Ultra-Resolution Cascaded Diffusion Model for Gigapixel Image Synthesis in Histopathology

Diagnoses from histopathology images rely on information from both high and low resolutions of Whole Slide Images. Ultra-Resolution Cascaded Diffusion Models (URCDMs) allow for the synthesis of high-resolution images that are realistic at all magnification levels, focusing not only on fidelity but also on long-distance spatial coherency. Our model beats existing methods, improving the pFID-50k [2] score by 110.63 to 39.52 pFID-50k. Additionally, a human expert evaluation study was performed, reaching a weighted Mean Absolute Error (MAE) of 0.11 for the Lower Resolution Diffusion Models and a weighted MAE of 0.22 for the URCDM.

Exploring the Hyperparameter Space of Image Diffusion Models for Echocardiogram Generation

This work presents an extensive hyperparameter search on Image Diffusion Models for Echocardiogram generation. The objective is to establish foundational benchmarks and provide guidelines within the realm of ultrasound image and video generation. This study builds over the latest advancements, including cutting-edge model architectures and training methodologies. We also examine the distribution shift between real and generated samples and consider potential solutions, crucial to train efficient models on generated data. We determine an Optimal FID score of $0.88$ for our research problem and achieve an FID of $2.60$. This work is aimed at contributing valuable insights and serving as a reference for further developments in the specialized field of ultrasound image and video generation.

GenerateCT: Text-Guided 3D Chest CT Generation

Generative modeling has experienced substantial progress in recent years, particularly in text-to-image and text-to-video synthesis. However, the medical field has not yet fully exploited the potential of large-scale foundational models for synthetic data generation. In this paper, we introduce GenerateCT, the first method for text-conditional computed tomography (CT) generation, addressing the limitations in 3D medical imaging research and making our entire framework open-source. GenerateCT consists of a pre-trained large language model, a transformer-based text-conditional 3D chest CT generation architecture, and a text-conditional spatial super-resolution diffusion model. We also propose CT-ViT, which efficiently compresses CT volumes while preserving auto-regressiveness in-depth, enabling the generation of 3D CT volumes with variable numbers of axial slices. Our experiments demonstrate that GenerateCT can produce realistic, high-resolution, and high-fidelity 3D chest CT volumes consistent with medical language text prompts. We further investigate the potential of GenerateCT by training a model using generated CT volumes for multi-abnormality classification of chest CT volumes. Our contributions provide a valuable foundation for future research in text-conditional 3D medical image generation and have the potential to accelerate advancements in medical imaging research. Our code, pre-trained models, and generated data are available at https://github.com/ibrahimethemhamamci/GenerateCT.

Pay Attention: Accuracy Versus Interpretability Trade-off in Fine-tuned Diffusion Models

The recent progress of diffusion models in terms of image quality has led to a major shift in research related to generative models. Current approaches often fine-tune pre-trained foundation models using domain-specific text-to-image pairs. This approach is straightforward for X-ray image generation due to the high availability of radiology reports linked to specific images. However, current approaches hardly ever look at attention layers to verify whether the models understand what they are generating. In this paper, we discover an important trade-off between image fidelity and interpretability in generative diffusion models. In particular, we show that fine-tuning text-to-image models with learnable text encoder leads to a lack of interpretability of diffusion models. Finally, we demonstrate the interpretability of diffusion models by showing that keeping the language encoder frozen, enables diffusion models to achieve state-of-the-art phrase grounding performance on certain diseases for a challenging multi-label segmentation task, without any additional training. Code and models will be available at https://github.com/MischaD/chest-distillation.

Feature-Conditioned Cascaded Video Diffusion Models for Precise Echocardiogram Synthesis

Image synthesis is expected to provide value for the translation of machine learning methods into clinical practice. Fundamental problems like model robustness, domain transfer, causal modelling, and operator training become approachable through synthetic data. Especially, heavily operator-dependant modalities like Ultrasound imaging require robust frameworks for image and video generation. So far, video generation has only been possible by providing input data that is as rich as the output data, e.g., image sequence plus conditioning in, video out. However, clinical documentation is usually scarce and only single images are reported and stored, thus retrospective patient-specific analysis or the generation of rich training data becomes impossible with current approaches. In this paper, we extend elucidated diffusion models for video modelling to generate plausible video sequences from single images and arbitrary conditioning with clinical parameters. We explore this idea within the context of echocardiograms by looking into the variation of the Left Ventricle Ejection Fraction, the most essential clinical metric gained from these examinations. We use the publicly available EchoNet-Dynamic dataset for all our experiments. Our image to sequence approach achieves an $R^2$ score of 93%, which is 38 points higher than recently proposed sequence to sequence generation methods. Code and models will be available at: https://github.com/HReynaud/EchoDiffusion.

Zero-Shot Object Segmentation through Concept Distillation from Generative Image Foundation Models

Curating datasets for object segmentation is a difficult task. With the advent of large-scale pre-trained generative models, conditional image generation has been given a significant boost in result quality and ease of use. In this paper, we present a novel method that enables the generation of general foreground-background segmentation models from simple textual descriptions, without requiring segmentation labels. We leverage and explore pre-trained latent diffusion models, to automatically generate weak segmentation masks for concepts and objects. The masks are then used to fine-tune the diffusion model on an inpainting task, which enables fine-grained removal of the object, while at the same time providing a synthetic foreground and background dataset. We demonstrate that using this method beats previous methods in both discriminative and generative performance and closes the gap with fully supervised training while requiring no pixel-wise object labels. We show results on the task of segmenting four different objects (humans, dogs, cars, birds).

Is More Data All You Need? A Causal Exploration

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

D'ARTAGNAN: Counterfactual Video Generation

Causally-enabled machine learning frameworks could help clinicians to identify the best course of treatments by answering counterfactual questions. We explore this path for the case of echocardiograms by looking into the variation of the Left Ventricle Ejection Fraction, the most essential clinical metric gained from these examinations. We combine deep neural networks, twin causal networks and generative adversarial methods for the first time to build D'ARTAGNAN (Deep ARtificial Twin-Architecture GeNerAtive Networks), a novel causal generative model. We demonstrate the soundness of our approach on a synthetic dataset before applying it to cardiac ultrasound videos by answering the question: "What would this echocardiogram look like if the patient had a different ejection fraction?". To do so, we generate new ultrasound videos, retaining the video style and anatomy of the original patient, with variations of the Ejection Fraction conditioned on a given input. We achieve an SSIM score of 0.79 and an R2 score of 0.51 on the counterfactual videos. Code and models are available at https://github.com/HReynaud/dartagnan.

Cross Modality 3D Navigation Using Reinforcement Learning and Neural Style Transfer

This paper presents the use of Multi-Agent Reinforcement Learning (MARL) to perform navigation in 3D anatomical volumes from medical imaging. We utilize Neural Style Transfer to create synthetic Computed Tomography (CT) agent gym environments and assess the generalization capabilities of our agents to clinical CT volumes. Our framework does not require any labelled clinical data and integrates easily with several image translation techniques, enabling cross modality applications. Further, we solely condition our agents on 2D slices, breaking grounds for 3D guidance in much more difficult imaging modalities, such as ultrasound imaging. This is an important step towards user guidance during the acquisition of standardised diagnostic view planes, improving diagnostic consistency and facilitating better case comparison.

Ultrasound Video Transformers for Cardiac Ejection Fraction Estimation

Cardiac ultrasound imaging is used to diagnose various heart diseases. Common analysis pipelines involve manual processing of the video frames by expert clinicians. This suffers from intra- and inter-observer variability. We propose a novel approach to ultrasound video analysis using a transformer architecture based on a Residual Auto-Encoder Network and a BERT model adapted for token classification. This enables videos of any length to be processed. We apply our model to the task of End-Systolic (ES) and End-Diastolic (ED) frame detection and the automated computation of the left ventricular ejection fraction. We achieve an average frame distance of 3.36 frames for the ES and 7.17 frames for the ED on videos of arbitrary length. Our end-to-end learnable approach can estimate the ejection fraction with a MAE of 5.95 and $R^2$ of 0.52 in 0.15s per video, showing that segmentation is not the only way to predict ejection fraction. Code and models are available at https://github.com/HReynaud/UVT.