23,414 research outputs found
An Ontology-Based Artificial Intelligence Model for Medicine Side-Effect Prediction: Taking Traditional Chinese Medicine as An Example
In this work, an ontology-based model for AI-assisted medicine side-effect
(SE) prediction is developed, where three main components, including the drug
model, the treatment model, and the AI-assisted prediction model, of proposed
model are presented. To validate the proposed model, an ANN structure is
established and trained by two hundred and forty-two TCM prescriptions. These
data are gathered and classified from the most famous ancient TCM book and more
than one thousand SE reports, in which two ontology-based attributions, hot and
cold, are introduced to evaluate whether the prescription will cause SE or not.
The results preliminarily reveal that it is a relationship between the
ontology-based attributions and the corresponding predicted indicator that can
be learnt by AI for predicting the SE, which suggests the proposed model has a
potential in AI-assisted SE prediction. However, it should be noted that, the
proposed model highly depends on the sufficient clinic data, and hereby, much
deeper exploration is important for enhancing the accuracy of the prediction
Learning signals of adverse drug-drug interactions from the unstructured text of electronic health records.
Drug-drug interactions (DDI) account for 30% of all adverse drug reactions, which are the fourth leading cause of death in the US. Current methods for post marketing surveillance primarily use spontaneous reporting systems for learning DDI signals and validate their signals using the structured portions of Electronic Health Records (EHRs). We demonstrate a fast, annotation-based approach, which uses standard odds ratios for identifying signals of DDIs from the textual portion of EHRs directly and which, to our knowledge, is the first effort of its kind. We developed a gold standard of 1,120 DDIs spanning 14 adverse events and 1,164 drugs. Our evaluations on this gold standard using millions of clinical notes from the Stanford Hospital confirm that identifying DDI signals from clinical text is feasible (AUROC=81.5%). We conclude that the text in EHRs contain valuable information for learning DDI signals and has enormous utility in drug surveillance and clinical decision support
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction
Recent advances and achievements of artificial intelligence (AI) as well as
deep and graph learning models have established their usefulness in biomedical
applications, especially in drug-drug interactions (DDIs). DDIs refer to a
change in the effect of one drug to the presence of another drug in the human
body, which plays an essential role in drug discovery and clinical research.
DDIs prediction through traditional clinical trials and experiments is an
expensive and time-consuming process. To correctly apply the advanced AI and
deep learning, the developer and user meet various challenges such as the
availability and encoding of data resources, and the design of computational
methods. This review summarizes chemical structure based, network based, NLP
based and hybrid methods, providing an updated and accessible guide to the
broad researchers and development community with different domain knowledge. We
introduce widely-used molecular representation and describe the theoretical
frameworks of graph neural network models for representing molecular
structures. We present the advantages and disadvantages of deep and graph
learning methods by performing comparative experiments. We discuss the
potential technical challenges and highlight future directions of deep and
graph learning models for accelerating DDIs prediction.Comment: Accepted by Briefings in Bioinformatic
HyGNN: Drug-Drug Interaction Prediction via Hypergraph Neural Network
Drug-Drug Interactions (DDIs) may hamper the functionalities of drugs, and in
the worst scenario, they may lead to adverse drug reactions (ADRs). Predicting
all DDIs is a challenging and critical problem. Most existing computational
models integrate drug-centric information from different sources and leverage
them as features in machine learning classifiers to predict DDIs. However,
these models have a high chance of failure, especially for the new drugs when
all the information is not available. This paper proposes a novel Hypergraph
Neural Network (HyGNN) model based on only the SMILES string of drugs,
available for any drug, for the DDI prediction problem. To capture the drug
similarities, we create a hypergraph from drugs' chemical substructures
extracted from the SMILES strings. Then, we develop HyGNN consisting of a novel
attention-based hypergraph edge encoder to get the representation of drugs as
hyperedges and a decoder to predict the interactions between drug pairs.
Furthermore, we conduct extensive experiments to evaluate our model and compare
it with several state-of-the-art methods. Experimental results demonstrate that
our proposed HyGNN model effectively predicts DDIs and impressively outperforms
the baselines with a maximum ROC-AUC and PR-AUC of 97.9% and 98.1%,
respectively.Comment: Some new experiments have been added. One more dataset has been
considered. Theoretical part has been updated to
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