Neural Ordinary Differential Equation based Sequential Image Registration for Dynamic Characterization

Deformable image registration (DIR) is crucial in medical image analysis, enabling the exploration of biological dynamics such as organ motions and longitudinal changes in imaging. Leveraging Neural Ordinary Differential Equations (ODE) for registration, this extension work discusses how this framework can aid in the characterization of sequential biological processes. Utilizing the Neural ODE's ability to model state derivatives with neural networks, our Neural Ordinary Differential Equation Optimization-based (NODEO) framework considers voxels as particles within a dynamic system, defining deformation fields through the integration of neural differential equations. This method learns dynamics directly from data, bypassing the need for physical priors, making it exceptionally suitable for medical scenarios where such priors are unavailable or inapplicable. Consequently, the framework can discern underlying dynamics and use sequence data to regularize the transformation trajectory. We evaluated our framework on two clinical datasets: one for cardiac motion tracking and another for longitudinal brain MRI analysis. Demonstrating its efficacy in both 2D and 3D imaging scenarios, our framework offers flexibility and model agnosticism, capable of managing image sequences and facilitating label propagation throughout these sequences. This study provides a comprehensive understanding of how the Neural ODE-based framework uniquely benefits the image registration challenge.

FireANTs: Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration

Diffeomorphic Image Registration is a critical part of the analysis in various imaging modalities and downstream tasks like image translation, segmentation, and atlas building. Registration algorithms based on optimization have stood the test of time in terms of accuracy, reliability, and robustness across a wide spectrum of modalities and acquisition settings. However, these algorithms converge slowly, are prohibitively expensive to run, and their usage requires a steep learning curve, limiting their scalability to larger clinical and scientific studies. In this paper, we develop multi-scale Adaptive Riemannian Optimization algorithms for diffeomorphic image registration. We demonstrate compelling improvements on image registration across a spectrum of modalities and anatomies by measuring structural and landmark overlap of the registered image volumes. Our proposed framework leads to a consistent improvement in performance, and from 300x up to 2000x speedup over existing algorithms. Our modular library design makes it easy to use and allows customization via user-defined cost functions.

Towards Establishing Dense Correspondence on Multiview Coronary Angiography: From Point-to-Point to Curve-to-Curve Query Matching

Coronary angiography is the gold standard imaging technique for studying and diagnosing coronary artery disease. However, the resulting 2D X-ray projections lose 3D information and exhibit visual ambiguities. In this work, we aim to establish dense correspondence in multi-view angiography, serving as a fundamental basis for various clinical applications and downstream tasks. To overcome the challenge of unavailable annotated data, we designed a data simulation pipeline using 3D Coronary Computed Tomography Angiography (CCTA). We formulated the problem of dense correspondence estimation as a query matching task over all points of interest in the given views. We established point-to-point query matching and advanced it to curve-to-curve correspondence, significantly reducing errors by minimizing ambiguity and improving topological awareness. The method was evaluated on a set of 1260 image pairs from different views across 8 clinically relevant angulation groups, demonstrating compelling results and indicating the feasibility of establishing dense correspondence in multi-view angiography.

SplatArmor: Articulated Gaussian splatting for animatable humans from monocular RGB videos

We propose SplatArmor, a novel approach for recovering detailed and animatable human models by `armoring' a parameterized body model with 3D Gaussians. Our approach represents the human as a set of 3D Gaussians within a canonical space, whose articulation is defined by extending the skinning of the underlying SMPL geometry to arbitrary locations in the canonical space. To account for pose-dependent effects, we introduce a SE(3) field, which allows us to capture both the location and anisotropy of the Gaussians. Furthermore, we propose the use of a neural color field to provide color regularization and 3D supervision for the precise positioning of these Gaussians. We show that Gaussian splatting provides an interesting alternative to neural rendering based methods by leverging a rasterization primitive without facing any of the non-differentiability and optimization challenges typically faced in such approaches. The rasterization paradigms allows us to leverage forward skinning, and does not suffer from the ambiguities associated with inverse skinning and warping. We show compelling results on the ZJU MoCap and People Snapshot datasets, which underscore the effectiveness of our method for controllable human synthesis.

Mesh Strikes Back: Fast and Efficient Human Reconstruction from RGB videos

Human reconstruction and synthesis from monocular RGB videos is a challenging problem due to clothing, occlusion, texture discontinuities and sharpness, and framespecific pose changes. Many methods employ deferred rendering, NeRFs and implicit methods to represent clothed humans, on the premise that mesh-based representations cannot capture complex clothing and textures from RGB, silhouettes, and keypoints alone. We provide a counter viewpoint to this fundamental premise by optimizing a SMPL+D mesh and an efficient, multi-resolution texture representation using only RGB images, binary silhouettes and sparse 2D keypoints. Experimental results demonstrate that our approach is more capable of capturing geometric details compared to visual hull, mesh-based methods. We show competitive novel view synthesis and improvements in novel pose synthesis compared to NeRF-based methods, which introduce noticeable, unwanted artifacts. By restricting the solution space to the SMPL+D model combined with differentiable rendering, we obtain dramatic speedups in compute, training times (up to 24x) and inference times (up to 192x). Our method therefore can be used as is or as a fast initialization to NeRF-based methods.

Beyond mAP: Re-evaluating and Improving Performance in Instance Segmentation with Semantic Sorting and Contrastive Flow

Top-down instance segmentation methods improve mAP by hedging bets on low-confidence predictions to match a ground truth. Moreover, the query-key paradigm of top-down methods leads to the instance merging problem. An excessive number of duplicate predictions leads to the (over)counting error, and the independence of category and localization branches leads to the naming error. The de-facto mAP metric doesn't capture these errors, as we show that a trivial dithering scheme can simultaneously increase mAP with hedging errors. To this end, we propose two graph-based metrics that quantifies the amount of hedging both inter-and intra-class. We conjecture the source of the hedging problem is due to feature merging and propose a) Contrastive Flow Field to encode contextual differences between instances as a supervisory signal, and b) Semantic Sorting and NMS step to suppress duplicates and incorrectly categorized prediction. Ablations show that our method encodes contextual information better than baselines, and experiments on COCO our method simultaneously reduces merging and hedging errors compared to state-of-the-art instance segmentation methods.

Self-Supervised Vessel Enhancement Using Flow-Based Consistencies

Vessel segmenting is an essential task in many clinical applications. Although supervised methods have achieved state-of-art performance, acquiring expert annotation is laborious and mostly limited for two-dimensional datasets with a small sample size. On the contrary, unsupervised methods rely on handcrafted features to detect tube-like structures such as vessels. However, those methods require complex pipelines involving several hyper-parameters and design choices rendering the procedure sensitive, dataset-specific, and not generalizable. Also, unsupervised methods usually underperform supervised methods. We propose a self-supervised method with a limited number of hyper-parameters that is generalizable. Our method uses tube-like structure properties, such as connectivity, profile consistency, and bifurcation, to introduce inductive bias into a learning algorithm. To model those properties, we generate a vector field that we refer to as a flow. Our experiments on various datasets in 2D and 3D show that our method reduces the gap between supervised and unsupervised methods. Unlike generic self-supervised methods, the learned features are transferable for supervised approaches, which is essential when the number of annotated data is limited.

Predicting Human Strategies in Simulated Search and Rescue Task

In a search and rescue scenario, rescuers may have different knowledge of the environment and strategies for exploration. Understanding what is inside a rescuer's mind will enable an observer agent to proactively assist them with critical information that can help them perform their task efficiently. To this end, we propose to build models of the rescuers based on their trajectory observations to predict their strategies. In our efforts to model the rescuer's mind, we begin with a simple simulated search and rescue task in Minecraft with human participants. We formulate neural sequence models to predict the triage strategy and the next location of the rescuer. As the neural networks are data-driven, we design a diverse set of artificial "faux human" agents for training, to test them with limited human rescuer trajectory data. To evaluate the agents, we compare it to an evidence accumulation method that explicitly incorporates all available background knowledge and provides an intended upper bound for the expected performance. Further, we perform experiments where the observer/predictor is human. We show results in terms of prediction accuracy of our computational approaches as compared with that of human observers.

Addressing reward bias in Adversarial Imitation Learning with neutral reward functions

Generative Adversarial Imitation Learning suffers from the fundamental problem of reward bias stemming from the choice of reward functions used in the algorithm. Different types of biases also affect different types of environments - which are broadly divided into survival and task-based environments. We provide a theoretical sketch of why existing reward functions would fail in imitation learning scenarios in task based environments with multiple terminal states. We also propose a new reward function for GAIL which outperforms existing GAIL methods on task based environments with single and multiple terminal states and effectively overcomes both survival and termination bias.