相关论文: Efficient Algorithms for de novo Assembly of Alter…

In this paper, we present a collection of novel and scalable algorithms designed to tackle the challenges inherent in the $k$-clique densest subgraph problem (\kcdsp) within network analysis. We propose \psctl, a novel algorithm based on…

In this paper, we address the problem of recovering arbitrary-shaped data clusters from datasets while facing \emph{high space constraints}, as this is for instance the case in many real-world applications when analysis algorithms are…

Finding cliques in random graphs and the closely related "planted" clique variant, where a clique of size k is planted in a random G(n, 1/2) graph, have been the focus of substantial study in algorithm design. Despite much effort, the best…

The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…

In computational genomics, many analyses rely on efficient storage and traversal of $k$-mers, motivating compact representations such as spectrum-preserving string sets (SPSS), which store strings whose $k$-mer spectrum matches that of the…

Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Distributed in-memory data processing engines accelerate iterative applications by caching substantial datasets in memory rather than recomputing them in each iteration. Selecting a suitable cluster size for caching these datasets plays an…

We study the problem of counting the number of {\em isomorphic} copies of a given {\em template} graph, say $H$, in the input {\em base} graph, say $G$. In general, it is believed that polynomial time algorithms that solve this problem…

De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem…

In this paper we study the problem of discovering a timeline of events in a temporal network. We model events as dense subgraphs that occur within intervals of network activity. We formulate the event-discovery task as an optimization…

Entity resolution (ER; also known as record linkage or de-duplication) is the process of merging noisy databases, often in the absence of unique identifiers. A major advancement in ER methodology has been the application of Bayesian…

Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…

Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…

Biclustering, also called co-clustering, block clustering, or two-way clustering, involves the simultaneous clustering of both the rows and columns of a data matrix into distinct groups, such that the rows and columns within a group display…

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…

Best subset of groups selection (BSGS) is the process of selecting a small part of non-overlapping groups to achieve the best interpretability on the response variable. It has attracted increasing attention and has far-reaching applications…

We study the problem of approximating the number of $k$-cliques in a graph when given query access to the graph. We consider the standard query model for general graphs via (1) degree queries, (2) neighbor queries and (3) pair queries. Let…

The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…

The subset sum problem, also referred as SSP, is a NP-Hard computational problem. SSP has its applications in broad domains like cryptography, number theory, operation research and complexity theory. The most famous algorithm for solving…