Pancakes: Consistent Multi-Protocol Image Segmentation Across Biomedical Domains

A single biomedical image can be meaningfully segmented in multiple ways, depending on the desired application. For instance, a brain MRI can be segmented according to tissue types, vascular territories, broad anatomical regions, fine-grained anatomy, or pathology, etc. Existing automatic segmentation models typically either (1) support only a single protocol, the one they were trained on, or (2) require labor-intensive manual prompting to specify the desired segmentation. We introduce Pancakes, a framework that, given a new image from a previously unseen domain, automatically generates multi-label segmentation maps for multiple plausible protocols, while maintaining semantic consistency across related images. Pancakes introduces a new problem formulation that is not currently attainable by existing foundation models. In a series of experiments on seven held-out datasets, we demonstrate that our model can significantly outperform existing foundation models in producing several plausible whole-image segmentations, that are semantically coherent across images.

Refocusing Is Key to Transfer Learning

Transfer learning involves adapting a pre-trained model to novel downstream tasks. However, we observe that current transfer learning methods often fail to focus on task-relevant features. In this work, we emphasize the importance of refocusing the attention in transfer learning. We introduce Top-Down Attention Steering (TOAST), a novel transfer learning algorithm that keeps the pre-trained backbone frozen, while selecting the task-relevant elements in the output and feeding them back to the model to steer its attention to the task-specific features. By refocusing the attention only, TOAST achieves state-of-the-art results on a number of transfer learning benchmarks, while having a small portion of tunable parameters. Compared to fully fine-tuning, LoRA, and prompt tuning, TOAST substantially improves performance across a range of fine-grained visual classification datasets (e.g., 81.1% -> 86.2% on FGVC). TOAST also outperforms the fully fine-tuned Alpaca model on instruction-following language generation. Code is available at https://github.com/bfshi/TOAST.