Segment Anything in Medical Images and Videos: Benchmark and Deployment

Recent advances in segmentation foundation models have enabled accurate and efficient segmentation across a wide range of natural images and videos, but their utility to medical data remains unclear. In this work, we first present a comprehensive benchmarking of the Segment Anything Model 2 (SAM2) across 11 medical image modalities and videos and point out its strengths and weaknesses by comparing it to SAM1 and MedSAM. Then, we develop a transfer learning pipeline and demonstrate SAM2 can be quickly adapted to medical domain by fine-tuning. Furthermore, we implement SAM2 as a 3D slicer plugin and Gradio API for efficient 3D image and video segmentation. The code has been made publicly available at \url{https://github.com/bowang-lab/MedSAM}.

Harmony: A Joint Self-Supervised and Weakly-Supervised Framework for Learning General Purpose Visual Representations

Vision-language contrastive learning frameworks like CLIP enable learning representations from natural language supervision, and provide strong zero-shot classification capabilities. However, due to the nature of the supervisory signal in these paradigms, they lack the ability to learn localized features, leading to degraded performance on dense prediction tasks like segmentation and detection. On the other hand, self-supervised learning methods have shown the ability to learn granular representations, complementing the high-level features in vision-language training. In this work, we present Harmony, a framework that combines vision-language training with discriminative and generative self-supervision to learn visual features that can be generalized across vision downstream tasks. Our framework is specifically designed to work on web-scraped data by not relying on negative examples and addressing the one-to-one correspondence issue using soft CLIP targets generated by an EMA model. We comprehensively evaluate Harmony across various vision downstream tasks and find that it significantly outperforms the baseline CLIP and the previously leading joint self and weakly-supervised methods, MaskCLIP and SLIP. Specifically, when comparing against these methods, Harmony shows superior performance in fine-tuning and zero-shot classification on ImageNet-1k, semantic segmentation on ADE20K, and both object detection and instance segmentation on MS-COCO, when pre-training a ViT-S/16 on CC3M. We also show that Harmony outperforms other self-supervised learning methods like iBOT and MAE across all tasks evaluated. On https://github.com/MohammedSB/Harmony our code is publicly available.

Towards General Purpose Vision Foundation Models for Medical Image Analysis: An Experimental Study of DINOv2 on Radiology Benchmarks

The integration of deep learning systems into the medical domain has been hindered by the resource-intensive process of data annotation and the inability of these systems to generalize to different data distributions. Foundation models, which are models pre-trained on large datasets, have emerged as a solution to reduce reliance on annotated data and enhance model generalizability and robustness. DINOv2, an open-source foundation model pre-trained with self-supervised learning on 142 million curated natural images, excels in extracting general-purpose visual representations, exhibiting promising capabilities across various vision tasks. Nevertheless, a critical question remains unanswered regarding DINOv2's adaptability to radiological imaging, and the clarity on whether its features are sufficiently general to benefit radiology image analysis is yet to be established. Therefore, this study comprehensively evaluates DINOv2 for radiology, conducting over 100 experiments across diverse modalities (X-ray, CT, and MRI). Tasks include disease classification and organ segmentation on both 2D and 3D images, evaluated under different settings like kNN, few-shot learning, linear-probing, end-to-end fine-tuning, and parameter-efficient fine-tuning, to measure the effectiveness and generalizability of the DINOv2 feature embeddings. Comparative analyses with established medical image analysis models, U-Net and TransUnet for segmentation, and CNN and ViT models pre-trained via supervised, weakly supervised, and self-supervised learning for classification, reveal DINOv2's superior performance in segmentation tasks and competitive results in disease classification. The findings contribute insights to potential avenues for optimizing pre-training strategies for medical imaging and enhancing the broader understanding of DINOv2's role in bridging the gap between natural and radiological image analysis.

HyMNet: a Multimodal Deep Learning System for Hypertension Classification using Fundus Photographs and Cardiometabolic Risk Factors

In recent years, deep learning has shown promise in predicting hypertension (HTN) from fundus images. However, most prior research has primarily focused on analyzing a single type of data, which may not capture the full complexity of HTN risk. To address this limitation, this study introduces a multimodal deep learning (MMDL) system, dubbed HyMNet, which combines fundus images and cardiometabolic risk factors, specifically age and gender, to improve hypertension detection capabilities. Our MMDL system uses the DenseNet-201 architecture, pre-trained on ImageNet, for the fundus imaging path and a fully connected neural network for the age and gender path. The two paths are jointly trained by concatenating 64 features output from each path that are then fed into a fusion network. The system was trained on 1,143 retinal images from 626 individuals collected from the Saudi Ministry of National Guard Health Affairs. The results show that the multimodal model that integrates fundus images along with age and gender achieved an AUC of 0.791 [CI: 0.735, 0.848], which outperforms the unimodal model trained solely on fundus photographs that yielded an AUC of 0.766 [CI: 0.705, 0.828] for hypertension detection.