DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma

Abstract Lung cancer is the first leading cause of cancer‐related death in the United States, with lung adenocarcinoma as the major subtype accounting for 40% of all cases. To improve patient survival, image‐based prognostic models were developed due to the ready availability of pathological images at diagnosis. However, the application of these models is hampered by two main challenges: the lack of publicly available image datasets with high‐quality survival information and the poor interpretability of conventional convolutional neural network models. Here, we integrated matched transcriptomic and H&E staining data from TCGA (The Cancer Genome Atlas) to develop an image‐based prognostic model, termed Deep‐learning based Cell Graph (DeepCG) model. Instead of survival data, we used a gene signature to predict patient prognostic risks, which was then used as labels for training DeepCG. Importantly, by employing graph structures to capture cell patterns, DeepCG can provide cell‐level interpretation, which was more biologically relevant than previous region‐level insights. We validated the prognostic values of DeepCG in independent datasets and demonstrated its ability to identify prognostically informative cells in images.