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.
This paper shows how to embed a similarity relation between complex descriptions in concept lattices. We formalize similarity by a tolerance relation: objects are grouped within a same concept when having similar descriptions, extending the ability of FCA to deal with complex data. We propose two different approaches. A first classical manner defines a discretization procedure. A second way consists in representing data by pattern structures, from which a pattern concept lattice can be constructed directly. In this case, considering a tolerance relation can be mathematically defined by a projection in a meet-semi-lattice. This allows to use concept lattices for their knowledge representation and reasoning abilities without transforming data. We show finally that resulting lattices are useful for solving information fusion problems. From the Publisher: This is the first textbook on formal concept analysis. It gives a systematic presentation of the mathematical foundations and their relation to applications in computer science, especially in data analysis and knowledge processing. Above all, it presents graphical methods for representing conceptual systems that have proved themselves in communicating knowledge. Theory and graphical representation are thus closely coupled together. The mathematical foundations are treated thoroughly and illuminated by means of numerous examples. Pattern structures consist of objects with descriptions (called patterns) that allow a semilattice operation on them. Pattern structures arise naturally from ordered data, e.g., from labeled graphs ordered by graph morphisms. It is shown that pattern structures can be reduced to formal contexts, however sometimes processing the former is often more efficient and obvious than processing the latter. Concepts, implications, plausible hypotheses, and classifications are defined for data given by pattern structures. Since computation in pattern structures may be intractable, approximations of patterns by means of projections are introduced. It is shown how concepts, implications, hypotheses, and classifications in projected pattern structures are related to those in original ones. A numerical dataset is usually represented by a table where each entry denotes the value taken by an object in line for an attribute in column. A bicluster in a numerical data table is a subtable with close values different from values outside the subtable. Traditionally, largest biclusters were found by means of methods based on linear algebra. We propose an alternative approach based on concept lattices and lattices of interval pattern structures. In other words, this paper shows how formal concept analysis originally tackles the problem of biclustering and provides interesting perspectives of research.