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Bayesian network

Guoqi Li, Lei Deng, Gaoxi Xiao, Pei Tang, Changyun Wen, Wuhua Hu, Jing Pei, Luping Shi, H Eugene Stanley
Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a dynamical system from any initial state to any desired final state in finite time, with a suitable choice of inputs; and optimal control, which is a typical control approach to minimize the cost for driving the network to a predefined state with a given number of control inputs...
March 15, 2018: Scientific Reports
Hythem Sidky, Jonathan K Whitmer
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes...
March 14, 2018: Journal of Chemical Physics
Julia N Bailey, Laurence de Nijs, Dongsheng Bai, Toshimitsu Suzuki, Hiroyuki Miyamoto, Miyabi Tanaka, Christopher Patterson, Yu-Chen Lin, Marco T Medina, María E Alonso, José M Serratosa, Reyna M Durón, Viet H Nguyen, Jenny E Wight, Iris E Martínez-Juárez, Adriana Ochoa, Aurelio Jara-Prado, Laura Guilhoto, Yolly Molina, Elsa M Yacubian, Minerva López-Ruiz, Yushi Inoue, Sunao Kaneko, Shinichi Hirose, Makiko Osawa, Hirokazu Oguni, Shinji Fujimoto, Thierry M Grisar, John M Stern, Kazuhiro Yamakawa, Bernard Lakaye, Antonio V Delgado-Escueta
BACKGROUND: In juvenile myoclonic epilepsy, data are limited on the genetic basis of networks promoting convulsions with diffuse polyspikes on electroencephalography (EEG) and the subtle microscopic brain dysplasia called microdysgenesis. METHODS: Using Sanger sequencing, we sequenced the exomes of six members of a large family affected with juvenile myoclonic epilepsy and confirmed cosegregation in all 37 family members. We screened an additional 310 patients with this disorder for variants on DNA melting-curve analysis and targeted real-time DNA sequencing of the gene encoding intestinal-cell kinase ( ICK)...
March 15, 2018: New England Journal of Medicine
Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
Yuqing Zhang, Xinyu Zhou, Lining Yang, Sarah E Hetrick, John R Weisz, Pim Cuijpers, Jürgen Barth, Cinzia Del Giovane, Shuai Yuan, David Cohen, Donna Gillies, Xiaofeng Jiang, Teng Teng, Peng Xie
INTRODUCTION: Post-traumatic stress disorder (PTSD) is common among children and adolescents who are exposed to trauma, and it is often associated with significant negative impacts on their psychosocial functioning and quality of life. Many types of psychotherapies have been found to be effective for PTSD in children and adolescents. However, due to the lack of direct comparisons between different psychotherapies, the hierarchy of treatment efficacy is still unclear. Therefore, we plan to conduct a systematic review and network meta-analysis to evaluate the efficacy and acceptability of various types of psychotherapies for PTSD in children and adolescents...
March 12, 2018: BMJ Open
Jonathan P Rehfuss, Kenneth M DeSart, Jared M Rozowsky, Kerri A O'Malley, Lyle L Moldawer, Henry V Baker, Yaqun Wang, Rongling Wu, Peter R Nelson, Scott A Berceli
BACKGROUND: Despite being the definitive treatment for lower extremity peripheral arterial disease, vein bypass grafts fail in half of all cases. Early repair mechanisms after implantation, governed largely by the immune environment, contribute significantly to long-term outcomes. The current study investigates the early response patterns of circulating monocytes as a determinant of graft outcome. METHODS: In 48 patients undergoing infrainguinal vein bypass grafting, the transcriptomes of circulating monocytes were analyzed preoperatively and at 1, 7, and 28 days post-operation...
March 2018: Circ Genom Precis Med
Y Wang, X Mi, G J M Rosa, Z Chen, P Lin, S Wang, Z Bao
Neural networks (NN) have emerged as a new tool for genomic selection (GS) in animal breeding. However, the properties of NN used in GS for the prediction of phenotypical outcomes are not well characterized due to the problem of over-parameterization of NN and difficulties in using whole-genome marker sets as high-dimensional NN input. In this note, we have developed an R package called snnR that could find an optimal sparse structure of a NN by minimizing the square error subject to a penalty on the L1-norm of the parameters (weights and biases), therefore solve the problem of over-parameterization in NN...
February 24, 2018: Journal of Animal Science
Filip Huyghe, Marc Kochzius
In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci...
2018: PloS One
Georgios A Kotsakis, Qinshu Lian, Andreas L Ioannou, Bryan S Michalowicz, Mike John, Haitao Chu
BACKGROUND: A wide selection of Interdental Oral Hygiene (IOH) aids is available to consumers. Recommendations for selection are, however, limited by the lack of direct comparisons in available studies. We aimed to assess the comparative efficacy of IOH aids using Bayesian Network Meta-Analysis (BNMA). METHODS: Two independent reviewers performed a systematic literature review of randomized clinical trials assessing IOH aids, based on a focused question. Gingival inflammation (Gingival Index (GI), Bleeding-on-probing (BOP)) was the primary outcome and plaque and probing depth were secondary outcomes A random-effects arm-based BNMA model was run for each outcome; posterior medians and 95% credible-intervals (CIs) summarized marginal distributions of parameters...
February 19, 2018: Journal of Periodontology
Fattaneh Jabbari, Joseph Ramsey, Peter Spirtes, Gregory Cooper
Discovering causal structure from observational data in the presence of latent variables remains an active research area. Constraint-based causal discovery algorithms are relatively efficient at discovering such causal models from data using independence tests. Typically, however, they derive and output only one such model. In contrast, Bayesian methods can generate and probabilistically score multiple models, outputting the most probable one; however, they are often computationally infeasible to apply when modeling latent variables...
September 2017: Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD: Proceedings
Rômulo V Paixão, Josiane Ribolli, Evoy Zaniboni-Filho
Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank...
2018: Frontiers in Genetics
J Hadida, S N Sotiropoulos, R G Abeysuriya, M W Woolrich, S Jbabdi
The relationship between structure and function in the human brain is well established, but not yet well characterised. Large-scale biophysical models allow us to investigate this relationship, by leveraging structural information (e.g.derived from diffusion tractography) in order to couple dynamical models of local neuronal activity into networks of interacting regions distributed across the cortex. In practice however, these models are difficult to parametrise, and their simulation is often delicate and computationally expensive...
March 5, 2018: NeuroImage
Dingqiao Wen, Yun Yu, Jiafan Zhu, Luay Nakhleh
PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g...
March 5, 2018: Systematic Biology
Camila Viana Vieira Farhate, Zigomar Menezes de Souza, Stanley Robson de Medeiros Oliveira, Rose Luiza Moraes Tavares, João Luís Nunes Carvalho
Soil CO2 emissions are regarded as one of the largest flows of the global carbon cycle and small changes in their magnitude can have a large effect on the CO2 concentration in the atmosphere. Thus, a better understanding of this attribute would enable the identification of promoters and the development of strategies to mitigate the risks of climate change. Therefore, our study aimed at using data mining techniques to predict the soil CO2 emission induced by crop management in sugarcane areas in Brazil. To do so, we used different variable selection methods (correlation, chi-square, wrapper) and classification (Decision tree, Bayesian models, neural networks, support vector machine, bagging with logistic regression), and finally we tested the efficiency of different approaches through the Receiver Operating Characteristic (ROC) curve...
2018: PloS One
Elizabeth C Lee, Ali Arab, Sandra M Goldlust, Cécile Viboud, Bryan T Grenfell, Shweta Bansal
The surveillance of influenza activity is critical to early detection of epidemics and pandemics and the design of disease control strategies. Case reporting through a voluntary network of sentinel physicians is a commonly used method of passive surveillance for monitoring rates of influenza-like illness (ILI) worldwide. Despite its ubiquity, little attention has been given to the processes underlying the observation, collection, and spatial aggregation of sentinel surveillance data, and its subsequent effects on epidemiological understanding...
March 7, 2018: PLoS Computational Biology
Jeong-Hwa Yoon, Se Hee Min, Chang Ho Ahn, Young Min Cho, Seokyung Hahn
We aimed to evaluate the comparative efficacy and safety of dipeptidyl peptidase-4 inhibitors (DPP4i), glucagon-like peptide-1 receptor agonists (GLP-1RA), sodium-glucose co-transporter 2 inhibitors (SGLT2i), or thiazolidinedione (TZD) as an adjunctive treatment in patients with poorly controlled type 2 diabetes mellitus (T2DM) on insulin therapy. We searched Medline, Embase, the Cochrane Library, and through April 2016. Bayesian network meta-analyses were performed with covariate adjustment...
March 6, 2018: Scientific Reports
A M Ardi Handojoseno, Ganesh R Naik, Moran Gilat, James M Shine, Tuan N Nguyen, Quynh T Ly, Simon J G Lewis, Hung T Nguyen
Freezing of gait (FOG) is an episodic gait disturbance affecting initiation and continuation of locomotion in many Parkinson's disease (PD) patients, causing falls and a poor quality of life. FOG can be experienced on turning and start hesitation, passing through doorways or crowded areas dual tasking, and in stressful situations. Electroencephalography (EEG) offers an innovative technique that may be able to effectively foresee an impending FOG. From data of 16 PD patients, using directed transfer function (DTF) and independent component analysis (ICA) as data pre-processing, and an optimal Bayesian neural network as a predictor of a transition of 5 seconds before the impending FOG occurs in 11 in-group PD patients, we achieved sensitivity and specificity of 85...
2018: Studies in Health Technology and Informatics
Chunsong Yang, Zilong Hao, Ling-Li Zhang, Cai-Rong Zhu, Ping Zhu, Qin Guo
OBJECTIVE: The purpose of this study was to evaluate the efficacy and safety of antipsychotic drugs for tic disorders (TDs) in a network meta-analysis. METHODS: PubMed, Embase, Cochrane Library, and 4 Chinese databases were searched. Randomized controlled trials (RCTs) evaluating the efficacy of antipsychotic drugs for TDs were included. RESULTS: Sixty RCTs were included. In terms of tic symptom score, compared with placebo, haloperidol, risperidone, aripiprazole, quetiapine, olanzapine, and ziprasidone can significantly improve tic symptom score (standardized mean differences [SMD] ranged from -12...
March 5, 2018: Pharmacopsychiatry
Bhornsawan Thanathornwong
Objectives: In this study, a clinical decision support system was developed to help general practitioners assess the need for orthodontic treatment in patients with permanent dentition. Methods: We chose a Bayesian network (BN) as the underlying model for assessing the need for orthodontic treatment. One thousand permanent dentition patient data sets chosen from a hospital record system were prepared in which one data element represented one participant with information for all variables and their stated need for orthodontic treatment...
January 2018: Healthcare Informatics Research
Eric M Maiese, Claire Ainsworth, Jean-Gabriel Le Moine, Outi Ahdesmäki, Judith Bell, Emma Hawe
PURPOSE: New therapies, including daratumumab plus lenalidomide plus dexamethasone (DRd) and daratumumab plus bortezomib plus dexamethasone (DVd), have recently been approved in the United States for patients with multiple myeloma (MM) who have received at least 1 prior line of therapy. However, few treatments have been compared in head-to-head clinical trials to determine the most efficacious therapy. In an update of the POLLUX (Phase 3 Study Comparing DRd Versus Rd in Subjects with Relapsed or Refractory Multiple Myeloma [RRMM]) trial, median progression-free survival (PFS) for DRd was not reached; the hazard ratio compared with Rd was 0...
February 27, 2018: Clinical Therapeutics
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