Zhangsihao Yang

Zhangsihao Yang, Mengwei Ren, Kaize Ding et al.

Pretraining CNN models (i.e., UNet) through self-supervision has become a powerful approach to facilitate medical image segmentation under low annotation regimes. Recent contrastive learning methods encourage similar global representations when the same image undergoes different transformations, or enforce invariance across different image/patch features that are intrinsically correlated. However, CNN-extracted global and local features are limited in capturing long-range spatial dependencies that are essential in biological anatomy. To this end, we present a keypoint-augmented fusion layer that extracts representations preserving both short- and long-range self-attention. In particular, we augment the CNN feature map at multiple scales by incorporating an additional input that learns long-range spatial self-attention among localized keypoint features. Further, we introduce both global and local self-supervised pretraining for the framework. At the global scale, we obtain global representations from both the bottleneck of the UNet, and by aggregating multiscale keypoint features. These global features are subsequently regularized through image-level contrastive objectives. At the local scale, we define a distance-based criterion to first establish correspondences among keypoints and encourage similarity between their features. Through extensive experiments on both MRI and CT segmentation tasks, we demonstrate the architectural advantages of our proposed method in comparison to both CNN and Transformer-based UNets, when all architectures are trained with randomly initialized weights. With our proposed pretraining strategy, our method further outperforms existing SSL methods by producing more robust self-attention and achieving state-of-the-art segmentation results. The code is available at https://github.com/zshyang/kaf.git.

Xuanzhao Dong, Vamsi Krishna Vasa, Wenhui Zhu et al.

Retinal fundus photography is significant in diagnosing and monitoring retinal diseases. However, systemic imperfections and operator/patient-related factors can hinder the acquisition of high-quality retinal images. Previous efforts in retinal image enhancement primarily relied on GANs, which are limited by the trade-off between training stability and output diversity. In contrast, the Schrödinger Bridge (SB), offers a more stable solution by utilizing Optimal Transport (OT) theory to model a stochastic differential equation (SDE) between two arbitrary distributions. This allows SB to effectively transform low-quality retinal images into their high-quality counterparts. In this work, we leverage the SB framework to propose an image-to-image translation pipeline for retinal image enhancement. Additionally, previous methods often fail to capture fine structural details, such as blood vessels. To address this, we enhance our pipeline by introducing Dynamic Snake Convolution, whose tortuous receptive field can better preserve tubular structures. We name the resulting retinal fundus image enhancement framework the Context-aware Unpaired Neural Schrödinger Bridge (CUNSB-RFIE). To the best of our knowledge, this is the first endeavor to use the SB approach for retinal image enhancement. Experimental results on a large-scale dataset demonstrate the advantage of the proposed method compared to several state-of-the-art supervised and unsupervised methods in terms of image quality and performance on downstream tasks.The code is available at https://github.com/Retinal-Research/CUNSB-RFIE .

Mohammad Farazi, Zhangsihao Yang, Wenhui Zhu et al.

Convolutional neural networks (CNN) have been broadly studied on images, videos, graphs, and triangular meshes. However, it has seldom been studied on tetrahedral meshes. Given the merits of using volumetric meshes in applications like brain image analysis, we introduce a novel interpretable graph CNN framework for the tetrahedral mesh structure. Inspired by ChebyNet, our model exploits the volumetric Laplace-Beltrami Operator (LBO) to define filters over commonly used graph Laplacian which lacks the Riemannian metric information of 3D manifolds. For pooling adaptation, we introduce new objective functions for localized minimum cuts in the Graclus algorithm based on the LBO. We employ a piece-wise constant approximation scheme that uses the clustering assignment matrix to estimate the LBO on sampled meshes after each pooling. Finally, adapting the Gradient-weighted Class Activation Mapping algorithm for tetrahedral meshes, we use the obtained heatmaps to visualize discovered regions-of-interest as biomarkers. We demonstrate the effectiveness of our model on cortical tetrahedral meshes from patients with Alzheimer's disease, as there is scientific evidence showing the correlation of cortical thickness to neurodegenerative disease progression. Our results show the superiority of our LBO-based convolution layer and adapted pooling over the conventionally used unitary cortical thickness, graph Laplacian, and point cloud representation.

Mohammad Farazi, Wenhui Zhu, Zhangsihao Yang et al.

This paper studies 3D dense shape correspondence, a key shape analysis application in computer vision and graphics. We introduce a novel hybrid geometric deep learning-based model that learns geometrically meaningful and discretization-independent features with a U-Net model as the primary node feature extraction module, followed by a successive spectral-based graph convolutional network. To create a diverse set of filters, we use anisotropic wavelet basis filters, being sensitive to both different directions and band-passes. This filter set overcomes the over-smoothing behavior of conventional graph neural networks. To further improve the model's performance, we add a function that perturbs the feature maps in the last layer ahead of fully connected layers, forcing the network to learn more discriminative features overall. The resulting correspondence maps show state-of-the-art performance on the benchmark datasets based on average geodesic errors and superior robustness to discretization in 3D meshes. Our approach provides new insights and practical solutions to the dense shape correspondence research.

Wenhui Zhu, Peijie Qiu, Oana M. Dumitrascu et al.

Non-mydriatic retinal color fundus photography (CFP) is widely available due to the advantage of not requiring pupillary dilation, however, is prone to poor quality due to operators, systemic imperfections, or patient-related causes. Optimal retinal image quality is mandated for accurate medical diagnoses and automated analyses. Herein, we leveraged the Optimal Transport (OT) theory to propose an unpaired image-to-image translation scheme for mapping low-quality retinal CFPs to high-quality counterparts. Furthermore, to improve the flexibility, robustness, and applicability of our image enhancement pipeline in the clinical practice, we generalized a state-of-the-art model-based image reconstruction method, regularization by denoising, by plugging in priors learned by our OT-guided image-to-image translation network. We named it as regularization by enhancing (RE). We validated the integrated framework, OTRE, on three publicly available retinal image datasets by assessing the quality after enhancement and their performance on various downstream tasks, including diabetic retinopathy grading, vessel segmentation, and diabetic lesion segmentation. The experimental results demonstrated the superiority of our proposed framework over some state-of-the-art unsupervised competitors and a state-of-the-art supervised method.

Chuanyue Shen, Letian Zhang, Zhangsihao Yang et al.

Meeting online is becoming the new normal. Creating an immersive experience for online meetings is a necessity towards more diverse and seamless environments. Efficient photorealistic rendering of human 3D dynamics is the core of immersive meetings. Current popular applications achieve real-time conferencing but fall short in delivering photorealistic human dynamics, either due to limited 2D space or the use of avatars that lack realistic interactions between participants. Recent advances in neural rendering, such as the Neural Radiance Field (NeRF), offer the potential for greater realism in metaverse meetings. However, the slow rendering speed of NeRF poses challenges for real-time conferencing. We envision a pipeline for a future extended reality metaverse conferencing system that leverages monocular video acquisition and free-viewpoint synthesis to enhance data and hardware efficiency. Towards an immersive conferencing experience, we explore an accelerated NeRF-based free-viewpoint synthesis algorithm for rendering photorealistic human dynamics more efficiently. We show that our algorithm achieves comparable rendering quality while performing training and inference 44.5% and 213% faster than state-of-the-art methods, respectively. Our exploration provides a design basis for constructing metaverse conferencing systems that can handle complex application scenarios, including dynamic scene relighting with customized themes and multi-user conferencing that harmonizes real-world people into an extended world.

Zhangsihao Yang, Mingyuan Zhou, Mengyi Shan et al.

Our paper aims to generate diverse and realistic animal motion sequences from textual descriptions, without a large-scale animal text-motion dataset. While the task of text-driven human motion synthesis is already extensively studied and benchmarked, it remains challenging to transfer this success to other skeleton structures with limited data. In this work, we design a model architecture that imitates Generative Pretraining Transformer (GPT), utilizing prior knowledge learned from human data to the animal domain. We jointly train motion autoencoders for both animal and human motions and at the same time optimize through the similarity scores among human motion encoding, animal motion encoding, and text CLIP embedding. Presenting the first solution to this problem, we are able to generate animal motions with high diversity and fidelity, quantitatively and qualitatively outperforming the results of training human motion generation baselines on animal data. Additionally, we introduce AnimalML3D, the first text-animal motion dataset with 1240 animation sequences spanning 36 different animal identities. We hope this dataset would mediate the data scarcity problem in text-driven animal motion generation, providing a new playground for the research community.

Zhangsihao Yang, Mengyi Shan, Mohammad Farazi et al.

Human video generation task has gained significant attention with the advancement of deep generative models. Generating realistic videos with human movements is challenging in nature, due to the intricacies of human body topology and sensitivity to visual artifacts. The extensively studied 2D media generation methods take advantage of massive human media datasets, but struggle with 3D-aware control; whereas 3D avatar-based approaches, while offering more freedom in control, lack photorealism and cannot be harmonized seamlessly with background scene. We propose AMG, a method that combines the 2D photorealism and 3D controllability by conditioning video diffusion models on controlled rendering of 3D avatars. We additionally introduce a novel data processing pipeline that reconstructs and renders human avatar movements from dynamic camera videos. AMG is the first method that enables multi-person diffusion video generation with precise control over camera positions, human motions, and background style. We also demonstrate through extensive evaluation that it outperforms existing human video generation methods conditioned on pose sequences or driving videos in terms of realism and adaptability.

Wenhui Zhu, Peijie Qiu, Xiwen Chen et al.

Multiple Instance Learning (MIL) is a popular weakly-supervised method for various applications, with a particular interest in histological whole slide image (WSI) classification. Due to the gigapixel resolution of WSI, applications of MIL in WSI typically necessitate a two-stage training scheme: first, extract features from the pre-trained backbone and then perform MIL aggregation. However, it is well-known that this suboptimal training scheme suffers from "noisy" feature embeddings from the backbone and inherent weak supervision, hindering MIL from learning rich and generalizable features. However, the most commonly used technique (i.e., dropout) for mitigating this issue has yet to be explored in MIL. In this paper, we empirically explore how effective the dropout can be in MIL. Interestingly, we observe that dropping the top-k most important instances within a bag leads to better performance and generalization even under noise attack. Based on this key observation, we propose a novel MIL-specific dropout method, termed MIL-Dropout, which systematically determines which instances to drop. Experiments on five MIL benchmark datasets and two WSI datasets demonstrate that MIL-Dropout boosts the performance of current MIL methods with a negligible computational cost. The code is available at https://github.com/ChongQingNoSubway/MILDropout.

Wenhui Zhu, Xuanzhao Dong, Xin Li et al.

Over the past decade, generative models have achieved significant success in enhancement fundus images.However, the evaluation of these models still presents a considerable challenge. A comprehensive evaluation benchmark for fundus image enhancement is indispensable for three main reasons: 1) The existing denoising metrics (e.g., PSNR, SSIM) are hardly to extend to downstream real-world clinical research (e.g., Vessel morphology consistency). 2) There is a lack of comprehensive evaluation for both paired and unpaired enhancement methods, along with the need for expert protocols to accurately assess clinical value. 3) An ideal evaluation system should provide insights to inform future developments of fundus image enhancement. To this end, we propose a novel comprehensive benchmark, EyeBench, to provide insights that align enhancement models with clinical needs, offering a foundation for future work to improve the clinical relevance and applicability of generative models for fundus image enhancement. EyeBench has three appealing properties: 1) multi-dimensional clinical alignment downstream evaluation: In addition to evaluating the enhancement task, we provide several clinically significant downstream tasks for fundus images, including vessel segmentation, DR grading, denoising generalization, and lesion segmentation. 2) Medical expert-guided evaluation design: We introduce a novel dataset that promote comprehensive and fair comparisons between paired and unpaired methods and includes a manual evaluation protocol by medical experts. 3) Valuable insights: Our benchmark study provides a comprehensive and rigorous evaluation of existing methods across different downstream tasks, assisting medical experts in making informed choices. Additionally, we offer further analysis of the challenges faced by existing methods. The code is available at \url{https://github.com/Retinal-Research/EyeBench}

Yanxi Chen, Mohammad Farazi, Zhangsihao Yang et al.

Alzheimer's disease (AD) is a major neurodegenerative condition that affects millions around the world. As one of the main biomarkers in the AD diagnosis procedure, brain amyloid positivity is typically identified by positron emission tomography (PET), which is costly and invasive. Brain structural magnetic resonance imaging (sMRI) may provide a safer and more convenient solution for the AD diagnosis. Recent advances in geometric deep learning have facilitated sMRI analysis and early diagnosis of AD. However, determining AD pathology, such as brain amyloid deposition, in preclinical stage remains challenging, as less significant morphological changes can be observed. As a result, few AD classification models are generalizable to the brain amyloid positivity classification task. Blood-based biomarkers (BBBMs), on the other hand, have recently achieved remarkable success in predicting brain amyloid positivity and identifying individuals with high risk of being brain amyloid positive. However, individuals in medium risk group still require gold standard tests such as Amyloid PET for further evaluation. Inspired by the recent success of transformer architectures, we propose a geometric deep learning model based on transformer that is both scalable and robust to variations in input volumetric mesh size. Our work introduced a novel tokenization scheme for tetrahedral meshes, incorporating anatomical landmarks generated by a pre-trained Gaussian process model. Our model achieved superior classification performance in AD classification task. In addition, we showed that the model was also generalizable to the brain amyloid positivity prediction with individuals in the medium risk class, where BM alone cannot achieve a clear classification. Our work may enrich geometric deep learning research and improve AD diagnosis accuracy without using expensive and invasive PET scans.

Zhangsihao Yang, Or Litany, Tolga Birdal et al.

The majority of descriptor-based methods for geometric processing of non-rigid shape rely on hand-crafted descriptors. Recently, learning-based techniques have been shown effective, achieving state-of-the-art results in a variety of tasks. Yet, even though these methods can in principle work directly on raw data, most methods still rely on hand-crafted descriptors at the input layer. In this work, we wish to challenge this practice and use a neural network to learn descriptors directly from the raw mesh. To this end, we introduce two modules into our neural architecture. The first is a local reference frame (LRF) used to explicitly make the features invariant to rigid transformations. The second is continuous convolution kernels that provide robustness to sampling. We show the efficacy of our proposed network in learning on raw meshes using two cornerstone tasks: shape matching, and human body parts segmentation. Our results show superior results over baseline methods that use hand-crafted descriptors.

Wentai Zhang, Zhangsihao Yang, Haoliang Jiang et al.

We propose a data-driven 3D shape design method that can learn a generative model from a corpus of existing designs, and use this model to produce a wide range of new designs. The approach learns an encoding of the samples in the training corpus using an unsupervised variational autoencoder-decoder architecture, without the need for an explicit parametric representation of the original designs. To facilitate the generation of smooth final surfaces, we develop a 3D shape representation based on a distance transformation of the original 3D data, rather than using the commonly utilized binary voxel representation. Once established, the generator maps the latent space representations to the high-dimensional distance transformation fields, which are then automatically surfaced to produce 3D representations amenable to physics simulations or other objective function evaluation modules. We demonstrate our approach for the computational design of gliders that are optimized to attain prescribed performance scores. Our results show that when combined with genetic optimization, the proposed approach can generate a rich set of candidate concept designs that achieve prescribed functional goals, even when the original dataset has only a few or no solutions that achieve these goals.

Zhangsihao Yang, Haoliang Jiang, Zou Lan

This article proposes a data-driven methodology to achieve a fast design support, in order to generate or develop novel designs covering multiple object categories. This methodology implements two state-of-the-art Variational Autoencoder dealing with 3D model data. Our methodology constructs a self-defined loss function. The loss function, containing the outputs of certain layers in the autoencoder, obtains combination of different latent features from different 3D model categories. Additionally, this article provide detail explanation to utilize the Princeton ModelNet40 database, a comprehensive clean collection of 3D CAD models for objects. After convert the original 3D mesh file to voxel and point cloud data type, we enable to feed our autoencoder with data of the same size of dimension. The novelty of this work is to leverage the power of deep learning methods as an efficient latent feature extractor to explore unknown designing areas. Through this project, we expect the output can show a clear and smooth interpretation of model from different categories to develop a fast design support to generate novel shapes. This final report will explore 1) the theoretical ideas, 2) the progresses to implement Variantional Autoencoder to attain implicit features from input shapes, 3) the results of output shapes during training in selected domains of both 3D voxel data and 3D point cloud data, and 4) our conclusion and future work to achieve the more outstanding goal.

Wentai Zhang, Haoliang Jiang, Zhangsihao Yang et al.

High quality upsampling of sparse 3D point clouds is critically useful for a wide range of geometric operations such as reconstruction, rendering, meshing, and analysis. In this paper, we propose a data-driven algorithm that enables an upsampling of 3D point clouds without the need for hard-coded rules. Our approach uses a deep network with Chamfer distance as the loss function, capable of learning the latent features in point clouds belonging to different object categories. We evaluate our algorithm across different amplification factors, with upsampling learned and performed on objects belonging to the same category as well as different categories. We also explore the desirable characteristics of input point clouds as a function of the distribution of the point samples. Finally, we demonstrate the performance of our algorithm in single-category training versus multi-category training scenarios. The final proposed model is compared against a baseline, optimization-based upsampling method. Results indicate that our algorithm is capable of generating more uniform and accurate upsamplings.