Dataset Information

A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD.

ABSTRACT: In this paper, we propose a Bayesian hierarchical approach to infer network structures across multiple sample groups where both shared and differential edges may exist across the groups. In our approach, we link graphs through a Markov random field prior. This prior on network similarity provides a measure of pairwise relatedness that borrows strength only between related groups. We incorporate the computational efficiency of continuous shrinkage priors, improving scalability for network estimation in cases of larger dimensionality. Our model is applied to patient groups with increasing levels of chronic obstructive pulmonary disease severity, with the goal of better understanding the break down of gene pathways as the disease progresses. Our approach is able to identify critical hub genes for four targeted pathways. Furthermore, it identifies gene connections that are disrupted with increased disease severity and that characterize the disease evolution. We also demonstrate the superior performance of our approach with respect to competing methods, using simulated data.

SUBMITTER: Shaddox E

PROVIDER: S-EPMC8078135 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD.

Shaddox Elin E Stingo Francesco C FC Peterson Christine B CB Jacobson Sean S Cruickshank-Quinn Charmion C Kechris Katerina K Bowler Russell R Vannucci Marina M

Statistics in biosciences 20161028 1

In this paper, we propose a Bayesian hierarchical approach to infer network structures across multiple sample groups where both shared and differential edges may exist across the groups. In our approach, we link graphs through a Markov random field prior. This prior on network similarity provides a measure of pairwise relatedness that borrows strength only between related groups. We incorporate the computational efficiency of continuous shrinkage priors, improving scalability for network estimat ...[more]

PMID: 33912251

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Project description:Manual identification of tomato leaf diseases is a time-consuming and laborious process that may lead to inaccurate results without professional assistance. Therefore, an automated, early, and precise leaf disease recognition system is essential for farmers to ensure the quality and quantity of tomato production by providing timely interventions to mitigate disease spread. In this study, we have proposed seven robust Bayesian optimized deep hybrid learning models leveraging the synergy between deep learning and machine learning for the automated classification of ten types of tomato leaves (nine diseased and one healthy). We customized the popular Convolutional Neural Network (CNN) algorithm for automatic feature extraction due to its ability to capture spatial hierarchies of features directly from raw data and classical machine learning techniques [Random Forest (RF), XGBoost, GaussianNB (GNB), Support Vector Machines (SVM), Multinomial Logistic Regression (MLR), K-Nearest Neighbor (KNN)], and stacking for classifications. Additionally, the study incorported a Boruta feature filtering layer to capture the statistically significant features. The standard, research-oriented PlantVillage dataset was used for the performance testing, which facilitates benchmarking against prior research and enables meaningful comparisons of classification performance across different approaches. We utilized a variety of statistical classification metrics to demonstrate the robustness of our models. Using the CNN-Stacking model, this study achieved the highest classification performance among the seven hybrid models. On an unseen dataset, this model achieved average precision, recall, f1-score, mcc, and accuracy values of 98.527%, 98.533%, 98.527%, 98.525%, and 98.268%, respectively. Our study requires only 0.174 s of testing time to correctly identify noisy, blurry, and transformed images. This indicates our approach's time efficiency and generalizability in images captured under challenging lighting conditions and with complex backgrounds. Based on the comparative analysis, our approach is superior and computationally inexpensive compared to the existing studies. This work will aid in developing a smartphone app to offer farmers a real-time disease diagnosis tool and management strategies.

Dataset Information

A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD.

Publications

A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD.

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