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Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…
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…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
We present sublinear-time (randomized) algorithms for finding simple cycles of length at least $k\geq 3$ and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being…
We focus on low-dimensional non-metric search, where tree-based approaches permit efficient and accurate retrieval while having short indexing time. These methods rely on space partitioning and require a pruning rule to avoid visiting…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
Merge trees are a common topological descriptor for data with a hierarchical component, such as terrains and scalar fields. The interleaving distance, in turn, is a common distance for comparing merge trees. However, the interleaving…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the…
We consider the problem of determining the proportion of edges that are discovered in an Erdos-Renyi graph when one constructs all shortest paths from a given source node to all other nodes. This problem is equivalent to the one of…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
The Spanning Tree Congestion (STC) problem is the following NP-hard problem: given a graph $G$, construct a spanning tree $T$ of $G$ minimizing its maximum edge congestion where the congestion of an edge $e\in T$ is the number of edges $uv$…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have…