Faculty Bibliography

INTRODUCTION/UNASSIGNED:Alzheimer's disease (AD) and Lewy body disease (LBD) are the two most common neurodegenerative dementias and can occur in combination (AD+LBD). Due to overlapping biomarkers and symptoms, clinical differentiation of these subtypes could be difficult. However, it is unclear how the magnitude of diagnostic uncertainty varies across dementia spectra and demographic variables. We aimed to compare clinical diagnosis and post-mortem autopsy-confirmed pathological results to assess the clinical subtype diagnosis quality across these factors. METHODS/UNASSIGNED:We studied data of 1,920 participants recorded by the National Alzheimer's Coordinating Center from 2005 to 2019. Selection criteria included autopsy-based neuropathological assessments for AD and LBD, and the initial visit with Clinical Dementia Rating (CDR) stage of normal, mild cognitive impairment, or mild dementia. Longitudinally, we analyzed the first visit at each subsequent CDR stage. This analysis included positive predictive values, specificity, sensitivity and false negative rates of clinical diagnosis, as well as disparities by sex, race, age, and education. If autopsy-confirmed AD and/or LBD was missed in the clinic, the alternative clinical diagnosis was analyzed. FINDINGS/UNASSIGNED:In our findings, clinical diagnosis of AD+LBD had poor sensitivities. Over 61% of participants with autopsy-confirmed AD+LBD were diagnosed clinically as AD. Clinical diagnosis of AD had a low sensitivity at the early dementia stage and low specificities at all stages. Among participants diagnosed as AD in the clinic, over 32% had concurrent LBD neuropathology at autopsy. Among participants diagnosed as LBD, 32% to 54% revealed concurrent autopsy-confirmed AD pathology. When three subtypes were missed by clinicians, "No cognitive impairment" and "primary progressive aphasia or behavioral variant frontotemporal dementia" were the leading primary etiologic clinical diagnoses. With increasing dementia stages, the clinical diagnosis accuracy of black participants became significantly worse than other races, and diagnosis quality significantly improved for males but not females. DISCUSSION/UNASSIGNED:These findings demonstrate that clinical diagnosis of AD, LBD, and AD+LBD are inaccurate and suffer from significant disparities on race and sex. They provide important implications for clinical management, anticipatory guidance, trial enrollment and applicability of potential therapies for AD, and promote research into better biomarker-based assessment of LBD pathology.

Early diagnosis of Alzheimer's disease plays a pivotal role in patient care and clinical trials. In this study, we have developed a new approach based on 3D deep convolutional neural networks to accurately differentiate mild Alzheimer's disease dementia from mild cognitive impairment and cognitively normal individuals using structural MRIs. For comparison, we have built a reference model based on the volumes and thickness of previously reported brain regions that are known to be implicated in disease progression. We validate both models on an internal held-out cohort from The Alzheimer's Disease Neuroimaging Initiative (ADNI) and on an external independent cohort from The National Alzheimer's Coordinating Center (NACC). The deep-learning model is accurate, achieved an area-under-the-curve (AUC) of 85.12 when distinguishing between cognitive normal subjects and subjects with either MCI or mild Alzheimer's dementia. In the more challenging task of detecting MCI, it achieves an AUC of 62.45. It is also significantly faster than the volume/thickness model in which the volumes and thickness need to be extracted beforehand. The model can also be used to forecast progression: subjects with mild cognitive impairment misclassified as having mild Alzheimer's disease dementia by the model were faster to progress to dementia over time. An analysis of the features learned by the proposed model shows that it relies on a wide range of regions associated with Alzheimer's disease. These findings suggest that deep neural networks can automatically learn to identify imaging biomarkers that are predictive of Alzheimer's disease, and leverage them to achieve accurate early detection of the disease.

PURPOSE/OBJECTIVE:Increasingly complex MRI studies and variable series naming conventions reveal limitations of rule-based image routing, especially in health systems with multiple scanners and sites. Accurate methods to identify series based on image content would aid post-processing and PACS viewing. Recent deep/machine learning efforts classify 5-8 basic brain MR sequences. We present an ensemble model combining a convolutional neural network and a random forest classifier to differentiate 25 brain sequences and image orientation. METHODS:Series were grouped by descriptions into 25 sequences and 4 orientations. Dataset A, obtained from our institution, was divided into training (16,828 studies; 48,512 series; 112,028 images), validation (4746 studies; 16,612 series; 26,222 images) and test sets (6348 studies; 58,705 series; 3,314,018 images). Dataset B, obtained from a separate hospital, was used for out-of-domain external validation (1252 studies; 2150 series; 234,944 images). We developed an ensemble model combining a 2D convolutional neural network with a custom multi-task learning architecture and random forest classifier trained on DICOM metadata to classify sequence and orientation by series. RESULTS:The neural network, random forest, and ensemble achieved 95%, 97%, and 98% overall sequence accuracy on dataset A, and 98%, 99%, and 99% accuracy on dataset B, respectively. All models achieved > 99% orientation accuracy on both datasets. CONCLUSION/CONCLUSIONS:The ensemble model for series identification accommodates the complexity of brain MRI studies in state-of-the-art clinical practice. Expanding on previous work demonstrating proof-of-concept, our approach is more comprehensive with greater sequence diversity and orientation classification.

Image-based analysis as a method for mutation detection can be advantageous in settings when tumor tissue is limited or unavailable for direct testing. Here, we utilize two distinct and complementary machine learning methods of analyzing whole slide images (WSI) for predicting mutated BRAF. In the first method, WSI of melanomas from 256 patients were used to train a deep convolutional neural network (CNN) in order to develop a fully automated model that first selects for tumor-rich areas (Area Under the Curve AUC=0.96) then predicts for mutated BRAF (AUC=0.71). Saliency mapping was performed and revealed that pixels corresponding to nuclei were the most relevant to network learning. In the second method, WSI were analyzed using a pathomics pipeline that first annotates nuclei and then quantifies nuclear features, demonstrating that mutated BRAF nuclei were significantly larger and rounder nuclei compared to BRAF WT nuclei. Lastly, we developed a model that combines clinical information, deep learning, and pathomics that improves the predictive performance for mutated BRAF to AUC=0.89. Not only does this provide additional insights on how BRAF mutations affect tumor structural characteristics, machine learning-based analysis of WSI has the potential to be integrated into higher order models for understanding tumor biology.

BACKGROUND: We previously developed and validated a predictive model to help clinicians identify hospitalized adults with coronavirus disease 2019 (COVID-19) who may be ready for discharge given their low risk of adverse events. Whether this algorithm can prompt more timely discharge for stable patients in practice is unknown. OBJECTIVES/OBJECTIVE: The aim of the study is to estimate the effect of displaying risk scores on length of stay (LOS). METHODS: We integrated model output into the electronic health record (EHR) at four hospitals in one health system by displaying a green/orange/red score indicating low/moderate/high-risk in a patient list column and a larger COVID-19 summary report visible for each patient. Display of the score was pseudo-randomized 1:1 into intervention and control arms using a patient identifier passed to the model execution code. Intervention effect was assessed by comparing LOS between intervention and control groups. Adverse safety outcomes of death, hospice, and re-presentation were tested separately and as a composite indicator. We tracked adoption and sustained use through daily counts of score displays. RESULTS: Enrolling 1,010 patients from May 15, 2020 to December 7, 2020, the trial found no detectable difference in LOS. The intervention had no impact on safety indicators of death, hospice or re-presentation after discharge. The scores were displayed consistently throughout the study period but the study lacks a causally linked process measure of provider actions based on the score. Secondary analysis revealed complex dynamics in LOS temporally, by primary symptom, and hospital location. CONCLUSION/CONCLUSIONS: An AI-based COVID-19 risk score displayed passively to clinicians during routine care of hospitalized adults with COVID-19 was safe but had no detectable impact on LOS. Health technology challenges such as insufficient adoption, nonuniform use, and provider trust compounded with temporal factors of the COVID-19 pandemic may have contributed to the null result. TRIAL REGISTRATION/BACKGROUND: ClinicalTrials.gov identifier: NCT04570488.

Biopsies of inflammatory tissue contain a complex network of interacting cells, orchestrating the immune or autoimmune response. While standard histological examination can identify relationships, it is clear that a great amount of data on each slide is not quantitated or categorized in standard microscopic examinations. To deal with the huge amount of data present in biopsy tissue in an unbiased and comprehensive way, we have developed a deep learning algorithm to identify immune cells in biopsies of inflammatory lesions. We focused on T follicular helper (Tfh) cell subsets and B cells in dermatomyositis biopsy images. We achieved strong performance on detection and classification of cells, including the rare Tfh cell subsets present in the tissue. This algorithm could be used to perform distance mapping between cell types in tissue, and could be easily adapted to other disease states.

BACKGROUND:It is estimated that up to 40% of Alzheimer's Disease and Related Dementias cases can be prevented or delayed by addressing modifiable factors including those that influence vascular risk (hypertension, obesity, smoking, physical activity, diabetes). Prevention may be particularly important in the vascular dementia subtypes. Despite the supporting evidence, the rates of medical therapy to reduce vascular risk are not well described. METHOD/METHODS:We assessed the utilization of statins, aspirin, and blood pressure (BP) medications in adults age ≥65 years cared for at NYU Langone Health, as recorded in the electronic health record. We included two cohorts: cohort 1 included patients who were diagnosed with vascular dementia (VaD) at NYU Langone Barlow Center for Memory Evaluation between January 1, 2015 and June 24, 2019. Cohort 2 extended the inclusion to seniors with VD diagnosis by any NYU Langone physician. Definitions for vascular dementia, the covariates assessed, and medications that we included in each category are shown in Tables 1-3. RESULT/RESULTS:We included 419 and 3745 patients in cohort 1 and cohort 2, respectively. Table 4 shows the characteristics and medication adherence in cohorts 1 and 2. In cohort 1, the prescription rates for statins, aspirin, and BP medications were 66%, 66%, 70%. In cohort 2, the rates for statin, aspirin, and BP medications were 56%, 46%, and 65%, respectively. The differences between prescription rates in cohort 1 and 2 for the three medication groups were statistically significant (p<0.05). CONCLUSION/CONCLUSIONS:Our analysis of the utilization of cardiovascular medications among patients with vascular dementia illuminates potential gaps both among patients who receive care at specialty clinics, as well as the overall population with vascular dementia. The rates of medication utilization are higher for patients under the care of cognitive neurologists. Electronic health records can help identify large cohorts of patients who may benefit from improved access to preventative measures including cardiovascular medications.

Introduction: Early detection of pancreatic cancer (PC) remains challenging largely due to the low population incidence and few known risk factors. However, screening in at-risk populations and detection of early cancer has the potential to significantly alter survival. We used an Electronic Health Records (EHR) based large-scale machine learning algorithm to identify disease codes that are associated with the development of PC at least 3 years before diagnosis and developed a predictive model to identify patients at risk for PC 27-33 months later.
Method(s): EHR data was analyzed between 2000 and 2021 and individuals with at least 3 years of continuous presence in the database were included. A 1:4 case-control matching based on age, sex, length of medical history to all diagnosed with PC was performed. In one model, all patients meeting database presence were included, whereas in a second model only those without known prior pancreatic disease were evaluated. Among demographic and 19,304 disease variables 27-33 months prior to PC diagnosis, we used the P-value of associations to select significant variables (cut-off P-value < 0.01), and trained a logistic regression model. Final predictive performance was tested on a held-out validation cohort.
Result(s): 544,000 patients were analyzed. 2091 patients with PC were matched to 8364 cancer-free patients. We identified 73 variables with significant association of development of PC, including pancreatic cysts, diabetes, family or personal history of breast cancer, and chronic pancreatitis (ranked results and statistical analysis are shown in Table 1). These variables were selected for the regression model, which we trained in over 541,602 patients. In our second model, in patients without prior pancreatic diseases, 541,377 patients were included. The area under the receiver operating characteristic curve (AUROC) were 0.790 [0.772, 0.809] and 0.779 [0.759, 0.789] in the two models respectively.
Conclusion(s): In a robust EHR-based analysis, we identified a list of diagnostic variables associated with pancreatic cancer development in a 3-year time frame and developed a model to identify patients at risk. Although the inclusion of additional variables such as laboratory results and radiomics will likely improve the accuracy of the model, the current algorithm will allow us to develop an EHR-based identification of patients at risk for PC. (Table Presented)