Search results for "computer.software_genre"
showing 10 items of 3858 documents
Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
2012
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the leng…
Causal Effect Identification from Multiple Incomplete Data Sources: A General Search-Based Approach
2021
Causal effect identification considers whether an interventional probability distribution can be uniquely determined without parametric assumptions from measured source distributions and structural knowledge on the generating system. While complete graphical criteria and procedures exist for many identification problems, there are still challenging but important extensions that have not been considered in the literature. To tackle these new settings, we present a search algorithm directly over the rules of do-calculus. Due to generality of do-calculus, the search is capable of taking more advanced data-generating mechanisms into account along with an arbitrary type of both observational and…
Bayesian Checking of the Second Levels of Hierarchical Models
2007
Hierarchical models are increasingly used in many applications. Along with this increased use comes a desire to investigate whether the model is compatible with the observed data. Bayesian methods are well suited to eliminate the many (nuisance) parameters in these complicated models; in this paper we investigate Bayesian methods for model checking. Since we contemplate model checking as a preliminary, exploratory analysis, we concentrate on objective Bayesian methods in which careful specification of an informative prior distribution is avoided. Numerous examples are given and different proposals are investigated and critically compared.
Centrality measures for networks with community structure
2016
Understanding the network structure, and finding out the influential nodes is a challenging issue in the large networks. Identifying the most influential nodes in the network can be useful in many applications like immunization of nodes in case of epidemic spreading, during intentional attacks on complex networks. A lot of research is done to devise centrality measures which could efficiently identify the most influential nodes in the network. There are two major approaches to the problem: On one hand, deterministic strategies that exploit knowledge about the overall network topology in order to find the influential nodes, while on the other end, random strategies are completely agnostic ab…
A multi-scale area-interaction model for spatio-temporal point patterns
2018
Models for fitting spatio-temporal point processes should incorporate spatio-temporal inhomogeneity and allow for different types of interaction between points (clustering or regularity). This paper proposes an extension of the spatial multi-scale area-interaction model to a spatio-temporal framework. This model allows for interaction between points at different spatio-temporal scales and the inclusion of covariates. We fit the proposed model to varicella cases registered during 2013 in Valencia, Spain. The fitted model indicates small scale clustering and regularity for higher spatio-temporal scales.
Imputation Procedures in Surveys Using Nonparametric and Machine Learning Methods: An Empirical Comparison
2020
Abstract Nonparametric and machine learning methods are flexible methods for obtaining accurate predictions. Nowadays, data sets with a large number of predictors and complex structures are fairly common. In the presence of item nonresponse, nonparametric and machine learning procedures may thus provide a useful alternative to traditional imputation procedures for deriving a set of imputed values used next for the estimation of study parameters defined as solution of population estimating equation. In this paper, we conduct an extensive empirical investigation that compares a number of imputation procedures in terms of bias and efficiency in a wide variety of settings, including high-dimens…
Alignment-free Genomic Analysis via a Big Data Spark Platform
2021
Abstract Motivation Alignment-free distance and similarity functions (AF functions, for short) are a well-established alternative to pairwise and multiple sequence alignments for many genomic, metagenomic and epigenomic tasks. Due to data-intensive applications, the computation of AF functions is a Big Data problem, with the recent literature indicating that the development of fast and scalable algorithms computing AF functions is a high-priority task. Somewhat surprisingly, despite the increasing popularity of Big Data technologies in computational biology, the development of a Big Data platform for those tasks has not been pursued, possibly due to its complexity. Results We fill this impo…
Introducing Traceability in GitHub for Medical Software Development
2021
Assuring traceability from requirements to implementation is a key element when developing safety critical software systems. Traditionally, this traceability is ensured by a waterfall-like process, where phases follow each other, and tracing between different phases can be managed. However, new software development paradigms, such as continuous software engineering and DevOps, which encourage a steady stream of new features, committed by developers in a seemingly uncontrolled fashion in terms of former phasing, challenge this view. In this paper, we introduce our approach that adds traceability capabilities to GitHub, so that the developers can act like they normally do in GitHub context bu…
Semantic Computing of Moods Based on Tags in Social Media of Music
2014
Social tags inherent in online music services such as Last.fm provide a rich source of information on musical moods. The abundance of social tags makes this data highly beneficial for developing techniques to manage and retrieve mood information, and enables study of the relationships between music content and mood representations with data substantially larger than that available for conventional emotion research. However, no systematic assessment has been done on the accuracy of social tags and derived semantic models at capturing mood information in music. We propose a novel technique called Affective Circumplex Transformation (ACT) for representing the moods of music tracks in an interp…
Measuring Semantic Coherence of a Conversation
2018
Conversational systems have become increasingly popular as a way for humans to interact with computers. To be able to provide intelligent responses, conversational systems must correctly model the structure and semantics of a conversation. We introduce the task of measuring semantic (in)coherence in a conversation with respect to background knowledge, which relies on the identification of semantic relations between concepts introduced during a conversation. We propose and evaluate graph-based and machine learning-based approaches for measuring semantic coherence using knowledge graphs, their vector space embeddings and word embedding models, as sources of background knowledge. We demonstrat…