arXiv subjects

Weidong Cai

Publications and source records attributed to Weidong Cai.

At least 127 records · Page 7Linked to original sources

arXiv2024

Exploiting Structural Consistency of Chest Anatomy for Unsupervised Anomaly Detection in Radiography Images

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

eess.IV↗

arXiv2024

Seeing Unseen: Discover Novel Biomedical Concepts via Geometry-Constrained Probabilistic Modeling

Machine learning holds tremendous promise for transforming the fundamental practice of scientific discovery by virtue of its data-driven nature. With the ever-increasing stream of research data collection, it would be appealing to autonomously explore patterns and insights from observational data for discovering novel classes of phenotypes and concepts. However, in the biomedical domain, there are several challenges inherently presented in the cumulated data which hamper the progress of novel class discovery. The non-i.i.d. data distribution accompanied by the severe imbalance among different groups of classes essentially leads to ambiguous and biased semantic representations. In this work, we present a geometry-constrained probabilistic modeling treatment to resolve the identified issues. First, we propose to parameterize the approximated posterior of instance embedding as a marginal von MisesFisher distribution to account for the interference of distributional latent bias. Then, we incorporate a suite of critical geometric properties to impose proper constraints on the layout of constructed embedding space, which in turn minimizes the uncontrollable risk for unknown class learning and structuring. Furthermore, a spectral graph-theoretic method is devised to estimate the number of potential novel classes. It inherits two intriguing merits compared to existent approaches, namely high computational efficiency and flexibility for taxonomy-adaptive estimation. Extensive experiments across various biomedical scenarios substantiate the effectiveness and general applicability of our method.

cs.LG↗

arXiv2024

Learning to Generalize over Subpartitions for Heterogeneity-aware Domain Adaptive Nuclei Segmentation

Annotation scarcity and cross-modality/stain data distribution shifts are two major obstacles hindering the application of deep learning models for nuclei analysis, which holds a broad spectrum of potential applications in digital pathology. Recently, unsupervised domain adaptation (UDA) methods have been proposed to mitigate the distributional gap between different imaging modalities for unsupervised nuclei segmentation in histopathology images. However, existing UDA methods are built upon the assumption that data distributions within each domain should be uniform. Based on the over-simplified supposition, they propose to align the histopathology target domain with the source domain integrally, neglecting severe intra-domain discrepancy over subpartitions incurred by mixed cancer types and sampling organs. In this paper, for the first time, we propose to explicitly consider the heterogeneity within the histopathology domain and introduce open compound domain adaptation (OCDA) to resolve the crux. In specific, a two-stage disentanglement framework is proposed to acquire domain-invariant feature representations at both image and instance levels. The holistic design addresses the limitations of existing OCDA approaches which struggle to capture instance-wise variations. Two regularization strategies are specifically devised herein to leverage the rich subpartition-specific characteristics in histopathology images and facilitate subdomain decomposition. Moreover, we propose a dual-branch nucleus shape and structure preserving module to prevent nucleus over-generation and deformation in the synthesized images. Experimental results on both cross-modality and cross-stain scenarios over a broad range of diverse datasets demonstrate the superiority of our method compared with state-of-the-art UDA and OCDA methods.

cs.CV↗

arXiv2024

A Deep Network for Explainable Prediction of Non-Imaging Phenotypes using Anatomical Multi-View Data

Large datasets often contain multiple distinct feature sets, or views, that offer complementary information that can be exploited by multi-view learning methods to improve results. We investigate anatomical multi-view data, where each brain anatomical structure is described with multiple feature sets. In particular, we focus on sets of white matter microstructure and connectivity features from diffusion MRI, as well as sets of gray matter area and thickness features from structural MRI. We investigate machine learning methodology that applies multi-view approaches to improve the prediction of non-imaging phenotypes, including demographics (age), motor (strength), and cognition (picture vocabulary). We present an explainable multi-view network (EMV-Net) that can use different anatomical views to improve prediction performance. In this network, each individual anatomical view is processed by a view-specific feature extractor and the extracted information from each view is fused using a learnable weight. This is followed by a wavelet transform-based module to obtain complementary information across views which is then applied to calibrate the view-specific information. Additionally, the calibrator produces an attention-based calibration score to indicate anatomical structures' importance for interpretation.

q-bio.QM↗

arXiv2023

V2A-Mapper: A Lightweight Solution for Vision-to-Audio Generation by Connecting Foundation Models

Building artificial intelligence (AI) systems on top of a set of foundation models (FMs) is becoming a new paradigm in AI research. Their representative and generative abilities learnt from vast amounts of data can be easily adapted and transferred to a wide range of downstream tasks without extra training from scratch. However, leveraging FMs in cross-modal generation remains under-researched when audio modality is involved. On the other hand, automatically generating semantically-relevant sound from visual input is an important problem in cross-modal generation studies. To solve this vision-to-audio (V2A) generation problem, existing methods tend to design and build complex systems from scratch using modestly sized datasets. In this paper, we propose a lightweight solution to this problem by leveraging foundation models, specifically CLIP, CLAP, and AudioLDM. We first investigate the domain gap between the latent space of the visual CLIP and the auditory CLAP models. Then we propose a simple yet effective mapper mechanism (V2A-Mapper) to bridge the domain gap by translating the visual input between CLIP and CLAP spaces. Conditioned on the translated CLAP embedding, pretrained audio generative FM AudioLDM is adopted to produce high-fidelity and visually-aligned sound. Compared to previous approaches, our method only requires a quick training of the V2A-Mapper. We further analyze and conduct extensive experiments on the choice of the V2A-Mapper and show that a generative mapper is better at fidelity and variability (FD) while a regression mapper is slightly better at relevance (CS). Both objective and subjective evaluation on two V2A datasets demonstrate the superiority of our proposed method compared to current state-of-the-art approaches - trained with 86% fewer parameters but achieving 53% and 19% improvement in FD and CS, respectively.

cs.CV↗

arXiv2023

Complex Organ Mask Guided Radiology Report Generation

The goal of automatic report generation is to generate a clinically accurate and coherent phrase from a single given X-ray image, which could alleviate the workload of traditional radiology reporting. However, in a real-world scenario, radiologists frequently face the challenge of producing extensive reports derived from numerous medical images, thereby medical report generation from multi-image perspective is needed. In this paper, we propose the Complex Organ Mask Guided (termed as COMG) report generation model, which incorporates masks from multiple organs (e.g., bones, lungs, heart, and mediastinum), to provide more detailed information and guide the model's attention to these crucial body regions. Specifically, we leverage prior knowledge of the disease corresponding to each organ in the fusion process to enhance the disease identification phase during the report generation process. Additionally, cosine similarity loss is introduced as target function to ensure the convergence of cross-modal consistency and facilitate model optimization.Experimental results on two public datasets show that COMG achieves a 11.4% and 9.7% improvement in terms of BLEU@4 scores over the SOTA model KiUT on IU-Xray and MIMIC, respectively. The code is publicly available at https://github.com/GaryGuTC/COMG_model.

cs.CV↗

arXiv2023

ODM3D: Alleviating Foreground Sparsity for Semi-Supervised Monocular 3D Object Detection

Monocular 3D object detection (M3OD) is a significant yet inherently challenging task in autonomous driving due to absence of explicit depth cues in a single RGB image. In this paper, we strive to boost currently underperforming monocular 3D object detectors by leveraging an abundance of unlabelled data via semi-supervised learning. Our proposed ODM3D framework entails cross-modal knowledge distillation at various levels to inject LiDAR-domain knowledge into a monocular detector during training. By identifying foreground sparsity as the main culprit behind existing methods' suboptimal training, we exploit the precise localisation information embedded in LiDAR points to enable more foreground-attentive and efficient distillation via the proposed BEV occupancy guidance mask, leading to notably improved knowledge transfer and M3OD performance. Besides, motivated by insights into why existing cross-modal GT-sampling techniques fail on our task at hand, we further design a novel cross-modal object-wise data augmentation strategy for effective RGB-LiDAR joint learning. Our method ranks 1st in both KITTI validation and test benchmarks, significantly surpassing all existing monocular methods, supervised or semi-supervised, on both BEV and 3D detection metrics.

cs.CV↗

arXiv2023

PaintHuman: Towards High-fidelity Text-to-3D Human Texturing via Denoised Score Distillation

Recent advances in zero-shot text-to-3D human generation, which employ the human model prior (eg, SMPL) or Score Distillation Sampling (SDS) with pre-trained text-to-image diffusion models, have been groundbreaking. However, SDS may provide inaccurate gradient directions under the weak diffusion guidance, as it tends to produce over-smoothed results and generate body textures that are inconsistent with the detailed mesh geometry. Therefore, directly leverage existing strategies for high-fidelity text-to-3D human texturing is challenging. In this work, we propose a model called PaintHuman to addresses the challenges from two aspects. We first propose a novel score function, Denoised Score Distillation (DSD), which directly modifies the SDS by introducing negative gradient components to iteratively correct the gradient direction and generate high-quality textures. In addition, we use the depth map as a geometric guidance to ensure the texture is semantically aligned to human mesh surfaces. To guarantee the quality of rendered results, we employ geometry-aware networks to predict surface materials and render realistic human textures. Extensive experiments, benchmarked against state-of-the-art methods, validate the efficacy of our approach.

cs.CV↗

arXiv2023

Improving Multiple Sclerosis Lesion Segmentation Across Clinical Sites: A Federated Learning Approach with Noise-Resilient Training

Accurately measuring the evolution of Multiple Sclerosis (MS) with magnetic resonance imaging (MRI) critically informs understanding of disease progression and helps to direct therapeutic strategy. Deep learning models have shown promise for automatically segmenting MS lesions, but the scarcity of accurately annotated data hinders progress in this area. Obtaining sufficient data from a single clinical site is challenging and does not address the heterogeneous need for model robustness. Conversely, the collection of data from multiple sites introduces data privacy concerns and potential label noise due to varying annotation standards. To address this dilemma, we explore the use of the federated learning framework while considering label noise. Our approach enables collaboration among multiple clinical sites without compromising data privacy under a federated learning paradigm that incorporates a noise-robust training strategy based on label correction. Specifically, we introduce a Decoupled Hard Label Correction (DHLC) strategy that considers the imbalanced distribution and fuzzy boundaries of MS lesions, enabling the correction of false annotations based on prediction confidence. We also introduce a Centrally Enhanced Label Correction (CELC) strategy, which leverages the aggregated central model as a correction teacher for all sites, enhancing the reliability of the correction process. Extensive experiments conducted on two multi-site datasets demonstrate the effectiveness and robustness of our proposed methods, indicating their potential for clinical applications in multi-site collaborations.

eess.IV↗

arXiv2023

Taxonomy Adaptive Cross-Domain Adaptation in Medical Imaging via Optimization Trajectory Distillation

The success of automated medical image analysis depends on large-scale and expert-annotated training sets. Unsupervised domain adaptation (UDA) has been raised as a promising approach to alleviate the burden of labeled data collection. However, they generally operate under the closed-set adaptation setting assuming an identical label set between the source and target domains, which is over-restrictive in clinical practice where new classes commonly exist across datasets due to taxonomic inconsistency. While several methods have been presented to tackle both domain shifts and incoherent label sets, none of them take into account the common characteristics of the two issues and consider the learning dynamics along network training. In this work, we propose optimization trajectory distillation, a unified approach to address the two technical challenges from a new perspective. It exploits the low-rank nature of gradient space and devises a dual-stream distillation algorithm to regularize the learning dynamics of insufficiently annotated domain and classes with the external guidance obtained from reliable sources. Our approach resolves the issue of inadequate navigation along network optimization, which is the major obstacle in the taxonomy adaptive cross-domain adaptation scenario. We evaluate the proposed method extensively on several tasks towards various endpoints with clinical and open-world significance. The results demonstrate its effectiveness and improvements over previous methods.

cs.CV↗

arXiv2023

TractCloud: Registration-free tractography parcellation with a novel local-global streamline point cloud representation

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/.

cs.CV↗

arXiv2023

TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance

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.

cs.CV↗

arXiv2023

Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation

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.

cs.CV↗

arXiv2023

Topology Repairing of Disconnected Pulmonary Airways and Vessels: Baselines and a Dataset

Accurate segmentation of pulmonary airways and vessels is crucial for the diagnosis and treatment of pulmonary diseases. However, current deep learning approaches suffer from disconnectivity issues that hinder their clinical usefulness. To address this challenge, we propose a post-processing approach that leverages a data-driven method to repair the topology of disconnected pulmonary tubular structures. Our approach formulates the problem as a keypoint detection task, where a neural network is trained to predict keypoints that can bridge disconnected components. We use a training data synthesis pipeline that generates disconnected data from complete pulmonary structures. Moreover, the new Pulmonary Tree Repairing (PTR) dataset is publicly available, which comprises 800 complete 3D models of pulmonary airways, arteries, and veins, as well as the synthetic disconnected data. Our code and data are available at https://github.com/M3DV/pulmonary-tree-repairing.

eess.IV↗

arXiv2023

Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes

Neuroimaging measures of the brain's white matter connections can enable the prediction of non-imaging phenotypes, such as demographic and cognitive measures. Existing works have investigated traditional microstructure and connectivity measures from diffusion MRI tractography, without considering the shape of the connections reconstructed by tractography. In this paper, we investigate the potential of fiber tract shape features for predicting non-imaging phenotypes, both individually and in combination with traditional features. We focus on three basic shape features: length, diameter, and elongation. Two different prediction methods are used, including a traditional regression method and a deep-learning-based prediction method. Experiments use an efficient two-stage fusion strategy for prediction using microstructure, connectivity, and shape measures. To reduce predictive bias due to brain size, normalized shape features are also investigated. Experimental results on the Human Connectome Project (HCP) young adult dataset (n=1065) demonstrate that individual shape features are predictive of non-imaging phenotypes. When combined with microstructure and connectivity features, shape features significantly improve performance for predicting the cognitive score TPVT (NIH Toolbox picture vocabulary test). Overall, this study demonstrates that the shape of fiber tracts contains useful information for the description and study of the living human brain using machine learning.

cs.CV↗

arXiv2023

SynthMix: Mixing up Aligned Synthesis for Medical Cross-Modality Domain Adaptation

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.

eess.IV↗

arXiv2023

Unsupervised Domain Adaptation for Neuron Membrane Segmentation based on Structural Features

AI-enhanced segmentation of neuronal boundaries in electron microscopy (EM) images is crucial for automatic and accurate neuroinformatics studies. To enhance the limited generalization ability of typical deep learning frameworks for medical image analysis, unsupervised domain adaptation (UDA) methods have been applied. In this work, we propose to improve the performance of UDA methods on cross-domain neuron membrane segmentation in EM images. First, we designed a feature weight module considering the structural features during adaptation. Second, we introduced a structural feature-based super-resolution approach to alleviating the domain gap by adjusting the cross-domain image resolutions. Third, we proposed an orthogonal decomposition module to facilitate the extraction of domain-invariant features. Extensive experiments on two domain adaptive membrane segmentation applications have indicated the effectiveness of our method.

cs.CV↗

arXiv2023

Precise Few-shot Fat-free Thigh Muscle Segmentation in T1-weighted MRI

Precise thigh muscle volumes are crucial to monitor the motor functionality of patients with diseases that may result in various degrees of thigh muscle loss. T1-weighted MRI is the default surrogate to obtain thigh muscle masks due to its contrast between muscle and fat signals. Deep learning approaches have recently been widely used to obtain these masks through segmentation. However, due to the insufficient amount of precise annotations, thigh muscle masks generated by deep learning approaches tend to misclassify intra-muscular fat (IMF) as muscle impacting the analysis of muscle volumetrics. As IMF is infiltrated inside the muscle, human annotations require expertise and time. Thus, precise muscle masks where IMF is excluded are limited in practice. To alleviate this, we propose a few-shot segmentation framework to generate thigh muscle masks excluding IMF. In our framework, we design a novel pseudo-label correction and evaluation scheme, together with a new noise robust loss for exploiting high certainty areas. The proposed framework only takes $1\%$ of the fine-annotated training dataset, and achieves comparable performance with fully supervised methods according to the experimental results.

eess.IV↗