Chaoyi Zhang

Tiange Xiang, Chaoyi Zhang, Xinyi Wang et al. · cmu

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.

Runkai Zhao, Heng Wang, Chaoyi Zhang et al.

Digital neuron reconstruction from 3D microscopy images is an essential technique for investigating brain connectomics and neuron morphology. Existing reconstruction frameworks use convolution-based segmentation networks to partition the neuron from noisy backgrounds before applying the tracing algorithm. The tracing results are sensitive to the raw image quality and segmentation accuracy. In this paper, we propose a novel framework for 3D neuron reconstruction. Our key idea is to use the geometric representation power of the point cloud to better explore the intrinsic structural information of neurons. Our proposed framework adopts one graph convolutional network to predict the neural skeleton points and another one to produce the connectivity of these points. We finally generate the target SWC file through the interpretation of the predicted point coordinates, radius, and connections. Evaluated on the Janelia-Fly dataset from the BigNeuron project, we show that our framework achieves competitive neuron reconstruction performance. Our geometry and topology learning of point clouds could further benefit 3D medical image analysis, such as cardiac surface reconstruction. Our code is available at https://github.com/RunkaiZhao/PointNeuron.

Zhiyuan Li, Dongnan Liu, Heng Wang et al.

Recently, training an image captioner without annotated image-sentence pairs has gained traction. Previous methods have faced limitations due to either using mismatched corpora for inaccurate pseudo annotations or relying on resource-intensive pre-training. To alleviate these challenges, we propose a new strategy where the prior knowledge from large pre-trained models (LPMs) is distilled and leveraged as supervision, and a retrieval process is integrated to further reinforce its effectiveness. Specifically, we introduce Retrieval-augmented Pseudo Sentence Generation (RaPSG), which can efficiently retrieve highly relevant short region descriptions from the mismatching corpora and use them to generate a variety of high-quality pseudo sentences via LPMs. Additionally, we introduce a fluency filter and a CLIP guidance objective to enhance contrastive information learning. Experimental results indicate that our method outperforms SOTA captioning models across various settings including zero-shot, unsupervised, semi-supervised, and cross-domain scenarios. Code is available at: https://github.com/Zhiyuan-Li-John/RaPSG.

Tengfei Xue, Fan Zhang, Chaoyi Zhang et al.

Diffusion MRI tractography is an advanced imaging technique that enables in vivo mapping of the brain's white matter connections. White matter parcellation classifies tractography streamlines into clusters or anatomically meaningful tracts. It enables quantification and visualization of whole-brain tractography. Currently, most parcellation methods focus on the deep white matter (DWM), whereas fewer methods address the superficial white matter (SWM) due to its complexity. We propose a novel two-stage 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 adapted to our SWM parcellation task, and supervised contrastive learning enables more discriminative representations between plausible streamlines and outliers for SWM. We train our model on a large-scale tractography dataset including streamline samples from labeled long- and medium-range (over 40 mm) SWM clusters and anatomically implausible streamline samples, and we perform testing on six independently acquired datasets of different ages and health conditions (including neonates and patients with space-occupying brain tumors). Compared to several state-of-the-art methods, SupWMA obtains highly consistent and accurate SWM parcellation results on all datasets, showing good generalization across the lifespan in health and disease. In addition, the computational speed of SupWMA is much faster than other methods.

Yuqian Chen, Chaoyi Zhang, Tengfei Xue et al.

White matter fiber clustering is an important strategy for white matter parcellation, which enables quantitative analysis of brain connections in health and disease. In combination with expert neuroanatomical labeling, data-driven white matter fiber clustering is a powerful tool for creating atlases that can model white matter anatomy across individuals. While widely used fiber clustering approaches have shown good performance using classical unsupervised machine learning techniques, recent advances in deep learning reveal a promising direction toward fast and effective fiber clustering. In this work, we propose a novel deep learning framework for white matter fiber clustering, Deep Fiber Clustering (DFC), which solves the unsupervised clustering problem as a self-supervised learning task with a domain-specific pretext task to predict pairwise fiber distances. This process learns a high-dimensional embedding feature representation for each fiber, regardless of the order of fiber points reconstructed during tractography. We design a novel network architecture that represents input fibers as point clouds and allows the incorporation of additional sources of input information from gray matter parcellation to improve anatomical coherence of clusters. In addition, DFC conducts outlier removal naturally by rejecting fibers with low cluster assignment probability. We evaluate DFC on three independently acquired cohorts, including data from 220 individuals across genders, ages (young and elderly adults), and different health conditions (healthy control and multiple neuropsychiatric disorders). We compare DFC to several state-of-the-art white matter fiber clustering algorithms. Experimental results demonstrate superior performance of DFC in terms of cluster compactness, generalization ability, anatomical coherence, and computational efficiency.

Zhiyuan Li, Heng Wang, Dongnan Liu et al.

Multimodal Large Language Models (MLLMs) have showcased exceptional Chain-of-Thought (CoT) reasoning ability in complex textual inference tasks including causal reasoning. However, will these causalities remain straightforward when crucial hints hide in visual details? If not, what factors might influence cross-modal generalization? Whether we can effectively enhance their capacity for robust causal inference across both text and vision? Motivated by these, we introduce MuCR - a novel Multimodal Causal Reasoning benchmark that leverages synthetic siamese images and text pairs to challenge MLLMs. Additionally, we develop tailored metrics from multiple perspectives, including image-level match, phrase-level understanding, and sentence-level explanation, to comprehensively assess MLLMs' comprehension abilities. Our experiments reveal that current MLLMs fall short in multimodal causal reasoning compared to their performance in purely textual settings. Additionally, we find that identifying visual cues across images is key to effective cross-modal generalization. Finally, we propose a VcCoT strategy that better highlights visual cues, and our results confirm its efficacy in enhancing multimodal causal reasoning. The project is available at: https://github.com/Zhiyuan-Li-John/MuCR

Yuqian Chen, Fan Zhang, Chaoyi Zhang et al.

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.

Yuqian Chen, Fan Zhang, Leo R. Zekelman et al.

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.

Yuqian Chen, Leo R. Zekelman, Chaoyi Zhang et al.

We propose a geometric deep-learning-based framework, TractGeoNet, for performing regression using diffusion magnetic resonance imaging (dMRI) tractography and associated pointwise tissue microstructure measurements. By employing a point cloud representation, TractGeoNet can directly utilize pointwise tissue microstructure and positional information from all points within a fiber tract. To improve regression performance, we propose a novel loss function, the Paired-Siamese Regression loss, which encourages the model to focus on accurately predicting the relative differences between regression label scores rather than just their absolute values. In addition, we propose a Critical Region Localization algorithm to identify highly predictive anatomical regions within the white matter fiber tracts for the regression task. We evaluate the effectiveness of the proposed method by predicting individual performance on two neuropsychological assessments of language using a dataset of 20 association white matter fiber tracts from 806 subjects from the Human Connectome Project. The results demonstrate superior prediction performance of TractGeoNet compared to several popular regression models. Of the twenty tracts studied, we find that the left arcuate fasciculus tract is the most highly predictive of the two studied language performance assessments. The localized critical regions are widespread and distributed across both hemispheres and all cerebral lobes, including areas of the brain considered important for language function such as superior and anterior temporal regions, pars opercularis, and precentral gyrus. Overall, TractGeoNet demonstrates the potential of geometric deep learning to enhance the study of the brain's white matter fiber tracts and to relate their structure to human traits such as language performance.

Tengfei Xue, Yuqian Chen, Chaoyi Zhang et al.

Diffusion MRI tractography parcellation classifies streamlines into anatomical fiber tracts to enable quantification and visualization for clinical and scientific applications. Current tractography parcellation methods rely heavily on registration, but registration inaccuracies can affect parcellation and the computational cost of registration is high for large-scale datasets. Recently, deep-learning-based methods have been proposed for tractography parcellation using various types of representations for streamlines. However, these methods only focus on the information from a single streamline, ignoring geometric relationships between the streamlines in the brain. We propose TractCloud, a registration-free framework that performs whole-brain tractography parcellation directly in individual subject space. We propose a novel, learnable, local-global streamline representation that leverages information from neighboring and whole-brain streamlines to describe the local anatomy and global pose of the brain. We train our framework on a large-scale labeled tractography dataset, which we augment by applying synthetic transforms including rotation, scaling, and translations. We test our framework on five independently acquired datasets across populations and health conditions. TractCloud significantly outperforms several state-of-the-art methods on all testing datasets. TractCloud achieves efficient and consistent whole-brain white matter parcellation across the lifespan (from neonates to elderly subjects, including brain tumor patients) without the need for registration. The robustness and high inference speed of TractCloud make it suitable for large-scale tractography data analysis. Our project page is available at https://tractcloud.github.io/.

Tengfei Xue, Fan Zhang, Leo R. Zekelman et al.

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.

Heng Wang, Chaoyi Zhang, Jianhui Yu et al.

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/ .

Shunqi Mao, Chaoyi Zhang, Hang Su et al.

Contextualized Image Captioning (CIC) evolves traditional image captioning into a more complex domain, necessitating the ability for multimodal reasoning. It aims to generate image captions given specific contextual information. This paper further introduces a novel domain of Controllable Contextualized Image Captioning (Ctrl-CIC). Unlike CIC, which solely relies on broad context, Ctrl-CIC accentuates a user-defined highlight, compelling the model to tailor captions that resonate with the highlighted aspects of the context. We present two approaches, Prompting-based Controller (P-Ctrl) and Recalibration-based Controller (R-Ctrl), to generate focused captions. P-Ctrl conditions the model generation on highlight by prepending captions with highlight-driven prefixes, whereas R-Ctrl tunes the model to selectively recalibrate the encoder embeddings for highlighted tokens. Additionally, we design a GPT-4V empowered evaluator to assess the quality of the controlled captions alongside standard assessment methods. Extensive experimental results demonstrate the efficient and effective controllability of our method, charting a new direction in achieving user-adaptive image captioning. Code is available at https://github.com/ShunqiM/Ctrl-CIC .

Peizhou Huang, Chaoyi Zhang, Xiaoliang Zhang et al.

Deep learning methods have been successfully used in various computer vision tasks. Inspired by that success, deep learning has been explored in magnetic resonance imaging (MRI) reconstruction. In particular, integrating deep learning and model-based optimization methods has shown considerable advantages. However, a large amount of labeled training data is typically needed for high reconstruction quality, which is challenging for some MRI applications. In this paper, we propose a novel reconstruction method, named DURED-Net, that enables interpretable self-supervised learning for MR image reconstruction by combining a self-supervised denoising network and a plug-and-play method. We aim to boost the reconstruction performance of Noise2Noise in MR reconstruction by adding an explicit prior that utilizes imaging physics. Specifically, the leverage of a denoising network for MRI reconstruction is achieved using Regularization by Denoising (RED). Experiment results demonstrate that the proposed method requires a reduced amount of training data to achieve high reconstruction quality among the state-of-art of MR reconstruction utilizing the Noise2Noise method.

Jianhui Yu, Chaoyi Zhang, Weidong Cai

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/.

Qianbi Yu, Dongnan Liu, Chaoyi Zhang et al.

Deep learning-based segmentation methods have been widely employed for automatic glaucoma diagnosis and prognosis. In practice, fundus images obtained by different fundus cameras vary significantly in terms of illumination and intensity. Although recent unsupervised domain adaptation (UDA) methods enhance the models' generalization ability on the unlabeled target fundus datasets, they always require sufficient labeled data from the source domain, bringing auxiliary data acquisition and annotation costs. To further facilitate the data efficiency of the cross-domain segmentation methods on the fundus images, we explore UDA optic disc and cup segmentation problems using few labeled source data in this work. We first design a Searching-based Multi-style Invariant Mechanism to diversify the source data style as well as increase the data amount. Next, a prototype consistency mechanism on the foreground objects is proposed to facilitate the feature alignment for each kind of tissue under different image styles. Moreover, a cross-style self-supervised learning stage is further designed to improve the segmentation performance on the target images. Our method has outperformed several state-of-the-art UDA segmentation methods under the UDA fundus segmentation with few labeled source data.

Yuqian Chen, Fan Zhang, Meng Wang et al.

The relationship between brain connections and non-imaging phenotypes is increasingly studied using deep neural networks. However, the local and global properties of brain white matter networks are often overlooked in convolutional network design. We introduce TractGraphFormer, a hybrid Graph CNN-Transformer deep learning framework tailored for diffusion MRI tractography. This model leverages local anatomical characteristics and global feature dependencies of white matter structures. The Graph CNN module captures white matter geometry and grey matter connectivity to aggregate local features from anatomically similar white matter connections, while the Transformer module uses self-attention to enhance global information learning. Additionally, TractGraphFormer includes an attention module for interpreting predictive white matter connections. We apply TractGraphFormer to tasks of sex and age prediction. TractGraphFormer shows strong performance in large datasets of children (n=9345) and young adults (n=1065). Overall, our approach suggests that widespread connections in the WM are predictive of the sex and age of an individual. For each prediction task, consistent predictive anatomical tracts are identified across the two datasets. The proposed approach highlights the potential of integrating local anatomical information and global feature dependencies to improve prediction performance in machine learning with diffusion MRI tractography.

Shunqi Mao, Chaoyi Zhang, Heng Wang et al.

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/.

Zhiyuan Li, Dongnan Liu, Chaoyi Zhang et al.

Recent advancements in Vision-Language (VL) research have sparked new benchmarks for complex visual reasoning, challenging models' advanced reasoning ability. Traditional Vision-Language Models (VLMs) perform well in visual perception tasks while struggling with complex reasoning scenarios. Conversely, Large Language Models (LLMs) demonstrate robust text reasoning capabilities; however, they lack visual acuity. To bridge this gap, we propose Complex Visual Reasoning Large Language Models (CVR-LLM), capitalizing on VLMs' visual perception proficiency and LLMs' extensive reasoning capability. Unlike recent multimodal large language models (MLLMs) that require a projection layer, our approach transforms images into detailed, context-aware descriptions using an iterative self-refinement loop and leverages LLMs' text knowledge for accurate predictions without extra training. We also introduce a novel multi-modal in-context learning (ICL) methodology to enhance LLMs' contextual understanding and reasoning. Additionally, we introduce Chain-of-Comparison (CoC), a step-by-step comparison technique enabling contrasting various aspects of predictions. Our CVR-LLM presents the first comprehensive study across a wide array of complex visual reasoning tasks and achieves SOTA performance among all.

Seed, Baisheng Li, Banggu Wu et al.

We introduce Virtual Width Networks (VWN), a framework that delivers the benefits of wider representations without incurring the quadratic cost of increasing the hidden size. VWN decouples representational width from backbone width, expanding the embedding space while keeping backbone compute nearly constant. In our large-scale experiment, an 8-times expansion accelerates optimization by over 2 times for next-token and 3 times for next-2-token prediction. The advantage amplifies over training as both the loss gap grows and the convergence-speedup ratio increases, showing that VWN is not only token-efficient but also increasingly effective with scale. Moreover, we identify an approximately log-linear scaling relation between virtual width and loss reduction, offering an initial empirical basis and motivation for exploring virtual-width scaling as a new dimension of large-model efficiency.

Dingxin Zhang, Jianhui Yu, Tengfei Xue et al.

Current models for point cloud recognition demonstrate promising performance on synthetic datasets. However, real-world point cloud data inevitably contains noise, impacting model robustness. While recent efforts focus on enhancing robustness through various strategies, there still remains a gap in comprehensive analyzes from the standpoint of network architecture design. Unlike traditional methods that rely on generic techniques, our approach optimizes model robustness to noise corruption through network architecture design. Inspired by the token-mixing technique applied in 2D images, we propose Set-Mixer, a noise-robust aggregation module which facilitates communication among all points to extract geometric shape information and mitigating the influence of individual noise points. A sorting strategy is designed to enable our module to be invariant to point permutation, which also tackles the unordered structure of point cloud and introduces consistent relative spatial information. Experiments conducted on ModelNet40-C indicate that Set-Mixer significantly enhances the model performance on noisy point clouds, underscoring its potential to advance real-world applicability in 3D recognition and perception tasks.

Tiange Xiang, Yixiao Zhang, Yongyi Lu et al.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. Exploiting this structured information could potentially ease the detection of anomalies from radiography images. To this end, we propose a Simple Space-Aware Memory Matrix for In-painting and Detecting anomalies from radiography images (abbreviated as SimSID). We formulate anomaly detection as an image reconstruction task, consisting of a space-aware memory matrix and an in-painting block in the feature space. During the training, SimSID can taxonomize the ingrained anatomical structures into recurrent visual patterns, and in the inference, it can identify anomalies (unseen/modified visual patterns) from the test image. Our SimSID surpasses the state of the arts in unsupervised anomaly detection by +8.0%, +5.0%, and +9.9% AUC scores on ZhangLab, COVIDx, and CheXpert benchmark datasets, respectively. Code: https://github.com/MrGiovanni/SimSID

Tiange Xiang, Chaoyi Zhang, Dongnan Liu et al.

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.

Mengzhao Chen, Chaoyi Zhang, Jing Liu et al. · bytedance

Large language models (LLMs) demand substantial computational and memory resources, creating deployment challenges. Quantization-aware training (QAT) addresses these challenges by reducing model precision while maintaining performance. However, the scaling behavior of QAT, especially at 4-bit precision (W4A4), is not well understood. Existing QAT scaling laws often ignore key factors such as the number of training tokens and quantization granularity, which limits their applicability. This paper proposes a unified scaling law for QAT that models quantization error as a function of model size, training data volume, and quantization group size. Through 268 QAT experiments, we show that quantization error decreases as model size increases, but rises with more training tokens and coarser quantization granularity. To identify the sources of W4A4 quantization error, we decompose it into weight and activation components. Both components follow the overall trend of W4A4 quantization error, but with different sensitivities. Specifically, weight quantization error increases more rapidly with more training tokens. Further analysis shows that the activation quantization error in the FC2 layer, caused by outliers, is the primary bottleneck of W4A4 QAT quantization error. By applying mixed-precision quantization to address this bottleneck, we demonstrate that weight and activation quantization errors can converge to similar levels. Additionally, with more training data, weight quantization error eventually exceeds activation quantization error, suggesting that reducing weight quantization error is also important in such scenarios. These findings offer key insights for improving QAT research and development.

Shunqi Mao, Chaoyi Zhang, Weidong Cai

Existing vision-language models (VLMs) often suffer from visual hallucination, where the generated responses contain inaccuracies that are not grounded in the visual input. Efforts to address this issue without model finetuning primarily mitigate hallucination by contrastively reducing language biases or amplifying the weights of visual embedding during decoding. However, these approaches remain limited in their ability to capture fine-grained visual details. In this work, we propose the Perception Magnifier (PM), a novel visual decoding method that iteratively isolates relevant visual tokens based on attention and magnifies the corresponding regions, spurring the model to concentrate on fine-grained visual details during decoding. By magnifying critical regions while preserving the structural and contextual information at each decoding step, PM allows the VLM to enhance its scrutiny of the visual input, hence producing more accurate and faithful responses. Extensive experimental results demonstrate that PM not only achieves superior hallucination mitigation but also enhances language generation while preserving strong reasoning capabilities.

Xinwen Zhang, Chaoyi Zhang, Dongnan Liu et al.

The adversarial methods showed advanced performance by producing synthetic images to mitigate the domain shift, a common problem due to the hardship of acquiring labelled data in medical field. Most existing studies focus on modifying the network architecture, but little has worked on the GAN training strategy. In this work, we propose SynthMix, an add-on module with a natural yet effective training policy that can promote synthetic quality without altering the network architecture. Following the adversarial philosophy of GAN, we designed a mix-up synthesis scheme termed SynthMix. It coherently mixed up aligned images of real and synthetic samples to stimulate the generation of fine-grained features, examined by an associated Inspector for the domain-specific details. We evaluated our method on two segmentation benchmarks among three publicly available datasets, where our method showed a significant performance gain compared with existing state-of-the-art approaches.

Tengfei Xue, Fan Zhang, Chaoyi Zhang et al.

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.

Dongnan Liu, Chaoyi Zhang, Yang Song et al.

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.

Jianhui Yu, Chaoyi Zhang, Heng Wang et al.

General point clouds have been increasingly investigated for different tasks, and recently Transformer-based networks are proposed for point cloud analysis. However, there are barely related works for medical point clouds, which are important for disease detection and treatment. In this work, we propose an attention-based model specifically for medical point clouds, namely 3D medical point Transformer (3DMedPT), to examine the complex biological structures. By augmenting contextual information and summarizing local responses at query, our attention module can capture both local context and global content feature interactions. However, the insufficient training samples of medical data may lead to poor feature learning, so we apply position embeddings to learn accurate local geometry and Multi-Graph Reasoning (MGR) to examine global knowledge propagation over channel graphs to enrich feature representations. Experiments conducted on IntrA dataset proves the superiority of 3DMedPT, where we achieve the best classification and segmentation results. Furthermore, the promising generalization ability of our method is validated on general 3D point cloud benchmarks: ModelNet40 and ShapeNetPart. Code is released.

Tiange Xiang, Yixiao Zhang, Yongyi Lu et al.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

Tiange Xiang, Yang Song, Chaoyi Zhang et al.

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.

Heng Wang, Chaoyi Zhang, Jianhui Yu et al.

Automatic 3D neuron reconstruction is critical for analysing the morphology and functionality of neurons in brain circuit activities. However, the performance of existing tracing algorithms is hinged by the low image quality. Recently, a series of deep learning based segmentation methods have been proposed to improve the quality of raw 3D optical image stacks by removing noises and restoring neuronal structures from low-contrast background. Due to the variety of neuron morphology and the lack of large neuron datasets, most of current neuron segmentation models rely on introducing complex and specially-designed submodules to a base architecture with the aim of encoding better feature representations. Though successful, extra burden would be put on computation during inference. Therefore, rather than modifying the base network, we shift our focus to the dataset itself. The encoder-decoder backbone used in most neuron segmentation models attends only intra-volume voxel points to learn structural features of neurons but neglect the shared intrinsic semantic features of voxels belonging to the same category among different volumes, which is also important for expressive representation learning. Hence, to better utilise the scarce dataset, we propose to explicitly exploit such intrinsic features of voxels through a novel voxel-level cross-volume representation learning paradigm on the basis of an encoder-decoder segmentation model. Our method introduces no extra cost during inference. Evaluated on 42 3D neuron images from BigNeuron project, our proposed method is demonstrated to improve the learning ability of the original segmentation model and further enhancing the reconstruction performance.

Yuqian Chen, Chaoyi Zhang, Yang Song et al.

White matter fiber clustering (WMFC) enables parcellation of white matter tractography for applications such as disease classification and anatomical tract segmentation. However, the lack of ground truth and the ambiguity of fiber data (the points along a fiber can equivalently be represented in forward or reverse order) pose challenges to this task. We propose a novel WMFC framework based on unsupervised deep learning. We solve the unsupervised clustering problem as a self-supervised learning task. Specifically, we use a convolutional neural network to learn embeddings of input fibers, using pairwise fiber distances as pseudo annotations. This enables WMFC that is insensitive to fiber point ordering. In addition, anatomical coherence of fiber clusters is improved by incorporating brain anatomical segmentation data. The proposed framework enables outlier removal in a natural way by rejecting fibers with low cluster assignment probability. We train and evaluate our method using 200 datasets from the Human Connectome Project. Results demonstrate superior performance and efficiency of the proposed approach.

Xinyi Wang, Tiange Xiang, Chaoyi Zhang et al.

The recurrent mechanism has recently been introduced into U-Net in various medical image segmentation tasks. Existing studies have focused on promoting network recursion via reusing building blocks. Although network parameters could be greatly saved, computational costs still increase inevitably in accordance with the pre-set iteration time. In this work, we study a multi-scale upgrade of a bi-directional skip connected network and then automatically discover an efficient architecture by a novel two-phase Neural Architecture Search (NAS) algorithm, namely BiX-NAS. Our proposed method reduces the network computational cost by sifting out ineffective multi-scale features at different levels and iterations. We evaluate BiX-NAS on two segmentation tasks using three different medical image datasets, and the experimental results show that our BiX-NAS searched architecture achieves the state-of-the-art performance with significantly lower computational cost.

Tiange Xiang, Chaoyi Zhang, Yang Song et al.

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.

Tiange Xiang, Chaoyi Zhang, Yang Song et al.

Discrete point cloud objects lack sufficient shape descriptors of 3D geometries. In this paper, we present a novel method for aggregating hypothetical curves in point clouds. Sequences of connected points (curves) are initially grouped by taking guided walks in the point clouds, and then subsequently aggregated back to augment their point-wise features. We provide an effective implementation of the proposed aggregation strategy including a novel curve grouping operator followed by a curve aggregation operator. Our method was benchmarked on several point cloud analysis tasks where we achieved the state-of-the-art classification accuracy of 94.2% on the ModelNet40 classification task, instance IoU of 86.8 on the ShapeNetPart segmentation task, and cosine error of 0.11 on the ModelNet40 normal estimation task.

Yang Ma, Chaoyi Zhang, Mariano Cabezas et al.

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.

Chaoyi Zhang, Jianhui Yu, Yang Song et al.

Scene understanding is a critical problem in computer vision. In this paper, we propose a 3D point-based scene graph generation ($\mathbf{SGG_{point}}$) framework to effectively bridge perception and reasoning to achieve scene understanding via three sequential stages, namely scene graph construction, reasoning, and inference. Within the reasoning stage, an EDGE-oriented Graph Convolutional Network ($\texttt{EdgeGCN}$) is created to exploit multi-dimensional edge features for explicit relationship modeling, together with the exploration of two associated twinning interaction mechanisms between nodes and edges for the independent evolution of scene graph representations. Overall, our integrated $\mathbf{SGG_{point}}$ framework is established to seek and infer scene structures of interest from both real-world and synthetic 3D point-based scenes. Our experimental results show promising edge-oriented reasoning effects on scene graph generation studies. We also demonstrate our method advantage on several traditional graph representation learning benchmark datasets, including the node-wise classification on citation networks and whole-graph recognition problems for molecular analysis.

Yuqian Chen, Yang Song, Chaoyi Zhang et al.

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.

Heng Wang, Yang Song, Chaoyi Zhang et al.

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.

Jianhui Yu, Chaoyi Zhang, Yang Song et al.

Micro-expressions are reflections of people's true feelings and motives, which attract an increasing number of researchers into the study of automatic facial micro-expression recognition. The short detection window, the subtle facial muscle movements, and the limited training samples make micro-expression recognition challenging. To this end, we propose a novel Identity-aware and Capsule-Enhanced Generative Adversarial Network with graph-based reasoning (ICE-GAN), introducing micro-expression synthesis as an auxiliary task to assist recognition. The generator produces synthetic faces with controllable micro-expressions and identity-aware features, whose long-ranged dependencies are captured through the graph reasoning module (GRM), and the discriminator detects the image authenticity and expression classes. Our ICE-GAN was evaluated on Micro-Expression Grand Challenge 2019 (MEGC2019) with a significant improvement (12.9%) over the winner and surpassed other state-of-the-art methods.

Chaoyi Zhang, Yang Song, Lina Yao et al.

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.