Related papers: A Data Structure for Nearest Common Ancestors with…
We present a compressed representation of tries based on top tree compression [ICALP 2013] that works on a standard, comparison-based, pointer machine model of computation and supports efficient prefix search queries. Namely, we show how to…
In this paper, we introduce a local search algorithm for hierarchical clustering. For the local step, we consider a tree re-arrangement operation, known as the {\em interchange}, which involves swapping two closely positioned sub-trees…
The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…
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…
Average linkage Hierarchical Agglomerative Clustering (HAC) is an extensively studied and applied method for hierarchical clustering. Recent applications to massive datasets have driven significant interest in near-linear-time and efficient…
Over the last decade, deep neural networks have transformed our society, and they are already widely applied in various machine learning applications. State-of-art deep neural networks are becoming larger in size every year to deliver…
We consider NCA labeling schemes: given a rooted tree $T$, label the nodes of $T$ with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the label of their nearest common…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Word and graph embeddings are widely used in deep learning applications. We present a data structure that captures inherent hierarchical properties from an unordered flat embedding space, particularly a sense of direction between pairs of…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
An algorithm is developed for finding a close to optimal junction tree of a given graph G. The algorithm has a worst case complexity O(c^k n^a) where a and c are constants, n is the number of vertices, and k is the size of the largest…
We present the first near-linear work and poly-logarithmic depth algorithm for computing a minimum cut in a graph, while previous parallel algorithms with poly-logarithmic depth required at least quadratic work in the number of vertices. In…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as…
In this paper we present novel algorithmic techniques with a O(H(N)+N/H(N)) time complexity for performing several types of queries and updates on general rooted trees, binary search trees and lists of size N. For rooted trees we introduce…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Common Neighbors (CNs) and their higher-order variants are important pairwise features widely used in state-of-the-art link prediction methods. However, existing methods often struggle with the repetition across different orders of CNs and…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
We consider the problem of augmenting an $n$-vertex tree with one shortcut in order to minimize the diameter of the resulting graph. The tree is embedded in an unknown space and we have access to an oracle that, when queried on a pair of…