Melanie Gaillochet

Anatomically-aware conformal prediction for medical image segmentation with random walks

Melanie Gaillochet

Christian Desrosiers

Hervé Lombaert

2026-01-25

ArXiv (preprint)

arxiv.org

Prompt learning with bounding box constraints for medical image segmentation.

Melanie Gaillochet

Mehrdad Noori

Sahar Dastani

Christian Desrosiers

Hervé Lombaert

Pixel-wise annotations are notoriously labourious and costly to obtain in the medical domain. To mitigate this burden, weakly supervised app… (see more)roaches based on bounding box annotations-much easier to acquire-offer a practical alternative. Vision foundation models have recently shown noteworthy segmentation performance when provided with prompts such as points or bounding boxes. Prompt learning exploits these models by adapting them to downstream tasks and automating segmentation, thereby reducing user intervention. However, existing prompt learning approaches depend on fully annotated segmentation masks. This paper proposes a novel framework that combines the representational power of foundation models with the annotation efficiency of weakly supervised segmentation. More specifically, our approach automates prompt generation for foundation models using only bounding box annotations. Our proposed optimization scheme integrates multiple constraints derived from box annotations with pseudo-labels generated by the prompted foundation model. Extensive experiments across multi-modal datasets reveal that our weakly supervised method achieves an average Dice score of 84.90% in a limited data setting, outperforming existing fully-supervised and weakly-supervised approaches. The code will be available upon acceptance

2025-06-24

IEEE transactions on bio-medical engineering (published)

doi.org

arxiv.org

Prompt learning with bounding box constraints for medical image segmentation.

Melanie Gaillochet

Mehrdad Noori

Sahar Dastani

Christian Desrosiers

Hervé Lombaert

Pixel-wise annotations are notoriously labourious and costly to obtain in the medical domain. To mitigate this burden, weakly supervised app… (see more)roaches based on bounding box annotations-much easier to acquire-offer a practical alternative. Vision foundation models have recently shown noteworthy segmentation performance when provided with prompts such as points or bounding boxes. Prompt learning exploits these models by adapting them to downstream tasks and automating segmentation, thereby reducing user intervention. However, existing prompt learning approaches depend on fully annotated segmentation masks. This paper proposes a novel framework that combines the representational power of foundation models with the annotation efficiency of weakly supervised segmentation. More specifically, our approach automates prompt generation for foundation models using only bounding box annotations. Our proposed optimization scheme integrates multiple constraints derived from box annotations with pseudo-labels generated by the prompted foundation model. Extensive experiments across multi-modal datasets reveal that our weakly supervised method achieves an average Dice score of 84.90% in a limited data setting, outperforming existing fully-supervised and weakly-supervised approaches. The code will be available upon acceptance

2025-06-23

IEEE transactions on bio-medical engineering (published)

doi.org

arxiv.org

Automating MedSAM by Learning Prompts with Weak Few-Shot Supervision

Melanie Gaillochet

Christian Desrosiers

Hervé Lombaert

2024-09-28

Lecture Notes in Computer Science (published)

doi.org

arxiv.org