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Natural and man-made networks often possess locally tree-like sub-structures. Taking such tree networks as our starting point, we show how the addition of links changes the synchronization properties of the network. We focus on two…
Link prediction, which aims to forecast unseen connections in graphs, is a fundamental task in graph machine learning. Heuristic methods, leveraging a range of different pairwise measures such as common neighbors and shortest paths, often…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
We consider the ``minimum degree spanning tree'' problem. As input, we receive an undirected, connected graph $G=(V, E)$ with $n$ nodes and $m$ edges, and our task is to find a spanning tree $T$ of $G$ that minimizes $\max_{u \in V}…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
We provide a method to obtain beyond-worst-case time complexity for any single-source-shortest-path (SSSP) algorithm by exploiting modular structures in graphs. The key novelty is a graph decomposition, called the acyclic-connected (A-C)…
Given a 2-edge connected, unweighted, and undirected graph $G$ with $n$ vertices and $m$ edges, a $\sigma$-tree spanner is a spanning tree $T$ of $G$ in which the ratio between the distance in $T$ of any pair of vertices and the…
Over the years, quantifying the similarity of nodes has been a hot topic in complex networks, yet little has been known about the distributions of node-similarity. In this paper, we consider a typical measure of node-similarity called the…
We introduce top trees as a design of a new simpler interface for data structures maintaining information in a fully-dynamic forest. We demonstrate how easy and versatile they are to use on a host of different applications. For example, we…
We give two fully dynamic algorithms that maintain a $(1+\varepsilon)$-approximation of the weight $M$ of a minimum spanning forest (MSF) of an $n$-node graph $G$ with edges weights in $[1,W]$, for any $\varepsilon>0$. (1) Our deterministic…
The neighbor-joining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbor-net algorithm is an extension of the neighbor-joining algorithm and is used for constructing split networks. We…
Relational data are ubiquitous in real-world data applications, e.g., in social network analysis or biological modeling, but networks are nearly always incompletely observed. The state-of-the-art for predicting missing links in the hard…
In the context of tree-search stochastic planning algorithms where a generative model is available, we consider on-line planning algorithms building trees in order to recommend an action. We investigate the question of avoiding re-planning…
Flat combining is a concurrency threaded technique whereby one thread performs all the operations in batch by scanning a queue of operations to-be-done and performing them together. Flat combining makes sense as long as k operations each…
We present an $\tilde O(m+n^{1.5})$-time randomized algorithm for maximum cardinality bipartite matching and related problems (e.g. transshipment, negative-weight shortest paths, and optimal transport) on $m$-edge, $n$-node graphs. For…