Related papers: Approximate Search for Known Gene Clusters in New …
Quantum Search Algorithm made a big impact by being able to solve the search problem for a set with $N$ elements using only $O(\sqrt{N})$ steps. Unfortunately, it is impossible to reduce the order of the complexity of this problem, however,…
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
Text clustering holds significant value across various domains due to its ability to identify patterns and group related information. Current approaches which rely heavily on a computed similarity measure between documents are often limited…
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…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Searching in partially ordered structures has been considered in the context of information retrieval and efficient tree-like indexes, as well as in hierarchy based knowledge representation. In this paper we focus on tree-like partial…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
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 Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…
Inferences in directed acyclic graphs associated with probability sets and probability intervals are NP-hard, even for polytrees. In this paper we focus on such inferences, and propose: 1) a substantial improvement on Tessems A / R…
Filtered approximate nearest neighbor search (ANNS) restricts the search to data objects whose attributes satisfy a given filter and retrieves the top-$K$ objects that are most semantically similar to the query object. Many graph-based ANNS…
Personalized medicine is expected to maximize the intended drug effects and minimize side effects by treating patients based on their genetic profiles. Thus, it is important to generate drugs based on the genetic profiles of diseases,…
We present APQ for efficient deep learning inference on resource-constrained hardware. Unlike previous methods that separately search the neural architecture, pruning policy, and quantization policy, we optimize them in a joint manner. To…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
We present a study of several generic tree search techniques applied to the Sequential Ordering Problem. This study enables us to propose a simple and competitive tree search algorithm. It consists of an iterative Beam Search algorithm that…
Schema matching is the process of identifying correspondences between the elements of two given schemata, essential for database management systems, data integration, and data warehousing. For datasets across different scenarios, the…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…