CT-Based Deep Foundation Model for Predicting Immune Checkpoint Inhibitor-Induced Pneumonitis Risk in Lung Cancer

Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy but can cause serious immune-related adverse events (irAEs), with pneumonitis (ICI-P) being among the most severe. Early identification of high-risk patients before ICI initiation is critical to close monitoring, enable timely intervention, and optimize outcomes.

To develop and validate a deep learning foundation model to predict ICI-P from baseline CT scans in patients with lung cancer.

We designed the Checkpoint-Inhibitor Pneumonitis Hazard EstimatoR (CIPHER), a deep learning-powered foundation model combining contrastive learning with a transformer-based masked autoencoder to predict ICI-P from baseline CT scans in lung cancer patients. Using self-supervised learning, CIPHER was pre-trained on 590,284 CT slices from 2,500 non-small cell lung cancer (NSCLC) patients, to understand heterogeneous lung parenchyma. Following pre-training, the model was fine-tuned on an internal NSCLC cohort for ICI-P risk prediction, with images from 254 patients used for model development and from 93 patients for internal validation. We compared CIPHER with classical radiomic models. We also validated CIPHER on an external NSCLC cohort of 116 patients.

In our internal immunotherapy cohort, CIPHER consistently distinguished patients at elevated risk of ICI-P from those without the event, with AUCs ranging from 0.77 to 0.85. In head-to-head benchmarking, CIPHER achieved an AUC of 0.83, outperforming radiomic model. In the external validation cohort, CIPHER maintained high performance (AUC=0.83; balanced accuracy=81.7%), exceeding the radiomic models (Delong p=0.0318) and demonstrating superior specificity without sacrificing sensitivity. By contrast, radiomic model, despite high sensitivity (85.0%), showed markedly lower specificity (45.8%). Confusion matrix analyses confirmed CIPHER's robust classification, correctly identifying 80 of 96 non-ICI-P cases and 16 of 20 ICI-P cases.

We developed and externally validated CIPHER for predicting future risk of developing ICI-P from pre-treatment CT scans. With prospective validation, CIPHER can be incorporated into routine patient management to improve outcomes.