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Weidong Cai

Weidong Cai contributes to research discovery and scholarly infrastructure.

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Computer Visioneess.IVMachine LearningApplicationsArtificial Intelligenceeess.ASRoboticsSound

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Published work

26 published item(s)

preprint2026arXiv

Aes3D: Aesthetic Assessment in 3D Gaussian Splatting

As 3D Gaussian Splatting (3DGS) gains attention in immersive media and digital content creation, assessing the aesthetics of 3D scenes becomes important in helping creators build more visually compelling 3D content. However, existing evaluation methods for 3D scenes primarily emphasize reconstruction fidelity and perceptual realism, largely overlooking higher-level aesthetic attributes such as composition, harmony, and visual appeal. This limitation comes from two key challenges: (1) the absence of general 3DGS datasets with aesthetic annotations, and (2) the intrinsic nature of 3DGS as a low-level primitive representation, which makes it difficult to capture high-level aesthetic features. To address these challenges, we propose Aes3D, the first systematic framework for assessing the aesthetics of 3D neural rendering scenes. Aes3D includes Aesthetic3D, the first dataset dedicated to 3D scene aesthetic assessment, built on our proposed annotation strategy for 3D scene aesthetics. In addition, we present Aes3DGSNet, a lightweight model that directly predicts scene-level aesthetic scores from 3DGS representations. Notably, our model operates solely on 3D Gaussian primitives, eliminating the need for rendering multi-view images and thus reducing computational cost and hardware requirements. Through aesthetics-supervised learning on multi-view 3DGS scene representations, Aes3DGSNet effectively captures high-level aesthetic cues and accurately regresses aesthetic scores. Experimental results demonstrate that our approach achieves strong performance while maintaining a lightweight design, establishing a new benchmark for 3D scene aesthetic assessment. Code and datasets will be made available in a future version.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

RNA-FM: Flow-Matching Generative Model for Genome-wide RNA-Seq Prediction

Histopathology whole-slide images (WSIs) are routinely acquired in clinical practice and contain rich tissue morphology but lack direct molecular architecture and functional programs defining pathological states, whereas RNA sequencing (RNA-seq) provides genome-wide transcriptional profiles at substantial cost, thereby motivating WSI-based genome-wide transcriptomic prediction. Existing approaches for predicting gene expression from WSIs predominantly rely on deterministic regression with one-to-one mapping, limiting their ability to capture biological heterogeneity and predictive uncertainty. We propose RNA-FM, a flow-matching generative framework for genome-wide bulk RNA-seq prediction from WSIs. RNA-FM formulates transcriptomic prediction as a continuous-time conditional transport problem, learning a velocity field that maps a simple prior to the target gene expression distribution conditioned on morphologies. By integrating pathway-level structure, RNA-FM enables scalable and biologically interpretable genome-wide gene expression imputation. Extensive experiments demonstrate that RNA-FM consistently outperforms state-of-the-art approaches while maintaining biological meaningfulness. Code is available at https://github.com/YXSong000/RNA-FM.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

TractGraphCNN: anatomically informed graph CNN for classification using diffusion MRI tractography

The structure and variability of the brain's connections can be investigated via prediction of non-imaging phenotypes using neural networks. However, known neuroanatomical relationships between input features are generally ignored in network design. We propose TractGraphCNN, a novel, anatomically informed graph CNN framework for machine learning tasks using diffusion MRI tractography. An EdgeConv module aggregates features from anatomically similar white matter connections indicated by graph edges, and an attention module enables interpretation of predictive white matter tracts. Results in a sex prediction testbed task demonstrate strong performance of TractGraphCNN in two large datasets (HCP and ABCD). Graphs informed by white matter geometry demonstrate higher performance than graphs informed by gray matter connectivity. Overall, the bilateral cingulum and left middle longitudinal fasciculus are consistently highly predictive of sex. This work shows the potential of incorporating anatomical information, especially known anatomical similarities between input features, to guide convolutions in neural networks.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

TractoSCR: A Novel Supervised Contrastive Regression Framework for Prediction of Neurocognitive Measures Using Multi-Site Harmonized Diffusion MRI Tractography

Neuroimaging-based prediction of neurocognitive measures is valuable for studying how the brain's structure relates to cognitive function. However, the accuracy of prediction using popular linear regression models is relatively low. We propose a novel deep regression method, namely TractoSCR, that allows full supervision for contrastive learning in regression tasks using diffusion MRI tractography. TractoSCR performs supervised contrastive learning by using the absolute difference between continuous regression labels (i.e. neurocognitive scores) to determine positive and negative pairs. We apply TractoSCR to analyze a large-scale dataset including multi-site harmonized diffusion MRI and neurocognitive data from 8735 participants in the Adolescent Brain Cognitive Development (ABCD) Study. We extract white matter microstructural measures using a fine parcellation of white matter tractography into fiber clusters. Using these measures, we predict three scores related to domains of higher-order cognition (general cognitive ability, executive function, and learning/memory). To identify important fiber clusters for prediction of these neurocognitive scores, we propose a permutation feature importance method for high-dimensional data. We find that TractoSCR improves the accuracy of neurocognitive score prediction compared to other state-of-the-art methods. We find that the most predictive fiber clusters are predominantly located within the superficial white matter and projection tracts, particularly the superficial frontal white matter and striato-frontal connections. Overall, our results demonstrate the utility of contrastive representation learning methods for regression, and in particular for improving neuroimaging-based prediction of higher-order cognitive abilities.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Decompose to Adapt: Cross-domain Object Detection via Feature Disentanglement

Recent advances in unsupervised domain adaptation (UDA) techniques have witnessed great success in cross-domain computer vision tasks, enhancing the generalization ability of data-driven deep learning architectures by bridging the domain distribution gaps. For the UDA-based cross-domain object detection methods, the majority of them alleviate the domain bias by inducing the domain-invariant feature generation via adversarial learning strategy. However, their domain discriminators have limited classification ability due to the unstable adversarial training process. Therefore, the extracted features induced by them cannot be perfectly domain-invariant and still contain domain-private factors, bringing obstacles to further alleviate the cross-domain discrepancy. To tackle this issue, we design a Domain Disentanglement Faster-RCNN (DDF) to eliminate the source-specific information in the features for detection task learning. Our DDF method facilitates the feature disentanglement at the global and local stages, with a Global Triplet Disentanglement (GTD) module and an Instance Similarity Disentanglement (ISD) module, respectively. By outperforming state-of-the-art methods on four benchmark UDA object detection tasks, our DDF method is demonstrated to be effective with wide applicability.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Domain Adaptive Nuclei Instance Segmentation and Classification via Category-aware Feature Alignment and Pseudo-labelling

Unsupervised domain adaptation (UDA) methods have been broadly utilized to improve the models' adaptation ability in general computer vision. However, different from the natural images, there exist huge semantic gaps for the nuclei from different categories in histopathology images. It is still under-explored how could we build generalized UDA models for precise segmentation or classification of nuclei instances across different datasets. In this work, we propose a novel deep neural network, namely Category-Aware feature alignment and Pseudo-Labelling Network (CAPL-Net) for UDA nuclei instance segmentation and classification. Specifically, we first propose a category-level feature alignment module with dynamic learnable trade-off weights. Second, we propose to facilitate the model performance on the target data via self-supervised training with pseudo labels based on nuclei-level prototype features. Comprehensive experiments on cross-domain nuclei instance segmentation and classification tasks demonstrate that our approach outperforms state-of-the-art UDA methods with a remarkable margin.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

DSNet: A Dual-Stream Framework for Weakly-Supervised Gigapixel Pathology Image Analysis

We present a novel weakly-supervised framework for classifying whole slide images (WSIs). WSIs, due to their gigapixel resolution, are commonly processed by patch-wise classification with patch-level labels. However, patch-level labels require precise annotations, which is expensive and usually unavailable on clinical data. With image-level labels only, patch-wise classification would be sub-optimal due to inconsistency between the patch appearance and image-level label. To address this issue, we posit that WSI analysis can be effectively conducted by integrating information at both high magnification (local) and low magnification (regional) levels. We auto-encode the visual signals in each patch into a latent embedding vector representing local information, and down-sample the raw WSI to hardware-acceptable thumbnails representing regional information. The WSI label is then predicted with a Dual-Stream Network (DSNet), which takes the transformed local patch embeddings and multi-scale thumbnail images as inputs and can be trained by the image-level label only. Experiments conducted on two large-scale public datasets demonstrate that our method outperforms all recent state-of-the-art weakly-supervised WSI classification methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

HNF-Netv2 for Brain Tumor Segmentation using multi-modal MR Imaging

In our previous work, $i.e.$, HNF-Net, high-resolution feature representation and light-weight non-local self-attention mechanism are exploited for brain tumor segmentation using multi-modal MR imaging. In this paper, we extend our HNF-Net to HNF-Netv2 by adding inter-scale and intra-scale semantic discrimination enhancing blocks to further exploit global semantic discrimination for the obtained high-resolution features. We trained and evaluated our HNF-Netv2 on the multi-modal Brain Tumor Segmentation Challenge (BraTS) 2021 dataset. The result on the test set shows that our HNF-Netv2 achieved the average Dice scores of 0.878514, 0.872985, and 0.924919, as well as the Hausdorff distances ($95\%$) of 8.9184, 16.2530, and 4.4895 for the enhancing tumor, tumor core, and whole tumor, respectively. Our method won the RSNA 2021 Brain Tumor AI Challenge Prize (Segmentation Task), which ranks 8th out of all 1250 submitted results.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

MS Lesion Segmentation: Revisiting Weighting Mechanisms for Federated Learning

Federated learning (FL) has been widely employed for medical image analysis to facilitate multi-client collaborative learning without sharing raw data. Despite great success, FL's performance is limited for multiple sclerosis (MS) lesion segmentation tasks, due to variance in lesion characteristics imparted by different scanners and acquisition parameters. In this work, we propose the first FL MS lesion segmentation framework via two effective re-weighting mechanisms. Specifically, a learnable weight is assigned to each local node during the aggregation process, based on its segmentation performance. In addition, the segmentation loss function in each client is also re-weighted according to the lesion volume for the data during training. Comparison experiments on two FL MS segmentation scenarios using public and clinical datasets have demonstrated the effectiveness of the proposed method by outperforming other FL methods significantly. Furthermore, the segmentation performance of FL incorporating our proposed aggregation mechanism can exceed centralised training with all the raw data. The extensive evaluation also indicated the superiority of our method when estimating brain volume differences estimation after lesion inpainting.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Multiple Sclerosis Lesion Analysis in Brain Magnetic Resonance Images: Techniques and Clinical Applications

Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system, characterized by the appearance of focal lesions in the white and gray matter that topographically correlate with an individual patient's neurological symptoms and signs. Magnetic resonance imaging (MRI) provides detailed in-vivo structural information, permitting the quantification and categorization of MS lesions that critically inform disease management. Traditionally, MS lesions have been manually annotated on 2D MRI slices, a process that is inefficient and prone to inter-/intra-observer errors. Recently, automated statistical imaging analysis techniques have been proposed to detect and segment MS lesions based on MRI voxel intensity. However, their effectiveness is limited by the heterogeneity of both MRI data acquisition techniques and the appearance of MS lesions. By learning complex lesion representations directly from images, deep learning techniques have achieved remarkable breakthroughs in the MS lesion segmentation task. Here, we provide a comprehensive review of state-of-the-art automatic statistical and deep-learning MS segmentation methods and discuss current and future clinical applications. Further, we review technical strategies, such as domain adaptation, to enhance MS lesion segmentation in real-world clinical settings.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Partial Graph Reasoning for Neural Network Regularization

Regularizers help deep neural networks prevent feature co-adaptations. Dropout, as a commonly used regularization technique, stochastically disables neuron activations during network optimization. However, such complete feature disposal can affect the feature representation and network understanding. Toward better descriptions of latent representations, we present DropGraph that learns a regularization function by constructing a stand-alone graph from the backbone features. DropGraph first samples stochastic spatial feature vectors and then incorporates graph reasoning methods to generate feature map distortions. This add-on graph regularizes the network during training and can be completely skipped during inference. We provide intuitions on the linkage between graph reasoning and Dropout with further discussions on how partial graph reasoning method reduces feature correlations. To this end, we extensively study the modeling of graph vertex dependencies and the utilization of the graph for distorting backbone feature maps. DropGraph was validated on 4 tasks with a total of 8 different datasets. The experimental results show that our method outperforms other state-of-the-art regularizers while leaving the base model structure unmodified during inference.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Rethinking Rotation Invariance with Point Cloud Registration

Recent investigations on rotation invariance for 3D point clouds have been devoted to devising rotation-invariant feature descriptors or learning canonical spaces where objects are semantically aligned. Examinations of learning frameworks for invariance have seldom been looked into. In this work, we review rotation invariance in terms of point cloud registration and propose an effective framework for rotation invariance learning via three sequential stages, namely rotation-invariant shape encoding, aligned feature integration, and deep feature registration. We first encode shape descriptors constructed with respect to reference frames defined over different scales, e.g., local patches and global topology, to generate rotation-invariant latent shape codes. Within the integration stage, we propose Aligned Integration Transformer to produce a discriminative feature representation by integrating point-wise self- and cross-relations established within the shape codes. Meanwhile, we adopt rigid transformations between reference frames to align the shape codes for feature consistency across different scales. Finally, the deep integrated feature is registered to both rotation-invariant shape codes to maximize feature similarities, such that rotation invariance of the integrated feature is preserved and shared semantic information is implicitly extracted from shape codes. Experimental results on 3D shape classification, part segmentation, and retrieval tasks prove the feasibility of our work. Our project page is released at: https://rotation3d.github.io/.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Spatiality-guided Transformer for 3D Dense Captioning on Point Clouds

Dense captioning in 3D point clouds is an emerging vision-and-language task involving object-level 3D scene understanding. Apart from coarse semantic class prediction and bounding box regression as in traditional 3D object detection, 3D dense captioning aims at producing a further and finer instance-level label of natural language description on visual appearance and spatial relations for each scene object of interest. To detect and describe objects in a scene, following the spirit of neural machine translation, we propose a transformer-based encoder-decoder architecture, namely SpaCap3D, to transform objects into descriptions, where we especially investigate the relative spatiality of objects in 3D scenes and design a spatiality-guided encoder via a token-to-token spatial relation learning objective and an object-centric decoder for precise and spatiality-enhanced object caption generation. Evaluated on two benchmark datasets, ScanRefer and ReferIt3D, our proposed SpaCap3D outperforms the baseline method Scan2Cap by 4.94% and 9.61% in CIDEr@0.5IoU, respectively. Our project page with source code and supplementary files is available at https://SpaCap3D.github.io/ .

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

SupWMA: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning

White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts to enable quantification and visualization. Most parcellation methods focus on the deep white matter (DWM), while fewer methods address the superficial white matter (SWM) due to its complexity. We propose a deep-learning-based framework, Superficial White Matter Analysis (SupWMA), that performs an efficient and consistent parcellation of 198 SWM clusters from whole-brain tractography. A point-cloud-based network is modified for our SWM parcellation task, and supervised contrastive learning enables more discriminative representations between plausible streamlines and outliers. We perform evaluation on a large tractography dataset with ground truth labels and on three independently acquired testing datasets from individuals across ages and health conditions. Compared to several state-of-the-art methods, SupWMA obtains a highly consistent and accurate SWM parcellation result. In addition, the computational speed of SupWMA is much faster than other methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Towards Bi-directional Skip Connections in Encoder-Decoder Architectures and Beyond

U-Net, as an encoder-decoder architecture with forward skip connections, has achieved promising results in various medical image analysis tasks. Many recent approaches have also extended U-Net with more complex building blocks, which typically increase the number of network parameters considerably. Such complexity makes the inference stage highly inefficient for clinical applications. Towards an effective yet economic segmentation network design, in this work, we propose backward skip connections that bring decoded features back to the encoder. Our design can be jointly adopted with forward skip connections in any encoder-decoder architecture forming a recurrence structure without introducing extra parameters. With the backward skip connections, we propose a U-Net based network family, namely Bi-directional O-shape networks, which set new benchmarks on multiple public medical imaging segmentation datasets. On the other hand, with the most plain architecture (BiO-Net), network computations inevitably increase along with the pre-set recurrence time. We have thus studied the deficiency bottleneck of such recurrent design and propose a novel two-phase Neural Architecture Search (NAS) algorithm, namely BiX-NAS, to search for the best multi-scale bi-directional skip connections. The ineffective skip connections are then discarded to reduce computational costs and speed up network inference. The finally searched BiX-Net yields the least network complexity and outperforms other state-of-the-art counterparts by large margins. We evaluate our methods on both 2D and 3D segmentation tasks in a total of six datasets. Extensive ablation studies have also been conducted to provide a comprehensive analysis for our proposed methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Towards Generalisable Audio Representations for Audio-Visual Navigation

In audio-visual navigation (AVN), an intelligent agent needs to navigate to a constantly sound-making object in complex 3D environments based on its audio and visual perceptions. While existing methods attempt to improve the navigation performance with preciously designed path planning or intricate task settings, none has improved the model generalisation on unheard sounds with task settings unchanged. We thus propose a contrastive learning-based method to tackle this challenge by regularising the audio encoder, where the sound-agnostic goal-driven latent representations can be learnt from various audio signals of different classes. In addition, we consider two data augmentation strategies to enrich the training sounds. We demonstrate that our designs can be easily equipped to existing AVN frameworks to obtain an immediate performance gain (13.4%$\uparrow$ in SPL on Replica and 12.2%$\uparrow$ in SPL on MP3D). Our project is available at https://AV-GeN.github.io/.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

TractoFormer: A Novel Fiber-level Whole Brain Tractography Analysis Framework Using Spectral Embedding and Vision Transformers

Diffusion MRI tractography is an advanced imaging technique for quantitative mapping of the brain's structural connectivity. Whole brain tractography (WBT) data contains over hundreds of thousands of individual fiber streamlines (estimated brain connections), and this data is usually parcellated to create compact representations for data analysis applications such as disease classification. In this paper, we propose a novel parcellation-free WBT analysis framework, TractoFormer, that leverages tractography information at the level of individual fiber streamlines and provides a natural mechanism for interpretation of results using the attention mechanism of transformers. TractoFormer includes two main contributions. First, we propose a novel and simple 2D image representation of WBT, TractoEmbedding, to encode 3D fiber spatial relationships and any feature of interest that can be computed from individual fibers (such as FA or MD). Second, we design a network based on vision transformers (ViTs) that includes: 1) data augmentation to overcome model overfitting on small datasets, 2) identification of discriminative fibers for interpretation of results, and 3) ensemble learning to leverage fiber information from different brain regions. In a synthetic data experiment, TractoFormer successfully identifies discriminative fibers with simulated group differences. In a disease classification experiment comparing several methods, TractoFormer achieves the highest accuracy in classifying schizophrenia vs control. Discriminative fibers are identified in left hemispheric frontal and parietal superficial white matter regions, which have previously been shown to be affected in schizophrenia patients.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

White Matter Tracts are Point Clouds: Neuropsychological Score Prediction and Critical Region Localization via Geometric Deep Learning

White matter tract microstructure has been shown to influence neuropsychological scores of cognitive performance. However, prediction of these scores from white matter tract data has not been attempted. In this paper, we propose a deep-learning-based framework for neuropsychological score prediction using microstructure measurements estimated from diffusion magnetic resonance imaging (dMRI) tractography, focusing on predicting performance on a receptive vocabulary assessment task based on a critical fiber tract for language, the arcuate fasciculus (AF). We directly utilize information from all points in a fiber tract, without the need to average data along the fiber as is traditionally required by diffusion MRI tractometry methods. Specifically, we represent the AF as a point cloud with microstructure measurements at each point, enabling adoption of point-based neural networks. We improve prediction performance with the proposed Paired-Siamese Loss that utilizes information about differences between continuous neuropsychological scores. Finally, we propose a Critical Region Localization (CRL) algorithm to localize informative anatomical regions containing points with strong contributions to the prediction results. Our method is evaluated on data from 806 subjects from the Human Connectome Project dataset. Results demonstrate superior neuropsychological score prediction performance compared to baseline methods. We discover that critical regions in the AF are strikingly consistent across subjects, with the highest number of strongly contributing points located in frontal cortical regions (i.e., the rostral middle frontal, pars opercularis, and pars triangularis), which are strongly implicated as critical areas for language processes.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

CellTrack R-CNN: A Novel End-To-End Deep Neural Network for Cell Segmentation and Tracking in Microscopy Images

Cell segmentation and tracking in microscopy images are of great significance to new discoveries in biology and medicine. In this study, we propose a novel approach to combine cell segmentation and cell tracking into a unified end-to-end deep learning based framework, where cell detection and segmentation are performed with a current instance segmentation pipeline and cell tracking is implemented by integrating Siamese Network with the pipeline. Besides, tracking performance is improved by incorporating spatial information into the network and fusing spatial and visual prediction. Our approach was evaluated on the DeepCell benchmark dataset. Despite being simple and efficient, our method outperforms state-of-the-art algorithms in terms of both cell segmentation and cell tracking accuracies.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Single Neuron Segmentation using Graph-based Global Reasoning with Auxiliary Skeleton Loss from 3D Optical Microscope Images

One of the critical steps in improving accurate single neuron reconstruction from three-dimensional (3D) optical microscope images is the neuronal structure segmentation. However, they are always hard to segment due to the lack in quality. Despite a series of attempts to apply convolutional neural networks (CNNs) on this task, noise and disconnected gaps are still challenging to alleviate with the neglect of the non-local features of graph-like tubular neural structures. Hence, we present an end-to-end segmentation network by jointly considering the local appearance and the global geometry traits through graph reasoning and a skeleton-based auxiliary loss. The evaluation results on the Janelia dataset from the BigNeuron project demonstrate that our proposed method exceeds the counterpart algorithms in performance.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access