Related papers: A Branch-and-Cut Algorithm for the 2-Species Dupli…
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…
Pruning has recently been widely adopted to reduce the parameter scale and improve the inference efficiency of Large Language Models (LLMs). Mainstream pruning techniques often rely on uniform layerwise pruning strategies, which can lead to…
Resource allocation in wireless networks, such as device-to-device (D2D) communications, is usually formulated as mixed integer nonlinear programming (MINLP) problems, which are generally NP-hard and difficult to get the optimal solutions.…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Network adaptation is essential for the efficient operation of Cloud-RANs. Unfortunately, it leads to highly intractable mixed-integer nonlinear programming problems. Existing solutions typically rely on convex relaxation, which yield…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
In this paper, we propose a cutting plane algorithm based on DC (Difference-of-Convex) programming and DC cut for globally solving Mixed-Binary Linear Program (MBLP). We first use a classical DC programming formulation via the exact…
We propose to generate Lagrangian cut for two-stage stochastic integer program by batch, in contrast to the existing methods which solve each Lagrangian subproblem at every iteration. We establish two convergence properties of the proposed…
We study the problem of complexity estimation in the context of parallelizing an advanced Branch and Bound-type algorithm over graphical models. The algorithm's pruning power makes load balancing, one crucial element of every distributed…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
The orienteering problem is a route optimization problem which consists in finding a simple cycle that maximizes the total collected profit subject to a maximum distance limitation. In the last few decades, the occurrence of this problem in…
In the recent years, branch-and-cut algorithms have been the target of data-driven approaches designed to enhance the decision making in different phases of the algorithm such as branching, or the choice of cutting planes (cuts). In…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
In this paper, we develop a novel weighted Laplacian method, which is partially inspired by the theory of graph Laplacian, to study recent popular graph problems, such as multilevel graph partitioning and balanced minimum cut problem, in a…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
A reduced-order model algorithm, called ALP, is proposed to solve nonlinear evolution partial differential equations. It is based on approximations of generalized Lax pairs. Contrary to other reduced-order methods, like Proper Orthogonal…