Related papers: Meraculous-2D: Haplotype-sensitive Assembly of Hig…
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…
Hypergraph data, which capture multi-way interactions among entities, are increasingly prevalent in the big data era. Generating new hyperlinks from an observed, usually high-dimensional hypergraph is an important yet challenging task with…
Hierarchical 3D grouping aims to recover scene groups across multiple granularities, from fine object parts to complete objects, without relying on semantic labels or a fixed vocabulary. The main challenge is to transform 2D…
We investigate the problem of multiplex graph embedding, that is, graphs in which nodes interact through multiple types of relations (dimensions). In recent years, several methods have been developed to address this problem. However, the…
Multi-view echocardiographic sequences segmentation is crucial for clinical diagnosis. However, this task is challenging due to limited labeled data, huge noise, and large gaps across views. Here we propose a recurrent aggregation learning…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
Molecular self-assembly plays a very important role in various aspects of technology as well as in biological systems. Governed by the covalent, hydrogen or van der Waals interactions - self-assembly of alike molecules results in a large…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
The two-scale computational homogenization method is proposed for modelling of locally periodic fluid-saturated media subjected a to large deformation induced by quasistatic loading. The periodic heterogeneities are relevant to the…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
We propose an algorithm for the computational homogenization of locally periodic hyperelastic structures undergoing large deformations due to external quasi-static loading. The algorithm performs clustering of macroscopic deformations into…
Understanding the three-dimensional motion of bubbles is essential for interpreting transport and mixing in multiphase flows, especially when bubbles deform under shear or move rapidly through the flow field. In many laboratory setups, only…
Establishing structure-property linkages in polycrystalline materials requires representative two- (2D) and three- (3D) dimensional microstructural inputs for full-field simulations. A core objective of microstructure characterization and…
We show that in a complex d-dimensional vector space, one can find O(d) bases whose elements form a 2-design. Such vector sets generalize the notion of a maximal collection of mutually unbiased bases (MUBs). MUBs have manifold applications…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Aggregation-based assays, using micro- and nano-particles have been widely accepted as an efficient and cost-effective bio-sensing tool, particularly in microbiology, where particle clustering events are used as a metric to infer the…
Segmenting gas bubbles in multiphase flows is a critical yet unsolved challenge in numerous industrial settings, from metallurgical processing to maritime drag reduction. Traditional approaches-and most recent learning-based methods-assume…
Generating graphs subject to strict structural constraints is a fundamental computational challenge in network science. Simultaneously preserving interacting properties-such as the diameter and the clustering coefficient- is particularly…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Biology is full of intricate molecular structures whose geometries are inextricably linked to their function. Many of these structures exhibit varying curvature, such as the helical structure of the bacterial flagellum, which is critical…