MersV1, Main, Exploration, bibRecord, 002A99

Constructing Treatment Portfolios Using Affinity Propagation

Identifieur interne : 002A99 ( Main/Exploration ); précédent : 002A98; suivant : 002B00

Constructing Treatment Portfolios Using Affinity Propagation

Auteurs : Delbert Dueck [Canada] ; Brendan J. Frey [Canada] ; Nebojsa Jojic [États-Unis] ; Vladimir Jojic [Canada, États-Unis] ; Guri Giaever [Canada] ; Andrew Emili [Canada] ; Gabe Musso [Canada] ; Robert Hegele [Canada]

Source :

Lecture Notes in Computer Science [ 0302-9743 ]

RBID : ISTEX:4E2DB7E9E3E0FA02EC2790BF840D404B35FFA7E1

Abstract

Abstract: A key problem of interest to biologists and medical researchers is the selection of a subset of queries or treatments that provide maximum utility for a population of targets. For example, when studying how gene deletion mutants respond to each of thousands of drugs, it is desirable to identify a small subset of genes that nearly uniquely define a drug ‘footprint’ that provides maximum predictability about the organism’s response to the drugs. As another example, when designing a cocktail of HIV genome sequences to be used as a vaccine, it is desirable to identify a small number of sequences that provide maximum immunological protection to a specified population of recipients. We refer to this task as ‘treatment portfolio design’ and formalize it as a facility location problem. Finding a treatment portfolio is NP-hard in the size of portfolio and number of targets, but a variety of greedy algorithms can be applied. We introduce a new algorithm for treatment portfolio design based on similar insights that made the recently-published affinity propagation algorithm work quite well for clustering tasks. We demonstrate this method using the two problems described above: selecting a subset of yeast genes that act as a drug-response footprint, and selecting a subset of vaccine sequences that provide maximum epitope coverage for an HIV genome population.

Url:

https://api.istex.fr/ark:/67375/HCB-SSMVNFLT-L/fulltext.pdf

DOI: 10.1007/978-3-540-78839-3_31

Affiliations:

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Le document en format XML

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Constructing Treatment Portfolios Using Affinity Propagation

Constructing Treatment Portfolios Using Affinity Propagation

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Abstract

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