Related papers: Inference of maximum parsimony phylogenetic trees …
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
Due to the expected disparity in quantum vs. classical clock speeds, quantum advantage for branch and bound algorithms is more likely achievable in settings involving large search trees and low operator evaluation costs. Therefore, in this…
Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for…
We show how to efficiently simulate a quantum many-body system with tree structure when its entanglement is bounded for any bipartite split along an edge of the tree. This is achieved by expanding the {\em time-evolving block decimation}…
When trying to use quantum-enhanced methods for optimization problems, the sheer number of options inhibits its adoption by industrial end users. Expert knowledge is required for the formulation and encoding of the use case, the selection…
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
The study of the fundamental limits of information systems is a central theme in information theory. Both the traditional analytical approach and the recently proposed computational approach have significant limitations, where the former is…
Hybrid Quantum Neural Networks (HQNNs) have gained attention for their potential to enhance computational performance by incorporating quantum layers into classical neural network (NN) architectures. However, a key question remains: Do…
Regression trees are one of the oldest forms of AI models, and their predictions can be made without a calculator, which makes them broadly useful, particularly for high-stakes applications. Within the large literature on regression trees,…
We propose and implement modern computational methods to enhance catastrophe excess-of-loss reinsurance contracts in practice. The underlying optimization problem involves attachment points, limits, and reinstatement clauses, and the…
Tackling simulation optimization problems with non-convex objective functions remains a fundamental challenge in operations research. In this paper, we propose a class of random search algorithms, called Regular Tree Search, which…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
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…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
We propose a new algorithm to the problem of polygonal curve approximation based on a multiresolution approach. This algorithm is suboptimal but still maintains some optimality between successive levels of resolution using dynamic…
Max-cut, clustering, and many other partitioning problems that are of significant importance to machine learning and other scientific fields are NP-hard, a reality that has motivated researchers to develop a wealth of approximation…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Optimization problems become fundamentally challenging as the number of variables increases. Because the volume of the search space grows exponentially, classical algorithms frequently fail to locate the global minimum of non-convex…
Complex networks theory has commonly been used for modelling and understanding the interactions taking place between the elements composing complex systems. More recently, the use of generative models has gained momentum, as they allow…