相关论文: On the optimality of the neighbor-joining algorith…

Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…

The complexity of nearest-neighbor search dominates the asymptotic running time of many sampling-based motion-planning algorithms. However, collision detection is often considered to be the computational bottleneck in practice. Examining…

In Connectivity Augmentation problems we are given a graph $H=(V,E_H)$ and an edge set $E$ on $V$, and seek a min-size edge set $J \subseteq E$ such that $H \cup J$ has larger edge/node connectivity than $H$. In the Edge-Connectivity…

Topology based dimensionality reduction methods such as t-SNE and UMAP have seen increasing success and popularity in high-dimensional data. These methods have strong mathematical foundations and are based on the intuition that the topology…

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…

We investigate uniqueness issues that arise in $l^\infty$-optimization to linear spaces and Bergman fans of matroids. For linear spaces, we give a polyhedral decomposition of $\mathbb{R}^n$ based on the dimension of the set of…

We consider networks of small, autonomous devices that communicate with each other wirelessly. Minimizing energy usage is an important consideration in designing algorithms for such networks, as battery life is a crucial and limited…

We compare the performance of three nearest neighbor search algorithms: the Orchard, ball tree, and VP-tree algorithms. These algorithms are commonly used for nearest-neighbor searches and are known for their efficiency in large datasets.…

Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…

K Nearest Neighbor (KNN) joins are used in scientific domains for data analysis, and are building blocks of several well-known algorithms. KNN-joins find the KNN of all points in a dataset. This paper focuses on a hybrid CPU/GPU approach…

We present an empirical analysis of data structures for approximate nearest neighbor searching. We compare the well-known optimized kd-tree splitting method against two alternative splitting methods. The first, called the sliding-midpoint…

Neighborhood finders and nearest neighbor queries are fundamental parts of sampling based motion planning algorithms. Using different distance metrics or otherwise changing the definition of a neighborhood produces different algorithms with…

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…

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…

Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…

Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…

2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…

We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…