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. . Our main contribution is to provide algorithms that do not use linear programming, are simple and… (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)
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)
We compare activation functions in terms of the approximation power of their feedforward nets. We consider the case of analog as well as boolean input.
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.
The paper studies the computational complexity and approximation algorithms for a new evolutionary distance between multi-chromosomal genomes introduced recently by F erretti, Nadeau and Sankoo. Here, a chromosome is represented as a set of genes and a genome is a collection of chromosomes. The syntenic distance between two genomes is deened as the minimum… (More)
A new combinatorial approach for modeling and reconstructing sibling relationships in a single generation of individuals without parental information is proposed in this paper. Simple genetic constraints on the full-sibling groups, imposed by the Mendelian inheritance rules, are employed to investigate data from codominant DNA markers. To extract the… (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)