Related papers: Approximate Search for Known Gene Clusters in New …
Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
Finding the nearest neighbor to a hyperplane (or Point-to-Hyperplane Nearest Neighbor Search, simply P2HNNS) is a new and challenging problem with applications in many research domains. While existing state-of-the-art hashing schemes (e.g.,…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
We propose a novel method for automatic program synthesis. P-Tree Programming represents the program search space through a single probabilistic prototype tree. From this prototype tree we form program instances which we evaluate on a given…
Probabilistic Structured Queries (PSQ) is a cross-language information retrieval (CLIR) method that uses translation probabilities statistically derived from aligned corpora. PSQ is a strong baseline for efficient CLIR using sparse…
In recent years, deep network pruning has attracted significant attention in order to enable the rapid deployment of AI into small devices with computation and memory constraints. Pruning is often achieved by dropping redundant weights,…
We focus on the average-case analysis: A function w : V -> Z+ is given which defines the likelihood for a node to be the one marked, and we want the strategy that minimizes the expected number of queries. Prior to this paper, very little…
Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory…
Improving the explainability of the results from machine learning methods has become an important research goal. Here, we study the problem of making clusters more interpretable by extending a recent approach of [Davidson et al., NeurIPS…
A computational challenge to validate the candidate disease genes identified in a high-throughput genomic study is to elucidate the associations between the set of candidate genes and disease phenotypes. The conventional gene set enrichment…
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over…
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…