Learning Drug-Disease-Target Embedding (DDTE) from knowledge graphs to inform drug repurposing hypotheses.

We aimed to develop and validate a new graph embedding algorithm for embedding drug-disease-target networks to generate novel drug repurposing hypotheses. Our model denotes drugs, diseases and targets as subjects, predicates and objects, respectively. Each entity is represented by a multidimensional vector and the predicate is regarded as a translation vector from a subject to an object vectors. These vectors are optimized so that when a subject-predicate-object triple represents a known drug-disease-target relationship, the summed vector between the subject and the predicate is to be close to that of the object; otherwise, the summed vector is distant from the object. The DTINet dataset was utilized to test this algorithm and discover unknown links between drugs and diseases. In cross-validation experiments, this new algorithm outperformed the original DTINet model. The MRR (Mean Reciprocal Rank) values of our models were around 0.80 while those of the original model were about 0.70. In addition, we have identified and verified several pairs of new therapeutic relations as well as adverse effect relations that were not recorded in the original DTINet dataset. This approach showed excellent performance, and the predicted drug-disease and drug-side-effect relationships were found to be consistent with literature reports. This novel method can be used to analyze diverse types of emerging biomedical and healthcare-related knowledge graphs (KG).

Using COVID-19 Vaccine Attitudes on Twitter to Improve Vaccine Uptake Forecast Models in the United States: Infodemiology Study of Tweets.

BACKGROUND: Since the onset of the COVID-19 pandemic, there has been a global effort to develop vaccines that protect against COVID-19. Individuals who are fully vaccinated are far less likely to contract and therefore transmit the virus to others. Researchers have found that the internet and social media both play a role in shaping personal choices about vaccinations. OBJECTIVE: This study aims to determine whether supplementing COVID-19 vaccine uptake forecast models with the attitudes found in tweets improves over baseline models that only use historical vaccination data. METHODS: Daily COVID-19 vaccination data at the county level was collected for the January 2021 to May 2021 study period. Twitter's streaming application programming interface was used to collect COVID-19 vaccine tweets during this same period. Several autoregressive integrated moving average models were executed to predict the vaccine uptake rate using only historical data (baseline autoregressive integrated moving average) and individual Twitter-derived features (autoregressive integrated moving average exogenous variable model). RESULTS: In this study, we found that supplementing baseline forecast models with both historical vaccination data and COVID-19 vaccine attitudes found in tweets reduced root mean square error by as much as 83%. CONCLUSIONS: Developing a predictive tool for vaccination uptake in the United States will empower public health researchers and decisionmakers to design targeted vaccination campaigns in hopes of achieving the vaccination threshold required for the United States to reach widespread population protection.

Enhancing short-term crime prediction with human mobility flows and deep learning architectures.

Place-based short-term crime prediction models leverage the spatio-temporal patterns of historical crimes to predict aggregate volumes of crime incidents at specific locations over time. Under the umbrella of the crime opportunity theory, that suggests that human mobility can play a role in crime generation, increasing attention has been paid to the predictive power of human mobility in place-based short-term crime models. Researchers have used call detail records (CDR), data from location-based services such as Foursquare or from social media to characterize human mobility; and have shown that mobility metrics, together with historical crime data, can improve short-term crime prediction accuracy. In this paper, we propose to use a publicly available fine-grained human mobility dataset from a location intelligence company to explore the effects of human mobility features on short-term crime prediction. For that purpose, we conduct a comprehensive evaluation across multiple cities with diverse demographic characteristics, different types of crimes and various deep learning models; and we show that adding human mobility flow features to historical crimes can improve the F1 scores for a variety of neural crime prediction models across cities and types of crimes, with improvements ranging from 2% to 7%. Our analysis also shows that some neural architectures can slightly improve the crime prediction performance when compared to non-neural regression models by at most 2%.