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Istituto di scienza dell'alimentazione

Torna all'elenco Contributi in rivista anno 2009

Contributo in rivista

Tipo: Articolo in rivista

Titolo: A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection

Anno di pubblicazione: 2009

Formato: Elettronico

Autori: Ceccarelli M; d'Acierno A; Facchiano A

Affiliazioni autori: Michele Ceccarelli -Department of Biological and Environmental Sciences, University of Sannio, Via Port'Arsa 11, 82100, Benevento, Italy and Bioinformatics Core, BIOGEM, Ariano Irpino, Italy and Antonio d'Acierno- Institute of Food Sciences, National Research Council, Via Roma 52 A/C, Avellino,Italy Angelo Facchiano -Institute of Food Sciences, National Research Council, Via Roma 52 A/C, Avellino,Italy

Autori CNR:

  • ANTONIO D'ACIERNO
  • ANGELO FACCHIANO

Lingua: inglese

Abstract: Background Mass spectrometry spectra, widely used in proteomics studies as a screening tool for protein profiling and to detect discriminatory signals, are high dimensional data. A large number of local maxima (a.k.a. peaks) have to be analyzed as part of computational pipelines aimed at the realization of efficient predictive and screening protocols. With this kind of data dimensions and samples size the risk of over-fitting and selection bias is pervasive. Therefore the development of bio-informatics methods based on unsupervised feature extraction can lead to general tools which can be applied to several fields of predictive proteomics. Results We propose a method for feature selection and extraction grounded on the theory of multi-scale spaces for high resolution spectra derived from analysis of serum. Then we use support vector machines for classification. In particular we use a database containing 216 samples spectra divided in 115 cancer and 91 control samples. The overall accuracy averaged over a large cross validation study is 98.18. The area under the ROC curve of the best selected model is 0.9962. Conclusion We improved previous known results on the problem on the same data, with the advantage that the proposed method has an unsupervised feature selection phase. All the developed code, as MATLAB scripts, can be downloaded from http://medeaserver.isa.cnr.it/dacierno/spectracode.htm

Rivista:

BMC bioinformatics BioMed Central,
Paese di pubblicazione: Regno Unito
Lingua: inglese
ISSN: 1471-2105

Numero volume: 10

DOI: 10.1186/1471-2105-10-S12-S9

Referee: Sì: Internazionale

Indicizzato da:

  • ISI Web of Science (WOS) [000271056600010]
  • Scopus [2-s2.0-70449504251]
  • PubMed [19828085]

URL: http://www.biomedcentral.com/1471-2105/10/S12/S9

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