Related papers: A Branch-and-Cut Algorithm for the 2-Species Dupli…
We tackle the challenge of detecting multiple change points in large time series by optimising a penalised likelihood derived from exponential family models. Dynamic programming algorithms can solve this task exactly with at most quadratic…
We consider the classical Minimum Balanced Cut problem: given a graph $G$, compute a partition of its vertices into two subsets of roughly equal volume, while minimizing the number of edges connecting the subsets. We present the first {\em…
We provide a method for parallelizing the branch-and-bound with isomorphism pruning algorithm developed by Margot [Symmetric ILP: Coloring and small integers, Discrete Optimization (4) (2007), 40-62]. We apply our method to classify…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
We study the complexity of cutting planes and branching schemes from a theoretical point of view. We give some rigorous underpinnings to the empirically observed phenomenon that combining cutting planes and branching into a branch-and-cut…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Segmenting an image into multiple components is a central task in computer vision. In many practical scenarios, prior knowledge about plausible components is available. Incorporating such prior knowledge into models and algorithms for image…
Layer pruning has emerged as a potent approach to remove redundant layers in the pre-trained network on the purpose of reducing network size and improve computational efficiency. However, existing layer pruning methods mostly overlook the…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
The talent scheduling problem is a simplified version of the real-world film shooting problem, which aims to determine a shooting sequence so as to minimize the total cost of the actors involved. In this article, we first formulate the…
We surely enjoy the larger the better models for their superior performance in the last couple of years when both the hardware and software support the birth of such extremely huge models. The applied fields include text mining and others.…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
The independent set problem is NP-hard and particularly difficult to solve in large sparse graphs. In this work, we develop an advanced evolutionary algorithm, which incorporates kernelization techniques to compute large independent sets in…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
Branch-and-bound approaches in integer programming require ordering portions of the space to explore next, a problem known as node comparison. We propose a new siamese graph neural network model to tackle this problem, where the nodes are…
As two fundamental problems, graph cuts and graph matching have been investigated over decades, resulting in vast literature in these two topics respectively. However the way of jointly applying and solving graph cuts and matching receives…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
We present a generic branch-and-bound algorithm for finding all the Pareto solutions of a biobjective mixed-integer linear program. The main contributions are new algorithms for obtaining dual bounds at a node, for checking node fathoming,…