相关论文: TwoPaCo: An efficient algorithm to build the compa…

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…

We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…

Kernel approximation using randomized feature maps has recently gained a lot of interest. In this work, we identify that previous approaches for polynomial kernel approximation create maps that are rank deficient, and therefore do not…

A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…

Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…

Mining dense subgraphs where vertices connect closely with each other is a common task when analyzing graphs. A very popular notion in subgraph analysis is core decomposition. Recently, Esfahani et al. presented a probabilistic core…

We show how to generate random derangements efficiently by two different techniques: random restricted transpositions and sequential importance sampling. The algorithm employing restricted transpositions can also be used to generate random…

We present an algorithm which computes a planar 2-spanner from an Unit Disk Graph when the node density is sufficient. The communication complexity in terms of number of node's identifier sent by the algorithm is $6n$, while the…

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…

There has been significant recent interest in parallel graph processing due to the need to quickly analyze the large graphs available today. Many graph codes have been designed for distributed memory or external memory. However, today even…

We describe and analyse a simple greedy algorithm \2G\ that finds a good 2-matching $M$ in the random graph $G=G_{n,cn}^{\d\geq 3}$ when $c\geq 15$. A 2-matching is a spanning subgraph of maximum degree two and $G$ is drawn uniformly from…

Cognitive brain imaging is accumulating datasets about the neural substrate of many different mental processes. Yet, most studies are based on few subjects and have low statistical power. Analyzing data across studies could bring more…

Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…

Graph-structured data are central to many scientific and industrial applications where the goal is to optimize expensive black-box objectives defined over graph structures or node configurations -- as seen in molecular design, supply…

The formation trajectory planning using complete graphs to model collaborative constraints becomes computationally intractable as the number of drones increases due to the curse of dimensionality. To tackle this issue, this paper presents a…

Human behavior emerges from planning over elaborate decompositions of tasks into goals, subgoals, and low-level actions. How are these decompositions created and used? Here, we propose and evaluate a normative framework for task…

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…

We provide a compact data structure for representing polyominoes that supports neighborhood and visibility queries. Neighborhood queries concern reporting adjacent cells to a given cell, and visibility queries determine whether a straight…

Imitation learning from human demonstrations is an effective means to teach robots manipulation skills. But data acquisition is a major bottleneck in applying this paradigm more broadly, due to the amount of cost and human effort involved.…

We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…