Abstract

In Machine Learning and Data Mining, most of the works in classification problems deal with flat classification, where each instance is classified in one of a set of possible classes and there is no hierarchical relationship between the classes. There are, however, more complex classification problems where the classes to be predicted are hierarchically related. This chapter presents a tutorial on the hierarchical classification techniques found in the literature. We also discuss how hierarchical classification techniques have been applied to the area of Bioinformatics (particularly the prediction of protein function), where hierarchical classification problems are often found.

Citations

897	Instance-Based Learning Algorithms - Aha, Kibler, et al. - 1991
775	Multi-Objective Optimization using Evolutionary Algorithms - Deb - 2001
363	Sahami M: Hierarchically classifying documents using very few words - Koller - 1997
319	PN: Introduction to data mining - Tan - 2006
71	Hierarchical text classification and evaluation - A, Lim - 2001
61	Class prediction and discovery using gene expression data - Slonim, Tamayo, et al. - 2000
46	The Gene Ontology Annotation (GOA) project: implementation - Camon, Magrane, et al. - 2003
36	R.D.: Knowledge discovery in multi-label phenotype data - Clare, King - 2001
35	Niculescu-Mizil A: Data Mining in Metric Space: An Empirical Analysis of Supervised Learning Performance Criteria - Caruana
35	Sun F: Prediction of protein function using protein-protein interaction data - Deng, Zhang, et al.
30	D (2005) Inference of protein function from protein structure Structure 13 - Pal, Eisenberg
26	Predicting gene function in Saccharomyces cerevisiae - Clare, King - 2003
26	Prediction of human protein function according to Gene Ontology categories - Jensen, Stærfeldt, et al. - 2003
26	Predicting gene function from patterns of annotation - King, Foulger, et al. - 2003
24	Dehaspe L: The utility of different representations of protein sequence for predicting functional class - RD, Karwath, et al.
22	Prediction of human protein function from post-translational modifications and localization features - LJ, Gupta, et al. - 2002
18	G: Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions - Hendlich, Bergner, et al.
17	Hierarchical multi-classification - Blockeel, Bruynooghe, et al. - 2002
17	Using a mixture of probabilistic decision trees for direct prediction of protein function - Syed, Yona - 2003
14	Gene Ontology: looking backwards and forwards - Lewis - 2005
12	Hierarchical Classification of GProtein-Coupled Receptors with a PSO/ACO Algorithm - Holden, Freitas - 2006
11	A critical review of multi-objective optimization in data mining: a position paper - Freitas - 2004
11	Brunak S: Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput - Gupta
10	Ashburner M: An Ontology for Cell Types. Genome Biology 2005 - Bard, Rhee
10	A hybrid particle swarm/ant colony algorithm for the classification of hierarchical biological data - Holden, Freitas - 2005
10	Performance Measurement Framework for Hierarchical Text Classification - Sun, Lim, et al. - 2003
9	Molecular biology of the cell, 4th ed - Alberts - 2002
9	Homology Induction: The Use of Machine Learning to Improve Sequence Similarity Searches - Karwath, King
9	Similarity Measures for Retrieval in Case-Based Reasoning - Liao, Zhang, et al. - 1998
9	Rule-based text categorization using hierarchical categories - Sasaki, Kita - 1998
8	Predicting Gene Ontology Biological Process from Temporal Gene Expression Patterns - Laegreid, Hvidsten, et al. - 2003
7	Can sequence determine function? Genome Biology - Gerlt, Babbitt - 2000
6	Bioinformatics and Molecular Evolution - Higgs, Attwood - 2005
6	Hierarchical Text Classification Methods and their - Sun, Lim, et al. - 2003
6	Learnability-Based Further Prediction of Gene Functions in Gene Ontology - Tu, Yu, et al. - 2004
5	Blocking reduction strategies in hierarchical text classification - Sun, Lim, et al. - 2004
5	Neural Networks for Protein Classification - Weinert, Lopes - 2004
2	Principles of Biochemistry with an Extended Discussion of Oxygen-Binding Proteins. (2nd Ed - Lenhinger, Nelson, et al. - 1998
1	Tolerating noisy, irrelevant and novel attributes in instance-based learning algorithms - Learning - 1992
1	Discovering Enzymes. Scientific American Library - Dressler, Potter - 1991
1	Eds.) Bioinformatics: genes, proteins, computers (pp - Orengo, Jones, et al.
1	Functions of the gene products of Eschirichia coli - Riley - 1993
1	predicting protein function from structure: unique features of Oglycosidases - in