Extended Data Fig. 8: Comparison of response and survival models using Shapley values.

a) Showing a comparison of response and survival hazard estimates. The points are color coded red for low responders (<10% probability response), yellow for medium responders (10-50% probability) and green for high responders(>50%). The estimates we obtained from XGboost models trained on representative biomarkers of the five latent factors across patients in the HMF-CPI cohort to predict CPI response and survival. b) Exploring the determinants of the distribution of hazards across patients with low probability of response (scatterplot). The patients in this group have been subdivided into two smaller groups based on their predicted hazard, represented by dots of different shades of red separated by the horizontal line in the value of predicted hazard 1.5. The line plots represent the distribution (quantiles) of Shapley values (see Methods) calculated for these two subgroups of patients for the five latent factors. The two lines appear more separated in the distributions of Shapley values of tumor proliferative potential and TGF-beta activity in the microenvironment. This indicates that it is the values of these two latent factors that contribute the most to the separation between these two groups of patients. c) Example of the predicted CPI response and survival of one patient in the HMF-CPI cohort broken down by Shapley values.