DeepCOVID-Fuse: A Multi-Modality Deep Learning Model Fusing Chest X-rays and Clinical Variables to Predict COVID-19 Risk Levels.

The COVID-19 pandemic has posed unprecedented challenges to global healthcare systems, highlighting the need for accurate and timely risk prediction models that can prioritize patient care and allocate resources effectively. This study presents DeepCOVID-Fuse, a deep learning fusion model that predicts risk levels in patients with confirmed COVID-19 by combining chest radiographs (CXRs) and clinical variables. The study collected initial CXRs, clinical variables, and outcomes (i.e., mortality, intubation, hospital length of stay, Intensive care units (ICU) admission) from February to April 2020, with risk levels determined by the outcomes. The fusion model was trained on 1657 patients (Age: 58.30 ± 17.74; Female: 807) and validated on 428 patients (56.41 ± 17.03; 190) from the local healthcare system and tested on 439 patients (56.51 ± 17.78; 205) from a different holdout hospital. The performance of well-trained fusion models on full or partial modalities was compared using DeLong and McNemar tests. Results show that DeepCOVID-Fuse significantly (p < 0.05) outperformed models trained only on CXRs or clinical variables, with an accuracy of 0.658 and an area under the receiver operating characteristic curve (AUC) of 0.842. The fusion model achieves good outcome predictions even when only one of the modalities is used in testing, demonstrating its ability to learn better feature representations across different modalities during training.

CNN approach for predicting survival outcome of patients with COVID-19

Coronavirus disease 2019 (COVID-19) has been challenged specifically with the new variant. The number of patients seeking treatment has increased significantly, putting tremendous pressure on hospitals and healthcare systems. With the potential of artificial intelligence (AI) to leverage clinicians to improve personalized medicine for COVID-19, we propose a deep learning model based on 1D and 3D convolutional neural networks (CNNs) to predict the survival outcome of COVID-19 patients. Our model consists of two CNN channels that operate with CT scans and the corresponding clinical variables. Specifically, each patient data set consists of CT images and the corresponding 44 clinical variables used in the 3D CNN and 1D CNN input, respectively. This model aims to combine imaging and clinical features to predict short-term from long-term survival. Our models demonstrate higher performance metrics compared to state-of-the-art models with AUC-ROC of 91.44 –91.60% versus 84.36 –88.10% and Accuracy of 83.39 –84.47% versus 79.06 –81.94% in predicting the survival groups of patients with COVID-19. Based on the findings, the combined clinical and imaging features in the deep CNN model can be used as a prognostic tool and help to distinguish censored and uncensored cases of COVID-19. IEEE

Deep Survival Analysis With Clinical Variables for COVID-19.

OBJECTIVE: Millions of people have been affected by coronavirus disease 2019 (COVID-19), which has caused millions of deaths around the world. Artificial intelligence (AI) plays an increasing role in all areas of patient care, including prognostics. This paper proposes a novel predictive model based on one dimensional convolutional neural networks (1D CNN) to use clinical variables in predicting the survival outcome of COVID-19 patients. METHODS AND PROCEDURES: We have considered two scenarios for survival analysis, 1) uni-variate analysis using the Log-rank test and Kaplan-Meier estimator and 2) combining all clinical variables ([Formula: see text]=44) for predicting the short-term from long-term survival. We considered the random forest (RF) model as a baseline model, comparing to our proposed 1D CNN in predicting survival groups. RESULTS: Our experiments using the univariate analysis show that nine clinical variables are significantly associated with the survival outcome with corrected p < 0.05. Our approach of 1D CNN shows a significant improvement in performance metrics compared to the RF and the state-of-the-art techniques (i.e., 1D CNN) in predicting the survival group of patients with COVID-19. CONCLUSION: Our model has been tested using clinical variables, where the performance is found promising. The 1D CNN model could be a useful tool for detecting the risk of mortality and developing treatment plans in a timely manner. CLINICAL IMPACT: The findings indicate that using both Heparin and Exnox for treatment is typically the most useful factor in predicting a patient's chances of survival from COVID-19. Moreover, our predictive model shows that the combination of AI and clinical data can be applied to point-of-care services through fast-learning healthcare systems.

Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York.

BACKGROUND: In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contributed to increased rates of breakthrough infections compared to unvaccinated controls. METHODS: We studied SARS-CoV-2 variant distribution, dynamics, and adaptive selection over time in relation to vaccine status, phylogenetic relatedness of viruses, full genome mutation profiles, and associated clinical and demographic parameters. FINDINGS: We show a steep and near-complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25 (14% in vaccinated, 7% in unvaccinated), its spike mutation S112L, and AY.44 (8% in vaccinated, 2% in unvaccinated) with its nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthrough infections increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. INTERPRETATION: We observed a modest adaptation of Delta genomes in breakthrough infections in New York, suggesting an improved genomic framework to support Delta's epidemic growth in times of waning vaccine protection despite limited impact on vaccine escape. FUNDING: The study was supported by NYU institutional funds. The NYULH Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center.

Predicting critical illness on initial diagnosis of COVID-19 based on easily obtained clinical variables: development and validation of the PRIORITY model.

OBJECTIVES: We aimed to develop and validate a prediction model, based on clinical history and examination findings on initial diagnosis of coronavirus disease 2019 (COVID-19), to identify patients at risk of critical outcomes. METHODS: We used data from the SEMI-COVID-19 Registry, a cohort of consecutive patients hospitalized for COVID-19 from 132 centres in Spain (23rd March to 21st May 2020). For the development cohort, tertiary referral hospitals were selected, while the validation cohort included smaller hospitals. The primary outcome was a composite of in-hospital death, mechanical ventilation, or admission to intensive care unit. Clinical signs and symptoms, demographics, and medical history ascertained at presentation were screened using least absolute shrinkage and selection operator, and logistic regression was used to construct the predictive model. RESULTS: There were 10 433 patients, 7850 in the development cohort (primary outcome 25.1%, 1967/7850) and 2583 in the validation cohort (outcome 27.0%, 698/2583). The PRIORITY model included: age, dependency, cardiovascular disease, chronic kidney disease, dyspnoea, tachypnoea, confusion, systolic blood pressure, and SpO2 ≤93% or oxygen requirement. The model showed high discrimination for critical illness in both the development (C-statistic 0.823; 95% confidence interval (CI) 0.813, 0.834) and validation (C-statistic 0.794; 95%CI 0.775, 0.813) cohorts. A freely available web-based calculator was developed based on this model (https://www.evidencio.com/models/show/2344). CONCLUSIONS: The PRIORITY model, based on easily obtained clinical information, had good discrimination and generalizability for identifying COVID-19 patients at risk of critical outcomes.

Time-to-Death Longitudinal Characterization of Clinical Variables and Longitudinal Prediction of Mortality in COVID-19 Patients: A Two-Center Study.

Objectives: To characterize the temporal characteristics of clinical variables with time lock to mortality and build a predictive model of mortality associated with COVID-19 using clinical variables. Design: Retrospective cohort study of the temporal characteristics of clinical variables with time lock to mortality. Setting: Stony Brook University Hospital (New York) and Tongji Hospital. Patients: Patients with confirmed positive for severe acute respiratory syndrome coronavirus-2 using polymerase chain reaction testing. Patients from the Stony Brook University Hospital data were used for training (80%, N = 1,002) and testing (20%, N = 250), and 375 patients from the Tongji Hospital (Wuhan, China) data were used for testing. Intervention: None. Measurements and Main Results: Longitudinal clinical variables were analyzed as a function of days from outcome with time-lock-to-day of death (non-survivors) or discharge (survivors). A predictive model using the significant earliest predictors was constructed. Performance was evaluated using receiver operating characteristics area under the curve (AUC). The predictive model found lactate dehydrogenase, lymphocytes, procalcitonin, D-dimer, C-reactive protein, respiratory rate, and white-blood cells to be early predictors of mortality. The AUC for the zero to 9 days prior to outcome were: 0.99, 0.96, 0.94, 0.90, 0.82, 0.75, 0.73, 0.77, 0.79, and 0.73, respectively (Stony Brook Hospital), and 1.0, 0.86, 0.88, 0.96, 0.91, 0.62, 0.67, 0.50, 0.63, and 0.57, respectively (Tongji Hospital). In comparison, prediction performance using hospital admission data was poor (AUC = 0.59). Temporal fluctuations of most clinical variables, indicative of physiological and biochemical instability, were markedly higher in non-survivors compared to survivors (p < 0.001). Conclusion: This study identified several clinical markers that demonstrated a temporal progression associated with mortality. These variables accurately predicted death within a few days prior to outcome, which provides objective indication that closer monitoring and interventions may be needed to prevent deterioration.