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.
Motivation: Understanding exact structure of an individual’s haplotype plays a significant role in various fields of human genetics. Despite tremendous research effort in recent years, fast and accurate haplotype reconstruction remains as an active research topic, mainly owing to the computational challenges involved. Existing haplotype assembly algorithms focus primarily on improving accuracy of the assembly, making them computationally challenging for applications on large high-throughput sequence data. Therefore, there is a need to develop haplotype reconstruction algorithms that are not only accurate but also highly scalable.Results: In this article, we introduce FastHap, a fast and accurate haplotype reconstruction approach, which is up to one order of magnitude faster than the state-of-the-art haplotype inference algorithms while also delivering higher accuracy than these algorithms. FastHap leverages a new similarity metric that allows us to precisely measure distances between pairs of fragments. The distance is then used in building the fuzzy conflict graphs of fragments. Given that optimal haplotype reconstruction based on minimum error correction is known to be NP-hard, we use our fuzzy conflict graphs to develop a fast heuristic for fragment partitioning and haplotype reconstruction.Availability: An implementation of FastHap is available for sharing on request.Contact: sepideh@cs.ucla.edu
Lifestyle interventions with the focus on diet are crucial in self-management and prevention of many chronic conditions, such as obesity, cardiovascular disease, diabetes, and cancer. Such interventions require a diet monitoring approach to estimate overall dietary composition and energy intake. Although wearable sensors have been used to estimate eating context (e.g., food type and eating time), accurate monitoring of dietary intake has remained a challenging problem. In particular, because monitoring dietary intake is a self-administered task that involves the end-user to record or report their nutrition intake, current diet monitoring technologies are prone to measurement errors related to challenges of human memory, estimation, and bias. New approaches based on mobile devices have been proposed to facilitate the process of dietary intake recording. These technologies require individuals to use mobile devices such as smartphones to record nutrition intake by either entering text or taking images of the food. Such approaches, however, suffer from errors due to low adherence to technology adoption and time sensitivity to the dietary intake context. In this article, we introduce EZNutriPal , 1 an interactive diet monitoring system that operates on unstructured mobile data such as speech and free-text to facilitate dietary recording, real-time prompting, and personalized nutrition monitoring. EZNutriPal features a natural language processing unit that learns incrementally to add user-specific nutrition data and rules to the system. To prevent missing data that are required for dietary monitoring (e.g., calorie intake estimation), EZNutriPal devises an interactive operating mode that prompts the end-user to complete missing data in real-time. Additionally, we propose a combinatorial optimization approach to identify the most appropriate pairs of food names and food quantities in complex input sentences. We evaluate the performance of EZNutriPal using real data collected from 23 human subjects who participated in two user studies conducted in 13 days each. The results demonstrate that EZNutriPal achieves an accuracy of 89.7% in calorie intake estimation. We also assess the impacts of the incremental training and interactive prompting technologies on the accuracy of nutrient intake estimation and show that incremental training and interactive prompting improve the performance of diet monitoring by 49.6% and 29.1%, respectively, compared to a system without such computing units.
Objectives: Toward common methods for system monitoring and evaluation, we proposed a key performance indicator framework and discussed lessons learned while implementing a statewide exposure notification (EN) system in California during the COVID-19 epidemic. Materials and Methods: California deployed the Google Apple Exposure Notification framework, branded CA Notify, on December 10, 2020, to supplement traditional COVID-19 contact tracing programs. For system evaluation, we defined 6 key performance indicators: adoption, retention, sharing of unique codes, identification of potential contacts, behavior change, and impact. We aggregated and analyzed data from December 10, 2020, to July 1, 2021, in compliance with the CA Notify privacy policy. Results: We estimated CA Notify adoption at nearly 11 million smartphone activations during the study period. Among 1 654 201 CA Notify users who received a positive test result for SARS-CoV-2, 446 634 (27%) shared their unique code, leading to ENs for other CA Notify users who were in close proximity to the SARS-CoV-2–positive individual. We identified at least 122 970 CA Notify users as contacts through this process. Contact identification occurred a median of 4 days after symptom onset or specimen collection date of the user who received a positive test result for SARS-CoV-2. Practice Implications: Smartphone-based EN systems are promising new tools to supplement traditional contact tracing and public health interventions, particularly when efficient scaling is not feasible for other approaches. Methods to collect and interpret appropriate measures of system performance must be refined while maintaining trust and privacy.
We sought to test a hypothesis that systemic blind spots in active learning are a barrier both for instructors—who cannot see what every student is actually thinking on each concept in each class—and for students—who often cannot tell precisely whether their thinking is right or wrong, let alone exactly how to fix it. We tested a strategy for eliminating these blind spots by having students answer open-ended, conceptual problems using a Web-based platform, and measured the effects on student attrition, engagement, and performance. In 4 years of testing both in class and using an online platform, this approach revealed (and provided specific resolution lessons for) more than 200 distinct conceptual errors, dramatically increased average student engagement, and reduced student attrition by approximately fourfold compared with the original lecture course format (down from 48.3% to 11.4%), especially for women undergraduates (down from 73.1% to 7.4%). Median exam scores increased from 53% to 72–80%, and the bottom half of students boosted their scores to the range in which the top half had scored before the pedagogical switch. By contrast, in our control year with the same active-learning content (but without this “zero blind spots” approach), these gains were not observed.
Detection of viral transmission clusters using molecular epidemiology is critical to the response pillar of the Ending the HIV Epidemic initiative. Here, we studied whether inference with an incomplete dataset would influence the accuracy of the reconstructed molecular transmission network. We analyzed viral sequence data available from ~ 13,000 individuals with diagnosed HIV (2012–2019) from Houston Health Department surveillance data with 53% completeness (n = 6852 individuals with sequences). We extracted random subsamples and compared the resulting reconstructed networks versus the full-size network. Increasing simulated completeness was associated with an increase in the number of detected clusters. We also subsampled based on the network node influence in the transmission of the virus where we measured Expected Force (ExF) for each node in the network. We simulated the removal of nodes with the highest and then lowest ExF from the full dataset and discovered that 4.7% and 60% of priority clusters were detected respectively. These results highlight the non-uniform impact of capturing high influence nodes in identifying transmission clusters. Although increasing sequence reporting completeness is the way to fully detect HIV transmission patterns, reaching high completeness has remained challenging in the real world. Hence, we suggest taking a network science approach to enhance performance of molecular cluster detection, augmented by node influence information.
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