WeakSupCon: Weakly Supervised Contrastive Learning for Encoder Pre-training

Weakly supervised multiple instance learning (MIL) is a challenging task given that only bag-level labels are provided, while each bag typically contains multiple instances. This topic has been extensively studied in histopathological image analysis, where labels are usually available only at the whole slide image (WSI) level, while each whole slide image can be divided into thousands of small image patches for training. The dominant MIL approaches take fixed patch features as inputs to address computational constraints and ensure model stability. These features are commonly generated by encoders pre-trained on ImageNet, foundation encoders pre-trained on large datasets, or through self-supervised learning on local datasets. While the self-supervised encoder pre-training on the same dataset as downstream MIL tasks helps mitigate domain shift and generate better features, the bag-level labels are not utilized during the process, and the features of patches from different categories may cluster together, reducing classification performance on MIL tasks. Recently, pre-training with supervised contrastive learning (SupCon) has demonstrated superior performance compared to self-supervised contrastive learning and even end-to-end training on traditional image classification tasks. In this paper, we propose a novel encoder pre-training method for downstream MIL tasks called Weakly Supervised Contrastive Learning (WeakSupCon) that utilizes bag-level labels. In our method, we employ multi-task learning and define distinct contrastive learning losses for samples with different bag labels. Our experiments demonstrate that the features generated using WeakSupCon significantly enhance MIL classification performance compared to self-supervised approaches across three datasets.