arXiv subjects

Yiqing Shen

Publications and source records attributed to Yiqing Shen.

71 records · Page 4Linked to original sources

arXiv2023

Towards the Unification of Generative and Discriminative Visual Foundation Model: A Survey

The advent of foundation models, which are pre-trained on vast datasets, has ushered in a new era of computer vision, characterized by their robustness and remarkable zero-shot generalization capabilities. Mirroring the transformative impact of foundation models like large language models (LLMs) in natural language processing, visual foundation models (VFMs) have become a catalyst for groundbreaking developments in computer vision. This review paper delineates the pivotal trajectories of VFMs, emphasizing their scalability and proficiency in generative tasks such as text-to-image synthesis, as well as their adeptness in discriminative tasks including image segmentation. While generative and discriminative models have historically charted distinct paths, we undertake a comprehensive examination of the recent strides made by VFMs in both domains, elucidating their origins, seminal breakthroughs, and pivotal methodologies. Additionally, we collate and discuss the extensive resources that facilitate the development of VFMs and address the challenges that pave the way for future research endeavors. A crucial direction for forthcoming innovation is the amalgamation of generative and discriminative paradigms. The nascent application of generative models within discriminative contexts signifies the early stages of this confluence. This survey aspires to be a contemporary compendium for scholars and practitioners alike, charting the course of VFMs and illuminating their multifaceted landscape.

cs.CV↗

arXiv2023

Tackling Heterogeneity in Medical Federated learning via Vision Transformers

Optimization-based regularization methods have been effective in addressing the challenges posed by data heterogeneity in medical federated learning, particularly in improving the performance of underrepresented clients. However, these methods often lead to lower overall model accuracy and slower convergence rates. In this paper, we demonstrate that using Vision Transformers can substantially improve the performance of underrepresented clients without a significant trade-off in overall accuracy. This improvement is attributed to the Vision transformer's ability to capture long-range dependencies within the input data.

cs.CV↗

arXiv2023

Graph Denoising Diffusion for Inverse Protein Folding

Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable sequences but also representing the sheer diversity of potential solutions. However, existing discriminative models, such as transformer-based auto-regressive models, struggle to encapsulate the diverse range of plausible solutions. In contrast, diffusion probabilistic models, as an emerging genre of generative approaches, offer the potential to generate a diverse set of sequence candidates for determined protein backbones. We propose a novel graph denoising diffusion model for inverse protein folding, where a given protein backbone guides the diffusion process on the corresponding amino acid residue types. The model infers the joint distribution of amino acids conditioned on the nodes' physiochemical properties and local environment. Moreover, we utilize amino acid replacement matrices for the diffusion forward process, encoding the biologically-meaningful prior knowledge of amino acids from their spatial and sequential neighbors as well as themselves, which reduces the sampling space of the generative process. Our model achieves state-of-the-art performance over a set of popular baseline methods in sequence recovery and exhibits great potential in generating diverse protein sequences for a determined protein backbone structure.

q-bio.QM↗

arXiv2023

MoViT: Memorizing Vision Transformers for Medical Image Analysis

The synergy of long-range dependencies from transformers and local representations of image content from convolutional neural networks (CNNs) has led to advanced architectures and increased performance for various medical image analysis tasks due to their complementary benefits. However, compared with CNNs, transformers require considerably more training data, due to a larger number of parameters and an absence of inductive bias. The need for increasingly large datasets continues to be problematic, particularly in the context of medical imaging, where both annotation efforts and data protection result in limited data availability. In this work, inspired by the human decision-making process of correlating new evidence with previously memorized experience, we propose a Memorizing Vision Transformer (MoViT) to alleviate the need for large-scale datasets to successfully train and deploy transformer-based architectures. MoViT leverages an external memory structure to cache history attention snapshots during the training stage. To prevent overfitting, we incorporate an innovative memory update scheme, attention temporal moving average, to update the stored external memories with the historical moving average. For inference speedup, we design a prototypical attention learning method to distill the external memory into smaller representative subsets. We evaluate our method on a public histology image dataset and an in-house MRI dataset, demonstrating that MoViT applied to varied medical image analysis tasks, can outperform vanilla transformer models across varied data regimes, especially in cases where only a small amount of annotated data is available. More importantly, MoViT can reach a competitive performance of ViT with only 3.0% of the training data.

cs.CV↗

arXiv2023

Artifact Restoration in Histology Images with Diffusion Probabilistic Models

Histological whole slide images (WSIs) can be usually compromised by artifacts, such as tissue folding and bubbles, which will increase the examination difficulty for both pathologists and Computer-Aided Diagnosis (CAD) systems. Existing approaches to restoring artifact images are confined to Generative Adversarial Networks (GANs), where the restoration process is formulated as an image-to-image transfer. Those methods are prone to suffer from mode collapse and unexpected mistransfer in the stain style, leading to unsatisfied and unrealistic restored images. Innovatively, we make the first attempt at a denoising diffusion probabilistic model for histological artifact restoration, namely ArtiFusion.Specifically, ArtiFusion formulates the artifact region restoration as a gradual denoising process, and its training relies solely on artifact-free images to simplify the training complexity.Furthermore, to capture local-global correlations in the regional artifact restoration, a novel Swin-Transformer denoising architecture is designed, along with a time token scheme. Our extensive evaluations demonstrate the effectiveness of ArtiFusion as a pre-processing method for histology analysis, which can successfully preserve the tissue structures and stain style in artifact-free regions during the restoration. Code is available at https://github.com/zhenqi-he/ArtiFusion.

eess.IV↗

arXiv2023

TransNuSeg: A Lightweight Multi-Task Transformer for Nuclei Segmentation

Nuclei appear small in size, yet, in real clinical practice, the global spatial information and correlation of the color or brightness contrast between nuclei and background, have been considered a crucial component for accurate nuclei segmentation. However, the field of automatic nuclei segmentation is dominated by Convolutional Neural Networks (CNNs), meanwhile, the potential of the recently prevalent Transformers has not been fully explored, which is powerful in capturing local-global correlations. To this end, we make the first attempt at a pure Transformer framework for nuclei segmentation, called TransNuSeg. Different from prior work, we decouple the challenging nuclei segmentation task into an intrinsic multi-task learning task, where a tri-decoder structure is employed for nuclei instance, nuclei edge, and clustered edge segmentation respectively. To eliminate the divergent predictions from different branches in previous work, a novel self distillation loss is introduced to explicitly impose consistency regulation between branches. Moreover, to formulate the high correlation between branches and also reduce the number of parameters, an efficient attention sharing scheme is proposed by partially sharing the self-attention heads amongst the tri-decoders. Finally, a token MLP bottleneck replaces the over-parameterized Transformer bottleneck for a further reduction in model complexity. Experiments on two datasets of different modalities, including MoNuSeg have shown that our methods can outperform state-of-the-art counterparts such as CA2.5-Net by 2-3% Dice with 30% fewer parameters. In conclusion, TransNuSeg confirms the strength of Transformer in the context of nuclei segmentation, which thus can serve as an efficient solution for real clinical practice. Code is available at https://github.com/zhenqi-he/transnuseg.

eess.IV↗

arXiv2023

SCRNet: a Retinex Structure-based Low-light Enhancement Model Guided by Spatial Consistency

Images captured under low-light conditions are often plagued by several challenges, including diminished contrast, increased noise, loss of fine details, and unnatural color reproduction. These factors can significantly hinder the performance of computer vision tasks such as object detection and image segmentation. As a result, improving the quality of low-light images is of paramount importance for practical applications in the computer vision domain.To effectively address these challenges, we present a novel low-light image enhancement model, termed Spatial Consistency Retinex Network (SCRNet), which leverages the Retinex-based structure and is guided by the principle of spatial consistency.Specifically, our proposed model incorporates three levels of consistency: channel level, semantic level, and texture level, inspired by the principle of spatial consistency.These levels of consistency enable our model to adaptively enhance image features, ensuring more accurate and visually pleasing results.Extensive experimental evaluations on various low-light image datasets demonstrate that our proposed SCRNet outshines existing state-of-the-art methods, highlighting the potential of SCRNet as an effective solution for enhancing low-light images.

cs.CV↗

arXiv2023

Mixed Sample Augmentation for Online Distillation

Mixed Sample Regularization (MSR), such as MixUp or CutMix, is a powerful data augmentation strategy to generalize convolutional neural networks. Previous empirical analysis has illustrated an orthogonal performance gain between MSR and conventional offline Knowledge Distillation (KD). To be more specific, student networks can be enhanced with the involvement of MSR in the training stage of sequential distillation. Yet, the interplay between MSR and online knowledge distillation, where an ensemble of peer students learn mutually from each other, remains unexplored. To bridge the gap, we make the first attempt at incorporating CutMix into online distillation, where we empirically observe a significant improvement. Encouraged by this fact, we propose an even stronger MSR specifically for online distillation, named as Cut\textsuperscript{n}Mix. Furthermore, a novel online distillation framework is designed upon Cut\textsuperscript{n}Mix, to enhance the distillation with feature level mutual learning and a self-ensemble teacher. Comprehensive evaluations on CIFAR10 and CIFAR100 with six network architectures show that our approach can consistently outperform state-of-the-art distillation methods.

cs.CV↗

arXiv2022

Federated Learning for Chronic Obstructive Pulmonary Disease Classification with Partial Personalized Attention Mechanism

Chronic Obstructive Pulmonary Disease (COPD) is the fourth leading cause of death worldwide. Yet, COPD diagnosis heavily relies on spirometric examination as well as functional airway limitation, which may cause a considerable portion of COPD patients underdiagnosed especially at the early stage. Recent advance in deep learning (DL) has shown their promising potential in COPD identification from CT images. However, with heterogeneous syndromes and distinct phenotypes, DL models trained with CTs from one data center fail to generalize on images from another center. Due to privacy regularizations, a collaboration of distributed CT images into one centralized center is not feasible. Federated learning (FL) approaches enable us to train with distributed private data. Yet, routine FL solutions suffer from performance degradation in the case where COPD CTs are not independent and identically distributed (Non-IID). To address this issue, we propose a novel personalized federated learning (PFL) method based on vision transformer (ViT) for distributed and heterogeneous COPD CTs. To be more specific, we partially personalize some heads in multiheaded self-attention layers to learn the personalized attention for local data and retain the other heads shared to extract the common attention. To the best of our knowledge, this is the first proposal of a PFL framework specifically for ViT to identify COPD. Our evaluation of a dataset set curated from six medical centers shows our method outperforms the PFL approaches for convolutional neural networks.

cs.CV↗

arXiv2022

RandStainNA: Learning Stain-Agnostic Features from Histology Slides by Bridging Stain Augmentation and Normalization

Stain variations often decrease the generalization ability of deep learning based approaches in digital histopathology analysis. Two separate proposals, namely stain normalization (SN) and stain augmentation (SA), have been spotlighted to reduce the generalization error, where the former alleviates the stain shift across different medical centers using template image and the latter enriches the accessible stain styles by the simulation of more stain variations. However, their applications are bounded by the selection of template images and the construction of unrealistic styles. To address the problems, we unify SN and SA with a novel RandStainNA scheme, which constrains variable stain styles in a practicable range to train a stain agnostic deep learning model. The RandStainNA is applicable to stain normalization in a collection of color spaces i.e. HED, HSV, LAB. Additionally, we propose a random color space selection scheme to gain extra performance improvement. We evaluate our method by two diagnostic tasks i.e. tissue subtype classification and nuclei segmentation, with various network backbones. The performance superiority over both SA and SN yields that the proposed RandStainNA can consistently improve the generalization ability, that our models can cope with more incoming clinical datasets with unpredicted stain styles. The codes is available at https://github.com/yiqings/RandStainNA.

cs.CV↗

arXiv2022

How GNNs Facilitate CNNs in Mining Geometric Information from Large-Scale Medical Images

Gigapixel medical images provide massive data, both morphological textures and spatial information, to be mined. Due to the large data scale in histology, deep learning methods play an increasingly significant role as feature extractors. Existing solutions heavily rely on convolutional neural networks (CNNs) for global pixel-level analysis, leaving the underlying local geometric structure such as the interaction between cells in the tumor microenvironment unexplored. The topological structure in medical images, as proven to be closely related to tumor evolution, can be well characterized by graphs. To obtain a more comprehensive representation for downstream oncology tasks, we propose a fusion framework for enhancing the global image-level representation captured by CNNs with the geometry of cell-level spatial information learned by graph neural networks (GNN). The fusion layer optimizes an integration between collaborative features of global images and cell graphs. Two fusion strategies have been developed: one with MLP which is simple but turns out efficient through fine-tuning, and the other with Transformer gains a champion in fusing multiple networks. We evaluate our fusion strategies on histology datasets curated from large patient cohorts of colorectal and gastric cancers for three biomarker prediction tasks. Both two models outperform plain CNNs or GNNs, reaching a consistent AUC improvement of more than 5% on various network backbones. The experimental results yield the necessity for combining image-level morphological features with cell spatial relations in medical image analysis. Codes are available at https://github.com/yiqings/HEGnnEnhanceCnn.

eess.IV↗

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

Self-Distillation from the Last Mini-Batch for Consistency Regularization

Knowledge distillation (KD) shows a bright promise as a powerful regularization strategy to boost generalization ability by leveraging learned sample-level soft targets. Yet, employing a complex pre-trained teacher network or an ensemble of peer students in existing KD is both time-consuming and computationally costly. Various self KD methods have been proposed to achieve higher distillation efficiency. However, they either require extra network architecture modification or are difficult to parallelize. To cope with these challenges, we propose an efficient and reliable self-distillation framework, named Self-Distillation from Last Mini-Batch (DLB). Specifically, we rearrange the sequential sampling by constraining half of each mini-batch coinciding with the previous iteration. Meanwhile, the rest half will coincide with the upcoming iteration. Afterwards, the former half mini-batch distills on-the-fly soft targets generated in the previous iteration. Our proposed mechanism guides the training stability and consistency, resulting in robustness to label noise. Moreover, our method is easy to implement, without taking up extra run-time memory or requiring model structure modification. Experimental results on three classification benchmarks illustrate that our approach can consistently outperform state-of-the-art self-distillation approaches with different network architectures. Additionally, our method shows strong compatibility with augmentation strategies by gaining additional performance improvement. The code is available at https://github.com/Meta-knowledge-Lab/DLB.

cs.CV↗

arXiv2021

A Deep Learning-based Quality Assessment and Segmentation System with a Large-scale Benchmark Dataset for Optical Coherence Tomographic Angiography Image

Optical Coherence Tomography Angiography (OCTA) is a non-invasive and non-contacting imaging technique providing visualization of microvasculature of retina and optic nerve head in human eyes in vivo. The adequate image quality of OCTA is the prerequisite for the subsequent quantification of retinal microvasculature. Traditionally, the image quality score based on signal strength is used for discriminating low quality. However, it is insufficient for identifying artefacts such as motion and off-centration, which rely specialized knowledge and need tedious and time-consuming manual identification. One of the most primary issues in OCTA analysis is to sort out the foveal avascular zone (FAZ) region in the retina, which highly correlates with any visual acuity disease. However, the variations in OCTA visual quality affect the performance of deep learning in any downstream marginally. Moreover, filtering the low-quality OCTA images out is both labor-intensive and time-consuming. To address these issues, we develop an automated computer-aided OCTA image processing system using deep neural networks as the classifier and segmentor to help ophthalmologists in clinical diagnosis and research. This system can be an assistive tool as it can process OCTA images of different formats to assess the quality and segment the FAZ area. The source code is freely available at https://github.com/shanzha09/COIPS.git. Another major contribution is the large-scale OCTA dataset, namely OCTA-25K-IQA-SEG we publicize for performance evaluation. It is comprised of four subsets, namely sOCTA-3$\times$3-10k, sOCTA-6$\times$6-14k, sOCTA-3$\times$3-1.1k-seg, and dOCTA-6$\times$6-1.1k-seg, which contains a total number of 25,665 images. The large-scale OCTA dataset is available at https://doi.org/10.5281/zenodo.5111975, https://doi.org/10.5281/zenodo.5111972.

eess.IV↗

arXiv2020

A novel method for constructing high accurate and robust WENO-Z type scheme

A novel method for constructing robust and high-order accurate weighted essentially non-oscillatory (WENO) scheme is proposed in this paper. The method is mainly based on the WENO-Z type scheme, in which, an eighth-order global smoothness indicator (the square of the approximation of the fourth-order derivative on the five-point stencil used by the fifth-order WENO scheme) is used, and in order to keep the ENO property and robustness, the constant 1 used to calculate the un-normalized weights is replaced by a function of local smoothness indicators of candidate sub-stencils. This function is designed to have following adaptive property: if the five-point stencil contains a discontinuity, then the function approaches to a small value, otherwise, it approaches to a large value. Analysis and numerical results show that the resulted WENO-Z type (WENO-ZN) scheme is robust for capturing shock waves and, in smooth regions, achieves fifth-order accuracy at first-order critical point and fourth-order accuracy at second-order critical point.

math.NA↗

arXiv2020

An efficient targeted ENO scheme with local adaptive dissipation for compressible flow simulation

High fidelity numerical simulation of compressible flow requires the numerical method being used to have both stable shock-capturing capability and high spectral resolution. Recently, a family of Targeted Essentially Non-Oscillatory (TENO) schemes are developed to fulfill such requirements. Although TENO has very low dissipation for smooth flow, it introduces a cutoff value $C_T$ to maintain the non-oscillatory shock-capturing property. $C_T$ is problem depended and therefore needs adjustments by trial and error for different problems. As $C_T$ actually controls the dissipation property of TENO, the choice of $C_T$ for better shock-capturing capability always means higher dissipation. To overcome this, in this paper, a local adaptive method is proposed for the choice of $C_T$. By introducing a novel adaptive function based on the WENO smoothness indicators, $C_T$ is dynamically adjusted form $1.0 \times 10.0^{-10}$ for lower dissipation to $1.0 \times 10.0^{-4}$ for better capturing of shock according to the smoothness of the reconstruction stencil. Numerical results of the new method are compared with those of the original TENO method and the TENO-A method (Fu et al., JCP, 2017). It reveals that the new method is capable of better suppressing numerical oscillations near discontinuities while maintaining the low dissipation property of TENO at lower extra computational cost.

physics.flu-dyn↗

arXiv2019

An Adaptive Characteristic-wise Reconstruction WENOZ scheme for Gas Dynamic Euler Equations

Due to its excellent shock-capturing capability and high resolution, the WENO scheme family has been widely used in varieties of compressive flow simulation. However, for problems containing strong shocks and contact discontinuities, such as the Lax shock tube problem, the WENO scheme still produces numerical oscillations. To avoid such numerical oscillations, the characteristic-wise construction method should be applied. Compared to component-wise reconstruction, characteristic-wise reconstruction leads to much more computational cost and thus is not suite for large scale simulation such as direct numeric simulation of turbulence. In this paper, an adaptive characteristic-wise reconstruction WENO scheme, i.e. the AdaWENO scheme, is proposed to improve the computational efficiency of the characteristic-wise reconstruction method. The new scheme performs characteristic-wise reconstruction near discontinuities while switching to component-wise reconstruction for smooth regions. Meanwhile, a new calculation strategy for the WENO smoothness indicators is implemented to reduce over-all computational cost. Several one dimensional and two dimensional numerical tests are performed to validate and evaluate the AdaWENO scheme. Numerical results show that AdaWENO maintains essentially non-oscillatory flow field near discontinuities as the characteristic-wise reconstruction method. Besieds, compared to the component-wise reconstruction, AdaWENO is about 40\% faster which indicates its excellent efficiency.

physics.flu-dyn↗