Search results for " algorithms"
showing 10 items of 612 documents
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
2014
Abstract Motivation: Protein–protein interaction (PPI) networks are powerful models to represent the pairwise protein interactions of the organisms. Clustering PPI networks can be useful for isolating groups of interacting proteins that participate in the same biological processes or that perform together specific biological functions. Evolutionary orthologies can be inferred this way, as well as functions and properties of yet uncharacterized proteins. Results: We present an overview of the main state-of-the-art clustering methods that have been applied to PPI networks over the past decade. We distinguish five specific categories of approaches, describe and compare their main features and …
Adaptive reference-free compression of sequence quality scores
2014
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…
The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis
2021
Abstract Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either mi…
Contributed discussion on article by Pratola
2016
The author should be commended for his outstanding contribution to the literature on Bayesian regression tree models. The author introduces three innovative sampling approaches which allow for efficient traversal of the model space. In this response, we add a fourth alternative.
Stochastic algorithms for robust statistics in high dimension
2016
This thesis focus on stochastic algorithms in high dimension as well as their application in robust statistics. In what follows, the expression high dimension may be used when the the size of the studied sample is large or when the variables we consider take values in high dimensional spaces (not necessarily finite). In order to analyze these kind of data, it can be interesting to consider algorithms which are fast, which do not need to store all the data, and which allow to update easily the estimates. In large sample of high dimensional data, outliers detection is often complicated. Nevertheless, these outliers, even if they are not many, can strongly disturb simple indicators like the me…
A Differential Evolution Framework with Ensemble of Parameters and Strategies and Pool of Local Search Algorithms
2014
The file attached to this record is the author's final peer reviewed version. The publisher's final version can be found by following the DOI link. The ensemble structure is a computational intelligence supervised strategy consisting of a pool of multiple operators that compete among each other for being selected, and an adaptation mechanism that tends to reward the most successful operators. In this paper we extend the idea of the ensemble to multiple local search logics. In a memetic fashion, the search structure of an ensemble framework cooperatively/competitively optimizes the problem jointly with a pool of diverse local search algorithms. In this way, the algorithm progressively adapts…
Machine learning for a combined electroencephalographic anesthesia index to detect awareness under anesthesia
2020
Spontaneous electroencephalogram (EEG) and auditory evoked potentials (AEP) have been suggested to monitor the level of consciousness during anesthesia. As both signals reflect different neuronal pathways, a combination of parameters from both signals may provide broader information about the brain status during anesthesia. Appropriate parameter selection and combination to a single index is crucial to take advantage of this potential. The field of machine learning offers algorithms for both parameter selection and combination. In this study, several established machine learning approaches including a method for the selection of suitable signal parameters and classification algorithms are a…
Training label cleaning with ant colony optimization for classification of remote sensing imagery
2015
This paper presents an original approach for improving performances of the supervised classifiers in remote sensing imagery by proposing a technique to refine a given training set using Ant Colony Optimization (ACO). The new method called ACO-Training Label Cleaning (ACO-TLC) applies ACO model for selection of the significant training samples from a given set of labeled vectors in order to optimize the quality of a supervised classifier. This means to retain the most informative samples and to remove the uncertain or misclassified training samples, which lead to classification errors. As a result of the selection process, we can obtain a purified training set. The proposed model is implemen…
Algorithms for the calculation of the view factors between human body and rectangular surfaces in parallelepiped environments
1992
Abstract The thermal comfort conditions for people in moderate thermal environments are subjected to spatial changes, depending on the radiative exchanges of the human body with the surrounding surfaces. Radiative thermal exchanges are notably accounted for by means of the “view factors” between a person in a given posture and the surface of the enclosure. These important parameters can be evaluated by means of a large set of graphs by Fanger, for rectangular surfaces. But the handling of graphs could lead to reading errors. In this paper a simple algorithm is presented, which is able to compute the required view factors. A validation, by means of a comparison against experimental data, is …
Anamorphic Projection: Analogical/Digital Algorithms
2014
The study presents the first outcomes of a wider research dealing with the theme of “anamorphosis”, a specific technique of geometric projection of a shape on a surface. Anamorphosis represents the synthesis among geometry, art and architecture and is realized in scientific and empirical research approaches. In this study we investigated how new digital techniques allow to simplify the anamorphic applications even in case of projections on complex surfaces. After a short excursus of the most famous historical and contemporary applications, we propose some possible approaches that allow you to manage the geometry of anamorphic curves both in Descriptive Geometry field (by using interactive t…