Background
Drug development is an expensive and time-consuming process. Literature-based discovery has played a critical role in drug development and may be a supplementary method to help scientists speed up the discovery of drugs.
Methods
Here, we propose a relation path features embedding based convolutional neural network model with attention mechanism for drug discovery from literature, which we denote as PACNN. First, we use predications from biomedical abstracts to construct a biomedical knowledge graph, and then apply a path ranking algorithm to extract drug-disease relation path features on the biomedical knowledge graph. After that, we use these drug-disease relation features to train a convolutional neural network model which combined with the attention mechanism. Finally, we employ the trained models to mine drugs for treating diseases.
Results
The experiment shows that the proposed model achieved promising results, comparing to several random walk algorithms.
Conclusions
In this paper, we propose a relation path features embedding based convolutional neural network with attention mechanism for discovering potential drugs from literature. Our method could be an auxiliary method for drug discovery, which can speed up the discovery of new drugs for the incurable diseases.
Electronic supplementary material
The online version of this article (10.1186/s12911-019-0764-5) contains supplementary material, which is available to authorized users.
BackgroundThe use of traditional techniques to evaluate breast cancer is restricted by the subjective nature of assessment, variation across radiologists, and limited data. Radiomics may predict axillary lymph node metastasis (ALNM) of breast cancer more accurately.PurposeThe aim was to evaluate the diagnostic performance of a radiomics model based on ALNs themselves that used contrast-enhanced computed tomography (CECT) to detect ALNM of breast cancer.MethodsWe retrospectively enrolled 402 patients with breast cancer confirmed by pathology from January 2016 to October 2019. Three hundred and ninety-six features were extracted for all patients from axial CECT images of 825 ALNs using Artificial Intelligent Kit software (GE Medical Systems, Version V3.1.0.R). Next, the radiomics model was trained, validated, and tested for predicting ALNM in breast cancer by using a support vector machine algorithm. Finally, the performance of the radiomics model was evaluated in terms of its classification accuracy and the value of the area under the curve (AUC).ResultsThe radiomics model yielded the best classification accuracy of 89.1% and the highest AUC of 0.92 (95% CI: 0.91-0.93, p=0.002) for discriminating ALNM in breast cancer in the validation cohorts. In the testing cohorts, the model also demonstrated better performance, with an accuracy of 88.5% and an AUC of 0.94 (95% CI: 0.93-0.95, p=0.005) for predicting ALNM in breast cancer.ConclusionThe radiomics model based on CECT images can be used to predict ALNM in breast cancer and has significant potential in clinical noninvasive diagnosis and in the prediction of breast cancer metastasis.
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