Exact and Heuristic Algorithms for Constrained Biclustering

Abstract

Biclustering, also known as co-clustering or two-way clustering, simultaneously partitions the rows and columns of a data matrix to reveal submatrices with coherent patterns. Incorporating background knowledge into clustering to enhance solution quality and interpretability has attracted growing interest in mathematical optimization and machine learning research. Extending this paradigm to biclustering enables prior information to guide the joint grouping of rows and columns. We study constrained biclustering with pairwise constraints, namely must-link and cannot-link constraints, which specify whether objects should belong to the same or different biclusters. As a model problem, we address the constrained version of the k-densest disjoint biclique problem, which aims to identify k disjoint complete bipartite subgraphs (called bicliques) in a weighted complete bipartite graph, maximizing the total density while satisfying pairwise constraints. We propose both exact and heuristic algorithms. The exact approach is a tailored branch-and-cut algorithm based on a low-dimensional semidefinite programming (SDP) relaxation, strengthened with valid inequalities and solved in a cutting-plane fashion. Exploiting integer programming tools, a rounding scheme converts SDP solutions into feasible biclusterings at each node. For large-scale instances, we introduce an efficient heuristic based on the low-rank factorization of the SDP. The resulting nonlinear optimization problem is tackled with an augmented Lagrangian method, where the subproblem is solved by decomposition through a block-coordinate projected gradient algorithm. Extensive experiments on synthetic and real-world datasets show that the exact method significantly outperforms general-purpose solvers, while the heuristic achieves high-quality solutions efficiently on large instances.