Applying natural language processing to patient messages to identify depression concerns in cancer patients.

OBJECTIVE: This study aims to explore and develop tools for early identification of depression concerns among cancer patients by leveraging the novel data source of messages sent through a secure patient portal. MATERIALS AND METHODS: We developed classifiers based on logistic regression (LR), support vector machines (SVMs), and 2 Bidirectional Encoder Representations from Transformers (BERT) models (original and Reddit-pretrained) on 6600 patient messages from a cancer center (2009-2022), annotated by a panel of healthcare professionals. Performance was compared using AUROC scores, and model fairness and explainability were examined. We also examined correlations between model predictions and depression diagnosis and treatment. RESULTS: BERT and RedditBERT attained AUROC scores of 0.88 and 0.86, respectively, compared to 0.79 for LR and 0.83 for SVM. BERT showed bigger differences in performance across sex, race, and ethnicity than RedditBERT. Patients who sent messages classified as concerning had a higher chance of receiving a depression diagnosis, a prescription for antidepressants, or a referral to the psycho-oncologist. Explanations from BERT and RedditBERT differed, with no clear preference from annotators. DISCUSSION: We show the potential of BERT and RedditBERT in identifying depression concerns in messages from cancer patients. Performance disparities across demographic groups highlight the need for careful consideration of potential biases. Further research is needed to address biases, evaluate real-world impacts, and ensure responsible integration into clinical settings. CONCLUSION: This work represents a significant methodological advancement in the early identification of depression concerns among cancer patients. Our work contributes to a route to reduce clinical burden while enhancing overall patient care, leveraging BERT-based models.

Predicting Depression Risk in Patients With Cancer Using Multimodal Data: Algorithm Development Study.

BACKGROUND: Patients with cancer starting systemic treatment programs, such as chemotherapy, often develop depression. A prediction model may assist physicians and health care workers in the early identification of these vulnerable patients. OBJECTIVE: This study aimed to develop a prediction model for depression risk within the first month of cancer treatment. METHODS: We included 16,159 patients diagnosed with cancer starting chemo- or radiotherapy treatment between 2008 and 2021. Machine learning models (eg, least absolute shrinkage and selection operator [LASSO] logistic regression) and natural language processing models (Bidirectional Encoder Representations from Transformers [BERT]) were used to develop multimodal prediction models using both electronic health record data and unstructured text (patient emails and clinician notes). Model performance was assessed in an independent test set (n=5387, 33%) using area under the receiver operating characteristic curve (AUROC), calibration curves, and decision curve analysis to assess initial clinical impact use. RESULTS: Among 16,159 patients, 437 (2.7%) received a depression diagnosis within the first month of treatment. The LASSO logistic regression models based on the structured data (AUROC 0.74, 95% CI 0.71-0.78) and structured data with email classification scores (AUROC 0.74, 95% CI 0.71-0.78) had the best discriminative performance. The BERT models based on clinician notes and structured data with email classification scores had AUROCs around 0.71. The logistic regression model based on email classification scores alone performed poorly (AUROC 0.54, 95% CI 0.52-0.56), and the model based solely on clinician notes had the worst performance (AUROC 0.50, 95% CI 0.49-0.52). Calibration was good for the logistic regression models, whereas the BERT models produced overly extreme risk estimates even after recalibration. There was a small range of decision thresholds for which the best-performing model showed promising clinical effectiveness use. The risks were underestimated for female and Black patients. CONCLUSIONS: The results demonstrated the potential and limitations of machine learning and multimodal models for predicting depression risk in patients with cancer. Future research is needed to further validate these models, refine the outcome label and predictors related to mental health, and address biases across subgroups.

Natural Language Processing Methods to Identify Oncology Patients at High Risk for Acute Care with Clinical Notes.

Clinical notes are an essential component of a health record. This paper evaluates how natural language processing (NLP) can be used to identify the risk of acute care use (ACU) in oncology patients, once chemotherapy starts. Risk prediction using structured health data (SHD) is now standard, but predictions using free-text formats are complex. This paper explores the use of free-text notes for the prediction of ACU in leu of SHD. Deep Learning models were compared to manually engineered language features. Results show that SHD models minimally outperform NLP models; an ℓ1-penalised logistic regression with SHD achieved a C-statistic of 0.748 (95%-CI: 0.735, 0.762), while the same model with language features achieved 0.730 (95%-CI: 0.717, 0.745) and a transformer-based model achieved 0.702 (95%-CI: 0.688, 0.717). This paper shows how language models can be used in clinical applications and underlines how risk bias is different for diverse patient groups, even using only free-text data.

A Bayesian approach to predictive uncertainty in chemotherapy patients at risk of acute care utilization.

BACKGROUND: Machine learning (ML) predictions are becoming increasingly integrated into medical practice. One commonly used method, ℓ1-penalised logistic regression (LASSO), can estimate patient risk for disease outcomes but is limited by only providing point estimates. Instead, Bayesian logistic LASSO regression (BLLR) models provide distributions for risk predictions, giving clinicians a better understanding of predictive uncertainty, but they are not commonly implemented. METHODS: This study evaluates the predictive performance of different BLLRs compared to standard logistic LASSO regression, using real-world, high-dimensional, structured electronic health record (EHR) data from cancer patients initiating chemotherapy at a comprehensive cancer centre. Multiple BLLR models were compared against a LASSO model using an 80-20 random split using 10-fold cross-validation to predict the risk of acute care utilization (ACU) after starting chemotherapy. FINDINGS: This study included 8439 patients. The LASSO model predicted ACU with an area under the receiver operating characteristic curve (AUROC) of 0.806 (95% CI: 0.775-0.834). BLLR with a Horseshoe+ prior and a posterior approximated by Metropolis-Hastings sampling showed similar performance: 0.807 (95% CI: 0.780-0.834) and offers the advantage of uncertainty estimation for each prediction. In addition, BLLR could identify predictions too uncertain to be automatically classified. BLLR uncertainties were stratified by different patient subgroups, demonstrating that predictive uncertainties significantly differ across race, cancer type, and stage. INTERPRETATION: BLLRs are a promising yet underutilised tool that increases explainability by providing risk estimates while offering a similar level of performance to standard LASSO-based models. Additionally, these models can identify patient subgroups with higher uncertainty, which can augment clinical decision-making. FUNDING: This work was supported in part by the National Library Of Medicine of the National Institutes of Health under Award Number R01LM013362. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Predicting Depression Risk in Patients with Cancer Using Multimodal Data.

When patients with cancer develop depression, it is often left untreated. We developed a prediction model for depression risk within the first month after starting cancer treatment using machine learning and Natural Language Processing (NLP) models. The LASSO logistic regression model based on structured data performed well, whereas the NLP model based on only clinician notes did poorly. After further validation, prediction models for depression risk could lead to earlier identification and treatment of vulnerable patients, ultimately improving cancer care and treatment adherence.

Predict, diagnose, and treat chronic kidney disease with machine learning: a systematic literature review.

OBJECTIVES: In this systematic review we aimed at assessing how artificial intelligence (AI), including machine learning (ML) techniques have been deployed to predict, diagnose, and treat chronic kidney disease (CKD). We systematically reviewed the available evidence on these innovative techniques to improve CKD diagnosis and patient management. METHODS: We included English language studies retrieved from PubMed. The review is therefore to be classified as a "rapid review", since it includes one database only, and has language restrictions; the novelty and importance of the issue make missing relevant papers unlikely. We extracted 16 variables, including: main aim, studied population, data source, sample size, problem type (regression, classification), predictors used, and performance metrics. We followed the Preferred Reporting Items for Systematic Reviews (PRISMA) approach; all main steps were done in duplicate. RESULTS: From a total of 648 studies initially retrieved, 68 articles met the inclusion criteria. Models, as reported by authors, performed well, but the reported metrics were not homogeneous across articles and therefore direct comparison was not feasible. The most common aim was prediction of prognosis, followed by diagnosis of CKD. Algorithm generalizability, and testing on diverse populations was rarely taken into account. Furthermore, the clinical evaluation and validation of the models/algorithms was perused; only a fraction of the included studies, 6 out of 68, were performed in a clinical context. CONCLUSIONS: Machine learning is a promising tool for the prediction of risk, diagnosis, and therapy management for CKD patients. Nonetheless, future work is needed to address the interpretability, generalizability, and fairness of the models to ensure the safe application of such technologies in routine clinical practice.