Experimentally optimal nu in support vector regression for different noise models and parameter settings.
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Models, Theoretical↗
Biomedical subjects
Alex J Smola
Publications and source records attributed to Alex J Smola.
Protein function prediction via graph kernels.
MOTIVATION: Computational approaches to protein function prediction infer protein function by finding proteins with similar sequence, structure, surface clefts, chemical properties, amino acid motifs, interaction partners or phylogenetic profiles. We present a new approach that combines sequential, structural and chemical information into one graph model of proteins. We predict functional class membership of enzymes and non-enzymes using graph kernels and support vector machine classification on these protein graphs. RESULTS: Our graph model, derivable from protein sequence and structure only, is competitive with vector models that require additional protein information, such as the size of surface pockets. If we include this extra information into our graph model, our classifier yields significantly higher accuracy levels than the vector models. Hyperkernels allow us to select and to optimally combine the most relevant node attributes in our protein graphs. We have laid the foundation for a protein function prediction system that integrates protein information from various sources efficiently and effectively. AVAILABILITY: More information available via www.dbs.ifi.lmu.de/Mitarbeiter/borgwardt.html.
Algorithms↗
Experimentally optimal nu in support vector regression for different noise models and parameter settings.
In Support Vector (SV) regression, a parameter nu controls the number of Support Vectors and the number of points that come to lie outside of the so-called epsilon-insensitive tube. For various noise models and SV parameter settings, we experimentally determine the values of nu that lead to the lowest generalization error. We find good agreement with the values that had previously been predicted by a theoretical argument based on the asymptotic efficiency of a simplified model of SV regression. As a side effect of the experiments, valuable information about the generalization behavior of the remaining SVM parameters and their dependencies is gained. The experimental findings are valid even for complex 'real-world' data sets. Based on our results on the role of the nu-SVM parameters, we discuss various model selection methods.
Generalization, Psychological↗