IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine最新文献

Quantifying pain in patients admitted to intensive care units (ICUs) is challenging due to the increased prevalence of communication barriers in this patient population. Previous research has posited a positive correlation between pain and physical activity in critically ill patients. In this study, we advance this hypothesis by building machine learning classifiers to examine the ability of accelerometer data collected from daily wearables to predict self-reported pain levels experienced by patients in the ICU. We trained multiple Machine Learning (ML) models, including Logistic Regression, CatBoost, and XG-Boost, on statistical features extracted from the accelerometer data combined with previous pain measurements and patient demographics. Following previous studies that showed a change in pain sensitivity in ICU patients at night, we performed the task of pain classification separately for daytime and nighttime pain reports. In the pain versus no-pain classification setting, logistic regression gave the best classifier in daytime (AUC: 0.72, F1-score: 0.72), and CatBoost gave the best classifier at nighttime (AUC: 0.82, F1-score: 0.82). Performance of logistic regression dropped to 0.61 AUC, 0.62 F1-score (mild vs. moderate pain, nighttime), and CatBoost's performance was similarly affected with 0.61 AUC, 0.60 F1-score (moderate vs. severe pain, daytime). The inclusion of analgesic information benefited the classification between moderate and severe pain. SHAP analysis was conducted to find the most significant features in each setting. It assigned the highest importance to accelerometer-related features on all evaluated settings but also showed the contribution of the other features such as age and medications in specific contexts. In conclusion, accelerometer data combined with patient demographics and previous pain measurements can be used to screen painful from painless episodes in the ICU and can be combined with analgesic information to provide moderate classification between painful episodes of different severities.

The SARS-CoV-2 pandemic has been presenting in periodic waves and multiple variants, of which some dominated over time with increased transmissibility. SARS-CoV-2 is still adapting in the human population, thus it is crucial to understand its evolutionary patterns and dynamics ahead of time. In this work, we analyzed transmission clusters and topology of SARS-CoV-2 phylogenies at the global, regional (North America) and clade-specific (Delta and Omicron) epidemic scales. We used the Nextstrain's nCov open global all-time phylogeny (September 2022, 2,698 strains, 2,243 for North America, 499 for Delta21A, and 543 for Omicron20M), with Nextstrain's clade annotation and Pango lineages. Transmission clusters were identified using Phylopart, DYNAMITE, and several tree imbalance measures were calculated, including staircase-ness, Sackin and Colless index. We found that the phylogenetic clustering profiles of the global epidemic have highest diversification at a distance threshold of 3% (divergence of 10, where the tree sampled median is 49). Phylopart and DYNAMITE clusters moderately-to-highly agree with the Pango nomenclature and the Nextstrain's clade. At the regional and clade-specific scale, transmission clustering profiles tend to flatten and similar clusters are found at distance thresholds between 0.05% and 25%. All the considered phylogenies exhibit high tree imbalance with respect to what expected in random phylogenies, suggesting short infection times and antigenic drift, perhaps due to progressive transition from innate to adaptive immunity in the population.