The problem of biclustering consists of the simultaneous clustering of rows and columns of a matrix such that each of the submatrices induced by a pair of row and column clusters is as uniform as possible. In this paper we approximate the optimal biclustering by applying one-way clustering algorithms independently on the rows and on the columns of the input matrix. We show that such a solution yields a worst-case approximation ratio of 1+2 under L"1-norm for 0-1 valued matrices, and of 2 under L"2-norm for real valued matrices.
An alternative definition of the basic biclustering problem described in the introduction consists on finding the maximal bicluster in a given matrix. A well-known connection of this alternative formulation is its reduction to the problem of finding a biclique in a bipartite graph @cite_4 . Algorithms for detecting bicliques enumerate them in the graph by using the monotonicity property that a subset of a biclique is also a biclique @cite_3 @cite_6 . These algorithms usually have a high order of complexity.
@cite_4 @cite_6 @cite_3
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We consider the problem of identifying a sparse set of relevant columns and rows in a large data matrix with highly corrupted entries. This problem of identifying groups from a collection of bipartite variables such as proteins and drugs, biological species and gene sequences, malware and signatures, etc is commonly referred to as biclustering or co-clustering. Despite its great practical relevance, and although several ad-hoc methods are available for biclustering, theoretical analysis of the problem is largely non-existent. The problem we consider is also closely related to structured multiple hypothesis testing, an area of statistics that has recently witnessed a flurry of activity. We make the following contributions 1. We prove lower bounds on the minimum signal strength needed for successful recovery of a bicluster as a function of the noise variance, size of the matrix and bicluster of interest. 2. We show that a combinatorial procedure based on the scan statistic achieves this optimal limit. 3. We characterize the SNR required by several computationally tractable procedures for biclustering including element-wise thresholding, column row average thresholding and a convex relaxation approach to sparse singular vector decomposition. Biclustering has proved to be a powerful data analysis technique due to its wide success in various application domains. However, the existing literature presents efficient solutions only for enumerating maximal biclusters with constant values, or heuristic-based approaches which can not find all biclusters or even support the maximality of the obtained biclusters. Here, we present a general family of biclustering algorithms for enumerating all maximal biclusters with (i) constant values on rows, (ii) constant values on columns, or (iii) coherent values. Versions for perfect and for perturbed biclusters are provided. Our algorithms have four key properties (just the algorithm for perturbed biclusters with coherent values fails to exhibit the first property): they are (1) efficient (take polynomial time per pattern), (2) complete (find all maximal biclusters), (3) correct (all biclusters attend the user-defined measure of similarity), and (4) non-redundant (all the obtained biclusters are maximal and the same bicluster is not enumerated twice). They are based on a generalization of an efficient formal concept analysis algorithm called In-Close2. Experimental results point to the necessity of having efficient enumerative biclustering algorithms and provide a valuable insight into the scalability of our family of algorithms and its sensitivity to user-defined parameters. We present here 2-approximation algorithms for several node deletion and edge deletion biclique problems and for an edge deletion clique problem. The biclique problem is to find a node induced subgraph that is bipartite and complete. The objective is to minimize the total weight of nodes or edges deleted so that the remaining subgraph is bipartite complete. Several variants of the biclique problem are studied here, where the problem is defined on bipartite graph or on general graphs with or without the requirement that each side of the bipartition forms an independent set. The maximum clique problem is formulated as maximizing the number (or weight) of edges in the complete subgraph. A 2-approximation algorithm is given for the minimum edge deletion version of this problem. The approximation algorithms given here are derived as a special case of an approximation technique devised for a class of formulations introduced by Hochbaum. All approximation algorithms described (and the polynomial algorithms for two versions of the node biclique problem) involve calls to a minimum cut algorithm. One conclusion of our analysis of the NP-hard problems here is that all of these problems are MAX SNP-hard and at least as difficult to approximate as the vertex cover problem. Another conclusion is that the problem of finding the minimum node cut-set, the removal of which leaves two cliques in the graph, is NP-hard and 2-approximable. Mining matrices to find relevant biclusters, subsets of rows exhibiting a coherent pattern over a subset of columns, is a critical task for a wide-set of biomedical and social applications. Since biclustering is a challenging combinatorial optimization task, existing approaches place restrictions on the allowed structure, coherence and quality of biclusters. Biclustering approaches relying on pattern mining (PM) allow an exhaustive yet efficient space exploration together with the possibility to discover flexible structures of biclusters with parameterizable coherency and noise-tolerance. Still, state-of-the-art contributions are dispersed and the potential of their integration remains unclear.This work proposes a structured and integrated view of the contributions of state-of-the-art PM-based biclustering approaches, makes available a set of principles for a guided definition of new PM-based biclustering approaches, and discusses their relevance for applications in pattern recognition. Empirical evidence shows that these principles guarantee the robustness, efficiency and flexibility of PM-based biclustering. HighlightsPattern mining (PM) searches enable flexible, exhaustive and efficient biclusteringIntegration of existing dispersed PM-inspired contributions for biclustering.Principles for guided design and evaluation of new PM-based biclustering approachesPM-based biclustering solutions have parameterizable coherency and quality.