arXiv subjects

Leo Anthony Celi

Publications and source records attributed to Leo Anthony Celi.

72 records · Page 4Linked to original sources

arXiv2021

Developing and validating multi-modal models for mortality prediction in COVID-19 patients: a multi-center retrospective study

The unprecedented global crisis brought about by the COVID-19 pandemic has sparked numerous efforts to create predictive models for the detection and prognostication of SARS-CoV-2 infections with the goal of helping health systems allocate resources. Machine learning models, in particular, hold promise for their ability to leverage patient clinical information and medical images for prediction. However, most of the published COVID-19 prediction models thus far have little clinical utility due to methodological flaws and lack of appropriate validation. In this paper, we describe our methodology to develop and validate multi-modal models for COVID-19 mortality prediction using multi-center patient data. The models for COVID-19 mortality prediction were developed using retrospective data from Madrid, Spain (N=2547) and were externally validated in patient cohorts from a community hospital in New Jersey, USA (N=242) and an academic center in Seoul, Republic of Korea (N=336). The models we developed performed differently across various clinical settings, underscoring the need for a guided strategy when employing machine learning for clinical decision-making. We demonstrated that using features from both the structured electronic health records and chest X-ray imaging data resulted in better 30-day-mortality prediction performance across all three datasets (areas under the receiver operating characteristic curves: 0.85 (95% confidence interval: 0.83-0.87), 0.76 (0.70-0.82), and 0.95 (0.92-0.98)). We discuss the rationale for the decisions made at every step in developing the models and have made our code available to the research community. We employed the best machine learning practices for clinical model development. Our goal is to create a toolkit that would assist investigators and organizations in building multi-modal models for prediction, classification and/or optimization.

cs.LG↗

arXiv2021

Reading Race: AI Recognises Patient's Racial Identity In Medical Images

Background: In medical imaging, prior studies have demonstrated disparate AI performance by race, yet there is no known correlation for race on medical imaging that would be obvious to the human expert interpreting the images. Methods: Using private and public datasets we evaluate: A) performance quantification of deep learning models to detect race from medical images, including the ability of these models to generalize to external environments and across multiple imaging modalities, B) assessment of possible confounding anatomic and phenotype population features, such as disease distribution and body habitus as predictors of race, and C) investigation into the underlying mechanism by which AI models can recognize race. Findings: Standard deep learning models can be trained to predict race from medical images with high performance across multiple imaging modalities. Our findings hold under external validation conditions, as well as when models are optimized to perform clinically motivated tasks. We demonstrate this detection is not due to trivial proxies or imaging-related surrogate covariates for race, such as underlying disease distribution. Finally, we show that performance persists over all anatomical regions and frequency spectrum of the images suggesting that mitigation efforts will be challenging and demand further study. Interpretation: We emphasize that model ability to predict self-reported race is itself not the issue of importance. However, our findings that AI can trivially predict self-reported race -- even from corrupted, cropped, and noised medical images -- in a setting where clinical experts cannot, creates an enormous risk for all model deployments in medical imaging: if an AI model secretly used its knowledge of self-reported race to misclassify all Black patients, radiologists would not be able to tell using the same data the model has access to.

cs.CV↗

arXiv2021

Prediction of Blood Lactate Values in Critically Ill Patients: A Retrospective Multi-center Cohort Study

Purpose. Elevations in initially obtained serum lactate levels are strong predictors of mortality in critically ill patients. Identifying patients whose serum lactate levels are more likely to increase can alert physicians to intensify care and guide them in the frequency of tending the blood test. We investigate whether machine learning models can predict subsequent serum lactate changes. Methods. We investigated serum lactate change prediction using the MIMIC-III and eICU-CRD datasets in internal as well as external validation of the eICU cohort on the MIMIC-III cohort. Three subgroups were defined based on the initial lactate levels: i) normal group (<2 mmol/L), ii) mild group (2-4 mmol/L), and iii) severe group (>4 mmol/L). Outcomes were defined based on increase or decrease of serum lactate levels between the groups. We also performed sensitivity analysis by defining the outcome as lactate change of >10% and furthermore investigated the influence of the time interval between subsequent lactate measurements on predictive performance. Results. The LSTM models were able to predict deterioration of serum lactate values of MIMIC-III patients with an AUC of 0.77 (95% CI 0.762-0.771) for the normal group, 0.77 (95% CI 0.768-0.772) for the mild group, and 0.85 (95% CI 0.840-0.851) for the severe group, with a slightly lower performance in the external validation. Conclusion. The LSTM demonstrated good discrimination of patients who had deterioration in serum lactate levels. Clinical studies are needed to evaluate whether utilization of a clinical decision support tool based on these results could positively impact decision-making and patient outcomes.

q-bio.QM↗

arXiv2021

Predicting Hyperkalemia in the ICU and Evaluation of Generalizability and Interpretability

Hyperkalemia is a potentially life-threatening condition that can lead to fatal arrhythmias. Early identification of high risk patients can inform clinical care to mitigate the risk. While hyperkalemia is often a complication of acute kidney injury (AKI), it also occurs in the absence of AKI. We developed predictive models to identify intensive care unit (ICU) patients at risk of developing hyperkalemia by using the Medical Information Mart for Intensive Care (MIMIC) and the eICU Collaborative Research Database (eICU-CRD). Our methodology focused on building multiple models, optimizing for interpretability through model selection, and simulating various clinical scenarios. In order to determine if our models perform accurately on patients with and without AKI, we evaluated the following clinical cases: (i) predicting hyperkalemia after AKI within 14 days of ICU admission, (ii) predicting hyperkalemia within 14 days of ICU admission regardless of AKI status, and compared different lead times for (i) and (ii). Both clinical scenarios were modeled using logistic regression (LR), random forest (RF), and XGBoost. Using observations from the first day in the ICU, our models were able to predict hyperkalemia with an AUC of (i) 0.79, 0.81, 0.81 and (ii) 0.81, 0.85, 0.85 for LR, RF, and XGBoost respectively. We found that 4 out of the top 5 features were consistent across the models. AKI stage was significant in the models that included all patients with or without AKI, but not in the models which only included patients with AKI. This suggests that while AKI is important for hyperkalemia, the specific stage of AKI may not be as important. Our findings require further investigation and confirmation.

cs.LG↗

arXiv2021

Identifying Decision Points for Safe and Interpretable Reinforcement Learning in Hypotension Treatment

Many batch RL health applications first discretize time into fixed intervals. However, this discretization both loses resolution and forces a policy computation at each (potentially fine) interval. In this work, we develop a novel framework to compress continuous trajectories into a few, interpretable decision points --places where the batch data support multiple alternatives. We apply our approach to create recommendations from a cohort of hypotensive patients dataset. Our reduced state space results in faster planning and allows easy inspection by a clinical expert.

cs.LG↗

arXiv2021

Acronym Identification and Disambiguation Shared Tasks for Scientific Document Understanding

Acronyms are the short forms of longer phrases and they are frequently used in writing, especially scholarly writing, to save space and facilitate the communication of information. As such, every text understanding tool should be capable of recognizing acronyms in text (i.e., acronym identification) and also finding their correct meaning (i.e., acronym disambiguation). As most of the prior works on these tasks are restricted to the biomedical domain and use unsupervised methods or models trained on limited datasets, they fail to perform well for scientific document understanding. To push forward research in this direction, we have organized two shared task for acronym identification and acronym disambiguation in scientific documents, named AI@SDU and AD@SDU, respectively. The two shared tasks have attracted 52 and 43 participants, respectively. While the submitted systems make substantial improvements compared to the existing baselines, there are still far from the human-level performance. This paper reviews the two shared tasks and the prominent participating systems for each of them.

cs.CL↗

arXiv2020

Real-time Prediction of COVID-19 related Mortality using Electronic Health Records

Coronavirus Disease 2019 (COVID-19) is an emerging respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with rapid human-to-human transmission and a high case fatality rate particularly in older patients. Due to the exponential growth of infections, many healthcare systems across the world are under pressure to care for increasing amounts of at-risk patients. Given the high number of infected patients, identifying patients with the highest mortality risk early is critical to enable effective intervention and optimal prioritisation of care. Here, we present the COVID-19 Early Warning System (CovEWS), a clinical risk scoring system for assessing COVID-19 related mortality risk. CovEWS provides continuous real-time risk scores for individual patients with clinically meaningful predictive performance up to 192 hours (8 days) in advance, and is automatically derived from patients' electronic health records (EHRs) using machine learning. We trained and evaluated CovEWS using de-identified data from a cohort of 66430 COVID-19 positive patients seen at over 69 healthcare institutions in the United States (US), Australia, Malaysia and India amounting to an aggregated total of over 2863 years of patient observation time. On an external test cohort of 5005 patients, CovEWS predicts COVID-19 related mortality from $78.8\%$ ($95\%$ confidence interval [CI]: $76.0$, $84.7\%$) to $69.4\%$ ($95\%$ CI: $57.6, 75.2\%$) specificity at a sensitivity greater than $95\%$ between respectively 1 and 192 hours prior to observed mortality events - significantly outperforming existing generic and COVID-19 specific clinical risk scores. CovEWS could enable clinicians to intervene at an earlier stage, and may therefore help in preventing or mitigating COVID-19 related mortality.

stat.AP↗

arXiv2020

Interpretable Off-Policy Evaluation in Reinforcement Learning by Highlighting Influential Transitions

Off-policy evaluation in reinforcement learning offers the chance of using observational data to improve future outcomes in domains such as healthcare and education, but safe deployment in high stakes settings requires ways of assessing its validity. Traditional measures such as confidence intervals may be insufficient due to noise, limited data and confounding. In this paper we develop a method that could serve as a hybrid human-AI system, to enable human experts to analyze the validity of policy evaluation estimates. This is accomplished by highlighting observations in the data whose removal will have a large effect on the OPE estimate, and formulating a set of rules for choosing which ones to present to domain experts for validation. We develop methods to compute exactly the influence functions for fitted Q-evaluation with two different function classes: kernel-based and linear least squares, as well as importance sampling methods. Experiments on medical simulations and real-world intensive care unit data demonstrate that our method can be used to identify limitations in the evaluation process and make evaluation more robust.

cs.LG↗

arXiv2020

A Corpus for Detecting High-Context Medical Conditions in Intensive Care Patient Notes Focusing on Frequently Readmitted Patients

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

cs.CL↗

arXiv2020

Ensembles of Locally Independent Prediction Models

Ensembles depend on diversity for improved performance. Many ensemble training methods, therefore, attempt to optimize for diversity, which they almost always define in terms of differences in training set predictions. In this paper, however, we demonstrate the diversity of predictions on the training set does not necessarily imply diversity under mild covariate shift, which can harm generalization in practical settings. To address this issue, we introduce a new diversity metric and associated method of training ensembles of models that extrapolate differently on local patches of the data manifold. Across a variety of synthetic and real-world tasks, we find that our method improves generalization and diversity in qualitatively novel ways, especially under data limits and covariate shift.

cs.LG↗

arXiv2020

Interpretable Machine Learning Model for Early Prediction of Mortality in Elderly Patients with Multiple Organ Dysfunction Syndrome (MODS): a Multicenter Retrospective Study and Cross Validation

Background: Elderly patients with MODS have high risk of death and poor prognosis. The performance of current scoring systems assessing the severity of MODS and its mortality remains unsatisfactory. This study aims to develop an interpretable and generalizable model for early mortality prediction in elderly patients with MODS. Methods: The MIMIC-III, eICU-CRD and PLAGH-S databases were employed for model generation and evaluation. We used the eXtreme Gradient Boosting model with the SHapley Additive exPlanations method to conduct early and interpretable predictions of patients' hospital outcome. Three types of data source combinations and five typical evaluation indexes were adopted to develop a generalizable model. Findings: The interpretable model, with optimal performance developed by using MIMIC-III and eICU-CRD datasets, was separately validated in MIMIC-III, eICU-CRD and PLAGH-S datasets (no overlapping with training set). The performances of the model in predicting hospital mortality as validated by the three datasets were: AUC of 0.858, sensitivity of 0.834 and specificity of 0.705; AUC of 0.849, sensitivity of 0.763 and specificity of 0.784; and AUC of 0.838, sensitivity of 0.882 and specificity of 0.691, respectively. Comparisons of AUC between this model and baseline models with MIMIC-III dataset validation showed superior performances of this model; In addition, comparisons in AUC between this model and commonly used clinical scores showed significantly better performance of this model. Interpretation: The interpretable machine learning model developed in this study using fused datasets with large sample sizes was robust and generalizable. This model outperformed the baseline models and several clinical scores for early prediction of mortality in elderly ICU patients. The interpretative nature of this model provided clinicians with the ranking of mortality risk features.

physics.med-ph↗

arXiv2019

Modeling Mistrust in End-of-Life Care

In this work, we characterize the doctor-patient relationship using a machine learning-derived trust score. We show that this score has statistically significant racial associations, and that by modeling trust directly we find stronger disparities in care than by stratifying on race. We further demonstrate that mistrust is indicative of worse outcomes, but is only weakly associated with physiologically-created severity scores. Finally, we describe sentiment analysis experiments indicating patients with higher levels of mistrust have worse experiences and interactions with their caregivers. This work is a step towards measuring fairer machine learning in the healthcare domain.

cs.AI↗

arXiv2019

Withholding or withdrawing invasive interventions may not accelerate time to death among dying ICU patients

We considered observational data available from the MIMIC-III open-access ICU database and collected within a study period between year 2002 up to 2011. If a patient had multiple admissions to the ICU during the 30 days before death, only the first stay was analyzed, leading to a final set of 6,436 unique ICU admissions during the study period. We tested two hypotheses: (i) administration of invasive intervention during the ICU stay immediately preceding end-of-life would decrease over the study time period and (ii) time-to-death from ICU admission would also decrease, due to the decrease in invasive intervention administration. To investigate the latter hypothesis, we performed a subgroups analysis by considering patients with lowest and highest severity. To do so, we stratified the patients based on their SAPS I scores, and we considered patients within the first and the third tertiles of the score. We then assessed differences in trends within these groups between years 2002-05 vs. 2008-11. Comparing the period 2002-2005 vs. 2008-2011, we found a reduction in endotracheal ventilation among patients who died within 30 days of ICU admission (120.8 vs. 68.5 hours for the lowest severity patients, p<0.001; 47.7 vs. 46.0 hours for the highest severity patients, p=0.004). This is explained in part by an increase in the use of non-invasive ventilation. Comparing the period 2002-2005 vs. 2008-2011, we found a reduction in the use of vasopressors and inotropes among patients with the lowest severity who died within 30 days of ICU admission (41.8 vs. 36.2 hours, p<0.001) but not among those with the highest severity. Despite a reduction in the use of invasive interventions, we did not find a reduction in the time to death between 2002-2005 vs. 2008-2011 (7.8 days vs. 8.2 days for the lowest severity patients, p=0.32; 2.1 days vs. 2.0 days for the highest severity patients, p=0.74).

cs.CY↗

arXiv2018

Racial Disparities and Mistrust in End-of-Life Care

There are established racial disparities in healthcare, including during end-of-life care, when poor communication and trust can lead to suboptimal outcomes for patients and their families. In this work, we find that racial disparities which have been reported in existing literature are also present in the MIMIC-III database. We hypothesize that one underlying cause of this disparity is due to mistrust between patient and caregivers, and we develop multiple possible trust metric proxies (using coded interpersonal variables and clinical notes) to measure this phenomenon more directly. These metrics show even stronger disparities in end-of-life care than race does, and they also tend to demonstrate statistically significant higher levels of mistrust for black patients than white ones. Finally, we demonstrate that these metrics improve performance on three clinical tasks: in-hospital mortality, discharge against medical advice (AMA) and modified care status (e.g., DNR, DNI, etc.).

stat.AP↗

arXiv2018

Evaluating Reinforcement Learning Algorithms in Observational Health Settings

Much attention has been devoted recently to the development of machine learning algorithms with the goal of improving treatment policies in healthcare. Reinforcement learning (RL) is a sub-field within machine learning that is concerned with learning how to make sequences of decisions so as to optimize long-term effects. Already, RL algorithms have been proposed to identify decision-making strategies for mechanical ventilation, sepsis management and treatment of schizophrenia. However, before implementing treatment policies learned by black-box algorithms in high-stakes clinical decision problems, special care must be taken in the evaluation of these policies. In this document, our goal is to expose some of the subtleties associated with evaluating RL algorithms in healthcare. We aim to provide a conceptual starting point for clinical and computational researchers to ask the right questions when designing and evaluating algorithms for new ways of treating patients. In the following, we describe how choices about how to summarize a history, variance of statistical estimators, and confounders in more ad-hoc measures can result in unreliable, even misleading estimates of the quality of a treatment policy. We also provide suggestions for mitigating these effects---for while there is much promise for mining observational health data to uncover better treatment policies, evaluation must be performed thoughtfully.

cs.LG↗

arXiv2017

Continuous State-Space Models for Optimal Sepsis Treatment - a Deep Reinforcement Learning Approach

Sepsis is a leading cause of mortality in intensive care units (ICUs) and costs hospitals billions annually. Treating a septic patient is highly challenging, because individual patients respond very differently to medical interventions and there is no universally agreed-upon treatment for sepsis. Understanding more about a patient's physiological state at a given time could hold the key to effective treatment policies. In this work, we propose a new approach to deduce optimal treatment policies for septic patients by using continuous state-space models and deep reinforcement learning. Learning treatment policies over continuous spaces is important, because we retain more of the patient's physiological information. Our model is able to learn clinically interpretable treatment policies, similar in important aspects to the treatment policies of physicians. Evaluating our algorithm on past ICU patient data, we find that our model could reduce patient mortality in the hospital by up to 3.6% over observed clinical policies, from a baseline mortality of 13.7%. The learned treatment policies could be used to aid intensive care clinicians in medical decision making and improve the likelihood of patient survival.

cs.LG↗

arXiv2017

Clinical Intervention Prediction and Understanding using Deep Networks

Real-time prediction of clinical interventions remains a challenge within intensive care units (ICUs). This task is complicated by data sources that are noisy, sparse, heterogeneous and outcomes that are imbalanced. In this paper, we integrate data from all available ICU sources (vitals, labs, notes, demographics) and focus on learning rich representations of this data to predict onset and weaning of multiple invasive interventions. In particular, we compare both long short-term memory networks (LSTM) and convolutional neural networks (CNN) for prediction of five intervention tasks: invasive ventilation, non-invasive ventilation, vasopressors, colloid boluses, and crystalloid boluses. Our predictions are done in a forward-facing manner to enable "real-time" performance, and predictions are made with a six hour gap time to support clinically actionable planning. We achieve state-of-the-art results on our predictive tasks using deep architectures. We explore the use of feature occlusion to interpret LSTM models, and compare this to the interpretability gained from examining inputs that maximally activate CNN outputs. We show that our models are able to significantly outperform baselines in intervention prediction, and provide insight into model learning, which is crucial for the adoption of such models in practice.

cs.LG↗

arXiv2017

Comparing Rule-Based and Deep Learning Models for Patient Phenotyping

Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We assess the performance of deep learning algorithms and compare them with classical NLP approaches. Materials and Methods: We compare convolutional neural networks (CNNs), n-gram models, and approaches based on cTAKES that extract pre-defined medical concepts from clinical notes and use them to predict patient phenotypes. The performance is tested on 10 different phenotyping tasks using 1,610 discharge summaries extracted from the MIMIC-III database. Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our model having an F1-score up to 37 points higher than alternative approaches. We additionally assess the interpretability of our model by presenting a method that extracts the most salient phrases for a particular prediction. Conclusion: We show that NLP methods based on deep learning improve the performance of patient phenotyping. Our CNN-based algorithm automatically learns the phrases associated with each patient phenotype. As such, it reduces the annotation complexity for clinical domain experts, who are normally required to develop task-specific annotation rules and identify relevant phrases. Our method performs well in terms of both performance and interpretability, which indicates that deep learning is an effective approach to patient phenotyping based on clinicians' notes.

cs.CL↗