相关论文: Joint Overlap Analysis of Multiple Genomic Interva…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
Minimum Spanning Tree (MST) is an important graph algorithm that has wide ranging applications in the areas of computer networks, VLSI routing, wireless communications among others. Today virtually every computer is built out of multi-core…
Most approaches to prediction of protein function from primary structure are based on similarity between the query sequence and sequences of known function. This approach, however, disregards the occurrence of gene duplication (paralogy) or…
The dynamic trees problem is to maintain a forest undergoing edge insertions and deletions while supporting queries for information such as connectivity. There are many existing data structures for this problem, but few of them are capable…
The rapid development of high-throughput technologies has enabled the generation of data from biological or disease processes that span multiple layers, like genomic, proteomic or metabolomic data, and further pertain to multiple sources,…
Indexing intervals is a fundamental problem, finding a wide range of applications. Recent work on managing large collections of intervals in main memory focused on overlap joins and temporal aggregation problems. In this paper, we propose…
This paper presents a detailed comparison of a recently proposed algorithm for optimizing decision trees, tree alternating optimization (TAO), with other popular, established algorithms. We compare their performance on a number of…
Introduction: Epigenomic datasets from high-throughput sequencing experiments are commonly summarized as genomic intervals. As the volume of this data grows, so does interest in analyzing it through deep learning. However, the heterogeneity…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…
In this paper, the problem of using uncoordinated multiple access (UMA) to serve a massive amount of heterogeneous users is investigated. Leveraging the heterogeneity, we propose a novel UMA protocol, called iterative collision resolution…
Traditional decision tree models, which rely exclusively on numerical variables, often face challenges in handling high-dimensional data and are limited in their ability to incorporate textual information effectively. To address these…
Species tree estimation from multi-locus datasets is statistically challenging for multiple reasons, including gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Species tree estimation methods have been…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
The junction-tree representation provides an attractive structural property for organizing a decomposable graph. In this study, we present two novel stochastic algorithms, which we call the junction-tree expander and junction-tree collapser…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
We propose a time series analysis framework focused on higher-order temporal correlations in the event sequence beyond the interevent time distribution by employing the burst-tree decomposition method. Bursts are clustered events that…