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Quantum walks provide a versatile framework for probing the structural and dynamical properties of complex systems ranging from biological networks to synthetic materials. However, their realization on current noisy pre-fault-tolerant…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…
Graph is a fundamental mathematical structure in characterizing relations between different objects and has been widely used on various learning tasks. Most methods implicitly assume a given graph to be accurate and complete. However, real…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Hypergraphs, increasingly utilised to model complex and diverse relationships in modern networks, have gained significant attention for representing intricate higher-order interactions. Among various challenges, cohesive subgraph discovery…
Deep homography estimation has broad applications in computer vision and robotics. Remarkable progresses have been achieved while the existing methods typically treat it as a direct regression or iterative refinement problem and often…
Getting a labeling of vertices close to the structure of the graph has been proved to be of interest in many applications e.g., to follow smooth signals indexed by the vertices of the network. This question can be related to a graph…
(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…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Robotic assembly in architectural construction faces a persistent bottleneck: existing planners are either highly specialized, requiring prohibitive retraining for every new geometric design, or operationally inefficient, treating…
Reconstructing a complete object from its parts is a fundamental problem in many scientific domains. The purpose of this article is to provide a systematic survey on this topic. The reassembly problem requires understanding the attributes…
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…
We propose high-order hypergraph walks as a framework to generalize graph-based network science techniques to hypergraphs. Edge incidence in hypergraphs is quantitative, yielding hypergraph walks with both length and width. Graph methods…
A team consisting of an unknown number of mobile agents, starting from different nodes of an unknown network, possibly at different times, have to meet at the same node. Agents are anonymous (identical), execute the same deterministic…
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…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…