arXiv subjects

Wenhui Zhu

Publications and source records attributed to Wenhui Zhu.

71 records · Page 4Linked to original sources

arXiv2024

SC-MIL: Sparsely Coded Multiple Instance Learning for Whole Slide Image Classification

Multiple Instance Learning (MIL) has been widely used in weakly supervised whole slide image (WSI) classification. Typical MIL methods include a feature embedding part, which embeds the instances into features via a pre-trained feature extractor, and an MIL aggregator that combines instance embeddings into predictions. Most efforts have typically focused on improving these parts. This involves refining the feature embeddings through self-supervised pre-training as well as modeling the correlations between instances separately. In this paper, we proposed a sparsely coding MIL (SC-MIL) method that addresses those two aspects at the same time by leveraging sparse dictionary learning. The sparse dictionary learning captures the similarities of instances by expressing them as sparse linear combinations of atoms in an over-complete dictionary. In addition, imposing sparsity improves instance feature embeddings by suppressing irrelevant instances while retaining the most relevant ones. To make the conventional sparse coding algorithm compatible with deep learning, we unrolled it into a sparsely coded module leveraging deep unrolling. The proposed SC module can be incorporated into any existing MIL framework in a plug-and-play manner with an acceptable computational cost. The experimental results on multiple datasets demonstrated that the proposed SC module could substantially boost the performance of state-of-the-art MIL methods. The codes are available at \href{https://github.com/sotiraslab/SCMIL.git}{https://github.com/sotiraslab/SCMIL.git}.

cs.CV↗

arXiv2024

RBAD: A Dataset and Benchmark for Retinal Vessels Branching Angle Detection

Detecting retinal image analysis, particularly the geometrical features of branching points, plays an essential role in diagnosing eye diseases. However, existing methods used for this purpose often are coarse-level and lack fine-grained analysis for efficient annotation. To mitigate these issues, this paper proposes a novel method for detecting retinal branching angles using a self-configured image processing technique. Additionally, we offer an open-source annotation tool and a benchmark dataset comprising 40 images annotated with retinal branching angles. Our methodology for retinal branching angle detection and calculation is detailed, followed by a benchmark analysis comparing our method with previous approaches. The results indicate that our method is robust under various conditions with high accuracy and efficiency, which offers a valuable instrument for ophthalmic research and clinical applications.

cs.CV↗

arXiv2024

DGR-MIL: Exploring Diverse Global Representation in Multiple Instance Learning for Whole Slide Image Classification

Multiple instance learning (MIL) stands as a powerful approach in weakly supervised learning, regularly employed in histological whole slide image (WSI) classification for detecting tumorous lesions. However, existing mainstream MIL methods focus on modeling correlation between instances while overlooking the inherent diversity among instances. However, few MIL methods have aimed at diversity modeling, which empirically show inferior performance but with a high computational cost. To bridge this gap, we propose a novel MIL aggregation method based on diverse global representation (DGR-MIL), by modeling diversity among instances through a set of global vectors that serve as a summary of all instances. First, we turn the instance correlation into the similarity between instance embeddings and the predefined global vectors through a cross-attention mechanism. This stems from the fact that similar instance embeddings typically would result in a higher correlation with a certain global vector. Second, we propose two mechanisms to enforce the diversity among the global vectors to be more descriptive of the entire bag: (i) positive instance alignment and (ii) a novel, efficient, and theoretically guaranteed diversification learning paradigm. Specifically, the positive instance alignment module encourages the global vectors to align with the center of positive instances (e.g., instances containing tumors in WSI). To further diversify the global representations, we propose a novel diversification learning paradigm leveraging the determinantal point process. The proposed model outperforms the state-of-the-art MIL aggregation models by a substantial margin on the CAMELYON-16 and the TCGA-lung cancer datasets. The code is available at \url{https://github.com/ChongQingNoSubway/DGR-MIL}.

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arXiv2024

SelfReg-UNet: Self-Regularized UNet for Medical Image Segmentation

Since its introduction, UNet has been leading a variety of medical image segmentation tasks. Although numerous follow-up studies have also been dedicated to improving the performance of standard UNet, few have conducted in-depth analyses of the underlying interest pattern of UNet in medical image segmentation. In this paper, we explore the patterns learned in a UNet and observe two important factors that potentially affect its performance: (i) irrelative feature learned caused by asymmetric supervision; (ii) feature redundancy in the feature map. To this end, we propose to balance the supervision between encoder and decoder and reduce the redundant information in the UNet. Specifically, we use the feature map that contains the most semantic information (i.e., the last layer of the decoder) to provide additional supervision to other blocks to provide additional supervision and reduce feature redundancy by leveraging feature distillation. The proposed method can be easily integrated into existing UNet architecture in a plug-and-play fashion with negligible computational cost. The experimental results suggest that the proposed method consistently improves the performance of standard UNets on four medical image segmentation datasets. The code is available at \url{https://github.com/ChongQingNoSubway/SelfReg-UNet}

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arXiv2024

TimeMIL: Advancing Multivariate Time Series Classification via a Time-aware Multiple Instance Learning

Deep neural networks, including transformers and convolutional neural networks, have significantly improved multivariate time series classification (MTSC). However, these methods often rely on supervised learning, which does not fully account for the sparsity and locality of patterns in time series data (e.g., diseases-related anomalous points in ECG). To address this challenge, we formally reformulate MTSC as a weakly supervised problem, introducing a novel multiple-instance learning (MIL) framework for better localization of patterns of interest and modeling time dependencies within time series. Our novel approach, TimeMIL, formulates the temporal correlation and ordering within a time-aware MIL pooling, leveraging a tokenized transformer with a specialized learnable wavelet positional token. The proposed method surpassed 26 recent state-of-the-art methods, underscoring the effectiveness of the weakly supervised TimeMIL in MTSC. The code will be available at https://github.com/xiwenc1/TimeMIL.

cs.LG↗

arXiv2024

PDL: Regularizing Multiple Instance Learning with Progressive Dropout Layers

Multiple instance learning (MIL) was a weakly supervised learning approach that sought to assign binary class labels to collections of instances known as bags. However, due to their weak supervision nature, the MIL methods were susceptible to overfitting and required assistance in developing comprehensive representations of target instances. While regularization typically effectively combated overfitting, its integration with the MIL model has been frequently overlooked in prior studies. Meanwhile, current regularization methods for MIL have shown limitations in their capacity to uncover a diverse array of representations. In this study, we delve into the realm of regularization within the MIL model, presenting a novel approach in the form of a Progressive Dropout Layer (PDL). We aim to not only address overfitting but also empower the MIL model in uncovering intricate and impactful feature representations. The proposed method was orthogonal to existing MIL methods and could be easily integrated into them to boost performance. Our extensive evaluation across a range of MIL benchmark datasets demonstrated that the incorporation of the PDL into multiple MIL methods not only elevated their classification performance but also augmented their potential for weakly-supervised feature localizations.

cs.CV↗

arXiv2024

Imaging Signal Recovery Using Neural Network Priors Under Uncertain Forward Model Parameters

Inverse imaging problems (IIPs) arise in various applications, with the main objective of reconstructing an image from its compressed measurements. This problem is often ill-posed for being under-determined with multiple interchangeably consistent solutions. The best solution inherently depends on prior knowledge or assumptions, such as the sparsity of the image. Furthermore, the reconstruction process for most IIPs relies significantly on the imaging (i.e. forward model) parameters, which might not be fully known, or the measurement device may undergo calibration drifts. These uncertainties in the forward model create substantial challenges, where inaccurate reconstructions usually happen when the postulated parameters of the forward model do not fully match the actual ones. In this work, we devoted to tackling accurate reconstruction under the context of a set of possible forward model parameters that exist. Here, we propose a novel Moment-Aggregation (MA) framework that is compatible with the popular IIP solution by using a neural network prior. Specifically, our method can reconstruct the signal by considering all candidate parameters of the forward model simultaneously during the update of the neural network. We theoretically demonstrate the convergence of the MA framework, which has a similar complexity with reconstruction under the known forward model parameters. Proof-of-concept experiments demonstrate that the proposed MA achieves performance comparable to the forward model with the known precise parameter in reconstruction across both compressive sensing and phase retrieval applications, with a PSNR gap of 0.17 to 1.94 over various datasets, including MNIST, X-ray, Glas, and MoNuseg. This highlights our method's significant potential in reconstruction under an uncertain forward model.

cs.CV↗

arXiv2024

nnMobileNet: Rethinking CNN for Retinopathy Research

Over the past few decades, convolutional neural networks (CNNs) have been at the forefront of the detection and tracking of various retinal diseases (RD). Despite their success, the emergence of vision transformers (ViT) in the 2020s has shifted the trajectory of RD model development. The leading-edge performance of ViT-based models in RD can be largely credited to their scalability-their ability to improve as more parameters are added. As a result, ViT-based models tend to outshine traditional CNNs in RD applications, albeit at the cost of increased data and computational demands. ViTs also differ from CNNs in their approach to processing images, working with patches rather than local regions, which can complicate the precise localization of small, variably presented lesions in RD. In our study, we revisited and updated the architecture of a CNN model, specifically MobileNet, to enhance its utility in RD diagnostics. We found that an optimized MobileNet, through selective modifications, can surpass ViT-based models in various RD benchmarks, including diabetic retinopathy grading, detection of multiple fundus diseases, and classification of diabetic macular edema. The code is available at https://github.com/Retinal-Research/NN-MOBILENET

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arXiv2024

Reconstructing Retinal Visual Images from 3T fMRI Data Enhanced by Unsupervised Learning

The reconstruction of human visual inputs from brain activity, particularly through functional Magnetic Resonance Imaging (fMRI), holds promising avenues for unraveling the mechanisms of the human visual system. Despite the significant strides made by deep learning methods in improving the quality and interpretability of visual reconstruction, there remains a substantial demand for high-quality, long-duration, subject-specific 7-Tesla fMRI experiments. The challenge arises in integrating diverse smaller 3-Tesla datasets or accommodating new subjects with brief and low-quality fMRI scans. In response to these constraints, we propose a novel framework that generates enhanced 3T fMRI data through an unsupervised Generative Adversarial Network (GAN), leveraging unpaired training across two distinct fMRI datasets in 7T and 3T, respectively. This approach aims to overcome the limitations of the scarcity of high-quality 7-Tesla data and the challenges associated with brief and low-quality scans in 3-Tesla experiments. In this paper, we demonstrate the reconstruction capabilities of the enhanced 3T fMRI data, highlighting its proficiency in generating superior input visual images compared to data-intensive methods trained and tested on a single subject.

cs.CV↗

arXiv2023

OTRE: Where Optimal Transport Guided Unpaired Image-to-Image Translation Meets Regularization by Enhancing

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

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arXiv2023

A Surface-Based Federated Chow Test Model for Integrating APOE Status, Tau Deposition Measure, and Hippocampal Surface Morphometry

Background: Alzheimer's Disease (AD) is the most common type of age-related dementia, affecting 6.2 million people aged 65 or older according to CDC data. It is commonly agreed that discovering an effective AD diagnosis biomarker could have enormous public health benefits, potentially preventing or delaying up to 40% of dementia cases. Tau neurofibrillary tangles are the primary driver of downstream neurodegeneration and subsequent cognitive impairment in AD, resulting in structural deformations such as hippocampal atrophy that can be observed in magnetic resonance imaging (MRI) scans. Objective: To build a surface-based model to 1) detect differences between APOE subgroups in patterns of tau deposition and hippocampal atrophy, and 2) use the extracted surface-based features to predict cognitive decline. Methods: Using data obtained from different institutions, we develop a surface-based federated Chow test model to study the synergistic effects of APOE, a previously reported significant risk factor of AD, and tau on hippocampal surface morphometry. Results: We illustrate that the APOE-specific morphometry features correlate with AD progression and better predict future AD conversion than other MRI biomarkers. For example, a strong association between atrophy and abnormal tau was identified in hippocampal subregion cornu ammonis 1 (CA1 subfield) and subiculum in e4 homozygote cohort. Conclusion: Our model allows for identifying MRI biomarkers for AD and cognitive decline prediction and may uncover a corner of the neural mechanism of the influence of APOE and tau deposition on hippocampal morphology.

physics.med-ph↗

arXiv2023

TetCNN: Convolutional Neural Networks on Tetrahedral Meshes

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

cs.CV↗

arXiv2023

Optimal Transport Guided Unsupervised Learning for Enhancing low-quality Retinal Images

Real-world non-mydriatic retinal fundus photography is prone to artifacts, imperfections and low-quality when certain ocular or systemic co-morbidities exist. Artifacts may result in inaccuracy or ambiguity in clinical diagnoses. In this paper, we proposed a simple but effective end-to-end framework for enhancing poor-quality retinal fundus images. Leveraging the optimal transport theory, we proposed an unpaired image-to-image translation scheme for transporting low-quality images to their high-quality counterparts. We theoretically proved that a Generative Adversarial Networks (GAN) model with a generator and discriminator is sufficient for this task. Furthermore, to mitigate the inconsistency of information between the low-quality images and their enhancements, an information consistency mechanism was proposed to maximally maintain structural consistency (optical discs, blood vessels, lesions) between the source and enhanced domains. Extensive experiments were conducted on the EyeQ dataset to demonstrate the superiority of our proposed method perceptually and quantitatively.

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arXiv2022

Anisotropic Multi-Scale Graph Convolutional Network for Dense Shape Correspondence

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

cs.CV↗

arXiv2022

Improved Prediction of Beta-Amyloid and Tau Burden Using Hippocampal Surface Multivariate Morphometry Statistics and Sparse Coding

Background: Beta-amyloid (A$β$) plaques and tau protein tangles in the brain are the defining 'A' and 'T' hallmarks of Alzheimer's disease (AD), and together with structural atrophy detectable on brain magnetic resonance imaging (MRI) scans as one of the neurodegenerative ('N') biomarkers comprise the ''ATN framework'' of AD. Current methods to detect A$β$/tau pathology include cerebrospinal fluid (CSF; invasive), positron emission tomography (PET; costly and not widely available), and blood-based biomarkers (BBBM; promising but mainly still in development). Objective: To develop a non-invasive and widely available structural MRI-based framework to quantitatively predict the amyloid and tau measurements. Methods: With MRI-based hippocampal multivariate morphometry statistics (MMS) features, we apply our Patch Analysis-based Surface Correntropy-induced Sparse coding and max-pooling (PASCS-MP) method combined with the ridge regression model to individual amyloid/tau measure prediction. Results: We evaluate our framework on amyloid PET/MRI and tau PET/MRI datasets from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Each subject has one pair consisting of a PET image and MRI scan, collected at about the same time. Experimental results suggest that amyloid/tau measurements predicted with our PASCP-MP representations are closer to the real values than the measures derived from other approaches, such as hippocampal surface area, volume, and shape morphometry features based on spherical harmonics (SPHARM). Conclusion: The MMS-based PASCP-MP is an efficient tool that can bridge hippocampal atrophy with amyloid and tau pathology and thus help assess disease burden, progression, and treatment effects.

physics.med-ph↗

arXiv2022

Self-Supervised Equivariant Regularization Reconciles Multiple Instance Learning: Joint Referable Diabetic Retinopathy Classification and Lesion Segmentation

Lesion appearance is a crucial clue for medical providers to distinguish referable diabetic retinopathy (rDR) from non-referable DR. Most existing large-scale DR datasets contain only image-level labels rather than pixel-based annotations. This motivates us to develop algorithms to classify rDR and segment lesions via image-level labels. This paper leverages self-supervised equivariant learning and attention-based multi-instance learning (MIL) to tackle this problem. MIL is an effective strategy to differentiate positive and negative instances, helping us discard background regions (negative instances) while localizing lesion regions (positive ones). However, MIL only provides coarse lesion localization and cannot distinguish lesions located across adjacent patches. Conversely, a self-supervised equivariant attention mechanism (SEAM) generates a segmentation-level class activation map (CAM) that can guide patch extraction of lesions more accurately. Our work aims at integrating both methods to improve rDR classification accuracy. We conduct extensive validation experiments on the Eyepacs dataset, achieving an area under the receiver operating characteristic curve (AU ROC) of 0.958, outperforming current state-of-the-art algorithms.

eess.IV↗

arXiv2021

Predicting Tau Accumulation in Cerebral Cortex with Multivariate MRI Morphometry Measurements, Sparse Coding, and Correntropy

Biomarker-assisted diagnosis and intervention in Alzheimer's disease (AD) may be the key to prevention breakthroughs. One of the hallmarks of AD is the accumulation of tau plaques in the human brain. However, current methods to detect tau pathology are either invasive (lumbar puncture) or quite costly and not widely available (Tau PET). In our previous work, structural MRI-based hippocampal multivariate morphometry statistics (MMS) showed superior performance as an effective neurodegenerative biomarker for preclinical AD and Patch Analysis-based Surface Correntropy-induced Sparse coding and max-pooling (PASCS-MP) has excellent ability to generate low-dimensional representations with strong statistical power for brain amyloid prediction. In this work, we apply this framework together with ridge regression models to predict Tau deposition in Braak12 and Braak34 brain regions separately. We evaluate our framework on 925 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Each subject has one pair consisting of a PET image and MRI scan which were collected at about the same times. Experimental results suggest that the representations from our MMS and PASCS-MP have stronger predictive power and their predicted Braak12 and Braak34 are closer to the real values compared to the measures derived from other approaches such as hippocampal surface area and volume, and shape morphometry features based on spherical harmonics (SPHARM).

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