Adaptive Stochastic Optimization to Improve Protein Conformation Sampling.

We have long known that characterizing protein structures structure is key to understanding protein function. Computational approaches have largely addressed a narrow formulation of the problem, seeking to compute one native structure from an amino-acid sequence. Now AlphaFold2 is shown to be able to reveal a high-quality native structure for many proteins. However, researchers over the years have argued for broadening our view to account for the multiplicity of native structures. We now know that many protein molecules switch between different structures to regulate interactions with molecular partners in the cell. Elucidating such structures de novo is exceptionally difficult, as it requires exploration of possibly a very large structure space in search of competing, near-optimal structures. Here we report on a novel stochastic optimization method capable of revealing very different structures for a given protein from knowledge of its amino-acid sequence. The method leverages evolutionary search techniques and adapts its exploration of the search space to balance between exploration and exploitation in the presence of a computational budget. In addition to demonstrating the utility of this method for identifying multiple native structures, we additionally provide a benchmark dataset for researchers to continue work on this problem.

Investigating usability of mobile health applications in Bangladesh.

BACKGROUND: Lack of usability can be a major barrier for the rapid adoption of mobile services. Therefore, the purpose of this paper is to investigate the usability of Mobile Health applications in Bangladesh. METHOD: We followed a 3-stage approach in our research. First, we conducted a keyword-based application search in the popular app stores. We followed the affinity diagram approach and clustered the found applications into nine groups. Second, we randomly selected four apps from each group (36 apps in total) and conducted a heuristic evaluation. Finally, we selected the highest downloaded app from each group and conducted user studies with 30 participants. RESULTS: We found 61% usability problems are catastrophe or major in nature from heuristic inspection. The most (21%) violated heuristic is aesthetic and minimalist design. The user studies revealed low System Usability Scale (SUS) scores for those apps that had a high number of usability problems based on the heuristic evaluation. Thus, the results of heuristic evaluation and user studies complement each other. CONCLUSION: Overall, the findings suggest that the usability of the mobile health apps in Bangladesh is not satisfactory in general and could be a potential barrier for wider adoption of mobile health services.

A Systematic Review on the Use of AI and ML for Fighting the COVID-19 Pandemic.

Artificial intelligence (AI) and machine learning (ML) have caused a paradigm shift in healthcare that can be used for decision support and forecasting by exploring medical data. Recent studies have shown that AI and ML can be used to fight COVID-19. The objective of this article is to summarize the recent AI- and ML-based studies that have addressed the pandemic. From an initial set of 634 articles, a total of 49 articles were finally selected through an inclusion-exclusion process. In this article, we have explored the objectives of the existing studies (i.e., the role of AI/ML in fighting the COVID-19 pandemic); the context of the studies (i.e., whether it was focused on a specific country-context or with a global perspective; the type and volume of the dataset; and the methodology, algorithms, and techniques adopted in the prediction or diagnosis processes). We have mapped the algorithms and techniques with the data type by highlighting their prediction/classification accuracy. From our analysis, we categorized the objectives of the studies into four groups: disease detection, epidemic forecasting, sustainable development, and disease diagnosis. We observed that most of these studies used deep learning algorithms on image-data, more specifically on chest X-rays and CT scans. We have identified six future research opportunities that we have summarized in this paper. Impact Statement: Artificial intelligence (AI) and machine learning(ML) methods have been widely used to assist in the fight against COVID-19 pandemic. A very few in-depth literature reviews have been conducted to synthesize the knowledge and identify future research agenda including a previously published review on data science for COVID-19 in this article. In this article, we synthesized reviewed recent literature that focuses on the usages and applications of AI and ML to fight against COVID-19. We have identified seven future research directions that would guide researchers to conduct future research. The most significant of these are: develop new treatment options, explore the contextual effect and variation in research outcomes, support the health care workforce, and explore the effect and variation in research outcomes based on different types of data.