A multi-task deep sequential neural network for IgA nephropathy Oxford classification and prognosis prediction

Abstract

Background

While deep learning has advanced pathological analysis in IgA nephropathy (IgAN), the lack of integrated models that combine multi-label structural identification, Oxford classification, and prognosis prediction remains a significant clinical challenge.

Methods

We developed DeepSNN, a novel deep sequential neural network that serves as a multi-task model trained on multi-center multi-modal renal datasets. The architecture integrates lesion segmentation, glomerular classification, Oxford MEST-C scoring, and prognosis prediction subnets. To ensure interpretability, we conducted visualization experiments and comparative analyses with pathologists’ diagnostic patterns. Pathologist comparisons employed Cohen’s Kappa with blinded re-evaluation of test and validation sets.

Results

DeepSNN demonstrated exceptional lesion identification capabilities across the People’s Liberation Army General (PLAG) Hospital dataset (n = 245) and China-Japan Friendship (CJF) Hospital dataset (n = 32), achieving dice coefficients of 0.95 and 0.92, respectively. For Oxford classification, DeepSNN delivered outstanding outcomes with high Kappa values of 0.84, 0.79, 0.87, 0.87, and 0.82 for M, E, S, T, and C scores on the PLAG dataset. Notably, our method outperformed three junior pathologists and achieved comparable performance to senior pathologists across both datasets. During a median follow-up of 47.7 (IQR: 21.9–61.1) months, DeepSNN excelled in prognosis prediction (AUC: 0.810), demonstrating improvement over the International IgA Nephropathy Prediction Tool (IIPT) (AUC: 0.742, ΔAUC = +0.068) in PLAG Hospital dataset (n = 245). Furthermore, visualization maps showed consistent pathological region identification between pathologists and DeepSNN.

Conclusions

DeepSNN successfully integrates multiple diagnostic tasks with performance comparable to senior pathologists, demonstrating substantial potential for streamlining IgAN clinical workflows. This innovation addresses critical gaps in automated renal pathology analysis while maintaining clinical interpretability.