Prompt-MIL: Boosting Multi-Instance Learning Schemes via Task-specific Prompt Tuning

• URL: http://arxiv.org/abs/2303.12214v2
• Date: Thu, 5 Oct 2023 03:50:19 GMT
• Title: Prompt-MIL: Boosting Multi-Instance Learning Schemes via Task-specific Prompt Tuning
• Authors: Jingwei Zhang, Saarthak Kapse, Ke Ma, Prateek Prasanna, Joel Saltz, Maria Vakalopoulou, Dimitris Samaras
• Abstract summary: Whole slide image (WSI) classification is a critical task in computational pathology. Current state of the art methods are based on multi-instance learning schemes (MIL), which usually rely on pretrained features to represent the instances. We propose Prompt-MIL, an MIL framework that integrates prompts into WSI classification.
• Score: 31.0183821423397
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Whole slide image (WSI) classification is a critical task in computational pathology, requiring the processing of gigapixel-sized images, which is challenging for current deep-learning methods. Current state of the art methods are based on multi-instance learning schemes (MIL), which usually rely on pretrained features to represent the instances. Due to the lack of task-specific annotated data, these features are either obtained from well-established backbones on natural images, or, more recently from self-supervised models pretrained on histopathology. However, both approaches yield task-agnostic features, resulting in performance loss compared to the appropriate task-related supervision, if available. In this paper, we show that when task-specific annotations are limited, we can inject such supervision into downstream task training, to reduce the gap between fully task-tuned and task agnostic features. We propose Prompt-MIL, an MIL framework that integrates prompts into WSI classification. Prompt-MIL adopts a prompt tuning mechanism, where only a small fraction of parameters calibrates the pretrained features to encode task-specific information, rather than the conventional full fine-tuning approaches. Extensive experiments on three WSI datasets, TCGA-BRCA, TCGA-CRC, and BRIGHT, demonstrate the superiority of Prompt-MIL over conventional MIL methods, achieving a relative improvement of 1.49%-4.03% in accuracy and 0.25%-8.97% in AUROC while using fewer than 0.3% additional parameters. Compared to conventional full fine-tuning approaches, we fine-tune less than 1.3% of the parameters, yet achieve a relative improvement of 1.29%-13.61% in accuracy and 3.22%-27.18% in AUROC and reduce GPU memory consumption by 38%-45% while training 21%-27% faster. Our code is available at https://github.com/cvlab-stonybrook/PromptMIL.

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