Using Uncorrelated Discriminant Analysis for Tissue Classification with Gene Expression Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Simple and effective visual models for gene expression cancer diagnostics
Proceedings of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining
Iterative RELIEF for feature weighting
ICML '06 Proceedings of the 23rd international conference on Machine learning
Pattern classification in DNA microarray data of multiple tumor types
Pattern Recognition
Link test-A statistical method for finding prostate cancer biomarkers
Computational Biology and Chemistry
Margin Trees for High-dimensional Classification
The Journal of Machine Learning Research
Markov blanket-embedded genetic algorithm for gene selection
Pattern Recognition
Clustering gene expression data via mining ensembles of classification rules evolved using moses
Proceedings of the 9th annual conference on Genetic and evolutionary computation
Understanding microarray data through applying competent program evolution
Proceedings of the 9th annual conference on Genetic and evolutionary computation
Gene expression profile class prediction using linear Bayesian classifiers
Computers in Biology and Medicine
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Journal of Biomedical Informatics
Methodological Review: Towards knowledge-based gene expression data mining
Journal of Biomedical Informatics
Improved binary PSO for feature selection using gene expression data
Computational Biology and Chemistry
Evolutionary design of multiclass support vector machines
Journal of Intelligent & Fuzzy Systems: Applications in Engineering and Technology - VIII Brazilian Symposium on Neural Networks
Detecting reliable gene interactions by a hierarchy of Bayesian network classifiers
Computer Methods and Programs in Biomedicine
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Wrapper filtering criteria via linear neuron and kernel approaches
Computers in Biology and Medicine
On α-divergence based nonnegative matrix factorization for clustering cancer gene expression data
Artificial Intelligence in Medicine
Sparse p-norm Nonnegative Matrix Factorization for clustering gene expression data
International Journal of Data Mining and Bioinformatics
A Cost-Sensitive Approach to Feature Selection in Micro-Array Data Classification
WILF '07 Proceedings of the 7th international workshop on Fuzzy Logic and Applications: Applications of Fuzzy Sets Theory
Ensemble Neural Networks with Novel Gene-Subsets for Multiclass Cancer Classification
Neural Information Processing
APPLYING DATA MINING TECHNIQUES FOR CANCER CLASSIFICATION ON GENE EXPRESSION DATA
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Fuzzy rule induction and artificial immune systems in female breast cancer familiarity profiling
International Journal of Hybrid Intelligent Systems - Recent Advances in Intelligent Paradigms Fusion and Their Applications
Sparse p-norm Nonnegative Matrix Factorization for clustering gene expression data
International Journal of Data Mining and Bioinformatics
Survival prediction using gene expression data: A review and comparison
Computational Statistics & Data Analysis
An expert system to classify microarray gene expression data using gene selection by decision tree
Expert Systems with Applications: An International Journal
The Impact of Gene Selection on Imbalanced Microarray Expression Data
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Parallel Selection of Informative Genes for Classification
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Gene boosting for cancer classification based on gene expression profiles
Pattern Recognition
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Cancer classification using microarray and layered architecture genetic programming
Proceedings of the 11th Annual Conference Companion on Genetic and Evolutionary Computation Conference: Late Breaking Papers
International Journal of Bioinformatics Research and Applications
A Framework for Multi-class Learning in Micro-array Data Analysis
AIME '09 Proceedings of the 12th Conference on Artificial Intelligence in Medicine: Artificial Intelligence in Medicine
Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data Sets
BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Improving k-NN for Human Cancer Classification Using the Gene Expression Profiles
IDA '09 Proceedings of the 8th International Symposium on Intelligent Data Analysis: Advances in Intelligent Data Analysis VIII
AAAI'05 Proceedings of the 20th national conference on Artificial intelligence - Volume 4
IJCAI'07 Proceedings of the 20th international joint conference on Artifical intelligence
Comments on selected fundamental aspects of microarray analysis
Computational Biology and Chemistry
Microarray analysis of autoimmune diseases by machine learning procedures
IEEE Transactions on Information Technology in Biomedicine
Multi-category bioinformatics dataset classification using extreme learning machine
CEC'09 Proceedings of the Eleventh conference on Congress on Evolutionary Computation
Kernel Alignment k-NN for Human Cancer Classification Using the Gene Expression Profiles
ICANN '09 Proceedings of the 19th International Conference on Artificial Neural Networks: Part II
Ant Colony Optimisation Classification for Gene Expression Data Analysis
RSFDGrC '09 Proceedings of the 12th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
A novel measure for evaluating classifiers
Expert Systems with Applications: An International Journal
Artificial Intelligence in Medicine
The Journal of Machine Learning Research
Frequent variable sets based clustering for artificial neural networks particle classification
APWeb/WAIM'07 Proceedings of the joint 9th Asia-Pacific web and 8th international conference on web-age information management conference on Advances in data and web management
Expression microarray classification using topic models
Proceedings of the 2010 ACM Symposium on Applied Computing
Capturing heuristics and intelligent methods for improving micro-array data classification
IDEAL'07 Proceedings of the 8th international conference on Intelligent data engineering and automated learning
Identification of Full and Partial Class Relevant Genes
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Orthogonal linear discriminant analysis and feature selection for micro-array data classification
Expert Systems with Applications: An International Journal
Data mining of gene expression data by fuzzy and hybrid fuzzy methods
IEEE Transactions on Information Technology in Biomedicine
Computers in Biology and Medicine
Decision forest for classification of gene expression data
Computers in Biology and Medicine
Automated segmentation of tissue images for computerized IHC analysis
Computer Methods and Programs in Biomedicine
Mining patterns in disease classification forests
Journal of Biomedical Informatics
The Journal of Machine Learning Research
Wavelet selection for disease classification by DNA microarray data
Expert Systems with Applications: An International Journal
Supervised learning based power management for multicore processors
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Expert Systems with Applications: An International Journal
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The fuzzy gene filter: an adaptive fuzzy inference system for expression array feature selection
IEA/AIE'10 Proceedings of the 23rd international conference on Industrial engineering and other applications of applied intelligent systems - Volume Part III
A New and Fast Orthogonal Linear Discriminant Analysis on Undersampled Problems
SIAM Journal on Scientific Computing
Improving accuracy of microarray classification by a simple multi-task feature selection filter
International Journal of Data Mining and Bioinformatics
A hybrid feature selection method for DNA microarray data
Computers in Biology and Medicine
Two-Step Cross-Entropy Feature Selection for Microarrays—Power Through Complementarity
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Expert Systems with Applications: An International Journal
CHIRP: a new classifier based on composite hypercubes on iterated random projections
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Fast Kernel Discriminant Analysis for Classification of Liver Cancer Mass Spectra
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Expert Systems with Applications: An International Journal
Biclustering of expression microarray data using affinity propagation
PRIB'11 Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics
A new gene selection method based on random subspace ensemble for microarray cancer classification
PRIB'11 Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics
A comparison on score spaces for expression microarray data classification
PRIB'11 Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics
Evaluating feature selection for SVMs in high dimensions
ECML'06 Proceedings of the 17th European conference on Machine Learning
BioDM'06 Proceedings of the 2006 international conference on Data Mining for Biomedical Applications
Scoring method for tumor prediction from microarray data using an evolutionary fuzzy classifier
PAKDD'06 Proceedings of the 10th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining
Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features
Computers in Biology and Medicine
Computers and Operations Research
AIME'05 Proceedings of the 10th conference on Artificial Intelligence in Medicine
A new multi-task learning technique to predict classification of leukemia and prostate cancer
ICMB'10 Proceedings of the Second international conference on Medical Biometrics
Cancer classification by kernel principal component self-regression
AI'06 Proceedings of the 19th Australian joint conference on Artificial Intelligence: advances in Artificial Intelligence
Multivariate statistical tests for comparing classification algorithms
LION'05 Proceedings of the 5th international conference on Learning and Intelligent Optimization
Gene Classification Using Parameter-Free Semi-Supervised Manifold Learning
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An unsupervised approach to feature discretization and selection
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Model selection in omnivariate decision trees using Structural Risk Minimization
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A New Measure of Classifier Performance for Gene Expression Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Expert Systems with Applications: An International Journal
ACM Transactions on Knowledge Discovery from Data (TKDD) - Special Issue on the Best of SIGKDD 2011
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ESCAPE'07 Proceedings of the First international conference on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies
ICANN'12 Proceedings of the 22nd international conference on Artificial Neural Networks and Machine Learning - Volume Part II
Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Investigating Topic Models' Capabilities in Expression Microarray Data Classification
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Environmental Modelling & Software
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A Multiclass Classification Tool Using Cloud Computing Architecture
ASONAM '12 Proceedings of the 2012 International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2012)
Selection of interdependent genes via dynamic relevance analysis for cancer diagnosis
Journal of Biomedical Informatics
Algorithms for discovery of multiple Markov boundaries
The Journal of Machine Learning Research
Identification of micro RNA biomarkers for cancer by combining multiple feature selection techniques
Journal of Computational Methods in Sciences and Engineering
Unlabeled patterns to tighten Rademacher complexity error bounds for kernel classifiers
Pattern Recognition Letters
International Journal of Data Mining and Bioinformatics
MaskedPainter: Feature selection for microarray data analysis
Intelligent Data Analysis
Intelligent Data Analysis - Combined Learning Methods and Mining Complex Data
Diverse accurate feature selection for microarray cancer diagnosis
Intelligent Data Analysis
A novel class dependent feature selection method for cancer biomarker discovery
Computers in Biology and Medicine
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Motivation: Cancer diagnosis is one of the most important emerging clinical applications of gene expression microarray technology. We are seeking to develop a computer system for powerful and reliable cancer diagnostic model creation based on microarray data. To keep a realistic perspective on clinical applications we focus on multicategory diagnosis. To equip the system with the optimum combination of classifier, gene selection and cross-validation methods, we performed a systematic and comprehensive evaluation of several major algorithms for multicategory classification, several gene selection methods, multiple ensemble classifier methods and two cross-validation designs using 11 datasets spanning 74 diagnostic categories and 41 cancer types and 12 normal tissue types. Results: Multicategory support vector machines (MC-SVMs) are the most effective classifiers in performing accurate cancer diagnosis from gene expression data. The MC-SVM techniques by Crammer and Singer, Weston and Watkins and one-versus-rest were found to be the best methods in this domain. MC-SVMs outperform other popular machine learning algorithms, such as k-nearest neighbors, backpropagation and probabilistic neural networks, often to a remarkable degree. Gene selection techniques can significantly improve the classification performance of both MC-SVMs and other non-SVM learning algorithms. Ensemble classifiers do not generally improve performance of the best non-ensemble models. These results guided the construction of a software system GEMS (Gene Expression Model Selector) that automates high-quality model construction and enforces sound optimization and performance estimation procedures. This is the first such system to be informed by a rigorous comparative analysis of the available algorithms and datasets. Availability: The software system GEMS is available for download from http://www.gems-system.org for non-commercial use. Contact: alexander.statnikov@vanderbilt.edu