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Principal Investigator: Ulas Bagci
Organization: NORTHWESTERN UNIVERSITY AT CHICAGO
Fiscal Year: 2024
Award: $772,290
Funding agency: National Heart Lung and Blood Institute
PROJECT SUMMARY
Since the beginning of COVID-19 (SARS-CoV-2) pandemic, we have seen a number of prominent variants, and
two of them are very recent. COVID-19 continues to affect millions of people: over 771 million people were
affected and over 6.9 million deaths occurred (as of October 2023). A significant portion of patients who suffer
from severe COVID-19 disease are at risk for developing long-term Post-Acute Sequelae (PASC) with pulmonary
fibrosis. Identifying patients who are most at risk for post COVID-19 pulmonary fibrosis could allow early
intervention with anti-fibrotic drugs and other potential treatment strategies. Given the extent of people infected
with COVID-19, post COVID-19 pulmonary fibrosis is a significant cause of mortality and morbidity, yet there is
no strategy developed to address this unmet critical clinical need. Hence, the overall goal of this proposal is to
address this need for predicting post COVID-19 pulmonary fibrosis at an early stage by developing novel
explainable deep learning (DL) algorithms on multimodal data (combined imaging and electronic health record
(EHR) data) from multiple centers. Main Hypothesis: The proposed explainable DL algorithms will identify
patients at risk for development of post COVID-19 related pulmonary fibrosis at early phases by multimodal data
with high accuracy. In Aim 1, we will identify imaging and EHR characteristics associated with post COVID-19
fibrosis from patient data gathered from Northwestern, Columbia, NIH, and UPenn. We will automatically extract
imaging (CT scan) features in two ways: (i) pulmonary analysis (PA) and (ii) body composition analysis (BCA).
For each patient, we will collect EHR data consisting of demographic, clinical (including vital, medication,
vaccination, and comorbidity) and laboratory information. We expect to retrospectively collect a balanced dataset
of 1,150 initial CT scans and associated EHR data. In Aim 2, we will develop Transformer embedded explainable
capsule networks (X-TCaps) for prediction of post COVID-19 pulmonary fibrosis. We will integrate our newly
established visual explanation algorithm (called IBA) into the machine-generated results in addition to
radiographical explanations, and PA and BCA features captured by X-TCaps. In Aim 3, we will employ our
established optimal biomarker (OBM) method to determine the most potent features (biomarkers) from EHR and
imaging data to predict post COVID-19 pulmonary fibrosis at the highest accuracy possible. PASC is a massive
emergency and very little is known about it. Once accomplished, our proposed framework will provide early
prediction of post COVID-19 pulmonary fibrosis and determine biomarkers to understand pulmonary fibrosis
better. Our study is innovative as no previous study has investigated post COVID-19 pulmonary fibrosis, which
is paramount to developing a robust knowledge database and informing clinical practice in this area. With this
project, we will provide mechanistic understanding of post COVID-19 pulmonary fibrosis, which is central in
determining therapeutic options and will ultimately play a role in lung transplant considerations in the long term.
Terms: <Active Follow-up><Acute><Address><Adipose tissue><Adrenal Cortex Hormones><Affect><Airway challenge><Algorithms><Area><Biological Markers><Body Composition><Bone structure><Breathlessness><CAT scan><COVID crisis><COVID epidemic><COVID pandemic><COVID survivors><COVID-19><COVID-19 crisis><COVID-19 epidemic><COVID-19 era><COVID-19 global health crisis><COVID-19 global pandemic><COVID-19 health crisis><COVID-19 infection><COVID-19 infection survivors><COVID-19 pandemic><COVID-19 period><COVID-19 public health crisis><COVID-19 survivors><COVID-19 virus infection><COVID-19 years><COVID19 infection><CT X Ray><CT Xray><CT imaging><CT scan><CV-19><Capsules><Cessation of life><Characteristics><Clinical><Clinical Evaluation><Clinical Testing><Computed Tomography><Confidence Intervals><Coronavirus Infectious Disease 2019><Corticoids><Corticosteroids><Data><Data Bases><Data Set><Databases><Death><Detection><Development><Diagnosis><Diagnostic><Disease><Disorder><Drugs><Dyspnea><Early Diagnosis><Early Intervention><Early identification><Electronic Health Record><Emergencies><Emergency Situation><Evaluation><Exhibits><Factor Analyses><Factor Analysis><Fatty Tissue><Fibrosis><Fibrotic lesions in lung><Future><Goals><Health Care Systems><Healthcare><Healthcare Systems><Human><Image><Individual><Knowledge><Laboratories><Long COVID><Long COVID-19><Long coronavirus disease><Long coronavirus disease 2019><Long-Term Effects><Longterm Effects><Lung><Lung Grafting><Lung Respiratory System><Lung Tissue Fibrosis><Lung Transplantation><Lung damage><Lung scar><Lung symptom><Lung tissue scar><Measurement><Mechanical Ventilator Weaning><Medication><Methods><Modality><Modeling><Modern Man><Morbidity><Morbidity - disease rate><Muscle><Muscle Tissue><Musculoskeletal System><NIH><National Institutes of Health><Neurocognitive><Outcome><Patients><Pattern><Pennsylvania><Personal Satisfaction><Persons><Pharmaceutical Preparations><Phase><Population><Predicting Risk><Property><Public Health><Pulmonary Fibrosis><Pulmonary Graft><Pulmonary Scar><Pulmonary Tissue fibrosis><Pulmonary Transplant><Pulmonary Transplantation><Radiography><Reporting><Respirator Weaning><Risk><Roentgenography><SARS-CoV-2 epidemic><SARS-CoV-2 global health crisis><SARS-CoV-2 global pandemic><SARS-CoV-2 infection><SARS-CoV-2 pandemic><SARS-CoV-2 survivors><SARS-CoV2 infection><SARS-coronavirus-2 epidemic><SARS-coronavirus-2 pandemic><Scanning><Scarring at the lung><Scarring in the lung><Severe Acute Respiratory Syndrome CoV 2 epidemic><Severe Acute Respiratory Syndrome CoV 2 pandemic><Severe acute respiratory syndrome coronavirus 2 epidemic><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome coronavirus 2 pandemic><Severity of illness><Skeletal Muscle><Symptoms><Testing><Texture><Therapeutic><Thick><Thickness><Tomodensitometry><Training><Translations><United States National Institutes of Health><Universities><Vaccination><Variant><Variation><Ventilator Weaning><Visceral><Visual><Voluntary Muscle><Work><X-Ray CAT Scan><X-Ray Computed Tomography><X-Ray Computerized Tomography><Xray CAT scan><Xray Computed Tomography><Xray computerized tomography><active followup><adipose><bio-markers><biologic marker><biomarker><biomarker discovery><biomarker selection><capsule><care seeking><catscan><chest CT><chest computed tomography><chronic COVID><chronic COVID-19><chronic novel coronavirus disease 2019><chronic symptom><clinical center><clinical practice><clinical test><co-morbid><co-morbidity><combat><comorbidity><computed axial tomography><computer tomography><computerized axial tomography><computerized tomography><coronavirus disease 2019><coronavirus disease 2019 crisis><coronavirus disease 2019 epidemic><coronavirus disease 2019 global health crisis><coronavirus disease 2019 global pandemic><coronavirus disease 2019 health crisis><coronavirus disease 2019 infection><coronavirus disease 2019 pandemic><coronavirus disease 2019 public health crisis><coronavirus disease crisis><coronavirus disease epidemic><coronavirus disease pandemic><coronavirus disease-19><coronavirus disease-19 global pandemic><coronavirus disease-19 pandemic><coronavirus infectious disease-19><data base><deep learning><deep learning algorithm><deep learning method><deep learning strategy><developmental><disease severity><drug/agent><early detection><electronic health care record><electronic health medical record><electronic health plan record><electronic health registry><electronic medical health record><exhaust><experience><fibrosis in the lung><fibrotic lung><follow up><follow-up><followed up><followup><forecasting risk><health care><imaging><improved><individual patient><infected with COVID-19><infected with COVID19><infected with SARS-CoV-2><infected with SARS-CoV2><infected with coronavirus disease 2019><infected with severe acute respiratory syndrome coronavirus 2><innovate><innovation><innovative><life-threatening COVID><life-threatening COVID-19><life-threatening SARS-CoV-2><life-threatening coronavirus disease><life-threatening coronavirus disease 2019><life-threatening severe acute respiratory syndrome coronavirus 2><locomotor system><long haul COVID><long haul COVID-19><long haul coronavirus disease><long haul coronavirus disease 2019><long-hauler COVID><long-hauler COVID-19><long-hauler coronavirus disease 2019><long-hauler syndrome><long-term COVID><long-term COVID-19><long-term coronavirus disease><long-term coronavirus disease 2019><longterm COVID><longterm COVID-19><longterm coronavirus disease><longterm coronavirus disease 2019><lung fibrosis><lung function><lung injury><lung lobe><lung rehabilitation><lung transplant><mortality><multi-modal data><multi-modal datasets><multi-modality><multimodal data><multimodal datasets><multimodality><muscular><non-contrast CT><noncontrast CT><noncontrast computed tomography><novel><persistent COVID-19><persistent symptom><post COVID syndrome><post COVID-19 syndrome><post acute COVID syndrome><post acute COVID-19><post acute COVID-19 syndrome><post acute SARS-CoV-2><post acute coronavirus disease 2019><post acute coronavirus disease 2019 syndrome><post acute coronavirus disease syndrome><post acute severe acute respiratory syndrome coronavirus 2><post coronavirus disease 2019 syndrome><post coronavirus disease syndrome><post-COVID><post-COVID pulmonary fibrosis><post-COVID-19><post-COVID-19 pulmonary fibrosis><post-acute phases of COVID-19><post-coronavirus disease 2019><potential biological marker><potential biomarker><predict risk><predict risks><predicted risk><predicted risks><predicting risks><predictive risk><predicts risk><prolonged COVID-19 symptoms><pulmonary><pulmonary damage><pulmonary function><pulmonary injury><pulmonary rehabilitation><pulmonary symptom><pulmonary tissue damage><pulmonary tissue injury><radiologic imaging><radiological imaging><research clinical testing><respiratory challenge><risk prediction><risk predictions><serious COVID><serious COVID-19><serious SARS-CoV-2><serious coronavirus disease><serious coronavirus disease 2019><serious severe acute respiratory syndrome coronavirus 2><severe COVID><severe COVID-19><severe COVID19><severe SARS-CoV-2><severe acute respiratory syndrome coronavirus 2 global health crisis><severe acute respiratory syndrome coronavirus 2 global pandemic><severe coronavirus disease><severe coronavirus disease 19><severe coronavirus disease 2019><severe severe acute respiratory syndrome coronavirus 2><skeletal structure><standard of care><statistics><subcutaneous><subdermal><success><survive COVID-19><survive SARS-CoV-2><tool><translation><treatment strategy><well-being><wellbeing><white adipose tissue><yellow adipose tissue>