Thomas Kannampallil

Hanyang Liu, Sunny S. Lou, Benjamin C. Warner et al.

Burnout is a significant public health concern affecting nearly half of the healthcare workforce. This paper presents the first end-to-end deep learning framework for predicting physician burnout based on electronic health record (EHR) activity logs, digital traces of physician work activities that are available in any EHR system. In contrast to prior approaches that exclusively relied on surveys for burnout measurement, our framework directly learns deep representations of physician behaviors from large-scale clinician activity logs to predict burnout. We propose the Hierarchical burnout Prediction based on Activity Logs (HiPAL), featuring a pre-trained time-dependent activity embedding mechanism tailored for activity logs and a hierarchical predictive model, which mirrors the natural hierarchical structure of clinician activity logs and captures physicians' evolving burnout risk at both short-term and long-term levels. To utilize the large amount of unlabeled activity logs, we propose a semi-supervised framework that learns to transfer knowledge extracted from unlabeled clinician activities to the HiPAL-based prediction model. The experiment on over 15 million clinician activity logs collected from the EHR at a large academic medical center demonstrates the advantages of our proposed framework in predictive performance of physician burnout and training efficiency over state-of-the-art approaches.

Benjamin C. Warner, Ziqi Xu, Simon Haroutounian et al.

Survey data can contain a high number of features while having a comparatively low quantity of examples. Machine learning models that attempt to predict outcomes from survey data under these conditions can overfit and result in poor generalizability. One remedy to this issue is feature selection, which attempts to select an optimal subset of features to learn upon. A relatively unexplored source of information in the feature selection process is the usage of textual names of features, which may be semantically indicative of which features are relevant to a target outcome. The relationships between feature names and target names can be evaluated using language models (LMs) to produce semantic textual similarity (STS) scores, which can then be used to select features. We examine the performance using STS to select features directly and in the minimal-redundancy-maximal-relevance (mRMR) algorithm. The performance of STS as a feature selection metric is evaluated against preliminary survey data collected as a part of a clinical study on persistent post-surgical pain (PPSP). The results suggest that features selected with STS can result in higher performance models compared to traditional feature selection algorithms.

Benjamin C. Warner, Thomas Kannampallil, Seunghwan Kim

EHR audit logs are a highly granular stream of events that capture clinician activities, and is a significant area of interest for research in characterizing clinician workflow on the electronic health record (EHR). Existing techniques to measure the complexity of workflow through EHR audit logs (audit logs) involve time- or frequency-based cross-sectional aggregations that are unable to capture the full complexity of a EHR session. We briefly evaluate the usage of transformer-based tabular language model (tabular LM) in measuring the entropy or disorderedness of action sequences within workflow and release the evaluated models publicly.

Charles Alba, Bing Xue, Joanna Abraham et al.

Clinical notes recorded during a patient's perioperative journey holds immense informational value. Advances in large language models (LLMs) offer opportunities for bridging this gap. Using 84,875 pre-operative notes and its associated surgical cases from 2018 to 2021, we examine the performance of LLMs in predicting six postoperative risks using various fine-tuning strategies. Pretrained LLMs outperformed traditional word embeddings by an absolute AUROC of 38.3% and AUPRC of 33.2%. Self-supervised fine-tuning further improved performance by 3.2% and 1.5%. Incorporating labels into training further increased AUROC by 1.8% and AUPRC by 2%. The highest performance was achieved with a unified foundation model, with improvements of 3.6% for AUROC and 2.6% for AUPRC compared to self-supervision, highlighting the foundational capabilities of LLMs in predicting postoperative risks, which could be potentially beneficial when deployed for perioperative care

Sayantan Kumar, Sean Yu, Andrew Michelson et al.

Objective: We aimed to develop and validate a novel multimodal framework HiMAL (Hierarchical, Multi-task Auxiliary Learning) framework, for predicting cognitive composite functions as auxiliary tasks that estimate the longitudinal risk of transition from Mild Cognitive Impairment (MCI) to Alzheimer Disease (AD). Methods: HiMAL utilized multimodal longitudinal visit data including imaging features, cognitive assessment scores, and clinical variables from MCI patients in the Alzheimer Disease Neuroimaging Initiative (ADNI) dataset, to predict at each visit if an MCI patient will progress to AD within the next 6 months. Performance of HiMAL was compared with state-of-the-art single-task and multi-task baselines using area under the receiver operator curve (AUROC) and precision recall curve (AUPRC) metrics. An ablation study was performed to assess the impact of each input modality on model performance. Additionally, longitudinal explanations regarding risk of disease progression were provided to interpret the predicted cognitive decline. Results: Out of 634 MCI patients (mean [IQR] age : 72.8 [67-78], 60% men), 209 (32%) progressed to AD. HiMAL showed better prediction performance compared to all single-modality singe-task baselines (AUROC = 0.923 [0.915-0.937]; AUPRC= 0.623 [0.605-0.644]; all p<0.05). Ablation analysis highlighted that imaging and cognition scores with maximum contribution towards prediction of disease progression. Discussion: Clinically informative model explanations anticipate cognitive decline 6 months in advance, aiding clinicians in future disease progression assessment. HiMAL relies on routinely collected EHR variables for proximal (6 months) prediction of AD onset, indicating its translational potential for point-of-care monitoring and managing of high-risk patients.

Junbo Shen, Bing Xue, Thomas Kannampallil et al.

Early detection of surgical complications allows for timely therapy and proactive risk mitigation. Machine learning (ML) can be leveraged to identify and predict patient risks for postoperative complications. We developed and validated the effectiveness of predicting postoperative complications using a novel surgical Variational Autoencoder (surgVAE) that uncovers intrinsic patterns via cross-task and cross-cohort presentation learning. This retrospective cohort study used data from the electronic health records of adult surgical patients over four years (2018 - 2021). Six key postoperative complications for cardiac surgery were assessed: acute kidney injury, atrial fibrillation, cardiac arrest, deep vein thrombosis or pulmonary embolism, blood transfusion, and other intraoperative cardiac events. We compared prediction performances of surgVAE against widely-used ML models and advanced representation learning and generative models under 5-fold cross-validation. 89,246 surgeries (49% male, median (IQR) age: 57 (45-69)) were included, with 6,502 in the targeted cardiac surgery cohort (61% male, median (IQR) age: 60 (53-70)). surgVAE demonstrated superior performance over existing ML solutions across all postoperative complications of cardiac surgery patients, achieving macro-averaged AUPRC of 0.409 and macro-averaged AUROC of 0.831, which were 3.4% and 3.7% higher, respectively, than the best alternative method (by AUPRC scores). Model interpretation using Integrated Gradients highlighted key risk factors based on preoperative variable importance. surgVAE showed excellent discriminatory performance for predicting postoperative complications and addressing the challenges of data complexity, small cohort sizes, and low-frequency positive events. surgVAE enables data-driven predictions of patient risks and prognosis while enhancing the interpretability of patient risk profiles.

Sayantan Kumar, Sean C. Yu, Thomas Kannampallil et al.

Complex deep learning models show high prediction tasks in various clinical prediction tasks but their inherent complexity makes it more challenging to explain model predictions for clinicians and healthcare providers. Existing research on explainability of deep learning models in healthcare have two major limitations: using post-hoc explanations and using raw clinical variables as units of explanation, both of which are often difficult for human interpretation. In this work, we designed a self-explaining deep learning framework using the expert-knowledge driven clinical concepts or intermediate features as units of explanation. The self-explaining nature of our proposed model comes from generating both explanations and predictions within the same architectural framework via joint training. We tested our proposed approach on a publicly available Electronic Health Records (EHR) dataset for predicting patient mortality in the ICU. In order to analyze the performance-interpretability trade-off, we compared our proposed model with a baseline having the same set-up but without the explanation components. Experimental results suggest that adding explainability components to a deep learning framework does not impact prediction performance and the explanations generated by the model can provide insights to the clinicians to understand the possible reasons behind patient mortality.

Hanyang Liu, Michael C. Montana, Dingwen Li et al.

We present an end-to-end model using streaming physiological time series to predict near-term risk for hypoxemia, a rare, but life-threatening condition known to cause serious patient harm during surgery. Inspired by the fact that a hypoxemia event is defined based on a future sequence of low SpO2 (i.e., blood oxygen saturation) instances, we propose the hybrid inference network (hiNet) that makes hybrid inference on both future low SpO2 instances and hypoxemia outcomes. hiNet integrates 1) a joint sequence autoencoder that simultaneously optimizes a discriminative decoder for label prediction, and 2) two auxiliary decoders trained for data reconstruction and forecast, which seamlessly learn contextual latent representations that capture the transition from present states to future states. All decoders share a memory-based encoder that helps capture the global dynamics of patient measurement. For a large surgical cohort of 72,081 surgeries at a major academic medical center, our model outperforms strong baselines including the model used by the state-of-the-art hypoxemia prediction system. With its capability to make real-time predictions of near-term hypoxemic at clinically acceptable alarm rates, hiNet shows promise in improving clinical decision making and easing burden of perioperative care.