Spatially-explicit harvest scheduling models optimize the spatial and temporal layout of forest management actions in order to best meet management objectives such as profit maximization, even flow of products, or wildlife habitat preservation while satisfying a variety of constraints, including maximum harvest opening size constraints. A procedure is proposed that strengthens these arearestric...

Most of the analyses on the conservation of gene order are limited to orthologous genes. However, the organization of genes into operons might also result in the conservation of gene order of paralogous genes. Thus, we sought computational evidence that conservation of gene order of paralogous genes represents another level of conservation of genes in operons. We found that pairs of genes withi...

Common techniques in collaborative filtering rely on finding low-rank matrix approximations to the adjacency matrix (ratings that users assign to items), essentially representing users and items as a collection of a small number of latent features. One issue that arises in many real world datasets for collaborative filtering is that the number of observed entries per row/column follows a heavy-...

Comparative genomics, evolutionary biology, and cancer researches require tools to elucidate the evolutionary trajectories and reconstruct the ancestral genomes. Various methods have been developed to infer the genome content and gene ordering of ancestral genomes by using such genomic structural variants. There are mainly two kinds of computational approaches in the ancestral genome reconstruc...

A novel technique to search for functional modules in a protein-protein interaction network is presented. The network is represented by the adjacency matrix associated with the undirected graph modelling it. The algorithm introduces the concept of quality of a sub-matrix of the adjacency matrix, and applies a greedy search technique for finding local optimal solutions made of dense submatrices ...

The maximum order of a square (0, 1)-matrix A with a fixed rank r is considered, provided A has no repeated rows or columns. When A is the adjacency matrix of a graph, Kotlov and Lovász [A. Kotlov and L. Lovász. The rank and size of graphs. J. Graph Theory, 23:185–189, 1996.] proved that the maximum order equals Θ(2r/2). In this note, it is showed that this result remains correct if A is symmet...

One may assume w.l.o.g. that p(x) is a homogeneous polynomial (form). Indeed, as observed in [2], if p(x) = ∑d l=0 pl(x), where pl(x) is homogeneous of degree l, then minimizing p(x) over ∆ is equivalent to minimizing the degree d form p(x) := ∑d l=0 pl(x)( ∑n i=1 xi) . Problem (1) is an NP-hard problem, already for forms of degree d = 2, as it contains the maximum stable set problem. Indeed, f...

In this thesis, we provide a general background for inference and learning, using Bayesian networks and genetic algorithms. We introduce Bayesian Networks in Java, a Java-based Bayesian network API that we have developed. We describe our research with structure learning using a genetic algorithm to search the space of adjacency matrices for a Bayesian network. We first instantiate the populatio...