Search results for "Abstract"
showing 10 items of 1959 documents
SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search
2017
Computer architectures continue to develop rapidly towards massively parallel and heterogeneous systems. Thus, easily extensible yet highly efficient parallelization approaches for a variety of platforms are urgently needed. In this paper, we present SWhybrid, a hybrid computing framework for large-scale biological sequence database search on heterogeneous computing environments with multi-core or many-core processing units (PUs) based on the Smith- Waterman (SW) algorithm. To incorporate a diverse set of PUs such as combinations of CPUs, GPUs and Xeon Phis, we abstract them as SIMD vector execution units with different number of lanes. We propose a machine model, associated with a unified …
An Integrative Framework for the Construction of Big Functional Networks
2018
We present a methodology for biological data integration, aiming at building and analysing large functional networks which model complex genotype-phenotype associations. A functional network is a graph where nodes represent cellular components (e.g., genes, proteins, mRNA, etc.) and edges represent associations among such molecules. Different types of components may cohesist in the same network, and associations may be related to physical[biochemical interactions or functional/phenotipic relationships. Due to both the large amount of involved information and the computational complexity typical of the problems in this domain, the proposed framework is based on big data technologies (Spark a…
149. Immunogenicity, Safety, and Post-hoc Efficacy Assessment of the Adjuvanted Recombinant Zoster Vaccine in Adults with Hematologic Malignancies: A…
2018
Abstract Background Patients with hematologic malignancies treated with anticancer immunosuppressive therapies (ITs) are at increased risk of herpes zoster (HZ). In a previous report of this phase 3, observer-blind, multicenter trial (NCT01767467), the adjuvanted recombinant zoster vaccine (RZV) was shown to be immunogenic and well-tolerated in ≥18 years of age patients with hematologic malignancies who completed or were undergoing anticancer IT.1 Here we report end-of-study results from the same trial. Methods Participants were randomized 1:1 to receive 2 doses of RZV or placebo (PL) 1–2 months apart, either ≥10 days before or after a cancer therapy cycle, or 10 days to 6 months after canc…
Discovering unbounded unions of regular pattern languages from positive examples
1996
The problem of learning unions of certain pattern languages from positive examples is considered. We restrict to the regular patterns, i.e., patterns where each variable symbol can appear only once, and to the substring patterns, which is a subclass of regular patterns of the type xαy, where x and y are variables and α is a string of constant symbols. We present an algorithm that, given a set of strings, finds a good collection of patterns covering this set. The notion of a ‘good covering’ is defined as the most probable collection of patterns likely to be present in the examples, assuming a simple probabilistic model, or equivalently using the Minimum Description Length (MDL) principle. Ou…
Main Steps in Image Processing and Quantification: The Analysis Workflow
2019
In the last decades, the variety of programs, algorithms, and strategies that researchers have at their disposal to process and analyze image files has grown extensively. However, these are only pointless tools if not applied with the careful planning required to achieve a succesful image analysis. In order to do so, the analyst must establish a meaningful and effective sequence of orderly operations that is able to (1) overcome all the problems derived from the image manipulation and (2) successfully resolve the question that was originally posed. In this chapter, the authors suggest a set of strategies and present a reflection on the main milestones that compose the image processing workf…
Reverse-safe data structures for text indexing
2021
We introduce the notion of reverse-safe data structures. These are data structures that prevent the reconstruction of the data they encode (i.e., they cannot be easily reversed). A data structure D is called z-reverse-safe when there exist at least z datasets with the same set of answers as the ones stored by D. The main challenge is to ensure that D stores as many answers to useful queries as possible, is constructed efficiently, and has size close to the size of the original dataset it encodes. Given a text of length n and an integer z, we propose an algorithm which constructs a z-reverse-safe data structure that has size O(n) and answers pattern matching queries of length at most d optim…
Multi-class Text Complexity Evaluation via Deep Neural Networks
2019
Automatic Text Complexity Evaluation (ATE) is a natural language processing task which aims to assess texts difficulty taking into account many facets related to complexity. A large number of papers tackle the problem of ATE by means of machine learning algorithms in order to classify texts into complex or simple classes. In this paper, we try to go beyond the methodologies presented so far by introducing a preliminary system based on a deep neural network model whose objective is to classify sentences into more of two classes. Experiments have been carried out on a manually annotated corpus which has been preprocessed in order to make it suitable for the scope of the paper. The results sho…
Eventual Consistency Formalized
2019
Distribution of computation is well-known, and there are several frameworks, including some formal frameworks, that capture distributed computation. As yet, however, models of distributed computation are based on the idea that data is conceptually centralized. That is, they assume that data, even if it is distributed, is consistent. This assumption is not valid for many of the database systems in use today, where consistency is compromised to ensure availability and partition tolerance. Starting with an informal definition of eventual consistency, this paper explores several measures of inconsistency that quantify how far from consistency a system is. These measures capture key aspects of e…
Materiality and atmosphere. Two American beat artists painting Europe
2019
The article discusses how European painting heavily influenced two American Beat painters in the post war years. Post-war American painting was often concerned with breaking away from traditional iconography and style, but Jay DeFeo and Joan Brown chose to engage with European traditional painting. Both artists travelled to Europe early in their careers and both declare an intense interest in European painters, paintings, and architecture. In Brown’s case particularly the works of Goya, Velazquez, and Rembrandt become scrutinized and remodeled in her pasty abstract style. De Feo, on her hand, states a particular interest in how the European cities’ distinct colors, lights and textures inspi…
Does higher technical efficiency induce a higher service level? A paradox association in the context of port operations
2020
Abstract Researchers and practitioners are benchmarking technical efficiency of ports and exploring the drivers of high efficiency. Paradoxically, this study argues that high technical efficiency (TE = 1) is not always essential, but an optimal level needs to be achieved while balancing the port service level. This study applies data envelopment analysis (DEA) and free disposal hull (FDH) methods to perform efficiency rankings of 38 container terminals from 17 different ports in 12 Asian countries. Four terminals are technically efficient (TE = 1) in all frontier approaches, thereof one Bangladeshi, one Chinese, one Indian and one Vietnamese. Furthermore, this study presents a case study co…