PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI

Remarkable progress has been made by data-driven machine-learning methods in the analysis of MRI scans. However, most existing MRI analysis approaches are crafted for specific MR pulse sequences (MR contrasts) and usually require nearly isotropic acquisitions. This limits their applicability to diverse real-world clinical data, where scans commonly exhibit variations in appearances due to being obtained with varying sequence parameters, resolutions, and orientations -- especially in the presence of pathology. In this paper, we propose PEPSI, the first pathology-enhanced, and pulse-sequence-invariant feature representation learning model for brain MRI. PEPSI is trained entirely on synthetic images with a novel pathology encoding strategy, and enables co-training across datasets with diverse pathologies and missing modalities. Despite variations in pathology appearances across different MR pulse sequences or the quality of acquired images (e.g., resolution, orientation, artifacts, etc), PEPSI produces a high-resolution image of reference contrast (MP-RAGE) that captures anatomy, along with an image specifically highlighting the pathology. Our experiments demonstrate PEPSI's remarkable capability for image synthesis compared with the state-of-the-art, contrast-agnostic synthesis models, as it accurately reconstructs anatomical structures while differentiating between pathology and normal tissue. We further illustrate the efficiency and effectiveness of PEPSI features for downstream pathology segmentations on five public datasets covering white matter hyperintensities and stroke lesions. Code is available at https://github.com/peirong26/PEPSI.

Quantifying white matter hyperintensity and brain volumes in heterogeneous clinical and low-field portable MRI

Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis. Automated segmentation and quantification is desirable but existing methods require high-resolution MRI with good signal-to-noise ratio (SNR). This precludes application to clinical and low-field portable MRI (pMRI) scans, thus hampering large-scale tracking of atrophy and WMH progression, especially in underserved areas where pMRI has huge potential. Here we present a method that segments white matter hyperintensity and 36 brain regions from scans of any resolution and contrast (including pMRI) without retraining. We show results on six public datasets and on a private dataset with paired high- and low-field scans (3T and 64mT), where we attain strong correlation between the WMH ($\rho$=.85) and hippocampal volumes (r=.89) estimated at both fields. Our method is publicly available as part of FreeSurfer, at: http://surfer.nmr.mgh.harvard.edu/fswiki/WMH-SynthSeg.

Brain-ID: Learning Robust Feature Representations for Brain Imaging

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography, yet they struggle to generalize in uncalibrated modalities -- notoriously magnetic resonance imaging (MRI), where performance is highly sensitive to the differences in MR contrast, resolution, and orientation between the training and testing data. This prevents broad applicability to the diverse clinical acquisition protocols in the real world. We introduce Brain-ID, a robust feature representation learning strategy for brain imaging, which is contrast-agnostic, and robust to the brain anatomy of each subject regardless of the appearance of acquired images (i.e., deformation, contrast, resolution, orientation, artifacts, etc). Brain-ID is trained entirely on synthetic data, and easily adapts to downstream tasks with our proposed simple one-layer solution. We validate the robustness of Brain-ID features, and evaluate their performance in a variety of downstream applications, including both contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on 6 public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks, and more importantly, preserves its performance when only limited training data is available.

A Unified Model for Tracking and Image-Video Detection Has More Power

Objection detection (OD) has been one of the most fundamental tasks in computer vision. Recent developments in deep learning have pushed the performance of image OD to new heights by learning-based, data-driven approaches. On the other hand, video OD remains less explored, mostly due to much more expensive data annotation needs. At the same time, multi-object tracking (MOT) which requires reasoning about track identities and spatio-temporal trajectories, shares similar spirits with video OD. However, most MOT datasets are class-specific (e.g., person-annotated only), which constrains a model's flexibility to perform tracking on other objects. We propose TrIVD (Tracking and Image-Video Detection), the first framework that unifies image OD, video OD, and MOT within one end-to-end model. To handle the discrepancies and semantic overlaps across datasets, TrIVD formulates detection/tracking as grounding and reasons about object categories via visual-text alignments. The unified formulation enables cross-dataset, multi-task training, and thus equips TrIVD with the ability to leverage frame-level features, video-level spatio-temporal relations, as well as track identity associations. With such joint training, we can now extend the knowledge from OD data, that comes with much richer object category annotations, to MOT and achieve zero-shot tracking capability. Experiments demonstrate that TrIVD achieves state-of-the-art performances across all image/video OD and MOT tasks.

Efficient conditioned face animation using frontally-viewed embedding

As the quality of few shot facial animation from landmarks increases, new applications become possible, such as ultra low bandwidth video chat compression with a high degree of realism. However, there are some important challenges to tackle in order to improve the experience in real world conditions. In particular, the current approaches fail to represent profile views without distortions, while running in a low compute regime. We focus on this key problem by introducing a multi-frames embedding dubbed Frontalizer to improve profile views rendering. In addition to this core improvement, we explore the learning of a latent code conditioning generations along with landmarks to better convey facial expressions. Our dense models achieves 22% of improvement in perceptual quality and 73% reduction of landmark error over the first order model baseline on a subset of DFDC videos containing head movements. Declined with mobile architectures, our models outperform the previous state-of-the-art (improving perceptual quality by more than 16% and reducing landmark error by more than 47% on two datasets) while running on real time on iPhone 8 with very low bandwidth requirements.

Fluid registration between lung CT and stationary chest tomosynthesis images

Registration is widely used in image-guided therapy and image-guided surgery to estimate spatial correspondences between organs of interest between planning and treatment images. However, while high-quality computed tomography (CT) images are often available at planning time, limited angle acquisitions are frequently used during treatment because of radiation concerns or imaging time constraints. This requires algorithms to register CT images based on limited angle acquisitions. We, therefore, formulate a 3D/2D registration approach which infers a 3D deformation based on measured projections and digitally reconstructed radiographs of the CT. Most 3D/2D registration approaches use simple transformation models or require complex mathematical derivations to formulate the underlying optimization problem. Instead, our approach entirely relies on differentiable operations which can be combined with modern computational toolboxes supporting automatic differentiation. This then allows for rapid prototyping, integration with deep neural networks, and to support a variety of transformation models including fluid flow models. We demonstrate our approach for the registration between CT and stationary chest tomosynthesis (sDCT) images and show how it naturally leads to an iterative image reconstruction approach.

Deep Decomposition for Stochastic Normal-Abnormal Transport

Advection-diffusion equations describe a large family of natural transport processes, e.g., fluid flow, heat transfer, and wind transport. They are also used for optical flow and perfusion imaging computations. We develop a machine learning model, D^2-SONATA, built upon a stochastic advection-diffusion equation, which predicts the velocity and diffusion fields that drive 2D/3D image time-series of transport. In particular, our proposed model incorporates a model of transport atypicality, which isolates abnormal differences between expected normal transport behavior and the observed transport. In a medical context such a normal-abnormal decomposition can be used, for example, to quantify pathologies. Specifically, our model identifies the advection and diffusion contributions from the transport time-series and simultaneously predicts an anomaly value field to provide a decomposition into normal and abnormal advection and diffusion behavior. To achieve improved estimation performance for the velocity and diffusion-tensor fields underlying the advection-diffusion process and for the estimation of the anomaly fields, we create a 2D/3D anomaly-encoded advection-diffusion simulator, which allows for supervised learning. We further apply our model on a brain perfusion dataset from ischemic stroke patients via transfer learning. Extensive comparisons demonstrate that our model successfully distinguishes stroke lesions (abnormal) from normal brain regions, while reconstructing the underlying velocity and diffusion tensor fields.

Accurate Point Cloud Registration with Robust Optimal Transport

This work investigates the use of robust optimal transport (OT) for shape matching. Specifically, we show that recent OT solvers improve both optimization-based and deep learning methods for point cloud registration, boosting accuracy at an affordable computational cost. This manuscript starts with a practical overview of modern OT theory. We then provide solutions to the main difficulties in using this framework for shape matching. Finally, we showcase the performance of transport-enhanced registration models on a wide range of challenging tasks: rigid registration for partial shapes; scene flow estimation on the Kitti dataset; and nonparametric registration of lung vascular trees between inspiration and expiration. Our OT-based methods achieve state-of-the-art results on Kitti and for the challenging lung registration task, both in terms of accuracy and scalability. We also release PVT1010, a new public dataset of 1,010 pairs of lung vascular trees with densely sampled points. This dataset provides a challenging use case for point cloud registration algorithms with highly complex shapes and deformations. Our work demonstrates that robust OT enables fast pre-alignment and fine-tuning for a wide range of registration models, thereby providing a new key method for the computer vision toolbox. Our code and dataset are available online at: https://github.com/uncbiag/robot.

Self-appearance-aided Differential Evolution for Motion Transfer

Image animation transfers the motion of a driving video to a static object in a source image, while keeping the source identity unchanged. Great progress has been made in unsupervised motion transfer recently, where no labelled data or ground truth domain priors are needed. However, current unsupervised approaches still struggle when there are large motion or viewpoint discrepancies between the source and driving images. In this paper, we introduce three measures that we found to be effective for overcoming such large viewpoint changes. Firstly, to achieve more fine-grained motion deformation fields, we propose to apply Neural-ODEs for parametrizing the evolution dynamics of the motion transfer from source to driving. Secondly, to handle occlusions caused by large viewpoint and motion changes, we take advantage of the appearance flow obtained from the source image itself ("self-appearance"), which essentially "borrows" similar structures from other regions of an image to inpaint missing regions. Finally, our framework is also able to leverage the information from additional reference views which help to drive the source identity in spite of varying motion state. Extensive experiments demonstrate that our approach outperforms the state-of-the-arts by a significant margin (~40%), across six benchmarks varying from human faces, human bodies to robots and cartoon characters. Model generality analysis indicates that our approach generalises the best across different object categories as well.

Discovering Hidden Physics Behind Transport Dynamics

Transport processes are ubiquitous. They are, for example, at the heart of optical flow approaches; or of perfusion imaging, where blood transport is assessed, most commonly by injecting a tracer. An advection-diffusion equation is widely used to describe these transport phenomena. Our goal is estimating the underlying physics of advection-diffusion equations, expressed as velocity and diffusion tensor fields. We propose a learning framework (YETI) building on an auto-encoder structure between 2D and 3D image time-series, which incorporates the advection-diffusion model. To help with identifiability, we develop an advection-diffusion simulator which allows pre-training of our model by supervised learning using the velocity and diffusion tensor fields. Instead of directly learning these velocity and diffusion tensor fields, we introduce representations that assure incompressible flow and symmetric positive semi-definite diffusion fields and demonstrate the additional benefits of these representations on improving estimation accuracy. We further use transfer learning to apply YETI on a public brain magnetic resonance (MR) perfusion dataset of stroke patients and show its ability to successfully distinguish stroke lesions from normal brain regions via the estimated velocity and diffusion tensor fields.