pyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules.

The construction of a molecular topology file is a prerequisite for any classical molecular dynamics simulation. However, the generation of such a file may be very challenging at times, especially for large supramolecules. While many tools are available to provide topologies for large proteins and other biomolecules, the scientific community researching nonbiological systems is not equally well equipped. Here, we present a practical tool to generate topologies for arbitrary supramolecules: The pyPolyBuilder. In addition to linear polymer chains, it also provides the possibility to generate topologies of arbitrary, large, branched molecules, such as, e.g., dendrimers. Furthermore, it also generates reasonable starting structures for simulations of these molecules. pyPolyBuilder is a standalone command-line tool implemented in python. Therefore, it may be easily incorporated in persisting simulation pipelines on any operating systems and with different simulation engines. pyPolyBuilder is freely available on github: https://github.com/mssm-labmmol/pypolybuilder.

Machine learning associated with respiratory oscillometry: a computer-aided diagnosis system for the detection of respiratory abnormalities in systemic sclerosis.

INTRODUCTION: The use of machine learning (ML) methods would improve the diagnosis of respiratory changes in systemic sclerosis (SSc). This paper evaluates the performance of several ML algorithms associated with the respiratory oscillometry analysis to aid in the diagnostic of respiratory changes in SSc. We also find out the best configuration for this task. METHODS: Oscillometric and spirometric exams were performed in 82 individuals, including controls (n = 30) and patients with systemic sclerosis with normal (n = 22) and abnormal (n = 30) spirometry. Multiple instance classifiers and different supervised machine learning techniques were investigated, including k-Nearest Neighbors (KNN), Random Forests (RF), AdaBoost with decision trees (ADAB), and Extreme Gradient Boosting (XGB). RESULTS AND DISCUSSION: The first experiment of this study showed that the best oscillometric parameter (BOP) was dynamic compliance, which provided moderate accuracy (AUC = 0.77) in the scenario control group versus patients with sclerosis and normal spirometry (CGvsPSNS). In the scenario control group versus patients with sclerosis and altered spirometry (CGvsPSAS), the BOP obtained high accuracy (AUC = 0.94). In the second experiment, the ML techniques were used. In CGvsPSNS, KNN achieved the best result (AUC = 0.90), significantly improving the accuracy in comparison with the BOP (p < 0.01), while in CGvsPSAS, RF obtained the best results (AUC = 0.97), also significantly improving the diagnostic accuracy (p < 0.05). In the third, fourth, fifth, and sixth experiments, different feature selection techniques allowed us to spot the best oscillometric parameters. They resulted in a small increase in diagnostic accuracy in CGvsPSNS (respectively, 0.87, 0.86, 0.82, and 0.84), while in the CGvsPSAS, the best classifier's performance remained the same (AUC = 0.97). CONCLUSIONS: Oscillometric principles combined with machine learning algorithms provide a new method for diagnosing respiratory changes in patients with systemic sclerosis. The present study's findings provide evidence that this combination may help in the early diagnosis of respiratory changes in these patients.

Differential diagnosis of asthma and restrictive respiratory diseases by combining forced oscillation measurements, machine learning and neuro-fuzzy classifiers.

To design machine learning classifiers to facilitate the clinical use and increase the accuracy of the forced oscillation technique (FOT) in the differential diagnosis of patients with asthma and restrictive respiratory diseases. FOT and spirometric exams were performed in 97 individuals, including controls (n = 20), asthmatic patients (n = 38), and restrictive (n = 39) patients. The first experiment of this study showed that the best FOT parameter was the resonance frequency, providing moderate accuracy (AUC = 0.87). In the second experiment, a neuro-fuzzy classifier and different supervised machine learning techniques were investigated, including k-nearest neighbors, random forests, AdaBoost with decision trees, and support vector machines with a radial basis kernel. All classifiers achieved high accuracy (AUC ≥ 0.9) in the differentiation between patient groups. In the third and fourth experiments, the use of different feature selection techniques allowed us to achieve high accuracy with only three FOT parameters. In addition, the neuro-fuzzy classifier also provided rules to explain the classification. Neuro-fuzzy and machine learning classifiers can aid in the differential diagnosis of patients with asthma and restrictive respiratory diseases. They can assist clinicians as a support system providing accurate diagnostic options.

High-accuracy detection of airway obstruction in asthma using machine learning algorithms and forced oscillation measurements.

BACKGROUND AND OBJECTIVES: The main pathologic feature of asthma is episodic airway obstruction. This is usually detected by spirometry and body plethysmography. These tests, however, require a high degree of collaboration and maximal effort on the part of the patient. There is agreement in the literature that there is a demand of research into new technologies to improve non-invasive testing of lung function. The purpose of this study was to develop automatic classifiers to simplify the clinical use and to increase the accuracy of the forced oscillation technique (FOT) in the diagnosis of airway obstruction in patients with asthma. METHODS: The data consisted of FOT parameters obtained from 75 volunteers (39 with obstruction and 36 without). Different supervised machine learning (ML) techniques were investigated, including k-nearest neighbors (KNN), random forest (RF), AdaBoost with decision trees (ADAB) and feature-based dissimilarity space classifier (FDSC). RESULTS: The first part of this study showed that the best FOT parameter was the resonance frequency (AUC = 0.81), which indicates moderate accuracy (0.70-0.90). In the second part of this study, the use of the cited ML techniques was investigated. All the classifiers improved the diagnostic accuracy. Notably, ADAB and KNN were very close to achieving high accuracy (AUC = 0.88 and 0.89, respectively). Experiments including the cross products of the FOT parameters showed that all the classifiers improved the diagnosis accuracy and KNN was able to reach a higher accuracy range (AUC = 0.91). CONCLUSIONS: Machine learning classifiers can help in the diagnosis of airway obstruction in asthma patients, and they can assist clinicians in airway obstruction identification.

Machine learning algorithms and forced oscillation measurements to categorise the airway obstruction severity in chronic obstructive pulmonary disease.

The purpose of this study was to develop automatic classifiers to simplify the clinical use and increase the accuracy of the forced oscillation technique (FOT) in the categorisation of airway obstruction level in patients with chronic obstructive pulmonary disease (COPD). The data consisted of FOT parameters obtained from 168 volunteers (42 healthy and 126 COPD subjects with four different levels of obstruction). The first part of this study showed that FOT parameters do not provide adequate accuracy in identifying COPD subjects in the first levels of obstruction, as well as in discriminating between close levels of obstruction. In the second part of this study, different supervised machine learning (ML) techniques were investigated, including k-nearest neighbour (KNN), random forest (RF) and support vector machines with linear (SVML) and radial basis function kernels (SVMR). These algorithms were applied only in situations where high categorisation accuracy [area under the Receiver Operating Characteristic curve (AUC)≥0.9] was not achieved with the FOT parameter alone. It was observed that KNN and RF classifiers improved categorisation accuracy. Notably, in four of the six cases studied, an AUC≥0.9 was achieved. Even in situations where an AUC≥0.9 was not achieved, there was a significant improvement in categorisation performance (AUC≥0.83). In conclusion, machine learning classifiers can help in the categorisation of COPD airway obstruction. They can assist clinicians in tracking disease progression, evaluating the risk of future disease exacerbations and guiding therapy.

An improved method of early diagnosis of smoking-induced respiratory changes using machine learning algorithms.

The purpose of this study was to develop an automatic classifier to increase the accuracy of the forced oscillation technique (FOT) for diagnosing early respiratory abnormalities in smoking patients. The data consisted of FOT parameters obtained from 56 volunteers, 28 healthy and 28 smokers with low tobacco consumption. Many supervised learning techniques were investigated, including logistic linear classifiers, k nearest neighbor (KNN), neural networks and support vector machines (SVM). To evaluate performance, the ROC curve of the most accurate parameter was established as baseline. To determine the best input features and classifier parameters, we used genetic algorithms and a 10-fold cross-validation using the average area under the ROC curve (AUC). In the first experiment, the original FOT parameters were used as input. We observed a significant improvement in accuracy (KNN=0.89 and SVM=0.87) compared with the baseline (0.77). The second experiment performed a feature selection on the original FOT parameters. This selection did not cause any significant improvement in accuracy, but it was useful in identifying more adequate FOT parameters. In the third experiment, we performed a feature selection on the cross products of the FOT parameters. This selection resulted in a further increase in AUC (KNN=SVM=0.91), which allows for high diagnostic accuracy. In conclusion, machine learning classifiers can help identify early smoking-induced respiratory alterations. The use of FOT cross products and the search for the best features and classifier parameters can markedly improve the performance of machine learning classifiers.

Machine learning algorithms and forced oscillation measurements applied to the automatic identification of chronic obstructive pulmonary disease.

The purpose of this study is to develop a clinical decision support system based on machine learning (ML) algorithms to help the diagnostic of chronic obstructive pulmonary disease (COPD) using forced oscillation (FO) measurements. To this end, the performances of classification algorithms based on Linear Bayes Normal Classifier, K nearest neighbor (KNN), decision trees, artificial neural networks (ANN) and support vector machines (SVM) were compared in order to the search for the best classifier. Four feature selection methods were also used in order to identify a reduced set of the most relevant parameters. The available dataset consists of 7 possible input features (FO parameters) of 150 measurements made in 50 volunteers (COPD, n = 25; healthy, n = 25). The performance of the classifiers and reduced data sets were evaluated by the determination of sensitivity (Se), specificity (Sp) and area under the ROC curve (AUC). Among the studied classifiers, KNN, SVM and ANN classifiers were the most adequate, reaching values that allow a very accurate clinical diagnosis (Se > 87%, Sp > 94%, and AUC > 0.95). The use of the analysis of correlation as a ranking index of the FOT parameters, allowed us to simplify the analysis of the FOT parameters, while still maintaining a high degree of accuracy. In conclusion, the results of this study indicate that the proposed classifiers may contribute to easy the diagnostic of COPD by using forced oscillation measurements.

Automatic identification of Chronic Obstructive Pulmonary Disease Based on forced oscillation measurements and artificial neural networks.

The purpose of this study is to develop an automatic classifier based on Artificial Neural Networks (ANNs) to help the diagnostic of Chronic Obstructive Pulmonary Disease (COPD) using forced oscillation measurements (FOT). The classifier inputs are the parameters provided by the FOT and the output is the indication if the parameters indicate COPD or not. The available dataset consists of 7 possible input features (FOT parameters) of 90 measurements made in 30 volunteers. Two feature selection methods (the analysis of the linear correlation and forward search) were used in order to identify a reduced set of the most relevant parameters. Two different training strategies for the ANNs were used and the performance of resulting networks were evaluated by the determination of accuracy, sensitivity (Se), specificity (Sp) and AUC. The ANN classifiers presented high accuracy (Se > 0.9, Se > 0.9 and AUC > 0.9) both in the complete and the reduce sets of FOT parameters. This indicates that ANNs classifiers may contribute to easy the diagnostic of COPD using forced oscillation measurements.