological sequence families. In P. Langley (Ed.), Proceedings of the 17th International Conference on Machine Learning (631-638)
Start Date | Jun 29, 2000 |
---|---|
End Date | Jul 2, 2000 |
Publication Date | Jul 2, 2000 |
Deposit Date | Feb 16, 2009 |
Publicly Available Date | Feb 16, 2009 |
Pages | 631-638 |
Book Title | Proceedings of the 17th International Conference on Machine Learning |
ISBN | 1-55860-707-2 |
Publisher URL | https://dl.acm.org/doi/10.5555/645529.658131 |
Additional Information | Event Type : Conference |
Files
bryant_icml2k.pdf
(223 Kb)
PDF
You might also like
Pruning methods for rule induction
(2017)
Thesis
Pruning classification rules with instance reduction methods
(2015)
Journal Article
Preceding rule induction with instance reduction methods
(2013)
Conference Proceeding
Comparing the performance of object and object relational database systems on objects of varying complexity
(2012)
Conference Proceeding
Downloadable Citations
About USIR
Administrator e-mail: library-research@salford.ac.uk
This application uses the following open-source libraries:
SheetJS Community Edition
Apache License Version 2.0 (http://www.apache.org/licenses/)
PDF.js
Apache License Version 2.0 (http://www.apache.org/licenses/)
Font Awesome
SIL OFL 1.1 (http://scripts.sil.org/OFL)
MIT License (http://opensource.org/licenses/mit-license.html)
CC BY 3.0 ( http://creativecommons.org/licenses/by/3.0/)
Powered by Worktribe © 2024
Advanced Search