Abstract
The large-scale pretrained models from terabyte-level (TB) data are now broadly used in feature extraction, model initialization, and transfer learning in pathological image analyses. Most existing studies have focused on developing more powerful pretrained models, which are increasingly unscalable for academic institutes. Very few, if any, studies have investigated how to take advantage of existing, yet heterogeneous, pretrained models for downstream tasks. As an example, our experiments elucidated that self-supervised models (e.g., contrastive learning on the entire The Cancer Genome Atlas (TCGA) dataset) achieved a superior performance compared with supervised models (e.g., ImageNet pretraining) on a classification cohort. Surprisingly, it yielded an inferior performance when it was translated to a cancer prognosis task. Such a phenomenon inspired us to explore how to leverage the already trained supervised and self-supervised models for pathological survival analysis. In this paper, we present a simple and low-cost joint representation tuning (JRT) to aggregate task-agnostic vision representation (supervised ImageNet pretrained models) and pathological specific feature representation (self-supervised TCGA pretrained models) for downstream tasks. Our contribution is in three-fold: (1) we adapt and aggregate classification-based supervised and self-supervised representation to survival prediction via joint representation tuning, (2) comprehensive analyses on prevalent strategies of pretrained models are conducted, (3) the joint representation tuning provides a simple, yet computationally efficient, perspective to leverage large-scale pretrained models for both cancer diagnosis and prognosis. The proposed JRT method improved the c-index from 0.705 to 0.731 on the TCGA brain cancer survival dataset. The feature-direct JRT (f-JRT) method achieved \(60\times \) training speedup while maintaining 0.707 c-index score.
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Liu, Q. et al. (2022). Leverage Supervised and Self-supervised Pretrain Models for Pathological Survival Analysis via a Simple and Low-cost Joint Representation Tuning. In: Xu, X., Li, X., Mahapatra, D., Cheng, L., Petitjean, C., Fu, H. (eds) Resource-Efficient Medical Image Analysis. REMIA 2022. Lecture Notes in Computer Science, vol 13543. Springer, Cham. https://doi.org/10.1007/978-3-031-16876-5_8
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