Related papers: Approximate Cartesian Tree Matching with Substitut…
Motivated by alignment of correlated sparse random graphs, we introduce a hypothesis testing problem of deciding whether or not two random trees are correlated. We obtain sufficient conditions under which this testing is impossible or…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
Sparse coding consists in representing signals as sparse linear combinations of atoms selected from a dictionary. We consider an extension of this framework where the atoms are further assumed to be embedded in a tree. This is achieved…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
We study permutation (jumbled/Abelian) pattern matching over a general alphabet $\Sigma$. Given a pattern P of length m and a text T of length n, the classical task is to decide whether T contains a length-m substring whose Parikh vector…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
We consider the following generalization of binary search in sorted arrays to tree domains. In each step of the search, an algorithm is querying a vertex $q$, and as a reply, it receives an answer, which either states that $q$ is the…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
A rectilinear Steiner tree for a set $P$ of points in $\mathbb{R}^2$ is a tree that connects the points in $P$ using horizontal and vertical line segments. The goal of Minimal Rectilinear Steiner Tree is to find a rectilinear Steiner tree…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
In the Steiner Tree problem we are given an edge weighted undirected graph $G = (V,E)$ and a set of terminals $R \subseteq V$. The task is to find a connected subgraph of $G$ containing $R$ and minimizing the sum of weights of its edges. We…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…
We study the counting problem known as #PPM, whose input is a pair of permutations $\pi$ and $\tau$ (called pattern and text, respectively), and the task is to find the number of subsequences of $\tau$ that have the same relative order as…