Structured output prediction of anti-cancer drug activity

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Abstract

We present a structured output prediction approach for classifying potential anti-cancer drugs. Our QSAR model takes as input a description of a molecule and predicts the activity against a set of cancer cell lines in one shot. Statistical dependencies between the cell lines are encoded by a Markov network that has cell lines as nodes and edges represent similarity according to an auxiliary dataset. Molecules are represented via kernels based on molecular graphs. Margin-based learning is applied to separate correct multilabels from incorrect ones. The performance of the multilabel classification method is shown in our experiments with NCI-Cancer data containing the cancer inhibition potential of drug-like molecules against 59 cancer cell lines. In the experiments, our method outperforms the state-of-the-art SVM method.
Original languageEnglish
Title of host publicationPattern Recognition in Bioinformatics
Subtitle of host publication5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings
EditorsTjeerd M. H. Dijkstra, Evgeni Tsivtsivadze, Elena Marchiori, Tom Heskes
PublisherSpringer-Verlag
Pages38-49
ISBN (Electronic)978-3-642-16001-1
ISBN (Print)978-3-642-16000-4
DOIs
Publication statusPublished - 2010
MoE publication typeA4 Article in a conference publication
EventIAPR International Conference on Pattern Recognition in Bioinformatics - Nijmegen, Netherlands
Duration: 22 Sep 201024 Sep 2010
Conference number: 5

Publication series

Name Lecture Notes in Computer Science
PublisherSpringer
Volume6282
ISSN (Print)0302-9743

Conference

ConferenceIAPR International Conference on Pattern Recognition in Bioinformatics
Abbreviated titlePRIB
CountryNetherlands
CityNijmegen
Period22/09/201024/09/2010

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  • Cite this

    Su, H., Heinonen, M., & Rousu, J. (2010). Structured output prediction of anti-cancer drug activity. In T. M. H. Dijkstra, E. Tsivtsivadze, E. Marchiori, & T. Heskes (Eds.), Pattern Recognition in Bioinformatics: 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings (pp. 38-49). ( Lecture Notes in Computer Science; Vol. 6282). Springer-Verlag. https://doi.org/10.1007/978-3-642-16001-1_4