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Genetic algorithm

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https://www.readbyqxmd.com/read/28103198/harmonious-genetic-clustering
#1
Faliang Huang, Xuelong Li, Shichao Zhang, Jilian Zhang
To automatically determine the number of clusters and generate more quality clusters while clustering data samples, we propose a harmonious genetic clustering algorithm, named HGCA, which is based on harmonious mating in eugenic theory. Different from extant genetic clustering methods that only use fitness, HGCA aims to select the most suitable mate for each chromosome and takes into account chromosomes gender, age, and fitness when computing mating attractiveness. To avoid illegal mating, we design three mating prohibition schemes, i...
January 5, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28103060/a-new-algorithm-using-the-non-dominated-tree-to-improve-non-dominated-sorting
#2
Patrik Gustavsson, Anna Syberfeldt
Non-dominated sorting is a technique often used in evolutionary algorithms to determine the quality of solutions in a population. The most common algorithm is the Fast Non-dominated Sort (FNS). This algorithm, however, has the drawback that its performance deteriorates when the population size grows. The same drawback applies also to other non-dominating sorting algorithms such as the Efficient Non-dominated Sort with Binary Strategy (ENS-BS). An algorithm suggested to overcome this drawback is the Divide-and-Conquer Non-dominated Sort (DCNS) which works well on a limited number of objectives but deteriorates when the number of objectives grows...
January 19, 2017: Evolutionary Computation
https://www.readbyqxmd.com/read/28101727/reliable-prediction-of-adsorption-isotherms-via-genetic-algorithm-molecular-simulation
#3
L LoftiKatooli, A Shahsavand
Conventional molecular simulation techniques such as grand canonical Monte Carlo (GCMC) strictly rely on purely random search inside the simulation box for predicting the adsorption isotherms. This blind search is usually extremely time demanding for providing a faithful approximation of the real isotherm and in some cases may lead to non-optimal solutions. A novel approach is presented in this article which does not use any of the classical steps of the standard GCMC method, such as displacement, insertation, and removal...
January 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28100788/genomic-infectious-disease-epidemiology-in-partially-sampled-and-ongoing-outbreaks
#4
Xavier Didelot, Christophe Fraser, Jennifer Gardy, Caroline Colijn
Genomic data is increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom - a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by colouring the branches of a phylogeny according to which host those branches were in...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100066/identification-of-eggs-from-different-production-systems-based-on-hyperspectra-and-cs-svm
#5
J Sun, S Cong, H Mao, X Zhou, X Wu, X Zhang
1. To identify the origin of table eggs more accurately, a method based on hyperspectral imaging technology was studied. 2. The hyperspectral data of 200 samples of intensive and extensive eggs were collected. Standard normalised variables (SNV) combined with Savitzky-Golay (SG) were used to eliminate noise, then stepwise regression (SWR) was used for feature selection. Grid search algorithm (GS), genetic search algorithm (GA), particle swarm optimisation algorithm (PSO) and cuckoo search algorithm (CS) were applied by support vector machine (SVM) to establish a SVM identification model with the optimal parameters...
January 19, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28099159/reducing-false-arrhythmia-alarm-rates-using-robust-heart-rate-estimation-and-cost-sensitive-support-vector-machines
#6
Qiang Zhang, Xianxiang Chen, Zhen Fang, Qingyuan Zhan, Ting Yang, Shanhong Xia
To lessen the rate of false critical arrhythmia alarms, we used robust heart rate estimation and cost-sensitive support vector machines. The PhysioNet MIMIC II database and the 2015 PhysioNet/CinC Challenge public database were used as the training dataset; the 2015 Challenge hidden dataset was for testing. Each record had an alarm labeled with asystole, extreme bradycardia, extreme tachycardia, ventricular tachycardia or ventricular flutter/fibrillation. Before alarm onsets, 300 s multimodal data was provided, including electrocardiogram, arterial blood pressure and/or photoplethysmogram...
January 18, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28098149/characterising-private-and-shared-signatures-of-positive-selection-in-37-asian-populations
#7
Xuanyao Liu, Dongsheng Lu, Woei-Yuh Saw, Philip J Shaw, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Suthat Fucharoen, Worachart Lert-Itthiporn, Kwanrutai Chin-Inmanu, Tran Nguyen Bich Chau, Katie Anders, Anuradhani Kasturiratne, H Janaka de Silva, Tomohiro Katsuya, Ryosuke Kimura, Toru Nabika, Takayoshi Ohkubo, Yasuharu Tabara, Fumihiko Takeuchi, Ken Yamamoto, Mitsuhiro Yokota, Dolikun Mamatyusupu, Wenjun Yang, Yeun-Jun Chung, Li Jin, Boon-Peng Hoh, Ananda R Wickremasinghe, RickTwee-Hee Ong, Chiea-Chuen Khor, Sarah J Dunstan, Cameron Simmons, Sissades Tongsima, Prapat Suriyaphol, Norihiro Kato, Shuhua Xu, Yik-Ying Teo
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28097779/the-mcgill-interactive-pediatric-oncogenetic-guidelines-an-approach-to-identifying-pediatric-oncology-patients-most-likely-to-benefit-from-a-genetic-evaluation
#8
Catherine Goudie, Hallie Coltin, Leora Witkowski, Stephanie Mourad, David Malkin, William D Foulkes
Identifying cancer predisposition syndromes in children with tumors is crucial, yet few clinical guidelines exist to identify children at high risk of having germline mutations. The McGill Interactive Pediatric OncoGenetic Guidelines project aims to create a validated pediatric guideline in the form of a smartphone/tablet application using algorithms to process clinical data and help determine whether to refer a child for genetic assessment. This paper discusses the initial stages of the project, focusing on its overall structure, the methodology underpinning the algorithms, and the upcoming algorithm validation process...
January 18, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28096315/experimental-optimization-of-exposure-index-and-quality-of-service-in-wlan-networks
#9
David Plets, Günter Vermeeren, Eli De Poorter, Ingrid Moerman, Sotirios K Goudos, Martens Luc, Joseph Wout
This paper presents the first real-life optimization of the Exposure Index (EI). A genetic optimization algorithm is developed and applied to three real-life Wireless Local Area Network scenarios in an experimental testbed. The optimization accounts for downlink, uplink and uplink of other users, for realistic duty cycles, and ensures a sufficient Quality of Service to all users. EI reductions up to 97.5% compared to a reference configuration can be achieved in a downlink-only scenario, in combination with an improved Quality of Service...
January 17, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/28093659/clinical-and-molecular-relevance-of-mutant-allele-tumor-heterogeneity-in-breast-cancer
#10
Ding Ma, Yi-Zhou Jiang, Xi-Yu Liu, Yi-Rong Liu, Zhi-Ming Shao
PURPOSE: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. METHODS: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment...
January 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28092578/experienced-gray-wolf-optimization-through-reinforcement-learning-and-neural-networks
#11
E Emary, Hossam M Zawbaa, Crina Grosan
In this paper, a variant of gray wolf optimization (GWO) that uses reinforcement learning principles combined with neural networks to enhance the performance is proposed. The aim is to overcome, by reinforced learning, the common challenge of setting the right parameters for the algorithm. In GWO, a single parameter is used to control the exploration/exploitation rate, which influences the performance of the algorithm. Rather than using a global way to change this parameter for all the agents, we use reinforcement learning to set it on an individual basis...
January 10, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28091917/detection-of-rare-mutations-by-routine-analysis-of-kras-nras-and-braf-oncogenes
#12
D S Mikhailenko, G D Efremov, N Yu Safronova, V V Strelnikov, B Ya Alekseev
Molecular genetic analysis of KRAS, NRAS, and BRAF genes was carried out in order to develop an optimal algorithm for detection of minor mutations. We analyzed 35 melanoma and 33 colorectal cancer specimens. Frequent G12D/V/A/C/S mutations were detected in KRAS. The most frequent BRAF mutation in melanoma was V600E, the percentage of rare mutations is significant for DNA diagnosis (24%). Identification of rare BRAF mutations 1790C→G (L597R), 1798_1799delinsAA (V600K), 1798_1799delinsAG (V600R), and 1799_1800delinsAA (V600E) and NRAS mutation 38G→T (G13V) was possible only by Sanger sequencing...
January 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28090684/predict-pd-an-online-approach-to-prospectively-identify-risk-indicators-of-parkinson-s-disease
#13
Alastair J Noyce, Lea R'Bibo, Luisa Peress, Jonathan P Bestwick, Kerala L Adams-Carr, Niccolo E Mencacci, Christopher H Hawkes, Joseph M Masters, Nicholas Wood, John Hardy, Gavin Giovannoni, Andrew J Lees, Anette Schrag
BACKGROUND: A number of early features can precede the diagnosis of Parkinson's disease (PD). OBJECTIVE: To test an online, evidence-based algorithm to identify risk indicators of PD in the UK population. METHODS: Participants aged 60 to 80 years without PD completed an online survey and keyboard-tapping task annually over 3 years, and underwent smell tests and genotyping for glucocerebrosidase (GBA) and leucine-rich repeat kinase 2 (LRRK2) mutations...
January 16, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28090239/the-screening-and-ranking-algorithm-for-change-points-detection-in-multiple-samples
#14
Chi Song, Xiaoyi Min, Heping Zhang
The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based...
December 2016: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28087895/crohn-disease-risk-prediction-best-practices-and-pitfalls-with-exome-data
#15
Manuel Giollo, David T Jones, Marco Carraro, Emanuela Leonardi, Carlo Ferrari, Silvio C E Tosatto
The Critical Assessment of Genome Interpretation (CAGI) experiment is the first attempt to evaluate the state-of-the-art in genetic data interpretation. Among the proposed challenges, Crohn disease (CD) risk prediction has become the most classic problem spanning three editions. The scientific question is very hard: can anybody assess the risk to develop CD given the exome data alone? This is one of the ultimate goals of genetic analysis, which motivated most CAGI participants to look for powerful new methods...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28087426/next-generation-sequencing-of-a-large-gene-panel-in-patients-initially-diagnosed-with-idiopathic-ventricular-fibrillation
#16
Marloes Visser, Dennis Dooijes, Jasper J van der Smagt, Jeroen F van der Heijden, Pieter A Doevendans, Peter Loh, Folkert W Asselbergs, Rutger J Hassink
BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a rare primary cardiac arrhythmia syndrome that is diagnosed in a resuscitated cardiac arrest victim, with documented ventricular fibrillation, in whom no underlying cause is identified after comprehensive clinical evaluation. In some patients causative genetic mutations are detected which facilitate patient treatment and follow-up. The feasibility of next generation sequencing (NGS) has increased with its greater availability and decreasing costs...
January 10, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28087102/feature-selection-for-outcome-prediction-in-oesophageal-cancer-using-genetic-algorithm-and-random-forest-classifier
#17
Desbordes Paul, Ruan Su, Modzelewski Romain, Vauclin Sébastien, Vera Pierre, Gardin Isabelle
The outcome prediction of patients can greatly help to personalize cancer treatment. A large amount of quantitative features (clinical exams, imaging, …) are potentially useful to assess the patient outcome. The challenge is to choose the most predictive subset of features. In this paper, we propose a new feature selection strategy called GARF (genetic algorithm based on random forest) extracted from positron emission tomography (PET) images and clinical data. The most relevant features, predictive of the therapeutic response or which are prognoses of the patient survival 3 years after the end of treatment, were selected using GARF on a cohort of 65 patients with a local advanced oesophageal cancer eligible for chemo-radiation therapy...
December 28, 2016: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
https://www.readbyqxmd.com/read/28081509/in-silico-prediction-of-toxicity-of-phenols-to-tetrahymena-pyriformis-by-using-genetic-algorithm-and-decision-tree-based-modeling-approach
#18
Fatemeh Abbasitabar, Vahid Zare-Shahabadi
Risk assessment of chemicals is an important issue in environmental protection; however, there is a huge lack of experimental data for a large number of end-points. The experimental determination of toxicity of chemicals involves high costs and time-consuming process. In silico tools such as quantitative structure-toxicity relationship (QSTR) models, which are constructed on the basis of computational molecular descriptors, can predict missing data for toxic end-points for existing or even not yet synthesized chemicals...
January 2, 2017: Chemosphere
https://www.readbyqxmd.com/read/28079798/clinical-and-genetic-factors-associated-with-warfarin-maintenance-dose-in-northern-chinese-patients-with-mechanical-heart-valve-replacement
#19
Rui Liu, Jian Cao, Qian Zhang, Xin-Miao Shi, Xiao-Dong Pan, Ran Dong
The effects of genetic variants on warfarin dosing vary among different ethnic groups, especially in the Chinese population. The objective of this study was to recruit patients through a rigorous experimental design and to perform a comprehensive screen to identify gene polymorphisms that may influence warfarin dosing in northern Han Chinese patients with mechanical heart valve replacement. Consenting patients (n = 183) with a stable warfarin dose were included in this study. Ninety-six single nucleotide polymorphisms (SNPs) in 30 genes involved in warfarin pharmacological pathways were genotyped using the Illumina SNP GoldenGate Assay, and their associations with warfarin dosing were assessed using univariate regression analysis with post hoc comparison using least significant difference analysis...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28077634/characterization-of-hcv-envelope-diversification-from-acute-to-chronic-infection-using-smrt-sequencing-within-a-sexually-transmitted-hepatitis-c-virus-cluster
#20
Cynthia K Y Ho, Jayna Raghwani, Sylvie Koekkoek, Richard H Liang, Jan T M Van der Meer, Marc Van Der Valk, Menno De Jong, Oliver G Pybus, Janke Schinkel, Richard Molenkamp
: In contrast to other available next generation sequencing platforms, Pacbio Single Molecule, Real-Time (SMRT) sequencing has the advantage of generating long reads, albeit with a relatively higher error rate in unprocessed data. Using this platform we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1680 nt) from individuals belonging to a cluster of sexually-transmitted cases. All five subjects were HIV-1 coinfected and infected with a closely related strain of HCV genotype 4d...
January 11, 2017: Journal of Virology
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