arXiv subjects

Weidong Cai

Publications and source records attributed to Weidong Cai.

173 records · Page 10Linked to original sources

arXiv2021

Panoptic Feature Fusion Net: A Novel Instance Segmentation Paradigm for Biomedical and Biological Images

Instance segmentation is an important task for biomedical and biological image analysis. Due to the complicated background components, the high variability of object appearances, numerous overlapping objects, and ambiguous object boundaries, this task still remains challenging. Recently, deep learning based methods have been widely employed to solve these problems and can be categorized into proposal-free and proposal-based methods. However, both proposal-free and proposal-based methods suffer from information loss, as they focus on either global-level semantic or local-level instance features. To tackle this issue, we present a Panoptic Feature Fusion Net (PFFNet) that unifies the semantic and instance features in this work. Specifically, our proposed PFFNet contains a residual attention feature fusion mechanism to incorporate the instance prediction with the semantic features, in order to facilitate the semantic contextual information learning in the instance branch. Then, a mask quality sub-branch is designed to align the confidence score of each object with the quality of the mask prediction. Furthermore, a consistency regularization mechanism is designed between the semantic segmentation tasks in the semantic and instance branches, for the robust learning of both tasks. Extensive experiments demonstrate the effectiveness of our proposed PFFNet, which outperforms several state-of-the-art methods on various biomedical and biological datasets.

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arXiv2020

H2NF-Net for Brain Tumor Segmentation using Multimodal MR Imaging: 2nd Place Solution to BraTS Challenge 2020 Segmentation Task

In this paper, we propose a Hybrid High-resolution and Non-local Feature Network (H2NF-Net) to segment brain tumor in multimodal MR images. Our H2NF-Net uses the single and cascaded HNF-Nets to segment different brain tumor sub-regions and combines the predictions together as the final segmentation. We trained and evaluated our model on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 dataset. The results on the test set show that the combination of the single and cascaded models achieved average Dice scores of 0.78751, 0.91290, and 0.85461, as well as Hausdorff distances ($95\%$) of 26.57525, 4.18426, and 4.97162 for the enhancing tumor, whole tumor, and tumor core, respectively. Our method won the second place in the BraTS 2020 challenge segmentation task out of nearly 80 participants.

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arXiv2020

BiO-Net: Learning Recurrent Bi-directional Connections for Encoder-Decoder Architecture

U-Net has become one of the state-of-the-art deep learning-based approaches for modern computer vision tasks such as semantic segmentation, super resolution, image denoising, and inpainting. Previous extensions of U-Net have focused mainly on the modification of its existing building blocks or the development of new functional modules for performance gains. As a result, these variants usually lead to an unneglectable increase in model complexity. To tackle this issue in such U-Net variants, in this paper, we present a novel Bi-directional O-shape network (BiO-Net) that reuses the building blocks in a recurrent manner without introducing any extra parameters. Our proposed bi-directional skip connections can be directly adopted into any encoder-decoder architecture to further enhance its capabilities in various task domains. We evaluated our method on various medical image analysis tasks and the results show that our BiO-Net significantly outperforms the vanilla U-Net as well as other state-of-the-art methods. Our code is available at https://github.com/tiangexiang/BiO-Net.

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arXiv2020

Unsupervised Instance Segmentation in Microscopy Images via Panoptic Domain Adaptation and Task Re-weighting

Unsupervised domain adaptation (UDA) for nuclei instance segmentation is important for digital pathology, as it alleviates the burden of labor-intensive annotation and domain shift across datasets. In this work, we propose a Cycle Consistency Panoptic Domain Adaptive Mask R-CNN (CyC-PDAM) architecture for unsupervised nuclei segmentation in histopathology images, by learning from fluorescence microscopy images. More specifically, we first propose a nuclei inpainting mechanism to remove the auxiliary generated objects in the synthesized images. Secondly, a semantic branch with a domain discriminator is designed to achieve panoptic-level domain adaptation. Thirdly, in order to avoid the influence of the source-biased features, we propose a task re-weighting mechanism to dynamically add trade-off weights for the task-specific loss functions. Experimental results on three datasets indicate that our proposed method outperforms state-of-the-art UDA methods significantly, and demonstrates a similar performance as fully supervised methods.

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arXiv2020

Shape-Oriented Convolution Neural Network for Point Cloud Analysis

Point cloud is a principal data structure adopted for 3D geometric information encoding. Unlike other conventional visual data, such as images and videos, these irregular points describe the complex shape features of 3D objects, which makes shape feature learning an essential component of point cloud analysis. To this end, a shape-oriented message passing scheme dubbed ShapeConv is proposed to focus on the representation learning of the underlying shape formed by each local neighboring point. Despite this intra-shape relationship learning, ShapeConv is also designed to incorporate the contextual effects from the inter-shape relationship through capturing the long-ranged dependencies between local underlying shapes. This shape-oriented operator is stacked into our hierarchical learning architecture, namely Shape-Oriented Convolutional Neural Network (SOCNN), developed for point cloud analysis. Extensive experiments have been performed to evaluate its significance in the tasks of point cloud classification and part segmentation.

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arXiv2020

Graph Attention Network based Pruning for Reconstructing 3D Liver Vessel Morphology from Contrasted CT Images

With the injection of contrast material into blood vessels, multi-phase contrasted CT images can enhance the visibility of vessel networks in the human body. Reconstructing the 3D geometric morphology of liver vessels from the contrasted CT images can enable multiple liver preoperative surgical planning applications. Automatic reconstruction of liver vessel morphology remains a challenging problem due to the morphological complexity of liver vessels and the inconsistent vessel intensities among different multi-phase contrasted CT images. On the other side, high integrity is required for the 3D reconstruction to avoid decision making biases. In this paper, we propose a framework for liver vessel morphology reconstruction using both a fully convolutional neural network and a graph attention network. A fully convolutional neural network is first trained to produce the liver vessel centerline heatmap. An over-reconstructed liver vessel graph model is then traced based on the heatmap using an image processing based algorithm. We use a graph attention network to prune the false-positive branches by predicting the presence probability of each segmented branch in the initial reconstruction using the aggregated CNN features. We evaluated the proposed framework on an in-house dataset consisting of 418 multi-phase abdomen CT images with contrast. The proposed graph network pruning improves the overall reconstruction F1 score by 6.4% over the baseline. It also outperformed the other state-of-the-art curvilinear structure reconstruction algorithms.

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arXiv2019

Region and Object based Panoptic Image Synthesis through Conditional GANs

Image-to-image translation is significant to many computer vision and machine learning tasks such as image synthesis and video synthesis. It has primary applications in the graphics editing and animation industries. With the development of generative adversarial networks, a lot of attention has been drawn to image-to-image translation tasks. In this paper, we propose and investigate a novel task named as panoptic-level image-to-image translation and a naive baseline of solving this task. Panoptic-level image translation extends the current image translation task to two separate objectives of semantic style translation (adjust the style of objects to that of different domains) and instance transfiguration (swap between different types of objects). The proposed task generates an image from a complete and detailed panoptic perspective which can enrich the context of real-world vision synthesis. Our contribution consists of the proposal of a significant task worth investigating and a naive baseline of solving it. The proposed baseline consists of the multiple instances sequential translation and semantic-level translation with domain-invariant content code.

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arXiv2018

3D Global Convolutional Adversarial Network\\ for Prostate MR Volume Segmentation

Advanced deep learning methods have been developed to conduct prostate MR volume segmentation in either a 2D or 3D fully convolutional manner. However, 2D methods tend to have limited segmentation performance, since large amounts of spatial information of prostate volumes are discarded during the slice-by-slice segmentation process; and 3D methods also have room for improvement, since they use isotropic kernels to perform 3D convolutions whereas most prostate MR volumes have anisotropic spatial resolution. Besides, the fully convolutional structural methods achieve good performance for localization issues but neglect the per-voxel classification for segmentation tasks. In this paper, we propose a 3D Global Convolutional Adversarial Network (3D GCA-Net) to address efficient prostate MR volume segmentation. We first design a 3D ResNet encoder to extract 3D features from prostate scans, and then develop the decoder, which is composed of a multi-scale 3D global convolutional block and a 3D boundary refinement block, to address the classification and localization issues simultaneously for volumetric segmentation. Additionally, we combine the encoder-decoder segmentation network with an adversarial network in the training phrase to enforce the contiguity of long-range spatial predictions. Throughout the proposed model, we use anisotropic convolutional processing for better feature learning on prostate MR scans. We evaluated our 3D GCA-Net model on two public prostate MR datasets and achieved state-of-the-art performances.

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arXiv2017

3D Anisotropic Hybrid Network: Transferring Convolutional Features from 2D Images to 3D Anisotropic Volumes

While deep convolutional neural networks (CNN) have been successfully applied for 2D image analysis, it is still challenging to apply them to 3D anisotropic volumes, especially when the within-slice resolution is much higher than the between-slice resolution and when the amount of 3D volumes is relatively small. On one hand, direct learning of CNN with 3D convolution kernels suffers from the lack of data and likely ends up with poor generalization; insufficient GPU memory limits the model size or representational power. On the other hand, applying 2D CNN with generalizable features to 2D slices ignores between-slice information. Coupling 2D network with LSTM to further handle the between-slice information is not optimal due to the difficulty in LSTM learning. To overcome the above challenges, we propose a 3D Anisotropic Hybrid Network (AH-Net) that transfers convolutional features learned from 2D images to 3D anisotropic volumes. Such a transfer inherits the desired strong generalization capability for within-slice information while naturally exploiting between-slice information for more effective modelling. The focal loss is further utilized for more effective end-to-end learning. We experiment with the proposed 3D AH-Net on two different medical image analysis tasks, namely lesion detection from a Digital Breast Tomosynthesis volume, and liver and liver tumor segmentation from a Computed Tomography volume and obtain the state-of-the-art results.

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arXiv2017

Deep Clustering via Joint Convolutional Autoencoder Embedding and Relative Entropy Minimization

Image clustering is one of the most important computer vision applications, which has been extensively studied in literature. However, current clustering methods mostly suffer from lack of efficiency and scalability when dealing with large-scale and high-dimensional data. In this paper, we propose a new clustering model, called DEeP Embedded RegularIzed ClusTering (DEPICT), which efficiently maps data into a discriminative embedding subspace and precisely predicts cluster assignments. DEPICT generally consists of a multinomial logistic regression function stacked on top of a multi-layer convolutional autoencoder. We define a clustering objective function using relative entropy (KL divergence) minimization, regularized by a prior for the frequency of cluster assignments. An alternating strategy is then derived to optimize the objective by updating parameters and estimating cluster assignments. Furthermore, we employ the reconstruction loss functions in our autoencoder, as a data-dependent regularization term, to prevent the deep embedding function from overfitting. In order to benefit from end-to-end optimization and eliminate the necessity for layer-wise pretraining, we introduce a joint learning framework to minimize the unified clustering and reconstruction loss functions together and train all network layers simultaneously. Experimental results indicate the superiority and faster running time of DEPICT in real-world clustering tasks, where no labeled data is available for hyper-parameter tuning.

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arXiv2015

Morphometry-Based Longitudinal Neurodegeneration Simulation with MR Imaging

We present a longitudinal MR simulation framework which simulates the future neurodegenerative progression by outputting the predicted follow-up MR image and the voxel-based morphometry (VBM) map. This framework expects the patients to have at least 2 historical MR images available. The longitudinal and cross-sectional VBM maps are extracted to measure the affinity between the target subject and the template subjects collected for simulation. Then the follow-up simulation is performed by resampling the latest available target MR image with a weighted sum of non-linear transformations derived from the best-matched templates. The leave-one-out strategy was used to compare different simulation methods. Compared to the state-of-the-art voxel-based method, our proposed morphometry-based simulation achieves better accuracy in most cases.

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