Continuous Spatio-Temporal Memory Networks for 4D Cardiac Cine MRI Segmentation

Current cardiac cine magnetic resonance image (cMR) studies focus on the end diastole (ED) and end systole (ES) phases, while ignoring the abundant temporal information in the whole image sequence. This is because whole sequence segmentation is currently a tedious process and inaccurate. Conventional whole sequence segmentation approaches first estimate the motion field between frames, which is then used to propagate the mask along the temporal axis. However, the mask propagation results could be prone to error, especially for the basal and apex slices, where through-plane motion leads to significant morphology and structural change during the cardiac cycle. Inspired by recent advances in video object segmentation (VOS), based on spatio-temporal memory (STM) networks, we propose a continuous STM (CSTM) network for semi-supervised whole heart and whole sequence cMR segmentation. Our CSTM network takes full advantage of the spatial, scale, temporal and through-plane continuity prior of the underlying heart anatomy structures, to achieve accurate and fast 4D segmentation. Results of extensive experiments across multiple cMR datasets show that our method can improve the 4D cMR segmentation performance, especially for the hard-to-segment regions.

Empowering Interdisciplinary Insights with Dynamic Graph Embedding Trajectories

We developed DyGETViz, a novel framework for effectively visualizing dynamic graphs (DGs) that are ubiquitous across diverse real-world systems. This framework leverages recent advancements in discrete-time dynamic graph (DTDG) models to adeptly handle the temporal dynamics inherent in dynamic graphs. DyGETViz effectively captures both micro- and macro-level structural shifts within these graphs, offering a robust method for representing complex and massive dynamic graphs. The application of DyGETViz extends to a diverse array of domains, including ethology, epidemiology, finance, genetics, linguistics, communication studies, social studies, and international relations. Through its implementation, DyGETViz has revealed or confirmed various critical insights. These include the diversity of content sharing patterns and the degree of specialization within online communities, the chronological evolution of lexicons across decades, and the distinct trajectories exhibited by aging-related and non-related genes. Importantly, DyGETViz enhances the accessibility of scientific findings to non-domain experts by simplifying the complexities of dynamic graphs. Our framework is released as an open-source Python package for use across diverse disciplines. Our work not only addresses the ongoing challenges in visualizing and analyzing DTDG models but also establishes a foundational framework for future investigations into dynamic graph representation and analysis across various disciplines.

A Video is Worth 10,000 Words: Training and Benchmarking with Diverse Captions for Better Long Video Retrieval

Existing long video retrieval systems are trained and tested in the paragraph-to-video retrieval regime, where every long video is described by a single long paragraph. This neglects the richness and variety of possible valid descriptions of a video, which could be described in moment-by-moment detail, or in a single phrase summary, or anything in between. To provide a more thorough evaluation of the capabilities of long video retrieval systems, we propose a pipeline that leverages state-of-the-art large language models to carefully generate a diverse set of synthetic captions for long videos. We validate this pipeline's fidelity via rigorous human inspection. We then benchmark a representative set of video language models on these synthetic captions using a few long video datasets, showing that they struggle with the transformed data, especially the shortest captions. We also propose a lightweight fine-tuning method, where we use a contrastive loss to learn a hierarchical embedding loss based on the differing levels of information among the various captions. Our method improves performance both on the downstream paragraph-to-video retrieval task (+1.1% R@1 on ActivityNet), as well as for the various long video retrieval metrics we compute using our synthetic data (+3.6% R@1 for short descriptions on ActivityNet). For data access and other details, please refer to our project website at https://mgwillia.github.io/10k-words.

Fill the K-Space and Refine the Image: Prompting for Dynamic and Multi-Contrast MRI Reconstruction

The key to dynamic or multi-contrast magnetic resonance imaging (MRI) reconstruction lies in exploring inter-frame or inter-contrast information. Currently, the unrolled model, an approach combining iterative MRI reconstruction steps with learnable neural network layers, stands as the best-performing method for MRI reconstruction. However, there are two main limitations to overcome: firstly, the unrolled model structure and GPU memory constraints restrict the capacity of each denoising block in the network, impeding the effective extraction of detailed features for reconstruction; secondly, the existing model lacks the flexibility to adapt to variations in the input, such as different contrasts, resolutions or views, necessitating the training of separate models for each input type, which is inefficient and may lead to insufficient reconstruction. In this paper, we propose a two-stage MRI reconstruction pipeline to address these limitations. The first stage involves filling the missing k-space data, which we approach as a physics-based reconstruction problem. We first propose a simple yet efficient baseline model, which utilizes adjacent frames/contrasts and channel attention to capture the inherent inter-frame/-contrast correlation. Then, we extend the baseline model to a prompt-based learning approach, PromptMR, for all-in-one MRI reconstruction from different views, contrasts, adjacent types, and acceleration factors. The second stage is to refine the reconstruction from the first stage, which we treat as a general video restoration problem to further fuse features from neighboring frames/contrasts in the image domain. Extensive experiments show that our proposed method significantly outperforms previous state-of-the-art accelerated MRI reconstruction methods.

DeFormer: Integrating Transformers with Deformable Models for 3D Shape Abstraction from a Single Image

Accurate 3D shape abstraction from a single 2D image is a long-standing problem in computer vision and graphics. By leveraging a set of primitives to represent the target shape, recent methods have achieved promising results. However, these methods either use a relatively large number of primitives or lack geometric flexibility due to the limited expressibility of the primitives. In this paper, we propose a novel bi-channel Transformer architecture, integrated with parameterized deformable models, termed DeFormer, to simultaneously estimate the global and local deformations of primitives. In this way, DeFormer can abstract complex object shapes while using a small number of primitives which offer a broader geometry coverage and finer details. Then, we introduce a force-driven dynamic fitting and a cycle-consistent re-projection loss to optimize the primitive parameters. Extensive experiments on ShapeNet across various settings show that DeFormer achieves better reconstruction accuracy over the state-of-the-art, and visualizes with consistent semantic correspondences for improved interpretability.

Neural Deformable Models for 3D Bi-Ventricular Heart Shape Reconstruction and Modeling from 2D Sparse Cardiac Magnetic Resonance Imaging

We propose a novel neural deformable model (NDM) targeting at the reconstruction and modeling of 3D bi-ventricular shape of the heart from 2D sparse cardiac magnetic resonance (CMR) imaging data. We model the bi-ventricular shape using blended deformable superquadrics, which are parameterized by a set of geometric parameter functions and are capable of deforming globally and locally. While global geometric parameter functions and deformations capture gross shape features from visual data, local deformations, parameterized as neural diffeomorphic point flows, can be learned to recover the detailed heart shape.Different from iterative optimization methods used in conventional deformable model formulations, NDMs can be trained to learn such geometric parameter functions, global and local deformations from a shape distribution manifold. Our NDM can learn to densify a sparse cardiac point cloud with arbitrary scales and generate high-quality triangular meshes automatically. It also enables the implicit learning of dense correspondences among different heart shape instances for accurate cardiac shape registration. Furthermore, the parameters of NDM are intuitive, and can be used by a physician without sophisticated post-processing. Experimental results on a large CMR dataset demonstrate the improved performance of NDM over conventional methods.

Multilingual Content Moderation: A Case Study on Reddit

Content moderation is the process of flagging content based on pre-defined platform rules. There has been a growing need for AI moderators to safeguard users as well as protect the mental health of human moderators from traumatic content. While prior works have focused on identifying hateful/offensive language, they are not adequate for meeting the challenges of content moderation since 1) moderation decisions are based on violation of rules, which subsumes detection of offensive speech, and 2) such rules often differ across communities which entails an adaptive solution. We propose to study the challenges of content moderation by introducing a multilingual dataset of 1.8 Million Reddit comments spanning 56 subreddits in English, German, Spanish and French. We perform extensive experimental analysis to highlight the underlying challenges and suggest related research problems such as cross-lingual transfer, learning under label noise (human biases), transfer of moderation models, and predicting the violated rule. Our dataset and analysis can help better prepare for the challenges and opportunities of auto moderation.

DeepRecon: Joint 2D Cardiac Segmentation and 3D Volume Reconstruction via A Structure-Specific Generative Method

Joint 2D cardiac segmentation and 3D volume reconstruction are fundamental to building statistical cardiac anatomy models and understanding functional mechanisms from motion patterns. However, due to the low through-plane resolution of cine MR and high inter-subject variance, accurately segmenting cardiac images and reconstructing the 3D volume are challenging. In this study, we propose an end-to-end latent-space-based framework, DeepRecon, that generates multiple clinically essential outcomes, including accurate image segmentation, synthetic high-resolution 3D image, and 3D reconstructed volume. Our method identifies the optimal latent representation of the cine image that contains accurate semantic information for cardiac structures. In particular, our model jointly generates synthetic images with accurate semantic information and segmentation of the cardiac structures using the optimal latent representation. We further explore downstream applications of 3D shape reconstruction and 4D motion pattern adaptation by the different latent-space manipulation strategies.The simultaneously generated high-resolution images present a high interpretable value to assess the cardiac shape and motion.Experimental results demonstrate the effectiveness of our approach on multiple fronts including 2D segmentation, 3D reconstruction, downstream 4D motion pattern adaption performance.

Modular Adaptation for Cross-Domain Few-Shot Learning

Adapting pre-trained representations has become the go-to recipe for learning new downstream tasks with limited examples. While literature has demonstrated great successes via representation learning, in this work, we show that substantial performance improvement of downstream tasks can also be achieved by appropriate designs of the adaptation process. Specifically, we propose a modular adaptation method that selectively performs multiple state-of-the-art (SOTA) adaptation methods in sequence. As different downstream tasks may require different types of adaptation, our modular adaptation enables the dynamic configuration of the most suitable modules based on the downstream task. Moreover, as an extension to existing cross-domain 5-way k-shot benchmarks (e.g., miniImageNet -> CUB), we create a new high-way (~100) k-shot benchmark with data from 10 different datasets. This benchmark provides a diverse set of domains and allows the use of stronger representations learned from ImageNet. Experimental results show that by customizing adaptation process towards downstream tasks, our modular adaptation pipeline (MAP) improves 3.1% in 5-shot classification accuracy over baselines of finetuning and Prototypical Networks.

DeepTag: An Unsupervised Deep Learning Method for Motion Tracking on Cardiac Tagging Magnetic Resonance Images

Cardiac tagging magnetic resonance imaging (t-MRI) is the gold standard for regional myocardium deformation and cardiac strain estimation. However, this technique has not been widely used in clinical diagnosis, as a result of the difficulty of motion tracking encountered with t-MRI images. In this paper, we propose a novel deep learning-based fully unsupervised method for in vivo motion tracking on t-MRI images. We first estimate the motion field (INF) between any two consecutive t-MRI frames by a bi-directional generative diffeomorphic registration neural network. Using this result, we then estimate the Lagrangian motion field between the reference frame and any other frame through a differentiable composition layer. By utilizing temporal information to perform reasonable estimations on spatio-temporal motion fields, this novel method provides a useful solution for motion tracking and image registration in dynamic medical imaging. Our method has been validated on a representative clinical t-MRI dataset; the experimental results show that our method is superior to conventional motion tracking methods in terms of landmark tracking accuracy and inference efficiency.