Natural language processing to predict isocitrate dehydrogenase genotype in diffuse glioma using MR radiology reports.

OBJECTIVES: To evaluate the performance of natural language processing (NLP) models to predict isocitrate dehydrogenase (IDH) mutation status in diffuse glioma using routine MR radiology reports. MATERIALS AND METHODS: This retrospective, multi-center study included consecutive patients with diffuse glioma with known IDH mutation status from May 2009 to November 2021 whose initial MR radiology report was available prior to pathologic diagnosis. Five NLP models (long short-term memory [LSTM], bidirectional LSTM, bidirectional encoder representations from transformers [BERT], BERT graph convolutional network [GCN], BioBERT) were trained, and area under the receiver operating characteristic curve (AUC) was assessed to validate prediction of IDH mutation status in the internal and external validation sets. The performance of the best performing NLP model was compared with that of the human readers. RESULTS: A total of 1427 patients (mean age ± standard deviation, 54 ± 15; 779 men, 54.6%) with 720 patients in the training set, 180 patients in the internal validation set, and 527 patients in the external validation set were included. In the external validation set, BERT GCN showed the highest performance (AUC 0.85, 95% CI 0.81-0.89) in predicting IDH mutation status, which was higher than LSTM (AUC 0.77, 95% CI 0.72-0.81; p = .003) and BioBERT (AUC 0.81, 95% CI 0.76-0.85; p = .03). This was higher than that of a neuroradiologist (AUC 0.80, 95% CI 0.76-0.84; p = .005) and a neurosurgeon (AUC 0.79, 95% CI 0.76-0.84; p = .04). CONCLUSION: BERT GCN was externally validated to predict IDH mutation status in patients with diffuse glioma using routine MR radiology reports with superior or at least comparable performance to human reader. CLINICAL RELEVANCE STATEMENT: Natural language processing may be used to extract relevant information from routine radiology reports to predict cancer genotype and provide prognostic information that may aid in guiding treatment strategy and enabling personalized medicine. KEY POINTS: • A transformer-based natural language processing (NLP) model predicted isocitrate dehydrogenase mutation status in diffuse glioma with an AUC of 0.85 in the external validation set. • The best NLP models were superior or at least comparable to human readers in both internal and external validation sets. • Transformer-based models showed higher performance than conventional NLP model such as long short-term memory.

Multitask Deep Learning for Joint Detection of Necrotizing Viral and Noninfectious Retinitis From Common Blood and Serology Test Data.

Purpose: Necrotizing viral retinitis is a serious eye infection that requires immediate treatment to prevent permanent vision loss. Uncertain clinical suspicion can result in delayed diagnosis, inappropriate administration of corticosteroids, or repeated intraocular sampling. To quickly and accurately distinguish between viral and noninfectious retinitis, we aimed to develop deep learning (DL) models solely using noninvasive blood test data. Methods: This cross-sectional study trained DL models using common blood and serology test data from 3080 patients (noninfectious uveitis of the posterior segment [NIU-PS] = 2858, acute retinal necrosis [ARN] = 66, cytomegalovirus [CMV], retinitis = 156). Following the development of separate base DL models for ARN and CMV retinitis, multitask learning (MTL) was employed to enable simultaneous discrimination. Advanced MTL models incorporating adversarial training were used to enhance DL feature extraction from the small, imbalanced data. We evaluated model performance, disease-specific important features, and the causal relationship between DL features and detection results. Results: The presented models all achieved excellent detection performances, with the adversarial MTL model achieving the highest receiver operating characteristic curves (0.932 for ARN and 0.982 for CMV retinitis). Significant features for ARN detection included varicella-zoster virus (VZV) immunoglobulin M (IgM), herpes simplex virus immunoglobulin G, and neutrophil count, while for CMV retinitis, they encompassed VZV IgM, CMV IgM, and lymphocyte count. The adversarial MTL model exhibited substantial changes in detection outcomes when the key features were contaminated, indicating stronger causality between DL features and detection results. Conclusions: The adversarial MTL model, using blood test data, may serve as a reliable adjunct for the expedited diagnosis of ARN, CMV retinitis, and NIU-PS simultaneously in real clinical settings.