Related papers: The Geometry of the Neighbor-Joining Algorithm for…
Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and…
We introduce a semiparametric approach to neighbor-based classification. We build off the recently proposed Boundary Trees algorithm by Mathy et al.(2015) which enables fast neighbor-based classification, regression and retrieval in large…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
While Graph Neural Network (GNN) has shown superiority in learning node representations of homogeneous graphs, leveraging GNN on heterogeneous graphs remains a challenging problem. The dominating reason is that GNN learns node…
Network (or Graph) Alignment Algorithms aims to reveal structural similarities among graphs. In particular Local Network Alignment Algorithms (LNAs) finds local regions of similarity among two or more networks. Such algorithms are in…
Nearest neighbor (kNN) methods have been gaining popularity in recent years in light of advances in hardware and efficiency of algorithms. There is a plethora of methods to choose from today, each with their own advantages and…
Tree rearrangements such as Nearest Neighbor Interchange (NNI) and Subtree Prune and Regraft (SPR) are commonly used to explore phylogenetic treespace. Computing distances based on them, however, is often intractable, so the efficiently…
We consider the task of topology discovery of sparse random graphs using end-to-end random measurements (e.g., delay) between a subset of nodes, referred to as the participants. The rest of the nodes are hidden, and do not provide any…
Manifold Learning occupies a vital role in the field of nonlinear dimensionality reduction and its ideas also serve for other relevant methods. Graph-based methods such as Graph Convolutional Networks (GCN) show ideas in common with…
In Polyamorous Scheduling, we are given an edge-weighted graph and must find a periodic schedule of matchings in this graph which minimizes the maximal weighted waiting time between consecutive occurrences of the same edge. This NP-hard…
This paper, based on $k$-NN graph, presents symmetric $(k,j)$-NN graph $(1 \leq j < k)$, a brand new topology which could be adopted by a series of network-based structures. We show that the $k$ nearest neighbors of a node exert disparate…
A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…
In this work, Transition Probability Matrix (TPM) is proposed as a new method for extracting the features of nodes in the graph. The proposed method uses random walks to capture the connectivity structure of a node's close neighborhood. The…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
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…
Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over tree spaces has some nice properties such as convexity in terms of the tropical…
In this paper we present the first provable approximate nearest-neighbor (ANN) algorithms for Bregman divergences. Our first algorithm processes queries in O(log^d n) time using O(n log^d n) space and only uses general properties of the…