arXiv subjects

Benjamin Shickel

Publications and source records attributed to Benjamin Shickel.

29 records · Page 2Linked to original sources

arXiv2023

Transformers in Healthcare: A Survey

With Artificial Intelligence (AI) increasingly permeating various aspects of society, including healthcare, the adoption of the Transformers neural network architecture is rapidly changing many applications. Transformer is a type of deep learning architecture initially developed to solve general-purpose Natural Language Processing (NLP) tasks and has subsequently been adapted in many fields, including healthcare. In this survey paper, we provide an overview of how this architecture has been adopted to analyze various forms of data, including medical imaging, structured and unstructured Electronic Health Records (EHR), social media, physiological signals, and biomolecular sequences. Those models could help in clinical diagnosis, report generation, data reconstruction, and drug/protein synthesis. We identified relevant studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We also discuss the benefits and limitations of using transformers in healthcare and examine issues such as computational cost, model interpretability, fairness, alignment with human values, ethical implications, and environmental impact.

cs.AI↗

arXiv2023

Computable Phenotypes to Characterize Changing Patient Brain Dysfunction in the Intensive Care Unit

In the United States, more than 5 million patients are admitted annually to ICUs, with ICU mortality of 10%-29% and costs over $82 billion. Acute brain dysfunction status, delirium, is often underdiagnosed or undervalued. This study's objective was to develop automated computable phenotypes for acute brain dysfunction states and describe transitions among brain dysfunction states to illustrate the clinical trajectories of ICU patients. We created two single-center, longitudinal EHR datasets for 48,817 adult patients admitted to an ICU at UFH Gainesville (GNV) and Jacksonville (JAX). We developed algorithms to quantify acute brain dysfunction status including coma, delirium, normal, or death at 12-hour intervals of each ICU admission and to identify acute brain dysfunction phenotypes using continuous acute brain dysfunction status and k-means clustering approach. There were 49,770 admissions for 37,835 patients in UFH GNV dataset and 18,472 admissions for 10,982 patients in UFH JAX dataset. In total, 18% of patients had coma as the worst brain dysfunction status; every 12 hours, around 4%-7% would transit to delirium, 22%-25% would recover, 3%-4% would expire, and 67%-68% would remain in a coma in the ICU. Additionally, 7% of patients had delirium as the worst brain dysfunction status; around 6%-7% would transit to coma, 40%-42% would be no delirium, 1% would expire, and 51%-52% would remain delirium in the ICU. There were three phenotypes: persistent coma/delirium, persistently normal, and transition from coma/delirium to normal almost exclusively in first 48 hours after ICU admission. We developed phenotyping scoring algorithms that determined acute brain dysfunction status every 12 hours while admitted to the ICU. This approach may be useful in developing prognostic and decision-support tools to aid patients and clinicians in decision-making on resource use and escalation of care.

q-bio.QM↗

arXiv2022

Dynamic Predictions of Postoperative Complications from Explainable, Uncertainty-Aware, and Multi-Task Deep Neural Networks

Accurate prediction of postoperative complications can inform shared decisions regarding prognosis, preoperative risk-reduction, and postoperative resource use. We hypothesized that multi-task deep learning models would outperform random forest models in predicting postoperative complications, and that integrating high-resolution intraoperative physiological time series would result in more granular and personalized health representations that would improve prognostication compared to preoperative predictions. In a longitudinal cohort study of 56,242 patients undergoing 67,481 inpatient surgical procedures at a university medical center, we compared deep learning models with random forests for predicting nine common postoperative complications using preoperative, intraoperative, and perioperative patient data. Our study indicated several significant results across experimental settings that suggest the utility of deep learning for capturing more precise representations of patient health for augmented surgical decision support. Multi-task learning improved efficiency by reducing computational resources without compromising predictive performance. Integrated gradients interpretability mechanisms identified potentially modifiable risk factors for each complication. Monte Carlo dropout methods provided a quantitative measure of prediction uncertainty that has the potential to enhance clinical trust. Multi-task learning, interpretability mechanisms, and uncertainty metrics demonstrated potential to facilitate effective clinical implementation.

cs.LG↗

arXiv2021

Multi-Task Prediction of Clinical Outcomes in the Intensive Care Unit using Flexible Multimodal Transformers

Recent deep learning research based on Transformer model architectures has demonstrated state-of-the-art performance across a variety of domains and tasks, mostly within the computer vision and natural language processing domains. While some recent studies have implemented Transformers for clinical tasks using electronic health records data, they are limited in scope, flexibility, and comprehensiveness. In this study, we propose a flexible Transformer-based EHR embedding pipeline and predictive model framework that introduces several novel modifications of existing workflows that capitalize on data attributes unique to the healthcare domain. We showcase the feasibility of our flexible design in a case study in the intensive care unit, where our models accurately predict seven clinical outcomes pertaining to readmission and patient mortality over multiple future time horizons.

cs.LG↗

arXiv2020

Sequential Interpretability: Methods, Applications, and Future Direction for Understanding Deep Learning Models in the Context of Sequential Data

Deep learning continues to revolutionize an ever-growing number of critical application areas including healthcare, transportation, finance, and basic sciences. Despite their increased predictive power, model transparency and human explainability remain a significant challenge due to the "black box" nature of modern deep learning models. In many cases the desired balance between interpretability and performance is predominately task specific. Human-centric domains such as healthcare necessitate a renewed focus on understanding how and why these frameworks are arriving at critical and potentially life-or-death decisions. Given the quantity of research and empirical successes of deep learning for computer vision, most of the existing interpretability research has focused on image processing techniques. Comparatively, less attention has been paid to interpreting deep learning frameworks using sequential data. Given recent deep learning advancements in highly sequential domains such as natural language processing and physiological signal processing, the need for deep sequential explanations is at an all-time high. In this paper, we review current techniques for interpreting deep learning techniques involving sequential data, identify similarities to non-sequential methods, and discuss current limitations and future avenues of sequential interpretability research.

cs.LG↗

arXiv2019

Added Value of Intraoperative Data for Predicting Postoperative Complications: Development and Validation of a MySurgeryRisk Extension

To test the hypothesis that accuracy, discrimination, and precision in predicting postoperative complications improve when using both preoperative and intraoperative data input features versus preoperative data alone. Models that predict postoperative complications often ignore important intraoperative physiological changes. Incorporation of intraoperative physiological data may improve model performance. This retrospective cohort analysis included 52,529 inpatient surgeries at a single institution during a 5 year period. Random forest machine learning models in the validated MySurgeryRisk platform made patient-level predictions for three postoperative complications and mortality during hospital admission using electronic health record data and patient neighborhood characteristics. For each outcome, one model trained with preoperative data alone and one model trained with both preoperative and intraoperative data. Models were compared by accuracy, discrimination (expressed as AUROC), precision (expressed as AUPRC), and reclassification indices (NRI). Machine learning models incorporating both preoperative and intraoperative data had greater accuracy, discrimination, and precision than models using preoperative data alone for predicting all three postoperative complications (intensive care unit length of stay >48 hours, mechanical ventilation >48 hours, and neurological complications including delirium) and in-hospital mortality (accuracy: 88% vs. 77%, AUROC: 0.93 vs. 0.87, AUPRC: 0.21 vs. 0.15). Overall reclassification improvement was 2.9-10.0% for complications and 11.2% for in-hospital mortality. Incorporating both preoperative and intraoperative data significantly increased accuracy, discrimination, and precision for machine learning models predicting postoperative complications.

cs.CY↗

arXiv2019

Automatic Detection and Classification of Cognitive Distortions in Mental Health Text

In cognitive psychology, automatic and self-reinforcing irrational thought patterns are known as cognitive distortions. Left unchecked, patients exhibiting these types of thoughts can become stuck in negative feedback loops of unhealthy thinking, leading to inaccurate perceptions of reality commonly associated with anxiety and depression. In this paper, we present a machine learning framework for the automatic detection and classification of 15 common cognitive distortions in two novel mental health free text datasets collected from both crowdsourcing and a real-world online therapy program. When differentiating between distorted and non-distorted passages, our model achieved a weighted F1 score of 0.88. For classifying distorted passages into one of 15 distortion categories, our model yielded weighted F1 scores of 0.68 in the larger crowdsourced dataset and 0.45 in the smaller online counseling dataset, both of which outperformed random baseline metrics by a large margin. For both tasks, we also identified the most discriminative words and phrases between classes to highlight common thematic elements for improving targeted and therapist-guided mental health treatment. Furthermore, we performed an exploratory analysis using unsupervised content-based clustering and topic modeling algorithms as first efforts towards a data-driven perspective on the thematic relationship between similar cognitive distortions traditionally deemed unique. Finally, we highlight the difficulties in applying mental health-based machine learning in a real-world setting and comment on the implications and benefits of our framework for improving automated delivery of therapeutic treatment in conjunction with traditional cognitive-behavioral therapy.

cs.HC↗

arXiv2019

DeepSOFA: A Continuous Acuity Score for Critically Ill Patients using Clinically Interpretable Deep Learning

Traditional methods for assessing illness severity and predicting in-hospital mortality among critically ill patients require time-consuming, error-prone calculations using static variable thresholds. These methods do not capitalize on the emerging availability of streaming electronic health record data or capture time-sensitive individual physiological patterns, a critical task in the intensive care unit. We propose a novel acuity score framework (DeepSOFA) that leverages temporal measurements and interpretable deep learning models to assess illness severity at any point during an ICU stay. We compare DeepSOFA with SOFA (Sequential Organ Failure Assessment) baseline models using the same model inputs and find that at any point during an ICU admission, DeepSOFA yields significantly more accurate predictions of in-hospital mortality. A DeepSOFA model developed in a public database and validated in a single institutional cohort had a mean AUC for the entire ICU stay of 0.90 (95% CI 0.90-0.91) compared with baseline SOFA models with mean AUC 0.79 (95% CI 0.79-0.80) and 0.85 (95% CI 0.85-0.86). Deep models are well-suited to identify ICU patients in need of life-saving interventions prior to the occurrence of an unexpected adverse event and inform shared decision-making processes among patients, providers, and families regarding goals of care and optimal resource utilization.

cs.LG↗

arXiv2018

The Intelligent ICU Pilot Study: Using Artificial Intelligence Technology for Autonomous Patient Monitoring

Currently, many critical care indices are repetitively assessed and recorded by overburdened nurses, e.g. physical function or facial pain expressions of nonverbal patients. In addition, many essential information on patients and their environment are not captured at all, or are captured in a non-granular manner, e.g. sleep disturbance factors such as bright light, loud background noise, or excessive visitations. In this pilot study, we examined the feasibility of using pervasive sensing technology and artificial intelligence for autonomous and granular monitoring of critically ill patients and their environment in the Intensive Care Unit (ICU). As an exemplar prevalent condition, we also characterized delirious and non-delirious patients and their environment. We used wearable sensors, light and sound sensors, and a high-resolution camera to collected data on patients and their environment. We analyzed collected data using deep learning and statistical analysis. Our system performed face detection, face recognition, facial action unit detection, head pose detection, facial expression recognition, posture recognition, actigraphy analysis, sound pressure and light level detection, and visitation frequency detection. We were able to detect patient's face (Mean average precision (mAP)=0.94), recognize patient's face (mAP=0.80), and their postures (F1=0.94). We also found that all facial expressions, 11 activity features, visitation frequency during the day, visitation frequency during the night, light levels, and sound pressure levels during the night were significantly different between delirious and non-delirious patients (p-value<0.05). In summary, we showed that granular and autonomous monitoring of critically ill patients and their environment is feasible and can be used for characterizing critical care conditions and related environment factors.

cs.HC↗

arXiv2018

Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis

The past decade has seen an explosion in the amount of digital information stored in electronic health records (EHR). While primarily designed for archiving patient clinical information and administrative healthcare tasks, many researchers have found secondary use of these records for various clinical informatics tasks. Over the same period, the machine learning community has seen widespread advances in deep learning techniques, which also have been successfully applied to the vast amount of EHR data. In this paper, we review these deep EHR systems, examining architectures, technical aspects, and clinical applications. We also identify shortcomings of current techniques and discuss avenues of future research for EHR-based deep learning.

cs.LG↗

arXiv2017

Hashtag Healthcare: From Tweets to Mental Health Journals Using Deep Transfer Learning

As the popularity of social media platforms continues to rise, an ever-increasing amount of human communication and self- expression takes place online. Most recent research has focused on mining social media for public user opinion about external entities such as product reviews or sentiment towards political news. However, less attention has been paid to analyzing users' internalized thoughts and emotions from a mental health perspective. In this paper, we quantify the semantic difference between public Tweets and private mental health journals used in online cognitive behavioral therapy. We will use deep transfer learning techniques for analyzing the semantic gap between the two domains. We show that for the task of emotional valence prediction, social media can be successfully harnessed to create more accurate, robust, and personalized mental health models. Our results suggest that the semantic gap between public and private self-expression is small, and that utilizing the abundance of available social media is one way to overcome the small sample sizes of mental health data, which are commonly limited by availability and privacy concerns.

cs.CL↗