The automatic fitting of spiking neuron models to experimental data is a challenging problem. The integrate and fire model and Hodgkin–Huxley (HH) models represent the two complexity extremes of spiking neural models. Between these two extremes lies two and three differential-equation-based models. In this work, we investigate the problem of parameter estimation of two simple neuron models with a sharp reset in order to fit the spike timing of electro-physiological recordings based on two problem formulations. Five optimization algorithms are investigated; three of them have not been used to

The suffix array is an indexing data structure used in a wide range of applications in Bioinformatics. Biological DNA sequences are available to download from public servers in the form of compressed files, where the popular lossless compression program gzip [1] is employed. The straightforward method to construct the suffix array for this data involves decompressing the sequence file, storing it on disk, and then calling a suffix array construction program to build the suffix array. This scenario, albeit feasible, requires disk access and throws away valuable information in the compressed

Background: Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a very challenging task. For the most simple distance measures (the breakpoint distance and the reversal distance), the problem is NP-hard even if one considers only three genomes. Results: In this paper, we present a new heuristic algorithm that directly constructs a phylogenetic tree w.r.t. the weighted reversal and transposition distance. Experimental results on previously

Multi-slice short-axis acquisitions of the left ventricle are fundamental for estimating the volume and mass of the left ventricle in cardiac MRI scans. Manual segmentation of the myocardium in all time frames per each cross-section is a cumbersome task. Therefore, automatic myocardium segmentation methods are essential for cardiac functional analysis. Region growing has been proposed to segment the myocardium. Although the technique is simple and fast, non uniform intensity and low-contrast interfaces of the myocardium are major challenges of the technique that limit its use in myocardial

neurodegenerative diseases have complex pathological mechanisms. Detecting disease-associated genes with typical differentially expressed gene selection approaches are ineffective. Recent studies have shown that wrappers Evolutionary optimization methods perform well in feature selection for high dimensional data, but they are computationally costly. This paper proposes a simple method based on a genetic algorithm engaged with the Empirical Bays T-statistics test to enhance the disease-associated gene selection process. The proposed method is applied to Affymetrix microarray data from

Pervasive healthcare environments provide an effective solution for monitoring the wellbeing of the elderly where the general trend of an increasingly ageing population has placed significant burdens on current healthcare systems. An important pervasive healthcare system functionality is patient motion analysis where gait information can be used to detect walking behavior abnormalities that may indicate the onset of adverse health problems, for quantifying post-operative recovery, and to observe the progression of neurodegenerative diseases. The development of accurate motion analysis models

Taxonomic assignment is the core of targeted metagenomics approaches that aims to assign sequencing reads to their corresponding taxonomy. Sequence similarity searching and machine learning (ML) are two commonly used approaches for taxonomic assignment based on the 16S rRNA. Similarity based approaches require high computation resources, while ML approaches dont need these resources in prediction. The majority of these ML approaches depend on k-mer frequency rather than direct sequence, which leads to low accuracy on short reads as k-mer frequency doesnt consider k-mer position. Moreover

The coronavirus (COVID-2019) quickly spread throughout the world and came to be a pandemic. To avoid further spreading this epidemic and treat affected patients rapidly, it is important to recognize the positive cases as early as possible. In this paper, deep learning techniques are employed to detect COVID-19 from chest X-ray images quickly. The images of the two classes, COVID and No-findings are collected from three public datasets. The proposed approach consists of two phases; transfer learning and fine-tuning. Transfer learning is carried out by seven deep learning models: DenseNet

Pediatric septic shock is generally considered as a devastating clinical syndrome that can lead to tissue damage and organ failure due to the over exaggerated immune response to an infection. Therefore, in this paper, we attempted to early identify the clinical course of such disease with the aid of peripheral blood T-cells of 181 pediatric patients who admitted to Intensive Care Unit (ICU), Accordingly, 34 differential expressed genes have been identified as biological genetic biomarkers. Minimum redundancy and maximum relevance feature selection strategy has been proposed for the discovery