EndoFinder: Online Image Retrieval for Explainable Colorectal Polyp Diagnosis

Determining the necessity of resecting malignant polyps during colonoscopy screen is crucial for patient outcomes, yet challenging due to the time-consuming and costly nature of histopathology examination. While deep learning-based classification models have shown promise in achieving optical biopsy with endoscopic images, they often suffer from a lack of explainability. To overcome this limitation, we introduce EndoFinder, a content-based image retrieval framework to find the 'digital twin' polyp in the reference database given a newly detected polyp. The clinical semantics of the new polyp can be inferred referring to the matched ones. EndoFinder pioneers a polyp-aware image encoder that is pre-trained on a large polyp dataset in a self-supervised way, merging masked image modeling with contrastive learning. This results in a generic embedding space ready for different downstream clinical tasks based on image retrieval. We validate the framework on polyp re-identification and optical biopsy tasks, with extensive experiments demonstrating that EndoFinder not only achieves explainable diagnostics but also matches the performance of supervised classification models. EndoFinder's reliance on image retrieval has the potential to support diverse downstream decision-making tasks during real-time colonoscopy procedures.

Test-Time Generative Augmentation for Medical Image Segmentation

In this paper, we propose a novel approach to enhance medical image segmentation during test time. Instead of employing hand-crafted transforms or functions on the input test image to create multiple views for test-time augmentation, we advocate for the utilization of an advanced domain-fine-tuned generative model (GM), e.g., stable diffusion (SD), for test-time augmentation. Given that the GM has been trained to comprehend and encapsulate comprehensive domain data knowledge, it is superior than segmentation models in terms of representing the data characteristics and distribution. Hence, by integrating the GM into test-time augmentation, we can effectively generate multiple views of a given test sample, aligning with the content and appearance characteristics of the sample and the related local data distribution. This approach renders the augmentation process more adaptable and resilient compared to conventional handcrafted transforms. Comprehensive experiments conducted across three medical image segmentation tasks (nine datasets) demonstrate the efficacy and versatility of the proposed TTGA in enhancing segmentation outcomes. Moreover, TTGA significantly improves pixel-wise error estimation, thereby facilitating the deployment of a more reliable segmentation system. Code will be released at: https://github.com/maxiao0234/TTGA.

An Empirical Study on the Fairness of Foundation Models for Multi-Organ Image Segmentation

The segmentation foundation model, e.g., Segment Anything Model (SAM), has attracted increasing interest in the medical image community. Early pioneering studies primarily concentrated on assessing and improving SAM's performance from the perspectives of overall accuracy and efficiency, yet little attention was given to the fairness considerations. This oversight raises questions about the potential for performance biases that could mirror those found in task-specific deep learning models like nnU-Net. In this paper, we explored the fairness dilemma concerning large segmentation foundation models. We prospectively curate a benchmark dataset of 3D MRI and CT scans of the organs including liver, kidney, spleen, lung and aorta from a total of 1056 healthy subjects with expert segmentations. Crucially, we document demographic details such as gender, age, and body mass index (BMI) for each subject to facilitate a nuanced fairness analysis. We test state-of-the-art foundation models for medical image segmentation, including the original SAM, medical SAM and SAT models, to evaluate segmentation efficacy across different demographic groups and identify disparities. Our comprehensive analysis, which accounts for various confounding factors, reveals significant fairness concerns within these foundational models. Moreover, our findings highlight not only disparities in overall segmentation metrics, such as the Dice Similarity Coefficient but also significant variations in the spatial distribution of segmentation errors, offering empirical evidence of the nuanced challenges in ensuring fairness in medical image segmentation.

Boosting Medical Image Classification with Segmentation Foundation Model

The Segment Anything Model (SAM) exhibits impressive capabilities in zero-shot segmentation for natural images. Recently, SAM has gained a great deal of attention for its applications in medical image segmentation. However, to our best knowledge, no studies have shown how to harness the power of SAM for medical image classification. To fill this gap and make SAM a true ``foundation model'' for medical image analysis, it is highly desirable to customize SAM specifically for medical image classification. In this paper, we introduce SAMAug-C, an innovative augmentation method based on SAM for augmenting classification datasets by generating variants of the original images. The augmented datasets can be used to train a deep learning classification model, thereby boosting the classification performance. Furthermore, we propose a novel framework that simultaneously processes raw and SAMAug-C augmented image input, capitalizing on the complementary information that is offered by both. Experiments on three public datasets validate the effectiveness of our new approach.

Self Pre-training with Topology- and Spatiality-aware Masked Autoencoders for 3D Medical Image Segmentation

Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can aggregate contextual information for downstream tasks. But, existing MAE pre-training methods, which were specifically developed with the ViT architecture, lack the ability to capture geometric shape and spatial information, which is critical for medical image segmentation tasks. In this paper, we propose a novel extension of known MAEs for self pre-training (i.e., models pre-trained on the same target dataset) for 3D medical image segmentation. (1) We propose a new topological loss to preserve geometric shape information by computing topological signatures of both the input and reconstructed volumes, learning geometric shape information. (2) We introduce a pre-text task that predicts the positions of the centers and eight corners of 3D crops, enabling the MAE to aggregate spatial information. (3) We extend the MAE pre-training strategy to a hybrid state-of-the-art (SOTA) medical image segmentation architecture and co-pretrain it alongside the ViT. (4) We develop a fine-tuned model for downstream segmentation tasks by complementing the pre-trained ViT encoder with our pre-trained SOTA model. Extensive experiments on five public 3D segmentation datasets show the effectiveness of our new approach.

Improving Segment Anything on the Fly: Auxiliary Online Learning and Adaptive Fusion for Medical Image Segmentation

The current variants of the Segment Anything Model (SAM), which include the original SAM and Medical SAM, still lack the capability to produce sufficiently accurate segmentation for medical images. In medical imaging contexts, it is not uncommon for human experts to rectify segmentations of specific test samples after SAM generates its segmentation predictions. These rectifications typically entail manual or semi-manual corrections employing state-of-the-art annotation tools. Motivated by this process, we introduce a novel approach that leverages the advantages of online machine learning to enhance Segment Anything (SA) during test time. We employ rectified annotations to perform online learning, with the aim of improving the segmentation quality of SA on medical images. To improve the effectiveness and efficiency of online learning when integrated with large-scale vision models like SAM, we propose a new method called Auxiliary Online Learning (AuxOL). AuxOL creates and applies a small auxiliary model (specialist) in conjunction with SAM (generalist), entails adaptive online-batch and adaptive segmentation fusion. Experiments conducted on eight datasets covering four medical imaging modalities validate the effectiveness of the proposed method. Our work proposes and validates a new, practical, and effective approach for enhancing SA on downstream segmentation tasks (e.g., medical image segmentation).

Improving GFlowNets for Text-to-Image Diffusion Alignment

Diffusion models have become the \textit{de-facto} approach for generating visual data, which are trained to match the distribution of the training dataset. In addition, we also want to control generation to fulfill desired properties such as alignment to a text description, which can be specified with a black-box reward function. Prior works fine-tune pretrained diffusion models to achieve this goal through reinforcement learning-based algorithms. Nonetheless, they suffer from issues including slow credit assignment as well as low quality in their generated samples. In this work, we explore techniques that do not directly maximize the reward but rather generate high-reward images with relatively high probability -- a natural scenario for the framework of generative flow networks (GFlowNets). To this end, we propose the \textbf{D}iffusion \textbf{A}lignment with \textbf{G}FlowNet (DAG) algorithm to post-train diffusion models with black-box property functions. Extensive experiments on Stable Diffusion and various reward specifications corroborate that our method could effectively align large-scale text-to-image diffusion models with given reward information.

Kaleido Diffusion: Improving Conditional Diffusion Models with Autoregressive Latent Modeling

Diffusion models have emerged as a powerful tool for generating high-quality images from textual descriptions. Despite their successes, these models often exhibit limited diversity in the sampled images, particularly when sampling with a high classifier-free guidance weight. To address this issue, we present Kaleido, a novel approach that enhances the diversity of samples by incorporating autoregressive latent priors. Kaleido integrates an autoregressive language model that encodes the original caption and generates latent variables, serving as abstract and intermediary representations for guiding and facilitating the image generation process. In this paper, we explore a variety of discrete latent representations, including textual descriptions, detection bounding boxes, object blobs, and visual tokens. These representations diversify and enrich the input conditions to the diffusion models, enabling more diverse outputs. Our experimental results demonstrate that Kaleido effectively broadens the diversity of the generated image samples from a given textual description while maintaining high image quality. Furthermore, we show that Kaleido adheres closely to the guidance provided by the generated latent variables, demonstrating its capability to effectively control and direct the image generation process.

Navigating User Experience of ChatGPT-based Conversational Recommender Systems: The Effects of Prompt Guidance and Recommendation Domain

Conversational recommender systems (CRS) enable users to articulate their preferences and provide feedback through natural language. With the advent of large language models (LLMs), the potential to enhance user engagement with CRS and augment the recommendation process with LLM-generated content has received increasing attention. However, the efficacy of LLM-powered CRS is contingent upon the use of prompts, and the subjective perception of recommendation quality can differ across various recommendation domains. Therefore, we have developed a ChatGPT-based CRS to investigate the impact of these two factors, prompt guidance (PG) and recommendation domain (RD), on the overall user experience of the system. We conducted an online empirical study (N = 100) by employing a mixed-method approach that utilized a between-subjects design for the variable of PG (with vs. without) and a within-subjects design for RD (book recommendations vs. job recommendations). The findings reveal that PG can substantially enhance the system's explainability, adaptability, perceived ease of use, and transparency. Moreover, users are inclined to perceive a greater sense of novelty and demonstrate a higher propensity to engage with and try recommended items in the context of book recommendations as opposed to job recommendations. Furthermore, the influence of PG on certain user experience metrics and interactive behaviors appears to be modulated by the recommendation domain, as evidenced by the interaction effects between the two examined factors. This work contributes to the user-centered evaluation of ChatGPT-based CRS by investigating two prominent factors and offers practical design guidance.

Many-to-many Image Generation with Auto-regressive Diffusion Models

Recent advancements in image generation have made significant progress, yet existing models present limitations in perceiving and generating an arbitrary number of interrelated images within a broad context. This limitation becomes increasingly critical as the demand for multi-image scenarios, such as multi-view images and visual narratives, grows with the expansion of multimedia platforms. This paper introduces a domain-general framework for many-to-many image generation, capable of producing interrelated image series from a given set of images, offering a scalable solution that obviates the need for task-specific solutions across different multi-image scenarios. To facilitate this, we present MIS, a novel large-scale multi-image dataset, containing 12M synthetic multi-image samples, each with 25 interconnected images. Utilizing Stable Diffusion with varied latent noises, our method produces a set of interconnected images from a single caption. Leveraging MIS, we learn M2M, an autoregressive model for many-to-many generation, where each image is modeled within a diffusion framework. Throughout training on the synthetic MIS, the model excels in capturing style and content from preceding images - synthetic or real - and generates novel images following the captured patterns. Furthermore, through task-specific fine-tuning, our model demonstrates its adaptability to various multi-image generation tasks, including Novel View Synthesis and Visual Procedure Generation.