Dataset Information

A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds.

ABSTRACT: Medicinal plants and their extracts have been used as important sources for drug discovery. In particular, plant-derived natural compounds, including phytochemicals, antioxidants, vitamins, and minerals, are gaining attention as they promote health and prevent disease. Although several in vitro methods have been developed to confirm the biological activities of natural compounds, there is still considerable room to reduce time and cost. To overcome these limitations, several in silico methods have been proposed for conducting large-scale analysis, but they are still limited in terms of dealing with incomplete and heterogeneous natural compound data. Here, we propose a deep learning-based approach to identify the medicinal uses of natural compounds by exploiting massive and heterogeneous drug and natural compound data. The rationale behind this approach is that deep learning can effectively utilize heterogeneous features to alleviate incomplete information. Based on latent knowledge, molecular interactions, and chemical property features, we generated 686 dimensional features for 4,507 natural compounds and 2,882 approved and investigational drugs. The deep learning model was trained using the generated features and verified drug indication information. When the features of natural compounds were applied as input to the trained model, potential efficacies were successfully predicted with high accuracy, sensitivity, and specificity.

SUBMITTER: Yoo S

PROVIDER: S-EPMC7845697 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds.

Yoo Sunyong S Yang Hyung Chae HC Lee Seongyeong S Shin Jaewook J Min Seyoung S Lee Eunjoo E Song Minkeun M Lee Doheon D

Frontiers in pharmacology 20201130

Medicinal plants and their extracts have been used as important sources for drug discovery. In particular, plant-derived natural compounds, including phytochemicals, antioxidants, vitamins, and minerals, are gaining attention as they promote health and prevent disease. Although several <i>in vitro</i> methods have been developed to confirm the biological activities of natural compounds, there is still considerable room to reduce time and cost. To overcome these limitations, several <i>in silico< ...[more]

PMID: 33519445

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Project description:BackgroundSuicide is an important public health concern in the United States and around the world. There has been significant work examining machine learning approaches to identify and predict intentional self-harm and suicide using existing data sets. With recent advances in computing, deep learning applications in health care are gaining momentum.ObjectiveThis study aimed to leverage the information in clinical notes using deep neural networks (DNNs) to (1) improve the identification of patients treated for intentional self-harm and (2) predict future self-harm events.MethodsWe extracted clinical text notes from electronic health records (EHRs) of 835 patients with International Classification of Diseases (ICD) codes for intentional self-harm and 1670 matched controls who never had any intentional self-harm ICD codes. The data were divided into training and holdout test sets. We tested a number of algorithms on clinical notes associated with the intentional self-harm codes using the training set, including several traditional bag-of-words-based models and 2 DNN models: a convolutional neural network (CNN) and a long short-term memory model. We also evaluated the predictive performance of the DNNs on a subset of patients who had clinical notes 1 to 6 months before the first intentional self-harm event. Finally, we evaluated the impact of a pretrained model using Word2vec (W2V) on performance.ResultsThe area under the receiver operating characteristic curve (AUC) for the CNN on the phenotyping task, that is, the detection of intentional self-harm in clinical notes concurrent with the events was 0.999, with an F1 score of 0.985. In the predictive task, the CNN achieved the highest performance with an AUC of 0.882 and an F1 score of 0.769. Although pretraining with W2V shortened the DNN training time, it did not improve performance.ConclusionsThe strong performance on the first task, namely, phenotyping based on clinical notes, suggests that such models could be used effectively for surveillance of intentional self-harm in clinical text in an EHR. The modest performance on the predictive task notwithstanding, the results using DNN models on clinical text alone are competitive with other reports in the literature using risk factors from structured EHR data.

Dataset Information

A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds.

Publications

A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds.

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