Dataset Information

Improved Classification of Blood-Brain-Barrier Drugs Using Deep Learning.

ABSTRACT: Blood-Brain-Barrier (BBB) is a strict permeability barrier for maintaining the Central Nervous System (CNS) homeostasis. One of the most important conditions to judge a CNS drug is to figure out whether it has BBB permeability or not. In the past 20 years, the existing prediction approaches are usually based on the data of the physical characteristics and chemical structure of drugs. However, these methods are usually only applicable to small molecule compounds based on passive diffusion through BBB. To deal this problem, one of the most famous methods is multi-core SVM method, which is based on clinical phenotypes about Drug Side Effects and Drug Indications to predict drug penetration of BBB. This paper proposed a Deep Learning method to predict the Blood-Brain-Barrier permeability based on the clinical phenotypes data. The validation result on three datasets proved that Deep Learning method achieves better performance than the other existing methods. The average accuracy of our method reaches 0.97, AUC reaches 0.98, and the F1 score is 0.92. The results proved that Deep Learning methods can significantly improve the prediction accuracy of drug BBB permeability and it can help researchers to reduce clinical trials and find new CNS drugs.

SUBMITTER: Miao R

PROVIDER: S-EPMC6584536 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Publications

Improved Classification of Blood-Brain-Barrier Drugs Using Deep Learning.

Miao Rui R Xia Liang-Yong LY Chen Hao-Heng HH Huang Hai-Hui HH Liang Yong Y

Scientific reports 20190619 1

Blood-Brain-Barrier (BBB) is a strict permeability barrier for maintaining the Central Nervous System (CNS) homeostasis. One of the most important conditions to judge a CNS drug is to figure out whether it has BBB permeability or not. In the past 20 years, the existing prediction approaches are usually based on the data of the physical characteristics and chemical structure of drugs. However, these methods are usually only applicable to small molecule compounds based on passive diffusion through ...[more]

PMID: 31217424

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Project description:The blood-brain barrier plays a crucial role in regulating the passage of 98% of the compounds that enter the central nervous system (CNS). Compounds with high permeability must be identified to enable the synthesis of brain medications for the treatment of various brain diseases, such as Parkinson's, Alzheimer's, and brain tumors. Throughout the years, several models have been developed to solve this problem and have achieved acceptable accuracy scores in predicting compounds that penetrate the blood-brain barrier. However, predicting compounds with "low" permeability has been a challenging task. In this study, we present a deep learning (DL) classification model to predict blood-brain barrier permeability. The proposed model addresses the fundamental issues presented in former models: high dimensionality, class imbalances, and low specificity scores. We address these issues to enhance the high-dimensional, imbalanced dataset before developing the classification model: the imbalanced dataset is addressed using oversampling techniques and the high dimensionality using a non-linear dimensionality reduction technique known as kernel principal component analysis (KPCA). This technique transforms the high-dimensional dataset into a low-dimensional Euclidean space while retaining invaluable information. For the classification task, we developed an enhanced feed-forward deep learning model and a convolutional neural network model. In terms of specificity scores (i.e., predicting compounds with low permeability), the results obtained by the enhanced feed-forward deep learning model outperformed those obtained by other models in the literature that were developed using the same technique. In addition, the proposed convolutional neural network model surpassed models used in other studies in multiple accuracy measures, including overall accuracy and specificity. The proposed approach solves the problem inevitably faced with obtaining low specificity resulting in high false positive rate.

Project description:Purpose: This study proposes an S-TextBLCNN model for the efficacy of traditional Chinese medicine (TCM) formula classification. This model uses deep learning to analyze the relationship between herb efficacy and formula efficacy, which is helpful in further exploring the internal rules of formula combination. Methods: First, for the TCM herbs extracted from Chinese Pharmacopoeia, natural language processing (NLP) is used to learn and realize the quantitative expression of different TCM herbs. Three features of herb name, herb properties, and herb efficacy are selected to encode herbs and to construct formula-vector and herb-vector. Then, based on 2,664 formulae for stroke collected in TCM literature and 19 formula efficacy categories extracted from Yifang Jijie, an improved deep learning model TextBLCNN consists of a bidirectional long short-term memory (Bi-LSTM) neural network and a convolutional neural network (CNN) is proposed. Based on 19 formula efficacy categories, binary classifiers are established to classify the TCM formulae. Finally, aiming at the imbalance problem of formula data, the over-sampling method SMOTE is used to solve it and the S-TextBLCNN model is proposed. Results: The formula-vector composed of herb efficacy has the best effect on the classification model, so it can be inferred that there is a strong relationship between herb efficacy and formula efficacy. The TextBLCNN model has an accuracy of 0.858 and an F1-score of 0.762, both higher than the logistic regression (acc = 0.561, F1-score = 0.567), SVM (acc = 0.703, F1-score = 0.591), LSTM (acc = 0.723, F1-score = 0.621), and TextCNN (acc = 0.745, F1-score = 0.644) models. In addition, the over-sampling method SMOTE is used in our model to tackle data imbalance, and the F1-score is greatly improved by an average of 47.1% in 19 models. Conclusion: The combination of formula feature representation and the S-TextBLCNN model improve the accuracy in formula efficacy classification. It provides a new research idea for the study of TCM formula compatibility.

Project description:BackgroundThe proportion of overweight and obese people has increased tremendously in a short period, culminating in a worldwide trend of obesity that is reaching epidemic proportions. Overweight and obesity are serious issues, especially with regard to children. This is because obese children have twice the risk of becoming obese as adults, as compared to non-obese children. Nowadays, many methods for maintaining a caloric balance exist; however, these methods are not applicable to children. In this study, a new approach for helping children monitor their activities using a convolutional neural network (CNN) is proposed, which is applicable for real-time scenarios requiring high accuracy.MethodsA total of 136 participants (86 boys and 50 girls), aged between 8.5 years and 12.5 years (mean 10.5, standard deviation 1.1), took part in this study. The participants performed various movement while wearing custom-made three-axis accelerometer modules around their waists. The data acquired by the accelerometer module was preprocessed by dividing them into small sets (128 sample points for 2.8 s). Approximately 183,600 data samples were used by the developed CNN for learning to classify ten physical activities : slow walking, fast walking, slow running, fast running, walking up the stairs, walking down the stairs, jumping rope, standing up, sitting down, and remaining still.ResultsThe developed CNN classified the ten activities with an overall accuracy of 81.2%. When similar activities were merged, leading to seven merged activities, the CNN classified activities with an overall accuracy of 91.1%. Activity merging also improved performance indicators, for the maximum case of 66.4% in recall, 48.5% in precision, and 57.4% in f1 score . The developed CNN classifier was compared to conventional machine learning algorithms such as the support vector machine, decision tree, and k-nearest neighbor algorithms, and the proposed CNN classifier performed the best: CNN (81.2%) > SVM (64.8%) > DT (63.9%) > kNN (55.4%) (for ten activities); CNN (91.1%) > SVM (74.4%) > DT (73.2%) > kNN (65.3%) (for the merged seven activities).DiscussionThe developed algorithm distinguished physical activities with improved time resolution using short-time acceleration signals from the physical activities performed by children. This study involved algorithm development, participant recruitment, IRB approval, custom-design of a data acquisition module, and data collection. The self-selected moving speeds for walking and running (slow and fast) and the structure of staircase degraded the performance of the algorithm. However, after similar activities were merged, the effects caused by the self-selection of speed were reduced. The experimental results show that the proposed algorithm performed better than conventional algorithms. Owing to its simplicity, the proposed algorithm could be applied to real-time applicaitons.

Dataset Information

Improved Classification of Blood-Brain-Barrier Drugs Using Deep Learning.

Publications

Improved Classification of Blood-Brain-Barrier Drugs Using Deep Learning.

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