Diff-Def: Diffusion-Generated Deformation Fields for Conditional Atlases

Anatomical atlases are widely used for population analysis. Conditional atlases target a particular sub-population defined via certain conditions (e.g. demographics or pathologies) and allow for the investigation of fine-grained anatomical differences - such as morphological changes correlated with age. Existing approaches use either registration-based methods that are unable to handle large anatomical variations or generative models, which can suffer from training instabilities and hallucinations. To overcome these limitations, we use latent diffusion models to generate deformation fields, which transform a general population atlas into one representing a specific sub-population. By generating a deformation field and registering the conditional atlas to a neighbourhood of images, we ensure structural plausibility and avoid hallucinations, which can occur during direct image synthesis. We compare our method to several state-of-the-art atlas generation methods in experiments using 5000 brain as well as whole-body MR images from UK Biobank. Our method generates highly realistic atlases with smooth transformations and high anatomical fidelity, outperforming the baselines.

Style-Extracting Diffusion Models for Semi-Supervised Histopathology Segmentation

Deep learning-based image generation has seen significant advancements with diffusion models, notably improving the quality of generated images. Despite these developments, generating images with unseen characteristics beneficial for downstream tasks has received limited attention. To bridge this gap, we propose Style-Extracting Diffusion Models, featuring two conditioning mechanisms. Specifically, we utilize 1) a style conditioning mechanism which allows to inject style information of previously unseen images during image generation and 2) a content conditioning which can be targeted to a downstream task, e.g., layout for segmentation. We introduce a trainable style encoder to extract style information from images, and an aggregation block that merges style information from multiple style inputs. This architecture enables the generation of images with unseen styles in a zero-shot manner, by leveraging styles from unseen images, resulting in more diverse generations. In this work, we use the image layout as target condition and first show the capability of our method on a natural image dataset as a proof-of-concept. We further demonstrate its versatility in histopathology, where we combine prior knowledge about tissue composition and unannotated data to create diverse synthetic images with known layouts. This allows us to generate additional synthetic data to train a segmentation network in a semi-supervised fashion. We verify the added value of the generated images by showing improved segmentation results and lower performance variability between patients when synthetic images are included during segmentation training. Our code will be made publicly available at [LINK].

Arc2Face: A Foundation Model of Human Faces

This paper presents Arc2Face, an identity-conditioned face foundation model, which, given the ArcFace embedding of a person, can generate diverse photo-realistic images with an unparalleled degree of face similarity than existing models. Despite previous attempts to decode face recognition features into detailed images, we find that common high-resolution datasets (e.g. FFHQ) lack sufficient identities to reconstruct any subject. To that end, we meticulously upsample a significant portion of the WebFace42M database, the largest public dataset for face recognition (FR). Arc2Face builds upon a pretrained Stable Diffusion model, yet adapts it to the task of ID-to-face generation, conditioned solely on ID vectors. Deviating from recent works that combine ID with text embeddings for zero-shot personalization of text-to-image models, we emphasize on the compactness of FR features, which can fully capture the essence of the human face, as opposed to hand-crafted prompts. Crucially, text-augmented models struggle to decouple identity and text, usually necessitating some description of the given face to achieve satisfactory similarity. Arc2Face, however, only needs the discriminative features of ArcFace to guide the generation, offering a robust prior for a plethora of tasks where ID consistency is of paramount importance. As an example, we train a FR model on synthetic images from our model and achieve superior performance to existing synthetic datasets.

Whole-examination AI estimation of fetal biometrics from 20-week ultrasound scans

The current approach to fetal anomaly screening is based on biometric measurements derived from individually selected ultrasound images. In this paper, we introduce a paradigm shift that attains human-level performance in biometric measurement by aggregating automatically extracted biometrics from every frame across an entire scan, with no need for operator intervention. We use a convolutional neural network to classify each frame of an ultrasound video recording. We then measure fetal biometrics in every frame where appropriate anatomy is visible. We use a Bayesian method to estimate the true value of each biometric from a large number of measurements and probabilistically reject outliers. We performed a retrospective experiment on 1457 recordings (comprising 48 million frames) of 20-week ultrasound scans, estimated fetal biometrics in those scans and compared our estimates to the measurements sonographers took during the scan. Our method achieves human-level performance in estimating fetal biometrics and estimates well-calibrated credible intervals in which the true biometric value is expected to lie.

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.

Stochastic Vision Transformers with Wasserstein Distance-Aware Attention

Self-supervised learning is one of the most promising approaches to acquiring knowledge from limited labeled data. Despite the substantial advancements made in recent years, self-supervised models have posed a challenge to practitioners, as they do not readily provide insight into the model's confidence and uncertainty. Tackling this issue is no simple feat, primarily due to the complexity involved in implementing techniques that can make use of the latent representations learned during pre-training without relying on explicit labels. Motivated by this, we introduce a new stochastic vision transformer that integrates uncertainty and distance awareness into self-supervised learning (SSL) pipelines. Instead of the conventional deterministic vector embedding, our novel stochastic vision transformer encodes image patches into elliptical Gaussian distributional embeddings. Notably, the attention matrices of these stochastic representational embeddings are computed using Wasserstein distance-based attention, effectively capitalizing on the distributional nature of these embeddings. Additionally, we propose a regularization term based on Wasserstein distance for both pre-training and fine-tuning processes, thereby incorporating distance awareness into latent representations. We perform extensive experiments across different tasks such as in-distribution generalization, out-of-distribution detection, dataset corruption, semi-supervised settings, and transfer learning to other datasets and tasks. Our proposed method achieves superior accuracy and calibration, surpassing the self-supervised baseline in a wide range of experiments on a variety of datasets.

DISYRE: Diffusion-Inspired SYnthetic REstoration for Unsupervised Anomaly Detection

Unsupervised Anomaly Detection (UAD) techniques aim to identify and localize anomalies without relying on annotations, only leveraging a model trained on a dataset known to be free of anomalies. Diffusion models learn to modify inputs $x$ to increase the probability of it belonging to a desired distribution, i.e., they model the score function $\nabla_x \log p(x)$. Such a score function is potentially relevant for UAD, since $\nabla_x \log p(x)$ is itself a pixel-wise anomaly score. However, diffusion models are trained to invert a corruption process based on Gaussian noise and the learned score function is unlikely to generalize to medical anomalies. This work addresses the problem of how to learn a score function relevant for UAD and proposes DISYRE: Diffusion-Inspired SYnthetic REstoration. We retain the diffusion-like pipeline but replace the Gaussian noise corruption with a gradual, synthetic anomaly corruption so the learned score function generalizes to medical, naturally occurring anomalies. We evaluate DISYRE on three common Brain MRI UAD benchmarks and substantially outperform other methods in two out of the three tasks.

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.

Whole Slide Multiple Instance Learning for Predicting Axillary Lymph Node Metastasis

Breast cancer is a major concern for women's health globally, with axillary lymph node (ALN) metastasis identification being critical for prognosis evaluation and treatment guidance. This paper presents a deep learning (DL) classification pipeline for quantifying clinical information from digital core-needle biopsy (CNB) images, with one step less than existing methods. A publicly available dataset of 1058 patients was used to evaluate the performance of different baseline state-of-the-art (SOTA) DL models in classifying ALN metastatic status based on CNB images. An extensive ablation study of various data augmentation techniques was also conducted. Finally, the manual tumor segmentation and annotation step performed by the pathologists was assessed.

Sculpting Efficiency: Pruning Medical Imaging Models for On-Device Inference

Applying ML advancements to healthcare can improve patient outcomes. However, the sheer operational complexity of ML models, combined with legacy hardware and multi-modal gigapixel images, poses a severe deployment limitation for real-time, on-device inference. We consider filter pruning as a solution, exploring segmentation models in cardiology and ophthalmology. Our preliminary results show a compression rate of up to 1148x with minimal loss in quality, stressing the need to consider task complexity and architectural details when using off-the-shelf models. At high compression rates, filter-pruned models exhibit faster inference on a CPU than the GPU baseline. We also demonstrate that such models' robustness and generalisability characteristics exceed that of the baseline and weight-pruned counterparts. We uncover intriguing questions and take a step towards realising cost-effective disease diagnosis, monitoring, and preventive solutions.