OpenMEDLab: An Open-source Platform for Multi-modality Foundation Models in Medicine

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Increasing SAM Zero-Shot Performance on Multimodal Medical Images Using GPT-4 Generated Descriptive Prompts Without Human Annotation

This study develops and evaluates a novel multimodal medical image zero-shot segmentation algorithm named Text-Visual-Prompt SAM (TV-SAM) without any manual annotations. TV-SAM incorporates and integrates large language model GPT-4, Vision Language Model GLIP, and Segment Anything Model (SAM), to autonomously generate descriptive text prompts and visual bounding box prompts from medical images, thereby enhancing SAM for zero-shot segmentation. Comprehensive evaluations are implemented on seven public datasets encompassing eight imaging modalities to demonstrate that TV-SAM can effectively segment unseen targets across various modalities without additional training, significantly outperforming SAM AUTO and GSAM, closely matching the performance of SAM BBOX with gold standard bounding box prompts, and surpassing the state-of-the-art on specific datasets like ISIC and WBC. The study indicates that TV-SAM serves as an effective multimodal medical image zero-shot segmentation algorithm, highlighting the significant contribution of GPT-4 to zero-shot segmentation. By integrating foundational models such as GPT-4, GLIP, and SAM, it could enhance the capability to address complex problems in specialized domains. The code is available at: https://github.com/JZK00/TV-SAM.

Deblurring Masked Autoencoder is Better Recipe for Ultrasound Image Recognition

Masked autoencoder (MAE) has attracted unprecedented attention and achieves remarkable performance in many vision tasks. It reconstructs random masked image patches (known as proxy task) during pretraining and learns meaningful semantic representations that can be transferred to downstream tasks. However, MAE has not been thoroughly explored in ultrasound imaging. In this work, we investigate the potential of MAE for ultrasound image recognition. Motivated by the unique property of ultrasound imaging in high noise-to-signal ratio, we propose a novel deblurring MAE approach that incorporates deblurring into the proxy task during pretraining. The addition of deblurring facilitates the pretraining to better recover the subtle details presented in the ultrasound images, thus improving the performance of the downstream classification task. Our experimental results demonstrate the effectiveness of our deblurring MAE, achieving state-of-the-art performance in ultrasound image classification. Overall, our work highlights the potential of MAE for ultrasound image recognition and presents a novel approach that incorporates deblurring to further improve its effectiveness.

ConES: Concept Embedding Search for Parameter Efficient Tuning Large Vision Language Models

Large pre-trained vision-language models have shown great prominence in transferring pre-acquired knowledge to various domains and downstream tasks with appropriate prompting or tuning. Existing prevalent tuning methods can be generally categorized into three genres: 1) prompt engineering by creating suitable prompt texts, which is time-consuming and requires domain expertise; 2) or simply fine-tuning the whole model, which is extremely inefficient; 3) prompt tuning through parameterized prompt embeddings with the text encoder. Nevertheless, all methods rely on the text encoder for bridging the modality gap between vision and language. In this work, we question the necessity of the cumbersome text encoder for a more lightweight and efficient tuning paradigm as well as more representative prompt embeddings closer to the image representations. To achieve this, we propose a Concept Embedding Search (ConES) approach by optimizing prompt embeddings -- without the need of the text encoder -- to capture the 'concept' of the image modality through a variety of task objectives. By dropping the text encoder, we are able to significantly speed up the learning process, \eg, from about an hour to just ten minutes in our experiments for personalized text-to-image generation without impairing the generation quality. Moreover, our proposed approach is orthogonal to current existing tuning methods since the searched concept embeddings can be further utilized in the next stage of fine-tuning the pre-trained large models for boosting performance. Extensive experiments show that our approach can beat the prompt tuning and textual inversion methods in a variety of downstream tasks including objection detection, instance segmentation, and image generation. Our approach also shows better generalization capability for unseen concepts in specialized domains, such as the medical domain.

SAM on Medical Images: A Comprehensive Study on Three Prompt Modes

The Segment Anything Model (SAM) made an eye-catching debut recently and inspired many researchers to explore its potential and limitation in terms of zero-shot generalization capability. As the first promptable foundation model for segmentation tasks, it was trained on a large dataset with an unprecedented number of images and annotations. This large-scale dataset and its promptable nature endow the model with strong zero-shot generalization. Although the SAM has shown competitive performance on several datasets, we still want to investigate its zero-shot generalization on medical images. As we know, the acquisition of medical image annotation usually requires a lot of effort from professional practitioners. Therefore, if there exists a foundation model that can give high-quality mask prediction simply based on a few point prompts, this model will undoubtedly become the game changer for medical image analysis. To evaluate whether SAM has the potential to become the foundation model for medical image segmentation tasks, we collected more than 12 public medical image datasets that cover various organs and modalities. We also explore what kind of prompt can lead to the best zero-shot performance with different modalities. Furthermore, we find that a pattern shows that the perturbation of the box size will significantly change the prediction accuracy. Finally, Extensive experiments show that the predicted mask quality varied a lot among different datasets. And providing proper prompts, such as bounding boxes, to the SAM will significantly increase its performance.

Towards General Purpose Medical AI: Continual Learning Medical Foundation Model

Inevitable domain and task discrepancies in real-world scenarios can impair the generalization performance of the pre-trained deep models for medical data. Therefore, we audaciously propose that we should build a general-purpose medical AI system that can be seamlessly adapted to downstream domains/tasks. Since the domain/task adaption procedures usually involve additional labeling work for the target data, designing a data-efficient adaption algorithm is desired to save the cost of transferring the learned knowledge. Our recent work found that vision-language models (VLMs) are efficient learners with extraordinary cross-domain ability. Therefore, in this work, we further explore the possibility of leveraging pre-trained VLMs as medical foundation models for building general-purpose medical AI, where we thoroughly investigate three machine-learning paradigms, i.e., domain/task-specialized learning, joint learning, and continual learning, for training the VLMs and evaluate their generalization performance on cross-domain and cross-task test sets. To alleviate the catastrophic forgetting during sequential training, we employ rehearsal learning and receive a sharp boost in terms of generalization capability. In a nutshell, our empirical evidence suggests that continual learning may be a practical and efficient learning paradigm for the medical foundation model. And we hope researchers can use our empirical evidence as basement to further explore the path toward medical foundation model.

Medical Image Understanding with Pretrained Vision Language Models: A Comprehensive Study

The large-scale pre-trained vision language models (VLM) have shown remarkable domain transfer capability on natural images. However, it remains unknown whether this capability can also apply to the medical image domain. This paper thoroughly studies the knowledge transferability of pre-trained VLMs to the medical domain, where we show that well-designed medical prompts are the key to elicit knowledge from pre-trained VLMs. We demonstrate that by prompting with expressive attributes that are shared between domains, the VLM can carry the knowledge across domains and improve its generalization. This mechanism empowers VLMs to recognize novel objects with fewer or without image samples. Furthermore, to avoid the laborious manual designing process, we develop three approaches for automatic generation of medical prompts, which can inject expert-level medical knowledge and image-specific information into the prompts for fine-grained grounding. We conduct extensive experiments on thirteen different medical datasets across various modalities, showing that our well-designed prompts greatly improve the zero-shot performance compared to the default prompts, and our fine-tuned models surpass the supervised models by a significant margin.

FlowX: Towards Explainable Graph Neural Networks via Message Flows

We investigate the explainability of graph neural networks (GNNs) as a step towards elucidating their working mechanisms. While most current methods focus on explaining graph nodes, edges, or features, we argue that, as the inherent functional mechanism of GNNs, message flows are more natural for performing explainability. To this end, we propose a novel method here, known as FlowX, to explain GNNs by identifying important message flows. To quantify the importance of flows, we propose to follow the philosophy of Shapley values from cooperative game theory. To tackle the complexity of computing all coalitions' marginal contributions, we propose an approximation scheme to compute Shapley-like values as initial assessments of further redistribution training. We then propose a learning algorithm to train flow scores and improve explainability. Experimental studies on both synthetic and real-world datasets demonstrate that our proposed FlowX leads to improved explainability of GNNs.

Towards Adversarial Robustness via Transductive Learning

There has been emerging interest to use transductive learning for adversarial robustness (Goldwasser et al., NeurIPS 2020; Wu et al., ICML 2020). Compared to traditional "test-time" defenses, these defense mechanisms "dynamically retrain" the model based on test time input via transductive learning; and theoretically, attacking these defenses boils down to bilevel optimization, which seems to raise the difficulty for adaptive attacks. In this paper, we first formalize and analyze modeling aspects of transductive robustness. Then, we propose the principle of attacking model space for solving bilevel attack objectives, and present an instantiation of the principle which breaks previous transductive defenses. These attacks thus point to significant difficulties in the use of transductive learning to improve adversarial robustness. To this end, we present new theoretical and empirical evidence in support of the utility of transductive learning.