Related papers: The Geometry of the Neighbor-Joining Algorithm for…
Tree rearrangement operations typically induce a metric on the space of phylogenetic trees. One important property of these metrics is the size of the neighbourhood, that is, the number of trees exactly one operation from a given tree. We…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
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…
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…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
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…
The rapid advancement of large language models (LLMs) has enabled significant strides in various fields. This paper introduces a novel approach to evaluate the effectiveness of LLM embeddings in the context of inherent geometric properties.…
Upon a matrix representation of a binary bipartite network, via the permutation invariance, a coupling geometry is computed to approximate the minimum energy macrostate of a network's system. Such a macrostate is supposed to constitute the…
It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this…
We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson's optimal radius bound as a special case and explains many cases…
Local learning of sparse image models has proven to be very effective to solve inverse problems in many computer vision applications. To learn such models, the data samples are often clustered using the K-means algorithm with the Euclidean…
A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
In this paper, we introduce the Fixed Topology Minimum-Length Tree with Neighborhood Problem, which aims to embed a rooted tree-shaped graph into a $d$-dimensional metric space while minimizing its total length provided that the nodes must…
Manifold learning now plays a very important role in machine learning and many relevant applications. Although its superior performance in dealing with nonlinear data distribution, data sparsity is always a thorny knot. There are few…
UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves,…
In this paper, we propose an ensemble learning algorithm called \textit{under-bagging $k$-nearest neighbors} (\textit{under-bagging $k$-NN}) for imbalanced classification problems. On the theoretical side, by developing a new learning…
A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…