Rapid and accurate detection of community outbreaks is critical to address the threat of resurgent waves of COVID-19. A practical challenge in outbreak detection is balancing accuracy vs. speed. In particular, while estimation accuracy improves with longer fitting windows, speed degrades. This paper presents a machine learning framework to balance this tradeoff using generalized random forests (GRF), and applies it to detect county level COVID-19 outbreaks. This algorithm chooses an adaptive fitting window size for each county based on relevant features affecting the disease spread, such as changes in social distancing policies. Experiment results show that our method outperforms any non-adaptive window size choices in 7-day ahead COVID-19 outbreak case number predictions.
The global spread of COVID-19, the disease caused by the novel coronavirus SARS-CoV-2, has cast a significant threat to mankind. As the COVID-19 situation continues to evolve, predicting localized disease severity is crucial for advanced resource allocation. This paper proposes a method named COURAGE (COUnty aggRegation mixup AuGmEntation) to generate a short-term prediction of 2-week-ahead COVID-19 related deaths for each county in the United States, leveraging modern deep learning techniques. Specifically, our method adopts a self-attention model from Natural Language Processing, known as th…
Accurately forecasting county level COVID-19 confirmed cases is crucial to optimizing medical resources. Forecasting emerging outbreaks pose a particular challenge because many existing forecasting techniques learn from historical seasons trends. Recurrent neural networks (RNNs) with LSTM-based cells are a logical choice of model due to their ability to learn temporal dynamics. In this paper, we adapt the state and county level influenza model, TDEFSI-LONLY, proposed in Wang et a. [l2020] to national and county level COVID-19 data. We show that this model poorly forecasts the current pandemic.…
With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper we approach the forecasting task with an alternative technique - spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a Long Short-term M…
Interpretable machine learning plays a key role in healthcare because it is challenging in understanding feature importance in deep learning model predictions. We propose a novel framework that uses deep learning to study feature sensitivity for model predictions. This work combines sensitivity analysis with heterogeneous time-series deep learning model prediction, which corresponds to the interpretations of spatio-temporal features. We forecast county-level COVID-19 infection using the Temporal Fusion Transformer. We then use the sensitivity analysis extending Morris Method to see how sensiti…
Frankfurt Institute for Advanced Studies（法兰克福高等研究院）；Beihang University（北京航空航天大学）；Black Hole KG；Goethe University Frankfurt（法兰克福歌德大学）
As the COVID-19 pandemic continues to ravage the world, it is of critical significance to provide a timely risk prediction of the COVID-19 in multi-level. To implement it and evaluate the public health policies, we develop a framework with machine learning assisted to extract epidemic dynamics from the infection data, in which contains a county-level spatiotemporal epidemiological model that combines a spatial Cellular Automaton (CA) with a temporal Susceptible-Undiagnosed-Infected-Removed (SUIR) model. Compared with the existing time risk prediction models, the proposed CA-SUIR model shows th…
Using a hybrid of machine learning and epidemiological approaches, we propose a novel data-driven approach in predicting US COVID-19 deaths at a county level. The model gives a more complete description of the daily death distribution, outputting quantile-estimates instead of mean deaths, where the model's objective is to minimize the pinball loss on deaths reported by the New York Times coronavirus county dataset. The resulting quantile estimates accurately forecast deaths at an individual-county level for a variable-length forecast period, and the approach generalizes well across different f…
University of California, Berkeley（加利福尼亚大学伯克利分校）；University of California, San Francisco（加利福尼亚大学旧金山分校）；Chan Zuckerberg Biohub（陈·扎克伯格生物中心）
As the COVID-19 outbreak evolves, accurate forecasting continues to play an extremely important role in informing policy decisions. In this paper, we present our continuous curation of a large data repository containing COVID-19 information from a range of sources. We use this data to develop predictions and corresponding prediction intervals for the short-term trajectory of COVID-19 cumulative death counts at the county-level in the United States up to two weeks ahead. Using data from January 22 to June 20, 2020, we develop and combine multiple forecasts using ensembling techniques, resulting…
Virginia Tech（弗吉尼亚理工大学）；Mississippi State University（密西西比州立大学）
Modeling the spatiotemporal nature of the spread of infectious diseases can provide useful intuition in understanding the time-varying aspect of the disease spread and the underlying complex spatial dependency observed in people's mobility patterns. Besides, the county level multiple related time series information can be leveraged to make a forecast on an individual time series. Adding to this challenge is the fact that real-time data often deviates from the unimodal Gaussian distribution assumption and may show some complex mixed patterns. Motivated by this, we develop a deep learning-based …
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）；The Third Hospital of Jilin University（吉林大学第三医院）；Ruijin Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属瑞金医院）；Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology（华中科技大学同济医学院附属同济医院）；Shanghai Public Health Clinical Center, Fudan University（复旦大学附属上海市公共卫生临床中心）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能科技有限公司）；Qianjiang Central Hospital, Jishou University School of Medicine（吉首大学医学院附属黔江中心医院）
Chest computed tomography (CT) becomes an effective tool to assist the diagnosis of coronavirus disease-19 (COVID-19). Due to the outbreak of COVID-19 worldwide, using the computed-aided diagnosis technique for COVID-19 classification based on CT images could largely alleviate the burden of clinicians. In this paper, we propose an Adaptive Feature Selection guided Deep Forest (AFS-DF) for COVID-19 classification based on chest CT images. Specifically, we first extract location-specific features from CT images. Then, in order to capture the high-level representation of these features with the r…
Environmental Systems Research Institute (Esri)（环境系统研究所）；California State Polytechnic University, Pomona（加州州立理工大学波莫纳分校）
The paper quantifies the impact of race, poverty, politics, and age on COVID-19 vaccination rates in counties in the continental US. Both, OLS regression analysis and Random Forest machine learning algorithms are applied to quantify factors for county-level vaccination hesitancy. The machine learning model considers joint effects of variables (race/ethnicity, partisanship, age, etc.) simultaneously to capture the unique combination of these factors on the vaccination rate. By implementing a state-of-the-art Artificial Intelligence Explanations (AIX) algorithm, it is possible to solve the black…
Predicting the number of infections in the anti-epidemic process is extremely beneficial to the government in developing anti-epidemic strategies, especially in fine-grained geographic units. Previous works focus on low spatial resolution prediction, e.g., county-level, and preprocess data to the same geographic level, which loses some useful information. In this paper, we propose a fine-grained population mobility data-based model (FGC-COVID) utilizing data of two geographic levels for community-level COVID-19 prediction. We use the population mobility data between Census Block Groups (CBGs),…
This study explored how population mobility flows form commuting networks across US counties and influence the spread of COVID-19. We utilized 3-level mixed effects negative binomial regression models to estimate the impact of network COVID-19 exposure on county confirmed cases and deaths over time. We also conducted weighting-based analyses to estimate the causal effect of network exposure. Results showed that commuting networks matter for COVID-19 deaths and cases, net of spatial proximity, socioeconomic, and demographic factors. Different local racial and ethnic concentrations are also asso…
Investigating the importance of county-level characteristics in opioid-related mortality across the United States
Department of Mathematics, University of Tennessee（田纳西大学数学系）；Computational Sciences and Engineering Division, Oak Ridge National Laboratory（橡树岭国家实验室计算科学与工程 division）；Office of Mental Health and Suicide Prevention, Veterans Health Administration（退伍军人健康管理局心理健康与自杀预防办公室）
University of Minnesota（明尼苏达大学）；IQVIA（艾昆纬）；University of Virginia（弗吉尼亚大学）；Temple University（天普大学）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Accurate prediction of the transmission of epidemic diseases such as COVID-19 is crucial for implementing effective mitigation measures. In this work, we develop a tensor method to predict the evolution of epidemic trends for many regions simultaneously. We construct a 3-way spatio-temporal tensor (location, attribute, time) of case counts and propose a nonnegative tensor factorization with latent epidemiological model regularization named STELAR. Unlike standard tensor factorization methods which cannot predict slabs ahead, STELAR enables long-term prediction by incorporating latent temporal …
Princeton University（普林斯顿大学）；New York University（纽约大学）
With the severity of the COVID-19 outbreak, we characterize the nature of the growth trajectories of counties in the United States using a novel combination of spectral clustering and the correlation matrix. As the U.S. and the rest of the world are experiencing a severe second wave of infections, the importance of assigning growth membership to counties and understanding the determinants of the growth are increasingly evident. Subsequently, we select the demographic features that are most statistically significant in distinguishing the communities. Lastly, we effectively predict the future gr…
Worldwide 2019 million people have been infected and 4.5 million have lost their lives in the ongoing Covid-19 pandemic. Until vaccines became widely available, precautions and safety measures like wearing masks, physical distancing, avoiding face touching were some of the primary means to curb the spread of virus. Face touching is a compulsive human begavior that can not be prevented without making a continuous consious effort, even then it is inevitable. To address this problem, we have designed a smartwatch-based solution, CovidAlert, that leverages Random Forest algorithm trained on accele…
Recently, the Centers for Disease Control and Prevention (CDC) has worked with other federal agencies to identify counties with increasing coronavirus disease 2019 (COVID-19) incidence (hotspots) and offers support to local health departments to limit the spread of the disease. Understanding the spatio-temporal dynamics of hotspot events is of great importance to support policy decisions and prevent large-scale outbreaks. This paper presents a spatio-temporal Bayesian framework for early detection of COVID-19 hotspots (at the county level) in the United States. We assume both the observed numb…
We use the output of a random forest to define a family of local smoothers with spatially adaptive bandwidth matrices. The smoother inherits the flexibility of the original forest but, since it is a simple, linear smoother, it is very interpretable and it can be used for tasks that would be intractable for the original forest. This includes bias correction, confidence intervals, assessing variable importance and methods for exploring the structure of the forest. We illustrate the method on some synthetic examples and on data related to Covid-19.
Arizona State University（亚利桑那州立大学）；Georgia Institute of Technology（佐治亚理工学院）；Fred Hutchinson Cancer Research Center（弗雷德·哈钦森癌症研究中心）
In this paper, we present an efficient statistical method (denoted as "Adaptive Resources Allocation CUSUM") to robustly and efficiently detect the hotspot with limited sampling resources. Our main idea is to combine the multi-arm bandit (MAB) and change-point detection methods to balance the exploration and exploitation of resource allocation for hotspot detection. Further, a Bayesian weighted update is used to update the posterior distribution of the infection rate. Then, the upper confidence bound (UCB) is used for resource allocation and planning. Finally, CUSUM monitoring statistics to de…
The worldwide spread of coronavirus disease (COVID-19) has become a threatening risk for global public health. It is of great importance to rapidly and accurately screen patients with COVID-19 from community acquired pneumonia (CAP). In this study, a total of 1658 patients with COVID-19 and 1027 patients of CAP underwent thin-section CT. All images were preprocessed to obtain the segmentations of both infections and lung fields, which were used to extract location-specific features. An infection Size Aware Random Forest method (iSARF) was proposed, in which subjects were automated categorized …
Comparative Evaluation of Explainable Machine Learning Versus Linear Regression for Predicting County-Level Lung Cancer Mortality Rate in the United States
University of Tennessee Graduate School（田纳西大学研究生院）
Automated Detection of Persistent Inflammatory Biomarkers in Post-COVID-19 Patients Using Machine Learning Techniques
Era University（埃拉大学）；Era's Lucknow Medical College and Hospital（埃拉克克瑙医学院及医院）；College of Medicine, Kufa University（库法大学医学院）；University of Al-Qadisiyah（卡迪西亚大学）；Liverpool John Moors University（利物浦约翰摩尔大学）
The increase in people's use of mobile messaging services has led to the spread of social engineering attacks like phishing, considering that spam text is one of the main factors in the dissemination of phishing attacks to steal sensitive data such as credit cards and passwords. In addition, rumors and incorrect medical information regarding the COVID-19 pandemic are widely shared on social media leading to people's fear and confusion. Thus, filtering spam content is vital to reduce risks and threats. Previous studies relied on machine learning and deep learning approaches for spam classificat…
