Methodological Review: Towards knowledge-based gene expression data mining
Journal of Biomedical Informatics
Pattern identification in pareto-set approximations
Proceedings of the 10th annual conference on Genetic and evolutionary computation
Finding Additive Biclusters with Random Background
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ACM Transactions on Knowledge Discovery from Data (TKDD)
Biclustering Expression Data Based on Expanding Localized Substructures
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Mean Square Residue Biclustering with Missing Data and Row Inversions
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
A scalable framework for discovering coherent co-clusters in noisy data
ICML '09 Proceedings of the 26th Annual International Conference on Machine Learning
An association analysis approach to biclustering
Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining
Two FCA-Based Methods for Mining Gene Expression Data
ICFCA '09 Proceedings of the 7th International Conference on Formal Concept Analysis
Linear Coherent Bi-cluster Discovery via Line Detection and Sample Majority Voting
COCOA '09 Proceedings of the 3rd International Conference on Combinatorial Optimization and Applications
Bi-clustering of Gene Expression Data Using Conditional Entropy
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
BiHEA: A Hybrid Evolutionary Approach for Microarray Biclustering
BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
An automatic gene ontology software tool for bicluster and cluster comparisons
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Binary matrix factorization for analyzing gene expression data
Data Mining and Knowledge Discovery
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE Transactions on Information Technology in Biomedicine - Special section on body sensor networks
An integrated model for visualizing biclusters from gene expression data and PPI networks
ISB '10 Proceedings of the International Symposium on Biocomputing
Virtual error: a new measure for evolutionary biclustering
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
A framework to analyze biclustering results on microarray experiments
IDEAL'07 Proceedings of the 8th international conference on Intelligent data engineering and automated learning
Methods to bicluster validation and comparison in microarray data
IDEAL'07 Proceedings of the 8th international conference on Intelligent data engineering and automated learning
MIB: Using mutual information for biclustering gene expression data
Pattern Recognition
Block clustering for web pages categorization
IDEAL'09 Proceedings of the 10th international conference on Intelligent data engineering and automated learning
Mean squared residue based biclustering algorithms
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Mining gene expression patterns for the discovery of overlapping clusters
EvoBIO'08 Proceedings of the 6th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Phoenix: privacy preserving biclustering on horizontally partitioned data
PinKDD'07 Proceedings of the 1st ACM SIGKDD international conference on Privacy, security, and trust in KDD
Bayesian dimension reduction models for microarray data
ICANNGA'09 Proceedings of the 9th international conference on Adaptive and natural computing algorithms
A network flow model for biclustering via optimal re-ordering of data matrices
Journal of Global Optimization
Discovering significant relaxed order-preserving submatrices
Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining
Comparative analysis of biclustering algorithms
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Bagged Biclustering for Microarray Data
Proceedings of the 2010 conference on ECAI 2010: 19th European Conference on Artificial Intelligence
Stability-based validation of bicluster solutions
Pattern Recognition
A novel approach for biclustering gene expression data using modular singular value decomposition
CIBB'09 Proceedings of the 6th international conference on Computational intelligence methods for bioinformatics and biostatistics
Iterated local search for biclustering of microarray data
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Bagging for biclustering: application to microarray data
ECML PKDD'10 Proceedings of the 2010 European conference on Machine learning and knowledge discovery in databases: Part I
Noise-robust algorithm for identifying functionally associated biclusters from gene expression data
Information Sciences: an International Journal
Linear coherent bi-cluster discovery via beam detection and sample set clustering
COCOA'10 Proceedings of the 4th international conference on Combinatorial optimization and applications - Volume Part I
A Combinatoric biclustering algorithm
Proceedings of the 2011 conference on Neural Nets WIRN10: Proceedings of the 20th Italian Workshop on Neural Nets
WF-MSB: A weighted fuzzy-based biclustering method for gene expression data
International Journal of Data Mining and Bioinformatics
Mining gene expression data with pattern structures in formal concept analysis
Information Sciences: an International Journal
BARTMAP: A viable structure for biclustering
Neural Networks
Mining coherent biclusters with fish school search
ICSI'11 Proceedings of the Second international conference on Advances in swarm intelligence - Volume Part II
Approximate bicluster and tricluster boxes in the analysis of binary data
RSFDGrC'11 Proceedings of the 13th international conference on Rough sets, fuzzy sets, data mining and granular computing
Simultaneous clustering: a survey
PReMI'11 Proceedings of the 4th international conference on Pattern recognition and machine intelligence
Finding bicliques in digraphs: application into viral-host protein interactome
PReMI'11 Proceedings of the 4th international conference on Pattern recognition and machine intelligence
Generating and postprocessing of biclusters from discrete value matrices
ICCCI'11 Proceedings of the Third international conference on Computational collective intelligence: technologies and applications - Volume Part I
CarGene: Characterisation of sets of genes based on metabolic pathways analysis
International Journal of Data Mining and Bioinformatics
Biclustering of expression microarray data using affinity propagation
PRIB'11 Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Parallelized Evolutionary Learning for Detection of Biclusters in Gene Expression Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The impact of feature representation to the biclustering of symptoms-herbs in TCM
PAKDD'11 Proceedings of the 15th international conference on New Frontiers in Applied Data Mining
Bi-clustering gene expression data using co-similarity
ADMA'11 Proceedings of the 7th international conference on Advanced Data Mining and Applications - Volume Part I
eBi --- the algorithm for exact biclustering
ICAISC'12 Proceedings of the 11th international conference on Artificial Intelligence and Soft Computing - Volume Part II
Ensemble methods for biclustering tasks
Pattern Recognition
Biclustering-driven ensemble of Bayesian belief network classifiers for underdetermined problems
IJCAI'11 Proceedings of the Twenty-Second international joint conference on Artificial Intelligence - Volume Volume Two
Hypergraph based geometric biclustering algorithm
Pattern Recognition Letters
International Journal of Data Mining and Bioinformatics
Techniques of biclustering in gene expression analysis
ITIB'12 Proceedings of the Third international conference on Information Technologies in Biomedicine
BiMine+: An efficient algorithm for discovering relevant biclusters of DNA microarray data
Knowledge-Based Systems
δTRIMAX: erxtracting triclusters and analysing coregulation in time series gene expression data
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Sparse learning based linear coherent bi-clustering
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
A knowledge-driven bi-clustering method for mining noisy datasets
ICONIP'12 Proceedings of the 19th international conference on Neural Information Processing - Volume Part III
A unified adaptive co-identification framework for high-d expression data
PRIB'12 Proceedings of the 7th IAPR international conference on Pattern Recognition in Bioinformatics
A conceptual approach to gene expression analysis enhanced by visual analytics
Proceedings of the 28th Annual ACM Symposium on Applied Computing
Comparative analysis of network algorithms to address modularity with gene expression temporal data
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
CoBi: Pattern Based Co-Regulated Biclustering of Gene Expression Data
Pattern Recognition Letters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
BiETopti-BiClustering ensemble using optimization techniques
ICDM'13 Proceedings of the 13th international conference on Advances in Data Mining: applications and theoretical aspects
Mining order-preserving submatrices from probabilistic matrices
ACM Transactions on Database Systems (TODS)
A new measure for gene expression biclustering based on non-parametric correlation
Computer Methods and Programs in Biomedicine
A continuous characterization of the maximum-edge biclique problem
Journal of Global Optimization
A Probabilistic Latent Semantic Analysis Model for Coclustering the Mouse Brain Atlas
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Extracting and validating biclusters from binary datasets
AI Communications
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Motivation: In recent years, there have been various efforts to overcome the limitations of standard clustering approaches for the analysis of gene expression data by grouping genes and samples simultaneously. The underlying concept, which is often referred to as biclustering, allows to identify sets of genes sharing compatible expression patterns across subsets of samples, and its usefulness has been demonstrated for different organisms and datasets. Several biclustering methods have been proposed in the literature; however, it is not clear how the different techniques compare with each other with respect to the biological relevance of the clusters as well as with other characteristics such as robustness and sensitivity to noise. Accordingly, no guidelines concerning the choice of the biclustering method are currently available. Results: First, this paper provides a methodology for comparing and validating biclustering methods that includes a simple binary reference model. Although this model captures the essential features of most biclustering approaches, it is still simple enough to exactly determine all optimal groupings; to this end, we propose a fast divide-and-conquer algorithm (Bimax). Second, we evaluate the performance of five salient biclustering algorithms together with the reference model and a hierarchical clustering method on various synthetic and real datasets for Saccharomyces cerevisiae and Arabidopsis thaliana. The comparison reveals that (1) biclustering in general has advantages over a conventional hierarchical clustering approach, (2) there are considerable performance differences between the tested methods and (3) already the simple reference model delivers relevant patterns within all considered settings. Availability: The datasets used, the outcomes of the biclustering algorithms and the Bimax implementation for the reference model are available at http://www.tik.ee.ethz.ch/sop/bimax Contact: bleuler@tik.ee.ethz.ch Supplementary information: Supplementary data are available at http://www.tik.ee.ethz.ch/sop/bimax