Image segmentation is a very important step in the computerized analysis of digital images. The maxflow mincut approach has been successfully used to obtain minimum energy segmentations of images in many fields. Classical algorithms for maxflow in networks do not directly lend themselves to efficient parallel implementations on contemporary parallel processors. We present the results of an implementation of Goldberg-Tarjan preflow-push algorithm on the Cray XMT-2 massively multithreaded supercomputer. This machine has hardware support for 128 threads in each physical processor, a uniformly accessible shared memory of up to 4 TB and hardware synchronization for 64 bit word. It is thus well-suited to the parallelization of graph theoretic algorithms, such as preflow-push. We describe the implementation of the preflow-push code on the XMT-2 and present the results of timing experiments on a series of synthetically generated as well as real images. Our results indicate very good performance on large images and pave the way for practical applications of this machine architecture for image analysis in a production setting. The largest images we have run are 32000 pixels in size, which are well beyond the largest previously reported in the literature.
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http://dx.doi.org/10.1002/cpe.3181 | DOI Listing |
Bioinformatics
December 2023
Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.
Motivation: Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like those produced by PacBio and Nanopore technologies. The recently proposed wavefront alignment (WFA) algorithm paves the way for more efficient alignment tools, improving time and memory complexity over previous methods.
View Article and Find Full Text PDFEntropy (Basel)
October 2023
Wuhan Geomatics Institute, Wuhan 430079, China.
The rapid development of information technology has made the amount of information in massive texts far exceed human intuitive cognition, and dependency parsing can effectively deal with information overload. In the background of domain specialization, the migration and application of syntactic treebanks and the speed improvement in syntactic analysis models become the key to the efficiency of syntactic analysis. To realize domain migration of syntactic tree library and improve the speed of text parsing, this paper proposes a novel approach-the Double-Array Trie and Multi-threading (DAT-MT) accelerated graph fusion dependency parsing model.
View Article and Find Full Text PDFPLoS One
October 2023
China-Singapore Tianjin Eco-city Technology Innovation Bureau, Tianjin, 300480, China.
The massive amount of vehicle plate data generated by intelligent transportation systems is widely used in the field of urban transportation information system construction and has a high scientific research and application value. The adoption of big data platforms to properly preserve, process, and exploit these valuable data resources has become a hot research area in recent years. To address the problems of implementing complex multi-conditional comprehensive query functions and flexible data applications in the key-value database storage environment of a big data platform, this paper proposes a data access model based on the jump hash consistency algorithm.
View Article and Find Full Text PDFGigascience
December 2022
School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW 2052, Australia.
Background: Third-generation nanopore sequencers offer selective sequencing or "Read Until" that allows genomic reads to be analyzed in real time and abandoned halfway if not belonging to a genomic region of "interest." This selective sequencing opens the door to important applications such as rapid and low-cost genetic tests. The latency in analyzing should be as low as possible for selective sequencing to be effective so that unnecessary reads can be rejected as early as possible.
View Article and Find Full Text PDFSensors (Basel)
August 2021
Computer Engineering and Software Engineering Department, Ecole Polytechnique Montreal, Montreal, QC h3t 1j4, Canada.
Integrated development environments (IDEs) provide many useful tools such as a code editor, a compiler, and a debugger for creating software. These tools are highly sophisticated, and their development requires a significant effort. Traditionally, an IDE supports different programming languages via plugins that are not usually reusable in other IDEs.
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