Related papers: Efficient Projection onto the Perfect Phylogeny Mo…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
We propose a simple and natural approximation algorithm for the problem of finding a 2-edge-connected spanning subgraph of minimum total edge cost in a graph. The algorithm maintains a spanning forest starting with an empty edge set. In…
Fault tree analysis is a well-known technique in reliability engineering and risk assessment, which supports decision-making processes and the management of complex systems. Traditionally, fault tree (FT) models are built manually together…
Surrogate assisted evolutionary algorithms (EA) are rapidly gaining popularity where applications of EA in complex real world problem domains are concerned. Although EAs are powerful global optimizers, finding optimal solution to complex…
In the $k$-dispersion problem, we need to select $k$ nodes of a given graph so as to maximize the minimum distance between any two chosen nodes. This can be seen as a generalization of the independent set problem, where the goal is to…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
Motif finding is one of the NP-complete problems in Computational Biology. Existing nondeterministic algorithms for motif finding do not guarantee the global optimality of results and are sensitive to initial parameters. To address this…
Neuroevolutionary algorithms, automatic searches of neural network structures by means of evolutionary techniques, are computationally costly procedures. In spite of this, due to the great performance provided by the architectures which are…
We present a tree structure algorithm for optimal control problems with state constraints. We prove a convergence result for a discrete time approximation of the value function based on a novel formulation of the constrained problem. Then…
We initiate a study of a query-driven approach to designing partition trees for range-searching problems. Our model assumes that a data structure is to be built for an unknown query distribution that we can access through a sampling oracle,…
Retrieving relevant targets from an extremely large target set under computational limits is a common challenge for information retrieval and recommendation systems. Tree models, which formulate targets as leaves of a tree with trainable…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Detecting elliptical objects from an image is a central task in robot navigation and industrial diagnosis where the detection time is always a critical issue. Existing methods are hardly applicable to these real-time scenarios of limited…
Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically…