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As a fundamental problem in many different fields, link prediction aims to estimate the likelihood of an existing link between two nodes based on the observed information. Since this problem is related to many applications ranging from…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We study the problem of exploring all vertices of an undirected weighted graph that is initially unknown to the searcher. An edge of the graph is only revealed when the searcher visits one of its endpoints. Beginning at some start node, the…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
Ordered set (and map) is one of the most used data type. In addition to standard set operations, like insert, delete and contains, it can provide set-set operations such as union, intersection, and difference. Each of these set-set…
We propose a new and strengthened Branch-and-Bound (BnB) algorithm for the maximum common (connected) induced subgraph problem based on two new operators, Long-Short Memory (LSM) and Leaf vertex Union Match (LUM). Given two graphs for which…
We design a generic method for reducing the task of finding weighted matchings to that of finding short augmenting paths in unweighted graphs. This method enables us to provide efficient implementations for approximating weighted matchings…
In this paper we describe a randomized algorithm which returns a maximal spanning forest of an unknown {\em weighted} undirected graph making $O(n)$ $\mathsf{CUT}$ queries in expectation. For weighted graphs, this is optimal due to a result…
We propose an efficient algorithm for graph matching based on similarity scores constructed from counting a certain family of weighted trees rooted at each vertex. For two Erd\H{o}s-R\'enyi graphs $\mathcal{G}(n,q)$ whose edges are…
Hierarchical agglomerative clustering (HAC) is a popular algorithm for clustering data, but despite its importance, no dynamic algorithms for HAC with good theoretical guarantees exist. In this paper, we study dynamic HAC on edge-weighted…
We introduce a technique that is capable to filter out information from complex systems, by mapping them to networks, and extracting a subgraph with the strongest links. This idea is based on the Minimum Spanning Tree, and it can be applied…
Finding optimal paths in connected graphs requires determining the smallest total cost for traveling along the graph's edges. This problem can be solved by several classical algorithms where, usually, costs are predefined for all edges.…
Evaluation of link prediction methods is a hard task in very large complex networks because of the inhibitive computational cost. By setting a lower bound of the number of common neighbors (CN), we propose a new framework to efficiently and…
We present algorithms that run in linear time on pointer machines for a collection of problems, each of which either directly or indirectly requires the evaluation of a function defined on paths in a tree. These problems previously had…
Let $G = (V, E)$ be an undirected connected simple graph on $n$ vertices. A cut-equivalent tree of $G$ is an edge-weighted tree on the same vertex set $V$, such that for any pair of vertices $s, t\in V$, the minimum $(s, t)$-cut in the tree…
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
In this paper we consider graph algorithms in models of computation where the space usage (random accessible storage, in addition to the read only input) is sublinear in the number of edges $m$ and the access to input data is constrained.…
Graph matching pairs corresponding nodes across two or more graphs. The problem is difficult as it is hard to capture the structural similarity across graphs, especially on large graphs. We propose to incorporate high-order information for…
We describe a synchronous distributed algorithm which identifies the edge-biconnected components of a connected network. It requires a leader, and uses messages of size O(log |V|). The main idea is to preorder a BFS spanning tree, and then…
Let G be a directed graph with n vertices and non-negative weights in its directed edges, embedded on a surface of genus g, and let f be an arbitrary face of G. We describe a randomized algorithm to preprocess the graph in O(gn log n) time…