Provenance-Centered Dataset of Drug-Drug Interactions

Over the years several studies have demonstrated the ability to identify potential drug-drug interactions via data mining from the literature (MEDLINE), electronic health records, public databases (Drugbank), etc. While each one of these approaches is properly statistically validated, they do not take into consideration the overlap between them as one of their decision making variables. In this paper we present LInked Drug-Drug Interactions (LIDDI), a public nanopublication-based RDF dataset with trusty URIs that encompasses some of the most cited prediction methods and sources to provide researchers a resource for leveraging the work of others into their prediction methods. As one of the main issues to overcome the usage of external resources is their mappings between drug names and identifiers used, we also provide the set of mappings we curated to be able to compare the multiple sources we aggregate in our dataset.Comment: In Proceedings of the 14th International Semantic Web Conference (ISWC) 201

Multimodal Machine Learning for Automated ICD Coding

This study presents a multimodal machine learning model to predict ICD-10 diagnostic codes. We developed separate machine learning models that can handle data from different modalities, including unstructured text, semi-structured text and structured tabular data. We further employed an ensemble method to integrate all modality-specific models to generate ICD-10 codes. Key evidence was also extracted to make our prediction more convincing and explainable. We used the Medical Information Mart for Intensive Care III (MIMIC -III) dataset to validate our approach. For ICD code prediction, our best-performing model (micro-F1 = 0.7633, micro-AUC = 0.9541) significantly outperforms other baseline models including TF-IDF (micro-F1 = 0.6721, micro-AUC = 0.7879) and Text-CNN model (micro-F1 = 0.6569, micro-AUC = 0.9235). For interpretability, our approach achieves a Jaccard Similarity Coefficient (JSC) of 0.1806 on text data and 0.3105 on tabular data, where well-trained physicians achieve 0.2780 and 0.5002 respectively.Comment: Machine Learning for Healthcare 201

Uncertainty-Aware Attention for Reliable Interpretation and Prediction

Department of Computer Science and EngineeringAttention mechanism is effective in both focusing the deep learning models on relevant features and interpreting them. However, attentions may be unreliable since the networks that generate them are often trained in a weakly-supervised manner. To overcome this limitation, we introduce the notion of input-dependent uncertainty to the attention mechanism, such that it generates attention for each feature with varying degrees of noise based on the given input, to learn larger variance on instances it is uncertain about. We learn this Uncertainty-aware Attention (UA) mechanism using variational inference, and validate it on various risk prediction tasks from electronic health records on which our model significantly outperforms existing attention models. The analysis of the learned attentions shows that our model generates attentions that comply with clinicians' interpretation, and provide richer interpretation via learned variance. Further evaluation of both the accuracy of the uncertainty calibration and the prediction performance with "I don't know'' decision show that UA yields networks with high reliability as well.ope

Predicting diabetes-related hospitalizations based on electronic health records

OBJECTIVE: To derive a predictive model to identify patients likely to be hospitalized during the following year due to complications attributed to Type II diabetes. METHODS: A variety of supervised machine learning classification methods were tested and a new method that discovers hidden patient clusters in the positive class (hospitalized) was developed while, at the same time, sparse linear support vector machine classifiers were derived to separate positive samples from the negative ones (non-hospitalized). The convergence of the new method was established and theoretical guarantees were proved on how the classifiers it produces generalize to a test set not seen during training. RESULTS: The methods were tested on a large set of patients from the Boston Medical Center - the largest safety net hospital in New England. It is found that our new joint clustering/classification method achieves an accuracy of 89% (measured in terms of area under the ROC Curve) and yields informative clusters which can help interpret the classification results, thus increasing the trust of physicians to the algorithmic output and providing some guidance towards preventive measures. While it is possible to increase accuracy to 92% with other methods, this comes with increased computational cost and lack of interpretability. The analysis shows that even a modest probability of preventive actions being effective (more than 19%) suffices to generate significant hospital care savings. CONCLUSIONS: Predictive models are proposed that can help avert hospitalizations, improve health outcomes and drastically reduce hospital expenditures. The scope for savings is significant as it has been estimated that in the USA alone, about $5.8 billion are spent each year on diabetes-related hospitalizations that could be prevented.Accepted manuscrip