Related papers: Practical algorithms for Hierarchical overlap grap…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
We consider a matrix completion problem that exploits social or item similarity graphs as side information. We develop a universal, parameter-free, and computationally efficient algorithm that starts with hierarchical graph clustering and…
Graph convolutional network (GCN) based approaches have achieved significant progress for solving complex, graph-structured problems. GCNs incorporate the graph structure information and the node (or edge) features through message passing…
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…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
We consider the problem of sampling and approximately counting an arbitrary given motif $H$ in a graph $G$, where access to $G$ is given via queries: degree, neighbor, and pair, as well as uniform edge sample queries. Previous algorithms…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
In earlier versions of the community discovering problem, the overlap between communities was restricted by a simple count upper-bound [17,5,11,8]. In this paper, we introduce the $\Pi$-Packing with $\alpha()$-Overlap problem to allow for…
Nucleus decompositions have been shown to be a useful tool for finding dense subgraphs. The coreness value of a clique represents its density based on the number of other cliques it is adjacent to. One useful output of nucleus decomposition…
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…
De Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in…
We present HARP, a novel method for learning low dimensional embeddings of a graph's nodes which preserves higher-order structural features. Our proposed method achieves this by compressing the input graph prior to embedding it, effectively…
One of the main challenges for hierarchical clustering is how to appropriately identify the representative points in the lower level of the cluster tree, which are going to be utilized as the roots in the higher level of the cluster tree…
An overlap representation is an assignment of sets to the vertices of a graph in such a way that two vertices are adjacent if and only if the sets assigned to them overlap. The overlap number of a graph is the minimum number of elements…
Hypergraphs tackle the limitations of traditional graphs by introducing {\em hyperedges}. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges. Also, the underlying message-passing…
Searching on bipartite graphs is basal and versatile to many real-world Web applications, e.g., online recommendation, database retrieval, and query-document searching. Given a query node, the conventional approaches rely on the similarity…
Various non-trivial spaces are becoming popular for embedding structured data such as graphs, texts, or images. Following spherical and hyperbolic spaces, more general product spaces have been proposed. However, searching for the best…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, information retrieval and many other areas related to the World Wide Web. There exist several algorithms for the problem with…