Mod/Resc Parsimony Inference

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.Comment: 11 pages, 3 figure

Nonnegative factorization and the maximum edge biclique problem

Nonnegative matrix factorization (NMF) is a data analysis technique based on the approximation of a nonnegative matrix with a product of two nonnegative factors, which allows compression and interpretation of nonnegative data. In this paper, we study the case of rank-one factorization and show that when the matrix to be factored is not required to be nonnegative, the corresponding problem (R1NF) becomes NP-hard. This sheds new light on the complexity of NMF since any algorithm for fixed-rank NMF must be able to solve at least implicitly such rank-one subproblems. Our proof relies on a reduction of the maximum edge biclique problem to R1NF. We also link stationary points of R1NF to feasible solutions of the biclique problem, which allows us to design a new type of biclique finding algorithm based on the application of a block-coordinate descent scheme to R1NF. We show that this algorithm, whose algorithmic complexity per iteration is proportional to the number of edges in the graph, is guaranteed to converge to a biclique and that it performs competitively with existing methods on random graphs and text mining datasets.nonnegative matrix factorization, rank-one factorization, maximum edge biclique problem, algorithmic complexity, biclique finding algorithm