No abstract

Data-driven phenotype analyses on Electronic Health Record (EHR) data have recently drawn benefits across many areas of clinical practice, uncovering new links in the medical sciences that can potentially affect the well-being of millions of patients. In this paper, EHR data is used to discover novel relationships between diseases by studying their comorbidities (co-occurrences in patients). A novel embedding model is designed to extract knowledge from disease comorbidities by learning from a large-scale EHR database comprising more than 35 million inpatient cases spanning nearly a decade, revealing significant improvements on disease phenotyping over current computational approaches. In addition, the use of the proposed methodology is extended to discover novel disease-gene associations by including valuable domain knowledge from genome-wide association studies. To evaluate our approach, its effectiveness is compared against a held-out set where, again, it revealed very compelling results. For selected diseases, we further identify candidate gene lists for which disease-gene associations were not studied previously. Thus, our approach provides biomedical researchers with new tools to filter genes of interest, thus, reducing costly lab studies.

In sponsored search it is critical to match ads that are relevant to a query and to accurately predict their likelihood of being clicked. Commercial search engines typically use machine learning models for both query-ad relevance matching and click-through-rate (CTR) prediction. However, matching models are based on the similarity between a query and an ad, ignoring the fact that a retrieved ad may not attract clicks, while click models rely on click history, being of limited use for new queries and ads. We propose a deeply supervised architecture that jointly learns the semantic embeddings of a query and an ad as well as their corresponding CTR. We also propose a novel cohort negative sampling technique for learning implicit negative signals. We trained the proposed architecture using one billion query-ad pairs from a major commercial web search engine. This architecture improves the best-performing baseline deep neural architectures by 2% of AUC for CTR prediction and by statistically significant 0.5% of NDCG for query-ad matching.

Increased availability of Electronic Health Record (EHR) data provides unique opportunities for improving the quality of health services. In this study, we couple EHRs with the advanced machine learning tools to predict three important parameters of healthcare quality. More specifically, we describe how to learn low-dimensional vector representations of patient conditions and clinical procedures in an unsupervised manner, and generate feature vectors of hospitalized patients useful for predicting their length of stay, total incurred charges, and mortality rates. In order to learn vector representations, we propose to employ state-of-the-art language models specifically designed for modeling co-occurrence of diseases and applied clinical procedures. The proposed model is trained on a large-scale EHR database comprising more than 35 million hospitalizations in California over a period of nine years. We compared the proposed approach to several alternatives and evaluated their effectiveness by measuring accuracy of regression and classification models used for three predictive tasks considered in this study. Our model outperformed the baseline models on all tasks, indicating a strong potential of the proposed approach for advancing quality of the healthcare system.

Objective Clinical trials, prospective research studies on human participants carried out by a distributed team of clinical investigators, play a crucial role in the development of new treatments in health care. This is a complex and expensive process where investigators aim to enroll volunteers with predetermined characteristics, administer treatment(s), and collect safety and efficacy data. Therefore, choosing top-enrolling investigators is essential for efficient clinical trial execution and is 1 of the primary drivers of drug development cost. Materials and Methods To facilitate clinical trials optimization, we propose DeepMatch (DM), a novel approach that builds on top of advances in deep learning. DM is designed to learn from both investigator and trial-related heterogeneous data sources and rank investigators based on their expected enrollment performance on new clinical trials. Results Large-scale evaluation conducted on 2618 studies provides evidence that the proposed ranking-based framework improves the current state-of-the-art by up to 19% on ranking investigators and up to 10% on detecting top/bottom performers when recruiting investigators for new clinical trials. Discussion The extensive experimental section suggests that DM can provide substantial improvement over current industry standards in several regards: (1) the enrollment potential of the investigator list, (2) the time it takes to generate the list, and (3) data-informed decisions about new investigators. Conclusion Due to the great significance of the problem at hand, related research efforts are set to shift the paradigm of how investigators are chosen for clinical trials, thereby optimizing and automating them and reducing the cost of new therapies.