arXiv subjects

Yuyin Zhou

Publications and source records attributed to Yuyin Zhou.

At least 109 records · Page 6Linked to original sources

arXiv2023

Boosting Dermatoscopic Lesion Segmentation via Diffusion Models with Visual and Textual Prompts

Image synthesis approaches, e.g., generative adversarial networks, have been popular as a form of data augmentation in medical image analysis tasks. It is primarily beneficial to overcome the shortage of publicly accessible data and associated quality annotations. However, the current techniques often lack control over the detailed contents in generated images, e.g., the type of disease patterns, the location of lesions, and attributes of the diagnosis. In this work, we adapt the latest advance in the generative model, i.e., the diffusion model, with the added control flow using lesion-specific visual and textual prompts for generating dermatoscopic images. We further demonstrate the advantage of our diffusion model-based framework over the classical generation models in both the image quality and boosting the segmentation performance on skin lesions. It can achieve a 9% increase in the SSIM image quality measure and an over 5% increase in Dice coefficients over the prior arts.

cs.CV↗

arXiv2023

SwinMM: Masked Multi-view with Swin Transformers for 3D Medical Image Segmentation

Recent advancements in large-scale Vision Transformers have made significant strides in improving pre-trained models for medical image segmentation. However, these methods face a notable challenge in acquiring a substantial amount of pre-training data, particularly within the medical field. To address this limitation, we present Masked Multi-view with Swin Transformers (SwinMM), a novel multi-view pipeline for enabling accurate and data-efficient self-supervised medical image analysis. Our strategy harnesses the potential of multi-view information by incorporating two principal components. In the pre-training phase, we deploy a masked multi-view encoder devised to concurrently train masked multi-view observations through a range of diverse proxy tasks. These tasks span image reconstruction, rotation, contrastive learning, and a novel task that employs a mutual learning paradigm. This new task capitalizes on the consistency between predictions from various perspectives, enabling the extraction of hidden multi-view information from 3D medical data. In the fine-tuning stage, a cross-view decoder is developed to aggregate the multi-view information through a cross-attention block. Compared with the previous state-of-the-art self-supervised learning method Swin UNETR, SwinMM demonstrates a notable advantage on several medical image segmentation tasks. It allows for a smooth integration of multi-view information, significantly boosting both the accuracy and data-efficiency of the model. Code and models are available at https://github.com/UCSC-VLAA/SwinMM/.

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arXiv2023

Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

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arXiv2023

Image Registration of In Vivo Micro-Ultrasound and Ex Vivo Pseudo-Whole Mount Histopathology Images of the Prostate: A Proof-of-Concept Study

Early diagnosis of prostate cancer significantly improves a patient's 5-year survival rate. Biopsy of small prostate cancers is improved with image-guided biopsy. MRI-ultrasound fusion-guided biopsy is sensitive to smaller tumors but is underutilized due to the high cost of MRI and fusion equipment. Micro-ultrasound (micro-US), a novel high-resolution ultrasound technology, provides a cost-effective alternative to MRI while delivering comparable diagnostic accuracy. However, the interpretation of micro-US is challenging due to subtle gray scale changes indicating cancer vs normal tissue. This challenge can be addressed by training urologists with a large dataset of micro-US images containing the ground truth cancer outlines. Such a dataset can be mapped from surgical specimens (histopathology) onto micro-US images via image registration. In this paper, we present a semi-automated pipeline for registering in vivo micro-US images with ex vivo whole-mount histopathology images. Our pipeline begins with the reconstruction of pseudo-whole-mount histopathology images and a 3-dimensional (3D) micro-US volume. Each pseudo-whole-mount histopathology image is then registered with the corresponding axial micro-US slice using a two-stage approach that estimates an affine transformation followed by a deformable transformation. We evaluated our registration pipeline using micro-US and histopathology images from 18 patients who underwent radical prostatectomy. The results showed a Dice coefficient of 0.94 and a landmark error of 2.7 mm, indicating the accuracy of our registration pipeline. This proof-of-concept study demonstrates the feasibility of accurately aligning micro-US and histopathology images. To promote transparency and collaboration in research, we will make our code and dataset publicly available.

cs.CV↗

arXiv2023

Unleashing the Power of Visual Prompting At the Pixel Level

This paper presents a simple and effective visual prompting method for adapting pre-trained models to downstream recognition tasks. Our method includes two key designs. First, rather than directly adding together the prompt and the image, we treat the prompt as an extra and independent learnable component. We show that the strategy of reconciling the prompt and the image matters, and find that warping the prompt around a properly shrinked image empirically works the best. Second, we re-introduce two "old tricks" commonly used in building transferable adversarial examples, i.e., input diversity and gradient normalization, into visual prompting. These techniques improve optimization and enable the prompt to generalize better. We provide extensive experimental results to demonstrate the effectiveness of our method. Using a CLIP model, our prompting method sets a new record of 82.8% average accuracy across 12 popular classification datasets, substantially surpassing the prior art by +5.6%. It is worth noting that this prompting performance already outperforms linear probing by +2.1% and can even match fully fine-tuning in certain datasets. In addition, our prompting method shows competitive performance across different data scales and against distribution shifts. The code is publicly available at https://github.com/UCSC-VLAA/EVP.

cs.CV↗

arXiv2023

Distribution Aligned Diffusion and Prototype-guided network for Unsupervised Domain Adaptive Segmentation

The Diffusion Probabilistic Model (DPM) has emerged as a highly effective generative model in the field of computer vision. Its intermediate latent vectors offer rich semantic information, making it an attractive option for various downstream tasks such as segmentation and detection. In order to explore its potential further, we have taken a step forward and considered a more complex scenario in the medical image domain, specifically, under an unsupervised adaptation condition. To this end, we propose a Diffusion-based and Prototype-guided network (DP-Net) for unsupervised domain adaptive segmentation. Concretely, our DP-Net consists of two stages: 1) Distribution Aligned Diffusion (DADiff), which involves training a domain discriminator to minimize the difference between the intermediate features generated by the DPM, thereby aligning the inter-domain distribution; and 2) Prototype-guided Consistency Learning (PCL), which utilizes feature centroids as prototypes and applies a prototype-guided loss to ensure that the segmentor learns consistent content from both source and target domains. Our approach is evaluated on fundus datasets through a series of experiments, which demonstrate that the performance of the proposed method is reliable and outperforms state-of-the-art methods. Our work presents a promising direction for using DPM in complex medical image scenarios, opening up new possibilities for further research in medical imaging.

cs.CV↗

arXiv2023

Can CNNs Be More Robust Than Transformers?

The recent success of Vision Transformers is shaking the long dominance of Convolutional Neural Networks (CNNs) in image recognition for a decade. Specifically, in terms of robustness on out-of-distribution samples, recent research finds that Transformers are inherently more robust than CNNs, regardless of different training setups. Moreover, it is believed that such superiority of Transformers should largely be credited to their self-attention-like architectures per se. In this paper, we question that belief by closely examining the design of Transformers. Our findings lead to three highly effective architecture designs for boosting robustness, yet simple enough to be implemented in several lines of code, namely a) patchifying input images, b) enlarging kernel size, and c) reducing activation layers and normalization layers. Bringing these components together, we are able to build pure CNN architectures without any attention-like operations that are as robust as, or even more robust than, Transformers. We hope this work can help the community better understand the design of robust neural architectures. The code is publicly available at https://github.com/UCSC-VLAA/RobustCNN.

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arXiv2023

Label-Efficient Self-Supervised Federated Learning for Tackling Data Heterogeneity in Medical Imaging

The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel Transformer-based self-supervised pre-training paradigm that pre-trains models directly on decentralized target task datasets using masked image modeling, to facilitate more robust representation learning on heterogeneous data and effective knowledge transfer to downstream models. Extensive empirical results on simulated and real-world medical imaging non-IID federated datasets show that masked image modeling with Transformers significantly improves the robustness of models against various degrees of data heterogeneity. Notably, under severe data heterogeneity, our method, without relying on any additional pre-training data, achieves an improvement of 5.06%, 1.53% and 4.58% in test accuracy on retinal, dermatology and chest X-ray classification compared to the supervised baseline with ImageNet pre-training. In addition, we show that our federated self-supervised pre-training methods yield models that generalize better to out-of-distribution data and perform more effectively when fine-tuning with limited labeled data, compared to existing FL algorithms. The code is available at https://github.com/rui-yan/SSL-FL.

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arXiv2022

Masked Autoencoders Enable Efficient Knowledge Distillers

This paper studies the potential of distilling knowledge from pre-trained models, especially Masked Autoencoders. Our approach is simple: in addition to optimizing the pixel reconstruction loss on masked inputs, we minimize the distance between the intermediate feature map of the teacher model and that of the student model. This design leads to a computationally efficient knowledge distillation framework, given 1) only a small visible subset of patches is used, and 2) the (cumbersome) teacher model only needs to be partially executed, ie, forward propagate inputs through the first few layers, for obtaining intermediate feature maps. Compared to directly distilling fine-tuned models, distilling pre-trained models substantially improves downstream performance. For example, by distilling the knowledge from an MAE pre-trained ViT-L into a ViT-B, our method achieves 84.0% ImageNet top-1 accuracy, outperforming the baseline of directly distilling a fine-tuned ViT-L by 1.2%. More intriguingly, our method can robustly distill knowledge from teacher models even with extremely high masking ratios: e.g., with 95% masking ratio where merely TEN patches are visible during distillation, our ViT-B competitively attains a top-1 ImageNet accuracy of 83.6%; surprisingly, it can still secure 82.4% top-1 ImageNet accuracy by aggressively training with just FOUR visible patches (98% masking ratio). The code and models are publicly available at https://github.com/UCSC-VLAA/DMAE.

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arXiv2022

Multi-Granularity Cross-modal Alignment for Generalized Medical Visual Representation Learning

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework.

cs.CV↗

arXiv2022

Bag of Tricks for FGSM Adversarial Training

Adversarial training (AT) with samples generated by Fast Gradient Sign Method (FGSM), also known as FGSM-AT, is a computationally simple method to train robust networks. However, during its training procedure, an unstable mode of "catastrophic overfitting" has been identified in arXiv:2001.03994 [cs.LG], where the robust accuracy abruptly drops to zero within a single training step. Existing methods use gradient regularizers or random initialization tricks to attenuate this issue, whereas they either take high computational cost or lead to lower robust accuracy. In this work, we provide the first study, which thoroughly examines a collection of tricks from three perspectives: Data Initialization, Network Structure, and Optimization, to overcome the catastrophic overfitting in FGSM-AT. Surprisingly, we find that simple tricks, i.e., a) masking partial pixels (even without randomness), b) setting a large convolution stride and smooth activation functions, or c) regularizing the weights of the first convolutional layer, can effectively tackle the overfitting issue. Extensive results on a range of network architectures validate the effectiveness of each proposed trick, and the combinations of tricks are also investigated. For example, trained with PreActResNet-18 on CIFAR-10, our method attains 49.8% accuracy against PGD-50 attacker and 46.4% accuracy against AutoAttack, demonstrating that pure FGSM-AT is capable of enabling robust learners. The code and models are publicly available at https://github.com/UCSC-VLAA/Bag-of-Tricks-for-FGSM-AT.

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arXiv2022

Multiple Instance Neuroimage Transformer

For the first time, we propose using a multiple instance learning based convolution-free transformer model, called Multiple Instance Neuroimage Transformer (MINiT), for the classification of T1weighted (T1w) MRIs. We first present several variants of transformer models adopted for neuroimages. These models extract non-overlapping 3D blocks from the input volume and perform multi-headed self-attention on a sequence of their linear projections. MINiT, on the other hand, treats each of the non-overlapping 3D blocks of the input MRI as its own instance, splitting it further into non-overlapping 3D patches, on which multi-headed self-attention is computed. As a proof-of-concept, we evaluate the efficacy of our model by training it to identify sex from T1w-MRIs of two public datasets: Adolescent Brain Cognitive Development (ABCD) and the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA). The learned attention maps highlight voxels contributing to identifying sex differences in brain morphometry. The code is available at https://github.com/singlaayush/MINIT.

cs.CV↗

arXiv2022

CateNorm: Categorical Normalization for Robust Medical Image Segmentation

Batch normalization (BN) uniformly shifts and scales the activations based on the statistics of a batch of images. However, the intensity distribution of the background pixels often dominates the BN statistics because the background accounts for a large proportion of the entire image. This paper focuses on enhancing BN with the intensity distribution of foreground pixels, the one that really matters for image segmentation. We propose a new normalization strategy, named categorical normalization (CateNorm), to normalize the activations according to categorical statistics. The categorical statistics are obtained by dynamically modulating specific regions in an image that belong to the foreground. CateNorm demonstrates both precise and robust segmentation results across five public datasets obtained from different domains, covering complex and variable data distributions. It is attributable to the ability of CateNorm to capture domain-invariant information from multiple domains (institutions) of medical data. Code is available at https://github.com/lambert-x/CateNorm.

eess.IV↗

arXiv2022

In Defense of Image Pre-Training for Spatiotemporal Recognition

Image pre-training, the current de-facto paradigm for a wide range of visual tasks, is generally less favored in the field of video recognition. By contrast, a common strategy is to directly train with spatiotemporal convolutional neural networks (CNNs) from scratch. Nonetheless, interestingly, by taking a closer look at these from-scratch learned CNNs, we note there exist certain 3D kernels that exhibit much stronger appearance modeling ability than others, arguably suggesting appearance information is already well disentangled in learning. Inspired by this observation, we hypothesize that the key to effectively leveraging image pre-training lies in the decomposition of learning spatial and temporal features, and revisiting image pre-training as the appearance prior to initializing 3D kernels. In addition, we propose Spatial-Temporal Separable (STS) convolution, which explicitly splits the feature channels into spatial and temporal groups, to further enable a more thorough decomposition of spatiotemporal features for fine-tuning 3D CNNs. Our experiments show that simply replacing 3D convolution with STS notably improves a wide range of 3D CNNs without increasing parameters and computation on both Kinetics-400 and Something-Something V2. Moreover, this new training pipeline consistently achieves better results on video recognition with significant speedup. For instance, we achieve +0.6% top-1 of Slowfast on Kinetics-400 over the strong 256-epoch 128-GPU baseline while fine-tuning for only 50 epochs with 4 GPUs. The code and models are available at https://github.com/UCSC-VLAA/Image-Pretraining-for-Video.

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arXiv2022

A Simple Data Mixing Prior for Improving Self-Supervised Learning

Data mixing (e.g., Mixup, Cutmix, ResizeMix) is an essential component for advancing recognition models. In this paper, we focus on studying its effectiveness in the self-supervised setting. By noticing the mixed images that share the same source images are intrinsically related to each other, we hereby propose SDMP, short for $\textbf{S}$imple $\textbf{D}$ata $\textbf{M}$ixing $\textbf{P}$rior, to capture this straightforward yet essential prior, and position such mixed images as additional $\textbf{positive pairs}$ to facilitate self-supervised representation learning. Our experiments verify that the proposed SDMP enables data mixing to help a set of self-supervised learning frameworks (e.g., MoCo) achieve better accuracy and out-of-distribution robustness. More notably, our SDMP is the first method that successfully leverages data mixing to improve (rather than hurt) the performance of Vision Transformers in the self-supervised setting. Code is publicly available at https://github.com/OliverRensu/SDMP

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arXiv2022

Rethinking Architecture Design for Tackling Data Heterogeneity in Federated Learning

Federated learning is an emerging research paradigm enabling collaborative training of machine learning models among different organizations while keeping data private at each institution. Despite recent progress, there remain fundamental challenges such as the lack of convergence and the potential for catastrophic forgetting across real-world heterogeneous devices. In this paper, we demonstrate that self-attention-based architectures (e.g., Transformers) are more robust to distribution shifts and hence improve federated learning over heterogeneous data. Concretely, we conduct the first rigorous empirical investigation of different neural architectures across a range of federated algorithms, real-world benchmarks, and heterogeneous data splits. Our experiments show that simply replacing convolutional networks with Transformers can greatly reduce catastrophic forgetting of previous devices, accelerate convergence, and reach a better global model, especially when dealing with heterogeneous data. We release our code and pretrained models at https://github.com/Liangqiong/ViT-FL-main to encourage future exploration in robust architectures as an alternative to current research efforts on the optimization front.

cs.LG↗

arXiv2022

CD$^2$-pFed: Cyclic Distillation-guided Channel Decoupling for Model Personalization in Federated Learning

Federated learning (FL) is a distributed learning paradigm that enables multiple clients to collaboratively learn a shared global model. Despite the recent progress, it remains challenging to deal with heterogeneous data clients, as the discrepant data distributions usually prevent the global model from delivering good generalization ability on each participating client. In this paper, we propose CD^2-pFed, a novel Cyclic Distillation-guided Channel Decoupling framework, to personalize the global model in FL, under various settings of data heterogeneity. Different from previous works which establish layer-wise personalization to overcome the non-IID data across different clients, we make the first attempt at channel-wise assignment for model personalization, referred to as channel decoupling. To further facilitate the collaboration between private and shared weights, we propose a novel cyclic distillation scheme to impose a consistent regularization between the local and global model representations during the federation. Guided by the cyclical distillation, our channel decoupling framework can deliver more accurate and generalized results for different kinds of heterogeneity, such as feature skew, label distribution skew, and concept shift. Comprehensive experiments on four benchmarks, including natural image and medical image analysis tasks, demonstrate the consistent effectiveness of our method on both local and external validations.

cs.CV↗

arXiv2022

External Attention Assisted Multi-Phase Splenic Vascular Injury Segmentation with Limited Data

The spleen is one of the most commonly injured solid organs in blunt abdominal trauma. The development of automatic segmentation systems from multi-phase CT for splenic vascular injury can augment severity grading for improving clinical decision support and outcome prediction. However, accurate segmentation of splenic vascular injury is challenging for the following reasons: 1) Splenic vascular injury can be highly variant in shape, texture, size, and overall appearance; and 2) Data acquisition is a complex and expensive procedure that requires intensive efforts from both data scientists and radiologists, which makes large-scale well-annotated datasets hard to acquire in general. In light of these challenges, we hereby design a novel framework for multi-phase splenic vascular injury segmentation, especially with limited data. On the one hand, we propose to leverage external data to mine pseudo splenic masks as the spatial attention, dubbed external attention, for guiding the segmentation of splenic vascular injury. On the other hand, we develop a synthetic phase augmentation module, which builds upon generative adversarial networks, for populating the internal data by fully leveraging the relation between different phases. By jointly enforcing external attention and populating internal data representation during training, our proposed method outperforms other competing methods and substantially improves the popular DeepLab-v3+ baseline by more than 7% in terms of average DSC, which confirms its effectiveness.

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