GP-Pi: Using Genetic Programming with Penalization and Initialization on Genome-Wide Association Study
Created by W.Langdon from
gp-bibliography.bib Revision:1.8178
- @InProceedings{conf/icaisc/Sze-ToLTWLTL13,
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author = "Ho-Yin Sze-To and Kwan-Yeung Lee and Kai-Yuen Tso and
Man Hon Wong and Kin-Hong Lee and Nelson L. S. Tang and
Kwong-Sak Leung",
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title = "{GP-Pi}: Using Genetic Programming with Penalization
and Initialization on Genome-Wide Association Study",
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bibdate = "2013-06-07",
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bibsource = "DBLP,
http://dblp.uni-trier.de/db/conf/icaisc/icaisc2013-2.html#Sze-ToLTWLTL13",
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booktitle = "Artificial Intelligence and Soft Computing - 12th
International Conference, {ICAISC} 2013, Zakopane,
Poland, June 9-13, 2013, Proceedings, Part {II}",
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publisher = "Springer",
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year = "2013",
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volume = "7895",
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editor = "Leszek Rutkowski and Marcin Korytkowski and
Rafal Scherer and Ryszard Tadeusiewicz and Lotfi A. Zadeh and
Jacek M. Zurada",
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keywords = "genetic algorithms, genetic programming",
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isbn13 = "978-3-642-38609-1",
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pages = "330--341",
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series = "Lecture Notes in Computer Science",
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URL = "http://dx.doi.org/10.1007/978-3-642-38610-7",
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DOI = "doi:10.1007/978-3-642-38610-7_31",
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abstract = "The advancement of chip-based technology has enabled
the measurement of millions of DNA sequence variations
across the human genome. Experiments revealed that
high-order, but not individual, interactions of single
nucleotide polymorphisms (SNPs) are responsible for
complex diseases such as cancer. The challenge of
genome-wide association studies (GWASs) is to sift
through high-dimensional datasets to find out
particular combinations of SNPs that are predictive of
these diseases. Genetic Programming (GP) has been
widely applied in GWASs. It serves two purposes:
attribute selection and/or discriminative modelling.
One advantage of discriminative modelling over
attribute selection lies in interpretability. However,
existing discriminative modelling algorithms do not
scale up well with the increase in the SNP dimension.
Here, we have developed GP-Pi. We have introduced a
penalising term in the fitness function to penalise
trees with common SNPs and an initialiser which uses
expert knowledge to seed the population with good
attributes. Experimental results on simulated data
suggested that GP-Pi outperforms GPAS with
statistically significance. GP-Pi was further evaluated
on a real GWAS dataset of Rheumatoid Arthritis,
obtained from the North American Rheumatoid Arthritis
Consortium. Our results, with potential new
discoveries, are found to be consistent with
literature.",
- }
Genetic Programming entries for
Ho-Yin Sze-To
Kwan-Yeung Lee
Kai-Yuen Tso
Man Hon Wong
Kin-Hong Lee
Nelson L S Tang
Kwong-Sak Leung
Citations