Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments

Smartwatches for non-invasive hypoglycaemia detection during cognitive and psychomotor stress.

ISSN:1462-8902ISSN:1463-132

FLIRT: A Feature Generation Toolkit for Wearable Data

Background and Objective: Researchers use wearable sensing data and machine learning (ML) models to predict various health and behavioral outcomes. However, sensor data from commercial wearables are prone to noise, missing, or artifacts. Even with the recent interest in deploying commercial wearables for long-term studies, there does not exist a standardized way to process the raw sensor data and researchers often use highly specific functions to preprocess, clean, normalize, and compute features. This leads to a lack of uniformity and reproducibility across different studies, making it difficult to compare results. To overcome these issues, we present FLIRT: A Feature Generation Toolkit for Wearable Data; it is an open-source Python package that focuses on processing physiological data specifically from commercial wearables with all its challenges from data cleaning to feature extraction. Methods: FLIRT leverages a variety of state-of-the-art algorithms (e.g., particle filters, ML-based artifact detection) to ensure a robust preprocessing of physiological data from wearables. In a subsequent step, FLIRT utilizes a sliding-window approach and calculates a feature vector of more than 100 dimensions – a basis for a wide variety of ML algorithms. Results: We evaluated FLIRT on the publicly available WESAD dataset, which focuses on stress detection with an Empatica E4 wearable. Preprocessing the data with FLIRT ensures that unintended noise and artifacts are appropriately filtered. In the classification task, FLIRT outperforms the preprocessing baseline of the original WESAD paper. Conclusion: FLIRT provides functionalities beyond existing packages that can address unmet needs in physiological data processing and feature generation: (a) integrated handling of common wearable file formats (e.g., Empatica E4 archives), (b) robust preprocessing, and (c) standardized feature generation that ensures reproducibility of results. Nevertheless, while FLIRT comes with a default configuration to accommodate most situations, it offers a highly configurable interface for all of its implemented algorithms to account for specific needs.ISSN:0169-2607ISSN:1872-756

Gated Domain Units for Multi-source Domain Generalization

The phenomenon of distribution shift (DS) occurs when a dataset at test time differs from the dataset at training time, which can significantly impair the performance of a machine learning model in practical settings due to a lack of knowledge about the data's distribution at test time. To address this problem, we postulate that real-world distributions are composed of latent Invariant Elementary Distributions (I.E.D) across different domains. This assumption implies an invariant structure in the solution space that enables knowledge transfer to unseen domains. To exploit this property for domain generalization, we introduce a modular neural network layer consisting of Gated Domain Units (GDUs) that learn a representation for each latent elementary distribution. During inference, a weighted ensemble of learning machines can be created by comparing new observations with the representations of each elementary distribution. Our flexible framework also accommodates scenarios where explicit domain information is not present. Extensive experiments on image, text, and graph data show consistent performance improvement on out-of-training target domains. These findings support the practicality of the I.E.D assumption and the effectiveness of GDUs for domain generalisation.ISSN:2835-885

A Scalable Risk-Scoring System Based on Consumer-Grade Wearables for Inpatients With COVID-19: Statistical Analysis and Model Development

Background: To provide effective care for inpatients with COVID-19, clinical practitioners need systems that monitor patient health and subsequently allow for risk scoring. Existing approaches for risk scoring in patients with COVID-19 focus primarily on intensive care units (ICUs) with specialized medical measurement devices but not on hospital general wards. Objective: In this paper, we aim to develop a risk score for inpatients with COVID-19 in general wards based on consumer-grade wearables (smartwatches). Methods: Patients wore consumer-grade wearables to record physiological measurements, such as the heart rate (HR), heart rate variability (HRV), and respiration frequency (RF). Based on Bayesian survival analysis, we validated the association between these measurements and patient outcomes (ie, discharge or ICU admission). To build our risk score, we generated a low-dimensional representation of the physiological features. Subsequently, a pooled ordinal regression with time-dependent covariates inferred the probability of either hospital discharge or ICU admission. We evaluated the predictive performance of our developed system for risk scoring in a single-center, prospective study based on 40 inpatients with COVID-19 in a general ward of a tertiary referral center in Switzerland. Results: First, Bayesian survival analysis showed that physiological measurements from consumer-grade wearables are significantly associated with patient outcomes (ie, discharge or ICU admission). Second, our risk score achieved a time-dependent area under the receiver operating characteristic curve (AUROC) of 0.73-0.90 based on leave-one-subject-out cross-validation. Conclusions: Our results demonstrate the effectiveness of consumer-grade wearables for risk scoring in inpatients with COVID-19. Due to their low cost and ease of use, consumer-grade wearables could enable a scalable monitoring system

A Scalable Risk Scoring System for COVID-19 Inpatients Based on Consumer-grade Wearables: Statistical Analysis and Model Development.

BACKGROUND To provide effective care for COVID-19 inpatients, clinical practitioners need systems that monitor patient health and subsequently allow for risk scoring. Existing approaches for risk scoring in COVID-19 patients focus primarily on intensive care units with specialized medical measurement devices, but not on hospital general wards. OBJECTIVE In this paper, we aim to develop a risk score for COVID-19 inpatients in general wards based on consumer-grade wearables (smartwatches). METHODS Patients wore consumer-grade wearables to record physiological measurements such as heart rate, heart rate variability, and respiration frequency. Based on Bayesian survival analysis, we validate the association between these measurements and the patient outcomes (i.e., discharge or intensive care unit admission). To build our risk score, we generate a low-dimensional representation of the physiological features. Subsequently, a pooled ordinal regression with time-dependent covariates infers the probability of either hospital discharge or intensive care unit (ICU) admission. RESULTS We evaluate the predictive performance of our developed system for risk scoring in a single-center, prospective study based on N = 40 inpatients with COVID-19 in a general ward of a tertiary referral center in Switzerland. First, the Bayesian survival analysis shows that physiological measurements from consumer-grade wearables are significantly associated with the patient outcomes (i.e., discharge or intensive care unit admission). Second, our risk score achieves a time-dependent area under the receiver operating characteristic curve of 0.73 to 0.90 based on leave-one-subject-out cross-validation. CONCLUSIONS Our results demonstrate the effectiveness of consumer-grade wearables for risk scoring in COVID-19 inpatients. Due to their low cost and ease of use, consumer-grade wearables could enable a scalable monitoring system. CLINICALTRIAL The study Wearable-based COVID-19 Markers for Prediction of Clinical Trajectories (WAVE) is registered at https://clinicaltrials.gov (Identifier: NCT04357834). The study followed the Declaration of Helsinki, the guidelines of good clinical practice, the Swiss health laws, and the ordinance on clinical research. The study was approved by the local ethics committee Bern, Switzerland (ID 2020-00874). Each patient gave informed written consent before any study-related procedure

Noninvasive Hypoglycemia Detection in People With Diabetes Using Smartwatch Data.

OBJECTIVE To develop a noninvasive hypoglycemia detection approach using smartwatch data. RESEARCH DESIGN AND METHODS We prospectively collected data from two wrist-worn wearables (Garmin vivoactive 4S, Empatica E4) and continuous glucose monitoring values in adults with diabetes on insulin treatment. Using these data, we developed a machine learning (ML) approach to detect hypoglycemia (<3.9 mmol/L) noninvasively in unseen individuals and solely based on wearable data. RESULTS Twenty-two individuals were included in the final analysis (age 54.5 ± 15.2 years, HbA1c 6.9 ± 0.6%, 16 males). Hypoglycemia was detected with an area under the receiver operating characteristic curve of 0.76 ± 0.07 solely based on wearable data. Feature analysis revealed that the ML model associated increased heart rate, decreased heart rate variability, and increased tonic electrodermal activity with hypoglycemia. CONCLUSIONS Our approach may allow for noninvasive hypoglycemia detection using wearables in people with diabetes and thus complement existing methods for hypoglycemia detection and warning

Glycaemic patterns of male professional athletes with type 1 diabetes during exercise, recovery and sleep: Retrospective, observational study over an entire competitive season

Aims To analyse glycaemic patterns of professional athletes with type 1 diabetes during a competitive season. Materials and Methods We analysed continuous glucose monitoring data of 12 professional male cyclists with type 1 diabetes during exercise, recovery and sleep on days with competitive exercise (CE) and non-competitive exercise (NCE). We assessed whether differences exist between CE and NCE days and analysed associations between exercise and dysglycaemia. Results The mean glycated haemoglobin was 50 ± 5 mmol/mol (6.7 ± 0.5%). The athletes cycled on 280.8 ± 28.1 days (entire season 332.6 ± 18.8 days). Overall, time in range (3.9-10 mmol/L) was 70.0 ± 13.7%, time in hypoglycaemia (10 mmol/L) was 23.6 ± 12.5%. During the nights of NCE days, athletes spent 10.1 ± 7.4% of time in hypoglycaemia, particularly after exercise in the endurance zones. The CE days were characterized by a higher time in hyperglycaemia compared with NCE days (25.2 ± 12.5% vs. 22.2 ± 12.1%, p = .012). This was driven by the CE phase, where time in range dropped to 60.4 ± 13.0% and time in hyperglycaemia was elevated (38.5 ± 12.9%). Mean glucose was higher during CE compared with NCE sessions (9.6 ± 0.9 mmol/L vs. 7.8 ± 1.1 mmol/L, p < .001). The probability of hyperglycaemia during exercise was particularly increased with longer duration, higher intensity and higher variability of exercise. Conclusions The analysis of glycaemic patterns of professional endurance athletes revealed that overall glycaemia was generally within targets. For further improvement, athletes, team staff and caregivers may focus on hyperglycaemia during competitions and nocturnal hypoglycaemia after NCE.ISSN:1462-8902ISSN:1463-132