- Title Pages
- Series Foreword
- Preface
-
1 Introduction to Semi-Supervised Learning -
1 A Taxonomy for Semi-Supervised Learning Methods -
3 Semi-Supervised Text Classification Using EM -
4 Risks of Semi-Supervised Learning: How Unlabeled Data Can Degrade Performance of Generative Classifiers -
5 Probabilistic Semi-Supervised Clustering with Constraints -
6 Transductive Support Vector Machines -
7 Semi-Supervised Learning Using Semi-Definite Programming -
8 Gaussian Processes and the Null-Category Noise Model -
9 Entropy Regularization -
10 Data-Dependent Regularization -
11 Label Propagation and Quadratic Criterion -
12 The Geometric Basis of Semi-Supervised Learning -
13 Discrete Regularization -
14 Semi-Supervised Learning with Conditional Harmonic Mixing -
15 Graph Kernels by Spectral Transforms -
16 Spectral Methods for Dimensionality Reduction -
17 Modifying Distances -
18 Large-Scale Algorithms -
19 Semi-Supervised Protein Classification Using Cluster Kernels -
20 Prediction of Protein Function from Networks -
25 Analysis of Benchmarks -
22 An Augmented PAC Model for Semi-Supervised Learning -
23 Metric-Based Approaches for Semi-Supervised Regression and Classification -
24 Transductive Inference and Semi-Supervised Learning -
25 A Discussion of Semi-Supervised Learning and Transduction - References
- Notation and Symbols
- Contributors
- Index
Semi-Supervised Protein Classification Using Cluster Kernels
Semi-Supervised Protein Classification Using Cluster Kernels
- Chapter:
- (p.342) (p.343) 19 Semi-Supervised Protein Classification Using Cluster Kernels
- Source:
- Semi-Supervised Learning
- Author(s):
Weston Jason
Leslie Christina
Ie Eugene
Noble William Stafford
- Publisher:
- The MIT Press
This chapter describes an experimental study of large-scale semi-supervised learning for the problem of protein classification. The protein classification problem, a central problem in computational biology, is to predict the structural class of a protein given its amino acid sequence. Such a classification helps biologists to understand the function of a protein. Building an accurate protein classification system, as with many tasks, depends critically upon choosing a good representation of the input sequences of amino acids. Early work using string kernels with support vector machines (SVMs) for protein classification achieved state-of-the-art classification performance. However, such representations are based only on labeled data—examples with known three-dimensional (3D) structures, organized into structural classes-while in practice, unlabeled data are far more plentiful.
Keywords: semi-supervised learning, protein classification problem, computational biology, amino acid sequence, input sequences, string kernels, support vector machines, SVMs, labeled data, unlabeled data
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- Title Pages
- Series Foreword
- Preface
-
1 Introduction to Semi-Supervised Learning -
1 A Taxonomy for Semi-Supervised Learning Methods -
3 Semi-Supervised Text Classification Using EM -
4 Risks of Semi-Supervised Learning: How Unlabeled Data Can Degrade Performance of Generative Classifiers -
5 Probabilistic Semi-Supervised Clustering with Constraints -
6 Transductive Support Vector Machines -
7 Semi-Supervised Learning Using Semi-Definite Programming -
8 Gaussian Processes and the Null-Category Noise Model -
9 Entropy Regularization -
10 Data-Dependent Regularization -
11 Label Propagation and Quadratic Criterion -
12 The Geometric Basis of Semi-Supervised Learning -
13 Discrete Regularization -
14 Semi-Supervised Learning with Conditional Harmonic Mixing -
15 Graph Kernels by Spectral Transforms -
16 Spectral Methods for Dimensionality Reduction -
17 Modifying Distances -
18 Large-Scale Algorithms -
19 Semi-Supervised Protein Classification Using Cluster Kernels -
20 Prediction of Protein Function from Networks -
25 Analysis of Benchmarks -
22 An Augmented PAC Model for Semi-Supervised Learning -
23 Metric-Based Approaches for Semi-Supervised Regression and Classification -
24 Transductive Inference and Semi-Supervised Learning -
25 A Discussion of Semi-Supervised Learning and Transduction - References
- Notation and Symbols
- Contributors
- Index
