Search results for "Speedup"
showing 10 items of 97 documents
An FPGA aligner for short read mapping
2012
The rapid growth of short read datasets poses a new challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. In this work, we present a parallel architecture for short read mapping utilizing field programmable gate array (FPGA)-based hardware. The computation intensive semi-global alignment and the hash table lookup operations are mapped onto an FPGA. The proposed Align Core is implemented with a parallel block structure to gain computational efficiency. We present a new parallel block-wise alignment structure to approximate the conventional dynamic programming algorithm. The performance of our FPGA aligner is compared to the GASSST and BWA …
Efficient distributed average consensus in wireless sensor networks
2020
International audience; Computing the distributed average consensus in Wireless Sensor Networks (WSNs) is investigated in this article. This problem, which is both natural and important, plays a significant role in various application fields such as mobile agents and fleet vehicle coordination, network synchronization, distributed voting and decision, load balancing of divisible loads in distributed computing network systems, and so on. By and large, the average consensus' objective is to have all nodes in the network converged to the average value of the initial nodes' measurements based only on local nodes' information states. In this paper, we introduce a fully distributed algorithm to a…
Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs
2014
Estimation of the pose in which two given molecules might bind together to form a potential complex is a crucial task in structural biology. To solve this so-called "docking problem", most algorithms initially generate large numbers of candidate poses (or decoys) which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the number of such candidates ranges from thousands to millions, performing the clustering on standard CPUs is highly time consuming. In this paper we analyze and evaluate different approaches to parallelize the nearest neighbor chain algorithm to perform hierarchical Ward clustering of protein structures usin…
OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys
2019
Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedback is especially important in studies that involve optogenetic cell type identification by enabling a systematic search for neurons of interest. However, such tools are scarce and limited to costly co…
Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences
2014
The degree of predictability of a sequence can be measured by its entropy and it is closely related to its repetitiveness and compressibility. Entropic profiles are useful tools to study the under- and over-representation of subsequences, providing also information about the scale of each conserved DNA region. On the other hand, compact classes of repetitive motifs, such as maximal motifs, have been proved to be useful for the identification of significant repetitions and for the compression of biological sequences. In this paper we show that there is a relationship between entropic profiles and maximal motifs, and in particular we prove that the former are a subset of the latter. As a furt…
Speeding up of microstructure reconstruction: I. Application to labyrinth patterns
2011
Recently, entropic descriptors based the Monte Carlo hybrid reconstruction of the microstructure of a binary/greyscale pattern has been proposed (Piasecki 2011 Proc. R. Soc. A 467 806). We try to speed up this method applied in this instance to the reconstruction of a binary labyrinth target. Instead of a random configuration, we propose to start with a suitable synthetic pattern created by cellular automaton. The occurrence of the characteristic attributes of the target is the key factor for reducing the computational cost that can be measured by the total number of MC steps required. For the same set of basic parameters, we investigated the following simulation scenarios: the biased/rando…
Exceptional Quantum Walk Search on the Cycle
2016
Quantum walks are standard tools for searching graphs for marked vertices, and they often yield quadratic speedups over a classical random walk's hitting time. In some exceptional cases, however, the system only evolves by sign flips, staying in a uniform probability distribution for all time. We prove that the one-dimensional periodic lattice or cycle with any arrangement of marked vertices is such an exceptional configuration. Using this discovery, we construct a search problem where the quantum walk's random sampling yields an arbitrary speedup in query complexity over the classical random walk's hitting time. In this context, however, the mixing time to prepare the initial uniform state…
Randomized renaming in shared memory systems.
2021
Abstract Renaming is a task in distributed computing where n processes are assigned new names from a name space of size m . The problem is called tight if m = n , and loose if m > n . In recent years renaming came to the fore again and new algorithms were developed. For tight renaming in asynchronous shared memory systems, Alistarh et al. describe a construction based on the AKS network that assigns all names within O ( log n ) steps per process. They also show that, depending on the size of the name space, loose renaming can be done considerably faster. For m = ( 1 + ϵ ) ⋅ n and constant ϵ , they achieve a step complexity of O ( log log n ) . In this paper we consider tight as well as loos…
Minimal nontrivial space complexity of probabilistic one- way turing machines
2005
Languages recognizable in o(log log n) space by probabilistic one — way Turing machines are proved to be regular. This solves an open problem in [4].