Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.

HIV molecular epidemiology estimates the transmission patterns from clustering genetically similar viruses. The process involves connecting genetically similar genotyped viral sequences in the network implying epidemiological transmissions. This technique relies on genotype data which is collected only from HIV diagnosed and in-care populations and leaves many persons with HIV (PWH) who have no access to consistent care out of the tracking process. We use machine learning algorithms to learn the non-linear correlation patterns between patient metadata and transmissions between HIV-positive cases. This enables us to expand the transmission network reconstruction beyond the molecular network. We employed multiple commonly used supervised classification algorithms to analyze the San Diego Primary Infection Resource Consortium (PIRC) cohort dataset, consisting of genotypes and nearly 80 additional non-genetic features. First, we trained classification models to determine genetically unrelated individuals from related ones. Our results show that random forest and decision tree achieved over 80% in accuracy, precision, recall, and F1-score by only using a subset of meta-features including age, birth sex, sexual orientation, race, transmission category, estimated date of infection, and first viral load date besides genetic data. Additionally, both algorithms achieved approximately 80% sensitivity and specificity. The Area Under Curve (AUC) is reported 97% and 94% for random forest and decision tree classifiers respectively. Next, we extended the models to identify clusters of similar viral sequences. Support vector machine demonstrated one order of magnitude improvement in accuracy of assigning the sequences to the correct cluster compared to dummy uniform random classifier. These results confirm that metadata carries important information about the dynamics of HIV transmission as embedded in transmission clusters. Hence, novel computational approaches are needed to apply the non-trivial knowledge collected from inter-individual genetic information to metadata from PWH in order to expand the estimated transmissions. We note that feature extraction alone will not be effective in identifying patterns of transmission and will result in random clustering of the data, but its utilization in conjunction with genetic data and the right algorithm can contribute to the expansion of the reconstructed network beyond individuals with genetic data.

Speech2Health: A Mobile Framework for Monitoring Dietary Composition From Spoken Data.

Diet and physical activity are known as important lifestyle factors in self-management and prevention of many chronic diseases. Mobile sensors such as accelerometers have been used to measure physical activity or detect eating time. In many intervention studies, however, stringent monitoring of overall dietary composition and energy intake is needed. Currently, such a monitoring relies on self-reported data by either entering text or taking an image that represents food intake. These approaches suffer from limitations such as low adherence in technology adoption and time sensitivity to the diet intake context. In order to address these limitations, we introduce development and validation of Speech2Health, a voice-based mobile nutrition monitoring system that devises speech processing, natural language processing (NLP), and text mining techniques in a unified platform to facilitate nutrition monitoring. After converting the spoken data to text, nutrition-specific data are identified within the text using an NLP-based approach that combines standard NLP with our introduced pattern mapping technique. We then develop a tiered matching algorithm to search the food name in our nutrition database and accurately compute calorie intake values. We evaluate Speech2Health using real data collected with 30 participants. Our experimental results show that Speech2Health achieves an accuracy of 92.2% in computing calorie intake. Furthermore, our user study demonstrates that Speech2Health achieves significantly higher scores on technology adoption metrics compared to text-based and image-based nutrition monitoring. Our research demonstrates that new sensor modalities such as voice can be used either standalone or as a complementary source of information to existing modalities to improve the accuracy and acceptability of mobile health technologies for dietary composition monitoring.