Siteng Chen | Searcharxiv

arXiv2023

Artificial intelligence for diagnosing and predicting survival of patients with renal cell carcinoma: Retrospective multi-center study

Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal-related tumor with high heterogeneity. There is still an urgent need for novel diagnostic and prognostic biomarkers for ccRCC. Methods: We proposed a weakly-supervised deep learning strategy using conventional histology of 1752 whole slide images from multiple centers. Our study was demonstrated through internal cross-validation and external validations for the deep learning-based models. Results: Automatic diagnosis for ccRCC through intelligent subtyping of renal cell carcinoma was proved in this study. Our graderisk achieved aera the curve (AUC) of 0.840 (95% confidence interval: 0.805-0.871) in the TCGA cohort, 0.840 (0.805-0.871) in the General cohort, and 0.840 (0.805-0.871) in the CPTAC cohort for the recognition of high-grade tumor. The OSrisk for the prediction of 5-year survival status achieved AUC of 0.784 (0.746-0.819) in the TCGA cohort, which was further verified in the independent General cohort and the CPTAC cohort, with AUC of 0.774 (0.723-0.820) and 0.702 (0.632-0.765), respectively. Cox regression analysis indicated that graderisk, OSrisk, tumor grade, and tumor stage were found to be independent prognostic factors, which were further incorporated into the competing-risk nomogram (CRN). Kaplan-Meier survival analyses further illustrated that our CRN could significantly distinguish patients with high survival risk, with hazard ratio of 5.664 (3.893-8.239, p < 0.0001) in the TCGA cohort, 35.740 (5.889-216.900, p < 0.0001) in the General cohort and 6.107 (1.815 to 20.540, p < 0.0001) in the CPTAC cohort. Comparison analyses conformed that our CRN outperformed current prognosis indicators in the prediction of survival status, with higher concordance index for clinical prognosis.

eess.IV↗

arXiv2022

Deep learning-based approach to reveal tumor mutational burden status from whole slide images across multiple cancer types

Tumor mutational burden (TMB) is a potential genomic biomarker of immunotherapy. However, TMB detected through whole exome sequencing lacks clinical penetration in low-resource settings. In this study, we proposed a multi-scale deep learning framework to address the detection of TMB status from routinely used whole slide images for a multiple cancer TMB prediction model (MC- TMB). The MC-TMB achieved a mean area under the curve (AUC) of 0.818 (0.804-0.831) in the cross-validation cohort, which showed superior performance to each single-scale model. The improvements of MC-TMB over the single-tumor models were also confirmed by the ablation tests on x10 magnification, and the highly concerned regions typically correspond to dense lymphocytic infiltration and heteromorphic tumor cells. MC-TMB algorithm also exhibited good generalization on the external validation cohort with an AUC of 0.732 (0.683-0.761), and better performance when compared to other methods. In conclusion, we proposed a deep learning-based approach to reveal tumor mutational burden status from routinely used pathological slides across multiple cancer types.

cs.CV↗