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

The well-known $k$-disjoint path problem ($k$-DPP) asks for pairwise vertex-disjoint paths between $k$ specified pairs of vertices $(s_i, t_i)$ in a given graph, if they exist. The decision version of the shortest $k$-DPP asks for the…

Applications involving telecommunication call data records, web pages, online transactions, medical records, stock markets, climate warning systems, etc., necessitate efficient management and processing of such massively exponential amount…

In high-dimensional generalized linear models, it is crucial to identify a sparse model that adequately accounts for response variation. Although the best subset section has been widely regarded as the Holy Grail of problems of this type,…

Listing k-cliques plays a fundamental role in various data mining tasks, such as community detection and mining of cohesive substructures. Existing algorithms for the k-clique listing problem are built upon a general framework, which finds…

We present an optimal and efficient algorithm for finding a shortest path in an elastic optical network. The algorithm is an adaptation of the Dijkstra shortest path algorithm, where we take into account the spectrum continuity and…

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves…

We give new sublinear and parallel algorithms for the extensively studied problem of approximating n-variable r-CSPs (constraint satisfaction problems with constraints of arity r up to an additive error. The running time of our algorithms…

Max-k-Cut and correlation clustering are fundamental graph partitioning problems. For a graph with G=(V,E) with n vertices, the methods with the best approximation guarantees for Max-k-Cut and the Max-Agree variant of correlation clustering…

RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…

In Bioinformatics, the applications of flow decomposition in directed acyclic graphs are highlighted in RNA Assembly problem. However, it admits multiple solutions where exactly one solution correctly represents the underlying transcripts.…

We present techniques for decreasing the error probability of randomized algorithms and for converting randomized algorithms to deterministic (non-uniform) algorithms. Unlike most existing techniques that involve repetition of the…

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…

We present improved deterministic algorithms for approximating shortest paths in the Congested Clique model of distributed computing. We obtain $poly(\log\log n)$-round algorithms for the following problems in unweighted undirected…

The computational equivalence between approximate counting and sampling is well established for polynomial-time algorithms. The most efficient general reduction from counting to sampling is achieved via simulated annealing, where the…

Effective causal discovery is essential for learning the causal graph from observational data. The linear non-Gaussian acyclic model (LiNGAM) operates under the assumption of a linear data generating process with non-Gaussian noise in…

In the graph clustering problem with a planted solution, the input is a graph on $n$ vertices partitioned into $k$ clusters, and the task is to infer the clusters from graph structure. A standard assumption is that clusters induce…

This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…

In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…

The subgraph enumeration problem asks us to find all subgraphs of a target graph that are isomorphic to a given pattern graph. Determining whether even one such isomorphic subgraph exists is NP-complete---and therefore finding all such…

Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausible matches between substrings of a read to subpaths of the…