Multimodal Machine Learning for Early Prediction of Metastasis in a Swedish Multi-Cancer Cohort

TL;DR

This study develops a multimodal machine learning framework to predict metastasis risk one month before diagnosis using diverse EHR data across four cancer types, demonstrating high predictive accuracy and interpretability.

Contribution

It introduces a comprehensive multimodal prediction framework with intermediate fusion strategies and SHAP-based interpretability for early metastasis detection in multiple cancers.

Findings

Intermediate fusion achieved highest F1 scores for breast, colon, and prostate cancers.

Deep learning classifiers outperformed traditional models across all modalities.

Text-only models performed best for lung cancer prediction.

Abstract

Multimodal Machine Learning offers a holistic view of a patient's status, integrating structured and unstructured data from electronic health records (EHR). We propose a framework to predict metastasis risk one month prior to diagnosis, using six months of clinical history from EHR data. Data from four cancer cohorts collected at Karolinska University Hospital (Stockholm, Sweden) were analyzed: breast (n = 743), colon (n = 387), lung (n = 870), and prostate (n = 1890). The dataset included demographics, comorbidities, laboratory results, medications, and clinical text. We compared traditional and deep learning classifiers across single modalities and multimodal combinations, using various fusion strategies and a Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) 2a design, with an 80-20 development-validation split to ensure a rigorous, repeatable evaluation. Performance was evaluated using AUROC, AUPRC, F1 score, sensitivity, and specificity. We then employed a multimodal adaptation of SHAP to analyze the classifiers' reasoning. Intermediate fusion achieved the highest F1 scores on breast (0.845), colon (0.786), and prostate cancer (0.845), demonstrating strong predictive performance. For lung cancer, the intermediate fusion achieved an F1 score of 0.819, while the text-only model achieved the highest, with an F1 score of 0.829. Deep learning classifiers consistently outperformed traditional models. Colon cancer, the smallest cohort, had the lowest performance, highlighting the importance of sufficient training data. SHAP analysis showed that the relative importance of modalities varied across cancer types. Fusion strategies offer distinct strengths and weaknesses. Intermediate fusion consistently delivered the best results, but strategy choices should align with data characteristics and organizational needs.