The challenges of deploying artificial intelligence models in a rapidly evolving pandemic

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2, emerged into a world being rapidly transformed by artificial intelligence (AI) based on big data, computational power and neural networks. The gaze of these networks has in recent years turned increasingly towards applications in healthcare. It was perhaps inevitable that COVID-19, a global disease propagating health and economic devastation, should capture the attention and resources of the world's computer scientists in academia and industry. The potential for AI to support the response to the pandemic has been proposed across a wide range of clinical and societal challenges, including disease forecasting, surveillance and antiviral drug discovery. This is likely to continue as the impact of the pandemic unfolds on the world's people, industries and economy but a surprising observation on the current pandemic has been the limited impact AI has had to date in the management of COVID-19. This correspondence focuses on exploring potential reasons behind the lack of successful adoption of AI models developed for COVID-19 diagnosis and prognosis, in front-line healthcare services. We highlight the moving clinical needs that models have had to address at different stages of the epidemic, and explain the importance of translating models to reflect local healthcare environments. We argue that both basic and applied research are essential to accelerate the potential of AI models, and this is particularly so during a rapidly evolving pandemic. This perspective on the response to COVID-19, may provide a glimpse into how the global scientific community should react to combat future disease outbreaks more effectively.Comment: Accepted in Nature Machine Intelligenc

Issue in Remote Assessment of Lung Disease and Impact on Physical and Mental Health (RALPMH): Protocol for Prospective Observational Study

Background: Chronic Lung disorders like COPD and IPF are characterised by exacerbations which are a significant problem: unpleasant for patients, and sometimes severe enough to cause hospital admission (and therefore NHS pressures) and death. Reducing the impact of exacerbations is very important. Moreover, due to the COVID-19 pandemic, the vulnerable populations with these disorders are at high risk and hence their routine care cannot be done properly. Remote monitoring offers a low cost and safe solution of gaining visibility into the health of people in their daily life. Thus, remote monitoring of patients in their daily lives using mobile and wearable devices could be useful especially in high vulnerability groups. A scenario we consider here is to monitor patients and detect disease exacerbation and progression and investigate the opportunity of detecting exacerbations in real-time with a future goal of real-time intervention. Objective: The primary objective is to assess the feasibility and acceptability of remote monitoring using wearable and mobile phones in patients with pulmonary diseases. The aims will be evaluated over these areas: Participant acceptability, drop-out rates and interpretation of data, Detection of clinically important events such as exacerbations and disease progression, Quantification of symptoms (physical and mental health), Impact of disease on mood and wellbeing/QoL and The trajectory-tracking of main outcome variables, symptom fluctuations and order. The secondary objective of this study is to provide power calculations for a larger longitudinal follow-up study. Methods: Participants will be recruited from 2 NHS sites in 3 different cohorts - COPD, IPF and Post hospitalised Covid. A total of 60 participants will be recruited, 20 in each cohort. Data collection will be done remotely using the RADAR-Base mHealth platform for different devices - Garmin wearable devices, smart spirometers, mobile app questionnaires, surveys and finger pulse oximeters. Passive data collected includes wearable derived continuous heart rate, SpO2, respiration rate, activity, and sleep. Active data collected includes disease-specific PROMs, mental health questionnaires and symptoms tracking to track disease trajectory in addition to speech sampling, spirometry and finger Pulse Oximetry. Analyses are intended to assess the feasibility of RADAR-Base for lung disorder remote monitoring (include quality of data, a cross-section of passive and active data, data completeness, the usability of the system, acceptability of the system). Where adequate data is collected, we will attempt to explore disease trajectory, patient stratification and identification of acute clinically interesting events such as exacerbations. A key part of this study is understanding the potential of real-time data collection, here we will simulate an intervention using the Exacerbation Rating Scale (ERS) to acquire responses at-time-of-event to assess the performance of a model for exacerbation identification from passive data collected. Results: RALPMH study provides a unique opportunity to assess the use of remote monitoring in the study of lung disorders. The study is set to be started in mid-May 2021. The data collection apparatus, questionnaires and wearable integrations have been set up and tested by clinical teams. While waiting for ethics approval, real-time detection models are currently being constructed. Conclusions: RALPMH will provide a reference infrastructure for the use of wearable data for monitoring lung diseases. Specifically information regarding the feasibility and acceptability of remote monitoring and the potential of real-time remote data collection and analysis in the context of chronic lung disorders. Moreover, it provides a unique standpoint to look into the specifics of novel coronavirus without burdensome interventions. It will help plan and inform decisions in any future studies that make use of remote monitoring in the area of Respiratory health. Clinical Trial: https://www.isrctn.com/ISRCTN1627560

Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles

BACKGROUND: Pseudomonas aeruginosa is a genetically complex bacterium which can adopt and switch between a free-living or biofilm lifestyle, a versatility that enables it to thrive in many different environments and contributes to its success as a human pathogen. RESULTS: Transcriptomes derived from growth states relevant to the lifestyle of P. aeruginosa were clustered using three different methods (K-means, K-means spectral and hierarchical clustering). The culture conditions used for this study were; biofilms incubated for 8, 14, 24 and 48 hrs, and planktonic culture (logarithmic and stationary phase). This cluster analysis revealed the existence and provided a clear illustration of distinct expression profiles present in the dataset. Moreover, it gave an insight into which genes are up-regulated in planktonic, developing biofilm and confluent biofilm states. In addition, this analysis confirmed the contribution of quorum sensing (QS) and RpoS regulated genes to the biofilm mode of growth, and enabled the identification of a 60.69 Kbp region of the genome associated with stationary phase growth (stationary phase planktonic culture and confluent biofilms). CONCLUSION: This is the first study to use clustering to separate a large P. aeruginosa microarray dataset consisting of transcriptomes obtained from diverse conditions relevant to its growth, into different expression profiles. These distinct expression profiles not only reveal novel aspects of P. aeruginosa gene expression but also provide a growth specific transcriptomic reference dataset for the research community

Home Monitoring to Detect Progression of Interstitial Lung Disease:A Prospective Cohort Study

In this prospective observational cohort study, 20 IPF and non-IPF patients, as diagnosed by a multidisciplinary team were recruited from the University College London Hospital (UCLH) between August 2021 and January 2022 using 2018 ATS criteria. Patients who met the criteria for ILD other than IPF, including those with sarcoidosis, and hypersensitivity pneumonitis, were grouped together as non-IPF. They were monitored over 26 weeks using the RADAR-Base mHealth platform. Data collection tools included: questionnaires, a Garmin wearable device, finger pulse oximeter and a NuvoAir smart-spirometer.7 In addition, participants underwent lung function testing in a hospital setting as part of their usual hospital visits. Patients were divided into two groups: progressed and stable. Progression was defined as a ≥5% decline in forced vital capacity (FVC) at6 months by hospital-based spirometry and/or death

Airway Measurement by Refinement of Synthetic Images Improves Mortality Prediction in Idiopathic Pulmonary Fibrosis

Several chronic lung diseases, like idiopathic pulmonary fibrosis (IPF) are characterised by abnormal dilatation of the airways. Quantification of airway features on computed tomography (CT) can help characterise disease progression. Physics based airway measurement algorithms have been developed, but have met with limited success in part due to the sheer diversity of airway morphology seen in clinical practice. Supervised learning methods are also not feasible due to the high cost of obtaining precise airway annotations. We propose synthesising airways by style transfer using perceptual losses to train our model, Airway Transfer Network (ATN). We compare our ATN model with a state-of-the-art GAN-based network (simGAN) using a) qualitative assessment; b) assessment of the ability of ATN and simGAN based CT airway metrics to predict mortality in a population of 113 patients with IPF. ATN was shown to be quicker and easier to train than simGAN. ATN-based airway measurements were also found to be consistently stronger predictors of mortality than simGAN-derived airway metrics on IPF CTs. Airway synthesis by a transformation network that refines synthetic data using perceptual losses is a realistic alternative to GAN-based methods for clinical CT analyses of idiopathic pulmonary fibrosis. Our source code can be found at https://github.com/ashkanpakzad/ATN that is compatible with the existing open-source airway analysis framework, AirQuant

Delineating COVID-19 subgroups using routine clinical data identifies distinct in-hospital outcomes

The COVID-19 pandemic has been a great challenge to healthcare systems worldwide. It highlighted the need for robust predictive models which can be readily deployed to uncover heterogeneities in disease course, aid decision-making and prioritise treatment. We adapted an unsupervised data-driven model-SuStaIn, to be utilised for short-term infectious disease like COVID-19, based on 11 commonly recorded clinical measures. We used 1344 patients from the National COVID-19 Chest Imaging Database (NCCID), hospitalised for RT-PCR confirmed COVID-19 disease, splitting them equally into a training and an independent validation cohort. We discovered three COVID-19 subtypes (General Haemodynamic, Renal and Immunological) and introduced disease severity stages, both of which were predictive of distinct risks of in-hospital mortality or escalation of treatment, when analysed using Cox Proportional Hazards models. A low-risk Normal-appearing subtype was also discovered. The model and our full pipeline are available online and can be adapted for future outbreaks of COVID-19 or other infectious disease