Streamlined Photoacoustic Image Processing with Foundation Models: A Training-Free Solution

Foundation models have rapidly evolved and have achieved significant accomplishments in computer vision tasks. Specifically, the prompt mechanism conveniently allows users to integrate image prior information into the model, making it possible to apply models without any training. Therefore, we propose a method based on foundation models and zero training to solve the tasks of photoacoustic (PA) image segmentation. We employed the segment anything model (SAM) by setting simple prompts and integrating the model's outputs with prior knowledge of the imaged objects to accomplish various tasks, including: (1) removing the skin signal in three-dimensional PA image rendering; (2) dual speed-of-sound reconstruction, and (3) segmentation of finger blood vessels. Through these demonstrations, we have concluded that deep learning can be directly applied in PA imaging without the requirement for network design and training. This potentially allows for a hands-on, convenient approach to achieving efficient and accurate segmentation of PA images. This letter serves as a comprehensive tutorial, facilitating the mastery of the technique through the provision of code and sample datasets.

FairCLIP: Harnessing Fairness in Vision-Language Learning

Fairness is a critical concern in deep learning, especially in healthcare, where these models influence diagnoses and treatment decisions. Although fairness has been investigated in the vision-only domain, the fairness of medical vision-language (VL) models remains unexplored due to the scarcity of medical VL datasets for studying fairness. To bridge this research gap, we introduce the first fair vision-language medical dataset Harvard-FairVLMed that provides detailed demographic attributes, ground-truth labels, and clinical notes to facilitate an in-depth examination of fairness within VL foundation models. Using Harvard-FairVLMed, we conduct a comprehensive fairness analysis of two widely-used VL models (CLIP and BLIP2), pre-trained on both natural and medical domains, across four different protected attributes. Our results highlight significant biases in all VL models, with Asian, Male, Non-Hispanic, and Spanish being the preferred subgroups across the protected attributes of race, gender, ethnicity, and language, respectively. In order to alleviate these biases, we propose FairCLIP, an optimal-transport-based approach that achieves a favorable trade-off between performance and fairness by reducing the Sinkhorn distance between the overall sample distribution and the distributions corresponding to each demographic group. As the first VL dataset of its kind, Harvard-FairVLMed holds the potential to catalyze advancements in the development of machine learning models that are both ethically aware and clinically effective. Our dataset and code are available at https://ophai.hms.harvard.edu/datasets/harvard-fairvlmed10k.

MedFLIP: Medical Vision-and-Language Self-supervised Fast Pre-Training with Masked Autoencoder

Within the domain of medical analysis, extensive research has explored the potential of mutual learning between Masked Autoencoders(MAEs) and multimodal data. However, the impact of MAEs on intermodality remains a key challenge. We introduce MedFLIP, a Fast Language-Image Pre-training method for Medical analysis. We explore MAEs for zero-shot learning with crossed domains, which enhances the model ability to learn from limited data, a common scenario in medical diagnostics. We verify that masking an image does not affect intermodal learning. Furthermore, we propose the SVD loss to enhance the representation learning for characteristics of medical images, aiming to improve classification accuracy by leveraging the structural intricacies of such data. Lastly, we validate using language will improve the zero-shot performance for the medical image analysis. MedFLIP scaling of the masking process marks an advancement in the field, offering a pathway to rapid and precise medical image analysis without the traditional computational bottlenecks. Through experiments and validation, MedFLIP demonstrates efficient performance improvements, setting an explored standard for future research and application in medical diagnostics.

TransFlower: An Explainable Transformer-Based Model with Flow-to-Flow Attention for Commuting Flow Prediction

Understanding the link between urban planning and commuting flows is crucial for guiding urban development and policymaking. This research, bridging computer science and urban studies, addresses the challenge of integrating these fields with their distinct focuses. Traditional urban studies methods, like the gravity and radiation models, often underperform in complex scenarios due to their limited handling of multiple variables and reliance on overly simplistic and unrealistic assumptions, such as spatial isotropy. While deep learning models offer improved accuracy, their black-box nature poses a trade-off between performance and explainability -- both vital for analyzing complex societal phenomena like commuting flows. To address this, we introduce TransFlower, an explainable, transformer-based model employing flow-to-flow attention to predict urban commuting patterns. It features a geospatial encoder with an anisotropy-aware relative location encoder for nuanced flow representation. Following this, the transformer-based flow predictor enhances this by leveraging attention mechanisms to efficiently capture flow interactions. Our model outperforms existing methods by up to 30.8% Common Part of Commuters, offering insights into mobility dynamics crucial for urban planning and policy decisions.

Prismatic: Interactive Multi-View Cluster Analysis of Concept Stocks

Financial cluster analysis allows investors to discover investment alternatives and avoid undertaking excessive risks. However, this analytical task faces substantial challenges arising from many pairwise comparisons, the dynamic correlations across time spans, and the ambiguity in deriving implications from business relational knowledge. We propose Prismatic, a visual analytics system that integrates quantitative analysis of historical performance and qualitative analysis of business relational knowledge to cluster correlated businesses interactively. Prismatic features three clustering processes: dynamic cluster generation, knowledge-based cluster exploration, and correlation-based cluster validation. Utilizing a multi-view clustering approach, it enriches data-driven clusters with knowledge-driven similarity, providing a nuanced understanding of business correlations. Through well-coordinated visual views, Prismatic facilitates a comprehensive interpretation of intertwined quantitative and qualitative features, demonstrating its usefulness and effectiveness via case studies on formulating concept stocks and extensive interviews with domain experts.

Cut-and-Paste: Subject-Driven Video Editing with Attention Control

This paper presents a novel framework termed Cut-and-Paste for real-word semantic video editing under the guidance of text prompt and additional reference image. While the text-driven video editing has demonstrated remarkable ability to generate highly diverse videos following given text prompts, the fine-grained semantic edits are hard to control by plain textual prompt only in terms of object details and edited region, and cumbersome long text descriptions are usually needed for the task. We therefore investigate subject-driven video editing for more precise control of both edited regions and background preservation, and fine-grained semantic generation. We achieve this goal by introducing an reference image as supplementary input to the text-driven video editing, which avoids racking your brain to come up with a cumbersome text prompt describing the detailed appearance of the object. To limit the editing area, we refer to a method of cross attention control in image editing and successfully extend it to video editing by fusing the attention map of adjacent frames, which strikes a balance between maintaining video background and spatio-temporal consistency. Compared with current methods, the whole process of our method is like ``cut" the source object to be edited and then ``paste" the target object provided by reference image. We demonstrate that our method performs favorably over prior arts for video editing under the guidance of text prompt and extra reference image, as measured by both quantitative and subjective evaluations.

FairSeg: A Large-scale Medical Image Segmentation Dataset for Fairness Learning with Fair Error-Bound Scaling

Fairness in artificial intelligence models has gained significantly more attention in recent years, especially in the area of medicine, as fairness in medical models is critical to people's well-being and lives. High-quality medical fairness datasets are needed to promote fairness learning research. Existing medical fairness datasets are all for classification tasks, and no fairness datasets are available for medical segmentation, while medical segmentation is an equally important clinical task as classifications, which can provide detailed spatial information on organ abnormalities ready to be assessed by clinicians. In this paper, we propose the first fairness dataset for medical segmentation named FairSeg with 10,000 subject samples. In addition, we propose a fair error-bound scaling approach to reweight the loss function with the upper error-bound in each identity group. We anticipate that the segmentation performance equity can be improved by explicitly tackling the hard cases with high training errors in each identity group. To facilitate fair comparisons, we propose new equity-scaled segmentation performance metrics, such as the equity-scaled Dice coefficient, which is calculated as the overall Dice coefficient divided by one plus the standard deviation of group Dice coefficients. Through comprehensive experiments, we demonstrate that our fair error-bound scaling approach either has superior or comparable fairness performance to the state-of-the-art fairness learning models. The dataset and code are publicly accessible via \url{https://github.com/Harvard-Ophthalmology-AI-Lab/FairSeg}.

Harvard Eye Fairness: A Large-Scale 3D Imaging Dataset for Equitable Eye Diseases Screening and Fair Identity Scaling

Fairness or equity in machine learning is profoundly important for societal well-being, but limited public datasets hinder its progress, especially in the area of medicine. It is undeniable that fairness in medicine is one of the most important areas for fairness learning's applications. Currently, no large-scale public medical datasets with 3D imaging data for fairness learning are available, while 3D imaging data in modern clinics are standard tests for disease diagnosis. In addition, existing medical fairness datasets are actually repurposed datasets, and therefore they typically have limited demographic identity attributes with at most three identity attributes of age, gender, and race for fairness modeling. To address this gap, we introduce our Eye Fairness dataset with 30,000 subjects (Harvard-EF) covering three major eye diseases including age-related macular degeneration, diabetic retinopathy, and glaucoma affecting 380 million patients globally. Our Harvard-EF dataset includes both 2D fundus photos and 3D optical coherence tomography scans with six demographic identity attributes including age, gender, race, ethnicity, preferred language, and marital status. We also propose a fair identity scaling (FIS) approach combining group and individual scaling together to improve model fairness. Our FIS approach is compared with various state-of-the-art fairness learning methods with superior performance in the racial, gender, and ethnicity fairness tasks with 2D and 3D imaging data, which demonstrate the utilities of our Harvard-EF dataset for fairness learning. To facilitate fairness comparisons between different models, we propose performance-scaled disparity measures, which can be used to compare model fairness accounting for overall performance levels. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-ef30k.

Harvard Glaucoma Detection and Progression: A Multimodal Multitask Dataset and Generalization-Reinforced Semi-Supervised Learning

Glaucoma is the number one cause of irreversible blindness globally. A major challenge for accurate glaucoma detection and progression forecasting is the bottleneck of limited labeled patients with the state-of-the-art (SOTA) 3D retinal imaging data of optical coherence tomography (OCT). To address the data scarcity issue, this paper proposes two solutions. First, we develop a novel generalization-reinforced semi-supervised learning (SSL) model called pseudo supervisor to optimally utilize unlabeled data. Compared with SOTA models, the proposed pseudo supervisor optimizes the policy of predicting pseudo labels with unlabeled samples to improve empirical generalization. Our pseudo supervisor model is evaluated with two clinical tasks consisting of glaucoma detection and progression forecasting. The progression forecasting task is evaluated both unimodally and multimodally. Our pseudo supervisor model demonstrates superior performance than SOTA SSL comparison models. Moreover, our model also achieves the best results on the publicly available LAG fundus dataset. Second, we introduce the Harvard Glaucoma Detection and Progression (Harvard-GDP) Dataset, a multimodal multitask dataset that includes data from 1,000 patients with OCT imaging data, as well as labels for glaucoma detection and progression. This is the largest glaucoma detection dataset with 3D OCT imaging data and the first glaucoma progression forecasting dataset that is publicly available. Detailed sex and racial analysis are provided, which can be used by interested researchers for fairness learning studies. Our released dataset is benchmarked with several SOTA supervised CNN and transformer deep learning models. The dataset and code are made publicly available via \url{https://ophai.hms.harvard.edu/datasets/harvard-gdp1000}.