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We consider the problem of off-line throughput maximization for job scheduling on one or more machines, where each job has a release time, a deadline and a profit. Most of the versions of the problem discussed here were already treated by Bar-Noy et al. [3]. Our main contribution is to provide algorithms that do not use linear programming, are simple and… (More)

In this paper, we investigate the test set problem and its variations that appear in a variety of applications. In general, we are given a universe of objects to be " distinguished " by a family of " tests " , and we want to find the smallest sufficient collection of tests. In the simplest version, a test is a subset of the universe and two objects are… (More)

Given a graph of interactions, a module (also called a community or cluster) is a subset of nodes whose fitness is a function of the statistical significance of the pairwise interactions of nodes in the module. The topic of this paper is a model-based community finding approach, commonly referred to as modularity clustering, that was originally proposed by… (More)

A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions which are optimal in an appropriate sense. In graph-theoretic language, the problems can be recast in terms of maximal… (More)

Reconstruction of sibling relationships from genetic data is an important component of many biological applications. In particular, the growing application of molecular markers (microsatellites) to study wild populations of plant and animals has created the need for new computational methods of establishing pedigree relationships, such as sibgroups, among… (More)

We p r o vide improved approximation algorithms for several rectangle tiling and packing problems (RTILE, DRTILE and d-RPACK) studied in the literature. Most of our algorithms are highly eecient since their running times are near-linear in the sparse input size rather than in the domain size. In addition, we improve the best known approximation ratios.

In this paper, we derive bounds on performance guarantees of online algorithms for real-time preemptive scheduling of jobs with deadlines on K machines when jobs are characterized in terms of their minimum stretch factor α (or, equivalently, their maximum execution rate r = 1/α). We consider two well known preemptive models that are of interest from… (More)

In this paper we consider the p-ary transitive reduction (TR p) problem where p > 0 is an integer; for p = 2 this problem arises in inferring a sparsest possible (biological) signal transduction network consistent with a set of experimental observations with a goal to minimize false positive inferences even if risking false negatives. Special cases of TR p… (More)

Computing a suitable measure of consensus among several clusterings on the same data is an important problem that arises in several areas such as computational biology and data mining. In this paper, we formalize a set-theoretic model for computing such a similarity measure. Roughly speaking, in this model we have k > 1 partitions (clusters) of the same… (More)

Kinship analysis using genetic data is important for many biological applications, including many in conservation biology. Wide availability of microsatellites has boosted studies in wild populations that rely on the knowledge of kinship, particularly sibling relationships (sibship). While there exist many methods for reconstructing sibling relationships,… (More)