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Modeling major histocompatibility complex binding by nonparametric averaging of multiple predictors and sequence encodings
- Source :
- Journal of Immunological Methods. 374:35-42
- Publication Year :
- 2011
- Publisher :
- Elsevier BV, 2011.
-
Abstract
- There has been considerable interest in statistical approaches that leverage the large volumes of experimental data to predict the binding of Major Histocompatibility Complex class I (MHC-I) molecules to peptides. Here we present our method for averaging together multiple predictors for MHC-peptide binding, where given a particular MHC molecule, a set of predictors and a set of training peptides, our method will average multiple simple predictors for MHC binding to produce a final prediction of the binding affinity between a given MHC molecule and a test peptide. The averaging of predictors is done using a nonparametric method, whereby for any test peptide, we identify similar peptides in the training set and average the predictions on the training set, weighted by each predictor's average accuracy for similar peptides in the training set. We show that our method significantly improves on individual predictors based on held-out data and also produces a predictor whose accuracy is competitive with state-of-the-art techniques based on the results from the Machine Learning in Immunology competition in which 21 submitted techniques were assessed on their accuracy in predicting the binding of HLA-A*0101, HLA-A*0201 and HLA-B*0702 molecules to 9-mer and 10-mer peptides.
- Subjects :
- Databases, Factual
Computer science
Immunology
Cytomegalovirus
Computational biology
Bioinformatics
Major histocompatibility complex
Statistics, Nonparametric
HLA-B7 Antigen
Viral Proteins
Major histocompatibility complex binding
Artificial Intelligence
HLA Antigens
HLA-A2 Antigen
Humans
Immunology and Allergy
Leverage (statistics)
HLA-A1 Antigen
Training set
biology
Models, Immunological
Nonparametric statistics
Nonparametric regression
biology.protein
Oligopeptides
Epitope Mapping
Subjects
Details
- ISSN :
- 00221759
- Volume :
- 374
- Database :
- OpenAIRE
- Journal :
- Journal of Immunological Methods
- Accession number :
- edsair.doi.dedup.....35e59e39544b3f7287b26946fb9d534c