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Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
In social networks, information and influence diffuse among users as cascades. While the importance of studying cascades has been recognized in various applications, it is difficult to observe the complete structure of cascades in practice.…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Trees can accelerate queries that search or aggregate values over large collections. They achieve this by storing metadata that enables quick pruning (or inclusion) of subtrees when predicates on that metadata can prove that none (or all)…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…
We consider the following problem: Let $H$ and $F$ be two graphs on $k$ vertices and assume $F \neq H$. We say that $H$ and $F$ are incomparable if neither $F$ nor $H$ contains the other. Let $H$ be a graph on $k$ vertices and let $G$ be a…
Inducing latent tree structures from sequential data is an emerging trend in the NLP research landscape today, largely popularized by recent methods such as Gumbel LSTM and Ordered Neurons (ON-LSTM). This paper proposes FASTTREES, a new…
A heavy path in a weighted graph represents a notion of connectivity and ordering that goes beyond two nodes. The heaviest path of length l in the graph, simply means a sequence of nodes with edges between them, such that the sum of edge…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
The ternary relation $B(x,y,z)$ of betweenness states that an element $y$ is between the elements $x$ and $z$, in some sense depending on the considered structure. In a partially ordered set $(N,\leq)$, $B(x,y,z):\Longleftrightarrow…
Admixed populations are formed by the merging of two or more ancestral populations, and the ancestry of each locus in an admixed genome derives from either source. Consider a simple "pulse" admixture model, where populations A and B merged…
In deep neural networks, better results can often be obtained by increasing the complexity of previously developed basic models. However, it is unclear whether there is a way to boost performance by decreasing the complexity of such models.…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…
We first show that increasing trees are in bijection with set compositions, extending simultaneously a recent result on trees due to Tonks and a classical result on increasing binary trees. We then consider algebraic structures on the…
In this paper, we describe the problem of cognate identification and its relation to phylogenetic inference. We introduce subsequence based features for discriminating cognates from non-cognates. We show that subsequence based features…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
This paper studies the important problem of finding all $k$-nearest neighbors to points of a query set $Q$ in another reference set $R$ within any metric space. Our previous work defined compressed cover trees and corrected the key…
Neural networks with tree-based sentence encoders have shown better results on many downstream tasks. Most of existing tree-based encoders adopt syntactic parsing trees as the explicit structure prior. To study the effectiveness of…