MedML: Fusing Medical Knowledge and Machine Learning Models for Early Pediatric COVID-19 Hospitalization and Severity Prediction (preprint)

The COVID-19 pandemic has caused devastating economic and social disruption, straining the resources of healthcare institutions worldwide. This has led to a nationwide call for models to predict hospitalization and severe illness in patients with COVID-19 to inform distribution of limited healthcare resources. We respond to one of these calls specific to the pediatric population. To address this challenge, we study two prediction tasks for the pediatric population using electronic health records: 1) predicting which children are more likely to be hospitalized, and 2) among hospitalized children, which individuals are more likely to develop severe symptoms. We respond to the national Pediatric COVID-19 data challenge with a novel machine learning model, MedML. MedML extracts the most predictive features based on medical knowledge and propensity scores from over 6 million medical concepts and incorporates the inter-feature relationships between heterogeneous medical features via graph neural networks (GNN). We evaluate MedML across 143,605 patients for the hospitalization prediction task and 11,465 patients for the severity prediction task using data from the National Cohort Collaborative (N3C) dataset. We also report detailed group-level and individual-level feature importance analyses to evaluate the model interpretability. MedML achieves up to a 7% higher AUROC score and up to a 14% higher AUPRC score compared to the best baseline machine learning models and performs well across all nine national geographic regions and over all three-month spans since the start of the pandemic. Our cross-disciplinary research team has developed a method of incorporating clinical domain knowledge as the framework for a new type of machine learning model that is more predictive and explainable than current state-of-the-art data-driven feature selection methods.

MTC: Multiresolution Tensor Completion from Partial and Coarse Observations (preprint)

Existing tensor completion formulation mostly relies on partial observations from a single tensor. However, tensors extracted from real-world data are often more complex due to: (i) Partial observation: Only a small subset (e.g., 5%) of tensor elements are available. (ii) Coarse observation: Some tensor modes only present coarse and aggregated patterns (e.g., monthly summary instead of daily reports). In this paper, we are given a subset of the tensor and some aggregated/coarse observations (along one or more modes) and seek to recover the original fine-granular tensor with low-rank factorization. We formulate a coupled tensor completion problem and propose an efficient Multi-resolution Tensor Completion model (MTC) to solve the problem. Our MTC model explores tensor mode properties and leverages the hierarchy of resolutions to recursively initialize an optimization setup, and optimizes on the coupled system using alternating least squares. MTC ensures low computational and space complexity. We evaluate our model on two COVID-19 related spatio-temporal tensors. The experiments show that MTC could provide 65.20% and 75.79% percentage of fitness (PoF) in tensor completion with only 5% fine granular observations, which is 27.96% relative improvement over the best baseline. To evaluate the learned low-rank factors, we also design a tensor prediction task for daily and cumulative disease case predictions, where MTC achieves 50% in PoF and 30% relative improvements over the best baseline.

Analyzing the Design Space of Re-opening Policies and COVID-19 Outcomes in the US (preprint)

Recent re-opening policies in the US, following a period of social distancing measures, introduced a significant increase in daily COVID-19 infections, calling for a roll-back or substantial revisiting of these policies in many states. The situation is suggestive of difficulties modeling the impact of partial distancing/re-opening policies on future epidemic spread for purposes of choosing safe alternatives. More specifically, one needs to understand the impact of manipulating the availability of social interaction venues (e.g., schools, workplaces, and retail establishments) on virus spread. We introduce a model, inspired by social networks research, that answers the above question. Our model compartmentalizes interaction venues into categories we call mixing domains, enabling one to predict COVID-19 contagion trends in different geographic regions under different what if assumptions on partial re-opening of individual domains. We apply our model to several highly impacted states showing (i) how accurately it predicts the extent of current resurgence (from available policy descriptions), and (ii) what alternatives might be more effective at mitigating the second wave. We further compare policies that rely on partial venue closure to policies that espouse wide-spread periodic testing instead (i.e., in lieu of social distancing). Our models predict that the benefits of (mandatory) testing out-shadow the benefits of partial venue closure, suggesting that perhaps more efforts should be directed to such a mitigation strategy.