Search results for "Speedup"
showing 7 items of 97 documents
Alignment-Free Sequence Comparison over Hadoop for Computational Biology
2015
Sequence comparison i.e., The assessment of how similar two biological sequences are to each other, is a fundamental and routine task in Computational Biology and Bioinformatics. Classically, alignment methods are the de facto standard for such an assessment. In fact, considerable research efforts for the development of efficient algorithms, both on classic and parallel architectures, has been carried out in the past 50 years. Due to the growing amount of sequence data being produced, a new class of methods has emerged: Alignment-free methods. Research in this ares has become very intense in the past few years, stimulated by the advent of Next Generation Sequencing technologies, since those…
Combining split-and-merge and multi-seed region growing algorithms for uterine fibroid segmentation in MRgFUS treatments
2016
Uterine fibroids are benign tumors that can affect female patients during reproductive years. Magnetic resonance-guided focused ultrasound (MRgFUS) represents a noninvasive approach that uses thermal ablation principles to treat symptomatic fibroids. During traditional treatment planning, uterus, fibroids, and surrounding organs at risk must be manually marked on MR images by an operator. After treatment, an operator must segment, again manually, treated areas to evaluate the non-perfused volume (NPV) inside the fibroids. Both pre- and post-treatment procedures are time-consuming and operator-dependent. This paper presents a novel method, based on an advanced direct region detection model, …
Artificial Intelligence + Distributed Systems = Agents
2009
The connection with Wirth’s book goes beyond the title, albeit confining the area to modern Artificial Intelligence (AI). Whereas thirty years ago, to devise effective programs, it became necessary to enhance the classical algorithmic framework with approaches applied to limited and focused subdomains, in the context of broad-band technology and semantic web, applications - running in open, heterogeneous, dynamic and uncertain environments-current paradigms are not enough, because of the shift from programs to processes. Beside the structure as position paper, to give more weight to some basic assertions, results of recent research are abridged and commented upon in line with new paradigms.…
A grid ant colony algorithm for the orienteering problem
2005
In this paper we propose a distributed ant colony algorithm to solve large scale orienteering problem instances. Our approach is based on a multi-colony strategy where each colony works in an independent portion (cluster) in the original graph. This results in no need for communicating pheromones information among colonies and in increasing speedup. We have implemented our algorithm as a .NET Web services infrastructure following a grid computing philosophy and we provide some promising experimental results to show the feasibility and effectiveness of our approach
Online Sparse Collapsed Hybrid Variational-Gibbs Algorithm for Hierarchical Dirichlet Process Topic Models
2017
Topic models for text analysis are most commonly trained using either Gibbs sampling or variational Bayes. Recently, hybrid variational-Gibbs algorithms have been found to combine the best of both worlds. Variational algorithms are fast to converge and more efficient for inference on new documents. Gibbs sampling enables sparse updates since each token is only associated with one topic instead of a distribution over all topics. Additionally, Gibbs sampling is unbiased. Although Gibbs sampling takes longer to converge, it is guaranteed to arrive at the true posterior after infinitely many iterations. By combining the two methods it is possible to reduce the bias of variational methods while …
PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment
2017
The progress of next-generation sequencing has a major impact on medical and genomic research. This technology can now produce billions of short DNA fragments (reads) in a single run. One of the most demanding computational problems used by almost every sequencing pipeline is short-read alignment; i.e. determining where each fragment originated from in the original genome. Most current solutions are based on a seed-and-extend approach, where promising candidate regions (seeds) are first identified and subsequently extended in order to verify whether a full high-scoring alignment actually exists in the vicinity of each seed. Seed verification is the main bottleneck in many state-of-the-art a…
An Abstract Generic Framework for Web Site Verification
2008
In this paper, we present an abstract framework for Web site verification which improves the performance of a previous, rewriting-based Web verification methodology. The approximated framework is formalized as a source-to-source transformation which is parametric w.r.t. the chosen abstraction. This transformation significantly reduces the size of the Web documents by dropping or merging contents that do not influence the properties to be checked. This allows us to reuse all verification facilities of the previous system WebVerdi-M to efficiently analyze Web sites. In order to ensure that the verified properties are not affected by the abstraction, we develop a methodology which derives the …