Lattice-based biclustering using Partition Pattern Structures

In this work we present a novel technique for exhaustive bicluster enumeration using formal concept analysis (FCA). Particularly, we use pattern structures (an extension of FCA dealing with complex data) to mine similar row/column biclusters, a specialization of biclustering when attribute values have coherent variations. We show how biclustering can benefit from the FCA framework through its robust theoretical description and efficient algorithms. Finally, we evaluate our bicluster mining approach w.r.t. a standard biclustering technique showing very good results in terms of bicluster quality and performance.

[1]  Jin-Kao Hao,et al.  Survey on Biclustering of Gene Expression Data , 2013 .

[2]  Derrick G. Kourie,et al.  AddIntent: A New Incremental Algorithm for Constructing Concept Lattices , 2004, ICFCA.

[3]  Sergei O. Kuznetsov,et al.  Comparing performance of algorithms for generating concept lattices , 2002, J. Exp. Theor. Artif. Intell..

[4]  Bernhard Ganter,et al.  Formal Concept Analysis: Mathematical Foundations , 1998 .

[5]  Amedeo Napoli,et al.  Biclustering meets triadic concept analysis , 2013, Annals of Mathematics and Artificial Intelligence.

[6]  Vipin Kumar,et al.  An association analysis approach to biclustering , 2009, KDD.

[7]  Bernhard Ganter,et al.  Pattern Structures and Their Projections , 2001, ICCS.

[8]  Amedeo Napoli,et al.  Characterizing functional dependencies in formal concept analysis with pattern structures , 2014, Annals of Mathematics and Artificial Intelligence.

[9]  Michelangelo Ceci,et al.  A Novel Biclustering Algorithm for the Discovery of Meaningful Biological Correlations between microRNAs and their Target Genes , 2013, BMC Bioinformatics.

[10]  Amedeo Napoli,et al.  Revisiting Numerical Pattern Mining with Formal Concept Analysis , 2011, IJCAI.

[11]  Sadaaki Miyamoto,et al.  Lattice-Valued Hierarchical Clustering for Analyzing Information Systems , 2006, RSCTC.

[12]  Sergei O. Kuznetsov,et al.  Galois Connections in Data Analysis: Contributions from the Soviet Era and Modern Russian Research , 2005, Formal Concept Analysis.

[13]  Arlindo L. Oliveira,et al.  Biclustering algorithms for biological data analysis: a survey , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[14]  George M. Church,et al.  Biclustering of Expression Data , 2000, ISMB.

[15]  Amedeo Napoli,et al.  Biclustering Numerical Data in Formal Concept Analysis , 2011, ICFCA.