We consider the task of representation learning for unsupervised segmentation of3Dvoxel-grid biomedical images.

Conversational generative AI has demonstrated remarkable promise for empowering biomedical practitioners, but current investigations focus on unimodal text. Multimodal conversational AI has seen rapid progress by leveraging billions of image-text pairs from the public web, but such general-domain vision-language models still lack sophistication in understanding and conversing about biomedical images. In this paper, we propose a cost-efficient approach for training a vision-language conversational assistant that can answer open-ended research questions of biomedical images. The key idea is to leverage a large-scale, broad-coverage biomedical figure-caption dataset extracted from PubMed Central, use GPT-4 to self-instruct open-ended instruction-following data from the captions, and then fine-tune a large general-domain vision-language model using a novel curriculum learning method. Specifically, the model first learns to align biomedical vocabulary using the figure-caption pairs as is, then learns to master open-ended conversational semantics using GPT-4 generated instruction-following data, broadly mimicking how a layperson gradually acquires biomedical knowledge. This enables us to train a Large Language and Vision Assistant for BioMedicine (LLaVA-Med) in less than 15 hours (with eight A100s). LLaVA-Med exhibits excellent multimodal conversational capability and can follow open-ended instruction to assist with inquiries about a biomedical image. On three standard biomedical visual question answering datasets, LLaVA-Med outperforms previous supervised state-of-the-art on certain metrics. To facilitate biomedical multimodal research, we will release our instruction-following data and the LLaVA-Med model.

We consider the task of representation learning for unsupervised segmentation of 3D voxel-grid biomedical images. We show that models that capture implicit hierarchical relationships between subvolumes are better suited for this task. To that end, we consider encoder-decoder architectures with a hyperbolic latent space, to explicitly capture hierarchical relationships present in subvolumes of the data. We propose utilizing a 3D hyperbolic variational autoencoder with a novel gyroplane convolutional layer to map from the embedding space back to 3D images. To capture these relationships, we introduce an essential self-supervised loss---in addition to the standard VAE loss---which infers approximate hierarchies and encourages implicitly related subvolumes to be mapped closer in the embedding space.

Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation performance.

We consider the task of representation learning for unsupervised segmentation of 3D voxel-grid biomedical images.

Prompt learning is one of the most effective paradigms for adapting pre-trained vision-language models (VLMs) to the biomedical image classification tasks in few shot scenarios. However, most of the current prompt learning methods only used the text prompts and ignored the particular structures (such as the complex anatomical structures and subtle pathological features) in the biomedical images. In this work, we propose Biomed-DPT, a knowledge-enhanced dual modality prompt tuning technique. In designing the text prompt, Biomed-DPT constructs a dual prompt including the template-driven clinical prompts and the large language model (LLM)-driven domain-adapted prompts, then extracts the clinical knowledge from the domain-adapted prompts through the knowledge distillation technique. In designing the vision prompt, Biomed-DPT introduces the zero vector as a soft prompt to leverage attention re-weighting so that the focus on non-diagnostic regions and the recognition of non-critical pathological features are avoided. Biomed-DPT achieves an average classification accuracy of 66.14\% across 11 biomedical image datasets covering 9 modalities and 10 organs, with performance reaching 78.06\% in base classes and 75.97\% in novel classes, surpassing the Context Optimization (CoOp) method by 6.20\%, 3.78\%, and 8.04\%, respectively. Our code are available at \underline{https://github.com/Kanyooo/Biomed-DPT}.