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Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…

Tree convex sets refer to a collection of sets such that each set in the collection is a subtree of a tree whose nodes are the elements of these sets. They extend the concept of row convex sets each of which is an interval over a total…

As a programming paradigm, answer set programming (ASP) brings about the usual issue of the human error. Hence, it is desirable to provide automated techniques that could help the programmer to find the error. This paper addresses the…

We are concerned with the problem of designing large families of subsets over a common labeled ground set that have small pairwise intersections and the property that the maximum discrepancy of the label values within each of the sets is…

Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…

We investigate the existence of heavy columns in binary matrices with distinct rows. A column of an m x n binary matrix is called heavy if the number of ones in it is at least m/2. We introduce two recursive algorithms, A1 and A2, that…

The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…

The best developed formulation of closed system quantum theory that handles multiple-time statements, is the consistent (or decoherent) histories approach. The most important weaknesses of the approach is that it gives rise to many…

Biclustering is the task of simultaneously clustering the rows and columns of the data matrix into different subgroups such that the rows and columns within a subgroup exhibit similar patterns. In this paper, we consider the case of…

The Minimum Spanning Tree with Conflicting Edge Pairs is a generalization that adds conflict constraints to a classical optimization problem on graphs used to model several real-world applications. In the last few years several approaches,…

Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…

Ordered sets and maps play important roles as index structures in relational data models. When a shared index in a multi-user system is modified concurrently, the current state of the index will diverge into multiple versions containing the…

A property $\Pi$ on a finite set $U$ is \emph{monotone} if for every $X \subseteq U$ satisfying $\Pi$, every superset $Y \subseteq U$ of $X$ also satisfies $\Pi$. Many combinatorial properties can be seen as monotone properties. The problem…

We study the problem of constructing concurrent objects in a setting where $P$ processes run in parallel and interact through a shared memory that is subject to write contention. Our goal is to transform hardware primitives that are subject…

A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…

The concurrent refinement algebra has been developed to support rely/guarantee reasoning about concurrent programs. The algebra supports atomic commands and defines parallel composition as a synchronous operation, as in Milner's SCCS. In…

Motivated by the problem of reducing the peak to average power ratio (PAPR) of transmitted signals, we consider a design of complementary set matrices whose column sequences satisfy a correlation constraint. The design algorithm recursively…

Two matrices are said to be principal minor equivalent if they have equal corresponding principal minors of all orders. We give a characterization of principal minor equivalence and a deterministic polynomial time algorithm to check if two…

In serial batch (s-batch) scheduling, jobs from similar families are grouped into batches and processed sequentially to avoid repetitive setups that are required when processing consecutive jobs of different families. Despite its large…