Point-Based Shape Representation Generation with a Correspondence-Preserving Diffusion Model

We propose a diffusion model designed to generate point-based shape representations with correspondences. Traditional statistical shape models have considered point correspondences extensively, but current deep learning methods do not take them into account, focusing on unordered point clouds instead. Current deep generative models for point clouds do not address generating shapes with point correspondences between generated shapes. This work aims to formulate a diffusion model that is capable of generating realistic point-based shape representations, which preserve point correspondences that are present in the training data. Using shape representation data with correspondences derived from Open Access Series of Imaging Studies 3 (OASIS-3), we demonstrate that our correspondence-preserving model effectively generates point-based hippocampal shape representations that are highly realistic compared to existing methods. We further demonstrate the applications of our generative model by downstream tasks, such as conditional generation of healthy and AD subjects and predicting morphological changes of disease progression by counterfactual generation.

MedIL: Implicit Latent Spaces for Generating Heterogeneous Medical Images at Arbitrary Resolutions

In this work, we introduce MedIL, a first-of-its-kind autoencoder built for encoding medical images with heterogeneous sizes and resolutions for image generation. Medical images are often large and heterogeneous, where fine details are of vital clinical importance. Image properties change drastically when considering acquisition equipment, patient demographics, and pathology, making realistic medical image generation challenging. Recent work in latent diffusion models (LDMs) has shown success in generating images resampled to a fixed-size. However, this is a narrow subset of the resolutions native to image acquisition, and resampling discards fine anatomical details. MedIL utilizes implicit neural representations to treat images as continuous signals, where encoding and decoding can be performed at arbitrary resolutions without prior resampling. We quantitatively and qualitatively show how MedIL compresses and preserves clinically-relevant features over large multi-site, multi-resolution datasets of both T1w brain MRIs and lung CTs. We further demonstrate how MedIL can influence the quality of images generated with a diffusion model, and discuss how MedIL can enhance generative models to resemble raw clinical acquisitions.

Measuring Feature Dependency of Neural Networks by Collapsing Feature Dimensions in the Data Manifold

This paper introduces a new technique to measure the feature dependency of neural network models. The motivation is to better understand a model by querying whether it is using information from human-understandable features, e.g., anatomical shape, volume, or image texture. Our method is based on the principle that if a model is dependent on a feature, then removal of that feature should significantly harm its performance. A targeted feature is "removed" by collapsing the dimension in the data distribution that corresponds to that feature. We perform this by moving data points along the feature dimension to a baseline feature value while staying on the data manifold, as estimated by a deep generative model. Then we observe how the model's performance changes on the modified test data set, with the target feature dimension removed. We test our method on deep neural network models trained on synthetic image data with known ground truth, an Alzheimer's disease prediction task using MRI and hippocampus segmentations from the OASIS-3 dataset, and a cell nuclei classification task using the Lizard dataset.

Feature Gradient Flow for Interpreting Deep Neural Networks in Head and Neck Cancer Prediction

This paper introduces feature gradient flow, a new technique for interpreting deep learning models in terms of features that are understandable to humans. The gradient flow of a model locally defines nonlinear coordinates in the input data space representing the information the model is using to make its decisions. Our idea is to measure the agreement of interpretable features with the gradient flow of a model. To then evaluate the importance of a particular feature to the model, we compare that feature's gradient flow measure versus that of a baseline noise feature. We then develop a technique for training neural networks to be more interpretable by adding a regularization term to the loss function that encourages the model gradients to align with those of chosen interpretable features. We test our method in a convolutional neural network prediction of distant metastasis of head and neck cancer from a computed tomography dataset from the Cancer Imaging Archive.