Related papers: Fast Cartesian Tree Matching
We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
Treemaps have been widely applied to the visualization of hierarchical data. A treemap takes a weighted tree and visualizes its leaves in a nested planar geometric shape, with sub-regions partitioned such that each sub-region has an area…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
Decision trees, owing to their interpretability, are attractive as control policies for (dynamical) systems. Unfortunately, constructing, or synthesising, such policies is a challenging task. Previous approaches do so by imitating a…
The domains of data mining and knowledge discovery make use of large amounts of textual data, which need to be handled efficiently. Specific problems, like finding the maximum weight ordered common subset of a set of ordered sets or…
Sparse decision trees are one of the most common forms of interpretable models. While recent advances have produced algorithms that fully optimize sparse decision trees for prediction, that work does not address policy design, because the…
Flat combining is a concurrency threaded technique whereby one thread performs all the operations in batch by scanning a queue of operations to-be-done and performing them together. Flat combining makes sense as long as k operations each…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
It has been shown that the parallel Lattice Linear Predicate (LLP) algorithm solves many combinatorial optimization problems such as the shortest path problem, the stable marriage problem and the market clearing price problem. In this…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Decision trees are well-known due to their ease of interpretability. To improve accuracy, we need to grow deep trees or ensembles of trees. These are hard to interpret, offsetting their original benefits. Shapley values have recently become…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
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,…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…