Foundational Models in Medical Imaging: A Comprehensive Survey and Future Vision

Foundation models, large-scale, pre-trained deep-learning models adapted to a wide range of downstream tasks have gained significant interest lately in various deep-learning problems undergoing a paradigm shift with the rise of these models. Trained on large-scale dataset to bridge the gap between different modalities, foundation models facilitate contextual reasoning, generalization, and prompt capabilities at test time. The predictions of these models can be adjusted for new tasks by augmenting the model input with task-specific hints called prompts without requiring extensive labeled data and retraining. Capitalizing on the advances in computer vision, medical imaging has also marked a growing interest in these models. To assist researchers in navigating this direction, this survey intends to provide a comprehensive overview of foundation models in the domain of medical imaging. Specifically, we initiate our exploration by providing an exposition of the fundamental concepts forming the basis of foundation models. Subsequently, we offer a methodical taxonomy of foundation models within the medical domain, proposing a classification system primarily structured around training strategies, while also incorporating additional facets such as application domains, imaging modalities, specific organs of interest, and the algorithms integral to these models. Furthermore, we emphasize the practical use case of some selected approaches and then discuss the opportunities, applications, and future directions of these large-scale pre-trained models, for analyzing medical images. In the same vein, we address the prevailing challenges and research pathways associated with foundational models in medical imaging. These encompass the areas of interpretability, data management, computational requirements, and the nuanced issue of contextual comprehension.Comment: The paper is currently in the process of being prepared for submission to MI

Contrastive Attention for Automatic Chest X-ray Report Generation

Recently, chest X-ray report generation, which aims to automatically generate descriptions of given chest X-ray images, has received growing research interests. The key challenge of chest X-ray report generation is to accurately capture and describe the abnormal regions. In most cases, the normal regions dominate the entire chest X-ray image, and the corresponding descriptions of these normal regions dominate the final report. Due to such data bias, learning-based models may fail to attend to abnormal regions. In this work, to effectively capture and describe abnormal regions, we propose the Contrastive Attention (CA) model. Instead of solely focusing on the current input image, the CA model compares the current input image with normal images to distill the contrastive information. The acquired contrastive information can better represent the visual features of abnormal regions. According to the experiments on the public IU-X-ray and MIMIC-CXR datasets, incorporating our CA into several existing models can boost their performance across most metrics. In addition, according to the analysis, the CA model can help existing models better attend to the abnormal regions and provide more accurate descriptions which are crucial for an interpretable diagnosis. Specifically, we achieve the state-of-the-art results on the two public datasets.Comment: Appear in Findings of ACL 2021 (The Joint Conference of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (ACL-IJCNLP 2021)

Competence-based Multimodal Curriculum Learning for Medical Report Generation

Medical report generation task, which targets to produce long and coherent descriptions of medical images, has attracted growing research interests recently. Different from the general image captioning tasks, medical report generation is more challenging for data-driven neural models. This is mainly due to 1) the serious data bias and 2) the limited medical data. To alleviate the data bias and make best use of available data, we propose a Competence-based Multimodal Curriculum Learning framework (CMCL). Specifically, CMCL simulates the learning process of radiologists and optimizes the model in a step by step manner. Firstly, CMCL estimates the difficulty of each training instance and evaluates the competence of current model; Secondly, CMCL selects the most suitable batch of training instances considering current model competence. By iterating above two steps, CMCL can gradually improve the model's performance. The experiments on the public IU-Xray and MIMIC-CXR datasets show that CMCL can be incorporated into existing models to improve their performance.Comment: Accepted by ACL 2021 (Oral

Deep reproductive feature generation framework for the diagnosis of COVID-19 and viral pneumonia using chest X-ray images

The rapid and accurate detection of COVID-19 cases is critical for timely treatment and preventing the spread of the disease. In this study, a two-stage feature extraction framework using eight state-of-the-art pre-trained deep Convolutional Neural Networks (CNNs) and an autoencoder is proposed to determine the health conditions of patients (COVID-19, Normal, Viral Pneumonia) based on chest X-rays. The X-ray scans are divided into four equally sized sections and analyzed by deep pre-trained CNNs. Subsequently, an autoencoder with three hidden layers is trained to extract reproductive features from the concatenated ouput of CNNs. To evaluate the performance of the proposed framework, three different classifiers, which are single-layer perceptron (SLP), multi-layer perceptron (MLP), and support vector machine (SVM) are used. Furthermore, the deep CNN architectures are used to create benchmark models and trained on the same dataset for comparision. The proposed framework outperforms other frameworks wih pre-trained feature extractors in binary classification and shows competitive results in three-class classification. The proposed methodology is task-independent and suitable for addressing various problems. The results show that the discriminative features are a subset of the reproductive features, suggesting that extracting task-independent features is superior to the extraction only task-based features. The flexibility and task-independence of the reproductive features make the conceptive information approach more favorable. The proposed methodology is novel and shows promising results for analyzing medical image data

Data-Centric Foundation Models in Computational Healthcare: A Survey

The advent of foundation models (FMs) as an emerging suite of AI techniques has struck a wave of opportunities in computational healthcare. The interactive nature of these models, guided by pre-training data and human instructions, has ignited a data-centric AI paradigm that emphasizes better data characterization, quality, and scale. In healthcare AI, obtaining and processing high-quality clinical data records has been a longstanding challenge, ranging from data quantity, annotation, patient privacy, and ethics. In this survey, we investigate a wide range of data-centric approaches in the FM era (from model pre-training to inference) towards improving the healthcare workflow. We discuss key perspectives in AI security, assessment, and alignment with human values. Finally, we offer a promising outlook of FM-based analytics to enhance the performance of patient outcome and clinical workflow in the evolving landscape of healthcare and medicine. We provide an up-to-date list of healthcare-related foundation models and datasets at https://github.com/Yunkun-Zhang/Data-Centric-FM-Healthcare

Generative models improve fairness of medical classifiers under distribution shifts

A ubiquitous challenge in machine learning is the problem of domain generalisation. This can exacerbate bias against groups or labels that are underrepresented in the datasets used for model development. Model bias can lead to unintended harms, especially in safety-critical applications like healthcare. Furthermore, the challenge is compounded by the difficulty of obtaining labelled data due to high cost or lack of readily available domain expertise. In our work, we show that learning realistic augmentations automatically from data is possible in a label-efficient manner using generative models. In particular, we leverage the higher abundance of unlabelled data to capture the underlying data distribution of different conditions and subgroups for an imaging modality. By conditioning generative models on appropriate labels, we can steer the distribution of synthetic examples according to specific requirements. We demonstrate that these learned augmentations can surpass heuristic ones by making models more robust and statistically fair in- and out-of-distribution. To evaluate the generality of our approach, we study 3 distinct medical imaging contexts of varying difficulty: (i) histopathology images from a publicly available generalisation benchmark, (ii) chest X-rays from publicly available clinical datasets, and (iii) dermatology images characterised by complex shifts and imaging conditions. Complementing real training samples with synthetic ones improves the robustness of models in all three medical tasks and increases fairness by improving the accuracy of diagnosis within underrepresented groups. This approach leads to stark improvements OOD across modalities: 7.7% prediction accuracy improvement in histopathology, 5.2% in chest radiology with 44.6% lower fairness gap and a striking 63.5% improvement in high-risk sensitivity for dermatology with a 7.5x reduction in fairness gap

Toward fairness in artificial intelligence for medical image analysis: Identification and mitigation of potential biases in the roadmap from data collection to model deployment

Purpose: To recognize and address various sources of bias essential for algorithmic fairness and trustworthiness and to contribute to a just and equitable deployment of AI in medical imaging, there is an increasing interest in developing medical imaging-based machine learning methods, also known as medical imaging artificial intelligence (AI), for the detection, diagnosis, prognosis, and risk assessment of disease with the goal of clinical implementation. These tools are intended to help improve traditional human decision-making in medical imaging. However, biases introduced in the steps toward clinical deployment may impede their intended function, potentially exacerbating inequities. Specifically, medical imaging AI can propagate or amplify biases introduced in the many steps from model inception to deployment, resulting in a systematic difference in the treatment of different groups. Approach: Our multi-institutional team included medical physicists, medical imaging artificial intelligence/machine learning (AI/ML) researchers, experts in AI/ML bias, statisticians, physicians, and scientists from regulatory bodies. We identified sources of bias in AI/ML, mitigation strategies for these biases, and developed recommendations for best practices in medical imaging AI/ML development. Results: Five main steps along the roadmap of medical imaging AI/ML were identified: (1) data collection, (2) data preparation and annotation, (3) model development, (4) model evaluation, and (5) model deployment. Within these steps, or bias categories, we identified 29 sources of potential bias, many of which can impact multiple steps, as well as mitigation strategies. Conclusions: Our findings provide a valuable resource to researchers, clinicians, and the public at large.</p