Dataset Information

Predicting Meridian in Chinese traditional medicine using machine learning approaches.

ABSTRACT: Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herbs, the rationale of Meridian classification remains poorly understood. In this study, we took a machine learning approach to explore the classification of Meridian. We determined the molecule features for 646 herbs and their active components including structure-based fingerprints and ADME properties (absorption, distribution, metabolism and excretion), and found that the Meridian can be predicted by machine learning approaches with a top accuracy of 0.83. We also identified the top compound features that were important for the Meridian prediction. To the best of our knowledge, this is the first time that molecular properties of the herb compounds are associated with the TCM Meridians. Taken together, the machine learning approach may provide novel insights for the understanding of molecular evidence of Meridians in TCM.

SUBMITTER: Wang Y

PROVIDER: S-EPMC6876772 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Predicting Meridian in Chinese traditional medicine using machine learning approaches.

Wang Yinyin Y Jafari Mohieddin M Tang Yun Y Tang Jing J

PLoS computational biology 20191125 11

Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herbs, the rationale of Meridian classification remains poorly understood. In this study, we took a machine learning approach to explore the classificatio ...[more]

PMID: 31765369

Similar Datasets

Project description:Biological pest control (i.e. 'biocontrol') agents can have direct and indirect non-target impacts, and predicting these effects (especially indirect impacts) remains a central challenge in biocontrol risk assessment. The analysis of ecological networks offers a promising approach to understanding the community-wide impacts of biocontrol agents (via direct and indirect interactions). Independently, species traits and phylogenies have been shown to successfully predict species interactions and network structure (alleviating the need to collect quantitative interaction data), but whether these approaches can be combined to predict indirect impacts of natural enemies remains untested. Whether predictions of interactions (i.e. direct effects) can be made equally well for generalists vs. specialists, abundant vs. less abundant species, and across different habitat types is also untested for consumer-prey interactions. Here, we used two machine-learning techniques (random forest and k-nearest neighbour; KNN) to test whether we could accurately predict empirically-observed quantitative host-parasitoid networks using trait and phylogenetic information. Then, we tested whether the accuracy of machine-learning-predicted interactions depended on the generality or abundance of the interacting partners, or on the source (habitat type) of the training data. Finally, we used these predicted networks to generate predictions of indirect effects via shared natural enemies (i.e. apparent competition), and tested these predictions against empirically observed indirect effects between hosts. We found that random-forest models predicted host-parasitoid pairwise interactions (which could be used to predict attack of non-target host species) more successfully than KNN. This predictive ability depended on the generality of the interacting partners for KNN models, and depended on species' abundances for both random-forest and KNN models, but did not depend on the source (habitat type) of data used to train the models. Further, although our machine-learning informed methods could significantly predict indirect effects, the explanatory power of our machine-learning models for indirect interactions was reasonably low. Combining machine-learning and network approaches provides a starting point for reducing risk in biocontrol introductions, and could be applied more generally to predicting species interactions such as impacts of invasive species.

Project description:Background: Individuals with major depressive disorder (MDD) vary in their response to antidepressants. However, identifying objective biomarkers, prior to or early in the course of treatment that can predict antidepressant efficacy, remains a challenge. Methods: Individuals with MDD participated in a 12-week antidepressant pharmacotherapy trial. Electroencephalographic (EEG) data was collected before and 1 week post-treatment initiation in 51 patients. Response status at week 12 was established with the Montgomery-Asberg Depression Scale (MADRS), with a ?50% decrease characterizing responders (N = 27/24 responders/non-responders). We used a machine learning (ML)-approach for predicting response status. We focused on Random Forests, though other ML methods were compared. First, we used a tree-based estimator to select a relatively small number of significant features from: (a) demographic/clinical data (age, sex, individual item/total MADRS scores at baseline, week 1, change scores); (b) scalp-level EEG power; (c) source-localized current density (via exact low-resolution electromagnetic tomography [eLORETA] software). Second, we applied kernel principal component analysis to reduce and map important features. Third, a set of ML models were constructed to classify response outcome based on mapped features. For each dataset, predictive features were extracted, followed by a model of all predictive features, and finally by a model of the most predictive features. Results: Fifty eLORETA features were predictive of response (across bands, both time-points); alpha1/theta eLORETA features showed the highest predictive value. Eighty-eight scalp EEG features were predictive of response (across bands, both time-points), with theta/alpha2 being most predictive. Clinical/demographic data consisted of 31 features, with the most important being week 1 "concentration difficulty" scores. When all features were included into one model, its predictive utility was high (88% accuracy). When the most important features were extracted in the final model, 12 predictive features emerged (78% accuracy), including baseline scalp-EEG frontopolar theta, parietal alpha2 and frontopolar alpha1. Conclusions: These findings suggest that ML models of pre- and early treatment-emergent EEG profiles and clinical features can serve as tools for predicting antidepressant response. While this must be replicated using large independent samples, it lays the groundwork for research on personalized, "biomarker"-based treatment approaches.

Dataset Information

Predicting Meridian in Chinese traditional medicine using machine learning approaches.

Publications

Predicting Meridian in Chinese traditional medicine using machine learning approaches.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure