Ge Wang

Zicheng Liu, Siyuan Li, Ge Wang et al.

Mixup is an efficient data augmentation approach that improves the generalization of neural networks by smoothing the decision boundary with mixed data. Recently, dynamic mixup methods have improved previous static policies effectively (e.g., linear interpolation) by maximizing target-related salient regions in mixed samples, but excessive additional time costs are not acceptable. These additional computational overheads mainly come from optimizing the mixed samples according to the mixed labels. However, we found that the extra optimizing step may be redundant because label-mismatched mixed samples are informative hard mixed samples for deep models to localize discriminative features. In this paper, we thus are not trying to propose a more complicated dynamic mixup policy but rather an efficient mixup objective function with a decoupled regularizer named Decoupled Mixup (DM). The primary effect is that DM can adaptively utilize those hard mixed samples to mine discriminative features without losing the original smoothness of mixup. As a result, DM enables static mixup methods to achieve comparable or even exceed the performance of dynamic methods without any extra computation. This also leads to an interesting objective design problem for mixup training that we need to focus on both smoothing the decision boundaries and identifying discriminative features. Extensive experiments on supervised and semi-supervised learning benchmarks across seven datasets validate the effectiveness of DM as a plug-and-play module. Source code and models are available at https://github.com/Westlake-AI/openmixup

Zhihao Chen, Chuang Niu, Qi Gao et al.

This paper studies 3D low-dose computed tomography (CT) imaging. Although various deep learning methods were developed in this context, typically they focus on 2D images and perform denoising due to low-dose and deblurring for super-resolution separately. Up to date, little work was done for simultaneous in-plane denoising and through-plane deblurring, which is important to obtain high-quality 3D CT images with lower radiation and faster imaging speed. For this task, a straightforward method is to directly train an end-to-end 3D network. However, it demands much more training data and expensive computational costs. Here, we propose to link in-plane and through-plane transformers for simultaneous in-plane denoising and through-plane deblurring, termed as LIT-Former, which can efficiently synergize in-plane and through-plane sub-tasks for 3D CT imaging and enjoy the advantages of both convolution and transformer networks. LIT-Former has two novel designs: efficient multi-head self-attention modules (eMSM) and efficient convolutional feedforward networks (eCFN). First, eMSM integrates in-plane 2D self-attention and through-plane 1D self-attention to efficiently capture global interactions of 3D self-attention, the core unit of transformer networks. Second, eCFN integrates 2D convolution and 1D convolution to extract local information of 3D convolution in the same fashion. As a result, the proposed LIT-Former synergize these two subtasks, significantly reducing the computational complexity as compared to 3D counterparts and enabling rapid convergence. Extensive experimental results on simulated and clinical datasets demonstrate superior performance over state-of-the-art models. The source code is made available at https://github.com/hao1635/LIT-Former.

Zilong Li, Qi Gao, Yaping Wu et al.

Metal implants and other high-density objects in patients introduce severe streaking artifacts in CT images, compromising image quality and diagnostic performance. Although various methods were developed for CT metal artifact reduction over the past decades, including the latest dual-domain deep networks, remaining metal artifacts are still clinically challenging in many cases. Here we extend the state-of-the-art dual-domain deep network approach into a quad-domain counterpart so that all the features in the sinogram, image, and their corresponding Fourier domains are synergized to eliminate metal artifacts optimally without compromising structural subtleties. Our proposed quad-domain network for MAR, referred to as Quad-Net, takes little additional computational cost since the Fourier transform is highly efficient, and works across the four receptive fields to learn both global and local features as well as their relations. Specifically, we first design a Sinogram-Fourier Restoration Network (SFR-Net) in the sinogram domain and its Fourier space to faithfully inpaint metal-corrupted traces. Then, we couple SFR-Net with an Image-Fourier Refinement Network (IFR-Net) which takes both an image and its Fourier spectrum to improve a CT image reconstructed from the SFR-Net output using cross-domain contextual information. Quad-Net is trained on clinical datasets to minimize a composite loss function. Quad-Net does not require precise metal masks, which is of great importance in clinical practice. Our experimental results demonstrate the superiority of Quad-Net over the state-of-the-art MAR methods quantitatively, visually, and statistically. The Quad-Net code is publicly available at https://github.com/longzilicart/Quad-Net.

Zelin Zang, Siyuan Li, Di Wu et al. · tsinghua

Manifold learning (ML) aims to seek low-dimensional embedding from high-dimensional data. The problem is challenging on real-world datasets, especially with under-sampling data, and we find that previous methods perform poorly in this case. Generally, ML methods first transform input data into a low-dimensional embedding space to maintain the data's geometric structure and subsequently perform downstream tasks therein. The poor local connectivity of under-sampling data in the former step and inappropriate optimization objectives in the latter step leads to two problems: structural distortion and underconstrained embedding. This paper proposes a novel ML framework named Deep Local-flatness Manifold Embedding (DLME) to solve these problems. The proposed DLME constructs semantic manifolds by data augmentation and overcomes the structural distortion problem using a smoothness constrained based on a local flatness assumption about the manifold. To overcome the underconstrained embedding problem, we design a loss and theoretically demonstrate that it leads to a more suitable embedding based on the local flatness. Experiments on three types of datasets (toy, biological, and image) for various downstream tasks (classification, clustering, and visualization) show that our proposed DLME outperforms state-of-the-art ML and contrastive learning methods.

Chuang Niu, Md Sayed Tanveer, Md Zabirul Islam et al.

Current LLMs for creating fully-structured reports face the challenges of formatting errors, content hallucinations, and privacy leakage issues when uploading data to external servers.We aim to develop an open-source, accurate LLM for creating fully-structured and standardized LCS reports from varying free-text reports across institutions and demonstrate its utility in automatic statistical analysis and individual lung nodule retrieval. With IRB approvals, our retrospective study included 5,442 de-identified LDCT LCS radiology reports from two institutions. We constructed two evaluation datasets by labeling 500 pairs of free-text and fully-structured radiology reports and one large-scale consecutive dataset from January 2021 to December 2023. Two radiologists created a standardized template for recording 27 lung nodule features on LCS. We designed a dynamic-template-constrained decoding method to enhance existing LLMs for creating fully-structured reports from free-text radiology reports. Using consecutive structured reports, we automated descriptive statistical analyses and a nodule retrieval prototype. Our best LLM for creating fully-structured reports achieved high performance on cross-institutional datasets with an F1 score of about 97%, with neither formatting errors nor content hallucinations. Our method consistently improved the best open-source LLMs by up to 10.42%, and outperformed GPT-4o by 17.19%. The automatically derived statistical distributions were consistent with prior findings regarding attenuation, location, size, stability, and Lung-RADS. The retrieval system with structured reports allowed flexible nodule-level search and complex statistical analysis. Our developed software is publicly available for local deployment and further research.

Yuhui Ruan, Qiao Yuan, Chuang Niu et al.

Deep learning has been successfully applied to low-dose CT (LDCT) image denoising for reducing potential radiation risk. However, the widely reported supervised LDCT denoising networks require a training set of paired images, which is expensive to obtain and cannot be perfectly simulated. Unsupervised learning utilizes unpaired data and is highly desirable for LDCT denoising. As an example, an artifact disentanglement network (ADN) relies on unparied images and obviates the need for supervision but the results of artifact reduction are not as good as those through supervised learning.An important observation is that there is often hidden similarity among unpaired data that can be utilized. This paper introduces a new learning mode, called quasi-supervised learning, to empower the ADN for LDCT image denoising.For every LDCT image, the best matched image is first found from an unpaired normal-dose CT (NDCT) dataset. Then, the matched pairs and the corresponding matching degree as prior information are used to construct and train our ADN-type network for LDCT denoising.The proposed method is different from (but compatible with) supervised and semi-supervised learning modes and can be easily implemented by modifying existing networks. The experimental results show that the method is competitive with state-of-the-art methods in terms of noise suppression and contextual fidelity. The code and working dataset are publicly available at https://github.com/ruanyuhui/ADN-QSDL.git.

Jiangbin Zheng, Yile Wang, Cheng Tan et al.

Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of large-scale available sign datasets becomes the main bottleneck for SLR. Most SLR works thereby adopt pretrained visual modules and develop two mainstream solutions. The multi-stream architectures extend multi-cue visual features, yielding the current SOTA performances but requiring complex designs and might introduce potential noise. Alternatively, the advanced single-cue SLR frameworks using explicit cross-modal alignment between visual and textual modalities are simple and effective, potentially competitive with the multi-cue framework. In this work, we propose a novel contrastive visual-textual transformation for SLR, CVT-SLR, to fully explore the pretrained knowledge of both the visual and language modalities. Based on the single-cue cross-modal alignment framework, we propose a variational autoencoder (VAE) for pretrained contextual knowledge while introducing the complete pretrained language module. The VAE implicitly aligns visual and textual modalities while benefiting from pretrained contextual knowledge as the traditional contextual module. Meanwhile, a contrastive cross-modal alignment algorithm is designed to explicitly enhance the consistency constraints. Extensive experiments on public datasets (PHOENIX-2014 and PHOENIX-2014T) demonstrate that our proposed CVT-SLR consistently outperforms existing single-cue methods and even outperforms SOTA multi-cue methods.

Qing Lyu, Josh Tan, Michael E. Zapadka et al.

The large language model called ChatGPT has drawn extensively attention because of its human-like expression and reasoning abilities. In this study, we investigate the feasibility of using ChatGPT in experiments on using ChatGPT to translate radiology reports into plain language for patients and healthcare providers so that they are educated for improved healthcare. Radiology reports from 62 low-dose chest CT lung cancer screening scans and 76 brain MRI metastases screening scans were collected in the first half of February for this study. According to the evaluation by radiologists, ChatGPT can successfully translate radiology reports into plain language with an average score of 4.27 in the five-point system with 0.08 places of information missing and 0.07 places of misinformation. In terms of the suggestions provided by ChatGPT, they are general relevant such as keeping following-up with doctors and closely monitoring any symptoms, and for about 37% of 138 cases in total ChatGPT offers specific suggestions based on findings in the report. ChatGPT also presents some randomness in its responses with occasionally over-simplified or neglected information, which can be mitigated using a more detailed prompt. Furthermore, ChatGPT results are compared with a newly released large model GPT-4, showing that GPT-4 can significantly improve the quality of translated reports. Our results show that it is feasible to utilize large language models in clinical education, and further efforts are needed to address limitations and maximize their potential.

Md Selim, Jie Zhang, Michael A. Brooks et al.

Computed tomography (CT) is one of the modalities for effective lung cancer screening, diagnosis, treatment, and prognosis. The features extracted from CT images are now used to quantify spatial and temporal variations in tumors. However, CT images obtained from various scanners with customized acquisition protocols may introduce considerable variations in texture features, even for the same patient. This presents a fundamental challenge to downstream studies that require consistent and reliable feature analysis. Existing CT image harmonization models rely on GAN-based supervised or semi-supervised learning, with limited performance. This work addresses the issue of CT image harmonization using a new diffusion-based model, named DiffusionCT, to standardize CT images acquired from different vendors and protocols. DiffusionCT operates in the latent space by mapping a latent non-standard distribution into a standard one. DiffusionCT incorporates an Unet-based encoder-decoder, augmented by a diffusion model integrated into the bottleneck part. The model is designed in two training phases. The encoder-decoder is first trained, without embedding the diffusion model, to learn the latent representation of the input data. The latent diffusion model is then trained in the next training phase while fixing the encoder-decoder. Finally, the decoder synthesizes a standardized image with the transformed latent representation. The experimental results demonstrate a significant improvement in the performance of the standardization task using DiffusionCT.

Huidong Xie, Zhao Liu, Luyao Shi et al.

In nuclear imaging, limited resolution causes partial volume effects (PVEs) that affect image sharpness and quantitative accuracy. Partial volume correction (PVC) methods incorporating high-resolution anatomical information from CT or MRI have been demonstrated to be effective. However, such anatomical-guided methods typically require tedious image registration and segmentation steps. Accurately segmented organ templates are also hard to obtain, particularly in cardiac SPECT imaging, due to the lack of hybrid SPECT/CT scanners with high-end CT and associated motion artifacts. Slight mis-registration/mis-segmentation would result in severe degradation in image quality after PVC. In this work, we develop a deep-learning-based method for fast cardiac SPECT PVC without anatomical information and associated organ segmentation. The proposed network involves a densely-connected multi-dimensional dynamic mechanism, allowing the convolutional kernels to be adapted based on the input images, even after the network is fully trained. Intramyocardial blood volume (IMBV) is introduced as an additional clinical-relevant loss function for network optimization. The proposed network demonstrated promising performance on 28 canine studies acquired on a GE Discovery NM/CT 570c dedicated cardiac SPECT scanner with a 64-slice CT using Technetium-99m-labeled red blood cells. This work showed that the proposed network with densely-connected dynamic mechanism produced superior results compared with the same network without such mechanism. Results also showed that the proposed network without anatomical information could produce images with statistically comparable IMBV measurements to the images generated by anatomical-guided PVC methods, which could be helpful in clinical translation.

Wenjun Xia, Hongming Shan, Ge Wang et al.

Since 2016, deep learning (DL) has advanced tomographic imaging with remarkable successes, especially in low-dose computed tomography (LDCT) imaging. Despite being driven by big data, the LDCT denoising and pure end-to-end reconstruction networks often suffer from the black box nature and major issues such as instabilities, which is a major barrier to apply deep learning methods in low-dose CT applications. An emerging trend is to integrate imaging physics and model into deep networks, enabling a hybridization of physics/model-based and data-driven elements. %This type of hybrid methods has become increasingly influential. In this paper, we systematically review the physics/model-based data-driven methods for LDCT, summarize the loss functions and training strategies, evaluate the performance of different methods, and discuss relevant issues and future directions.

Yufei Huang, Lirong Wu, Haitao Lin et al.

Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is more informative has become a promising research topic. However, there are three major challenges facing protein structure pretraining: insufficient sample diversity, physically unrealistic modeling, and the lack of protein-specific pretext tasks. To try to address these challenges, we present the 3D Geometric Pretraining. In this paper, we propose a unified framework for protein pretraining and a 3D geometric-based, data-efficient, and protein-specific pretext task: RefineDiff (Refine the Diffused Protein Structure Decoy). After pretraining our geometric-aware model with this task on limited data(less than 1% of SOTA models), we obtained informative protein representations that can achieve comparable performance for various downstream tasks.

Ge Wang, Jie Zhang, Hao Gao et al.

Current tomographic imaging systems need major improvements, especially when multi-dimensional, multi-scale, multi-temporal and multi-parametric phenomena are under investigation. Both preclinical and clinical imaging now depend on in vivo tomography, often requiring separate evaluations by different imaging modalities to define morphologic details, delineate interval changes due to disease or interventions, and study physiological functions that have interconnected aspects. Over the past decade, fusion of multimodality images has emerged with two different approaches: post-hoc image registration and combined acquisition on PET-CT, PET-MRI and other hybrid scanners. There are intrinsic limitations for both the post-hoc image analysis and dual/triple modality approaches defined by registration errors and physical constraints in the acquisition chain. We envision that tomography will evolve beyond current modality fusion and towards grand fusion, a large scale fusion of all or many imaging modalities, which may be referred to as omni-tomography or multi-tomography. Unlike modality fusion, grand fusion is here proposed for truly simultaneous but often localized reconstruction in terms of all or many relevant imaging mechanisms such as CT, MRI, PET, SPECT, US, optical, and possibly more. In this paper, the technical basis for omni-tomography is introduced and illustrated with a top-level design of a next generation scanner, interior tomographic reconstructions of representative modalities, and anticipated applications of omni-tomography.

Wenjun Xia, Wenxiang Cong, Ge Wang

Sparse-view computed tomography (CT) can be used to reduce radiation dose greatly but is suffers from severe image artifacts. Recently, the deep learning based method for sparse-view CT reconstruction has attracted a major attention. However, neural networks often have a limited ability to remove the artifacts when they only work in the image domain. Deep learning-based sinogram processing can achieve a better anti-artifact performance, but it inevitably requires feature maps of the whole image in a video memory, which makes handling large-scale or three-dimensional (3D) images rather challenging. In this paper, we propose a patch-based denoising diffusion probabilistic model (DDPM) for sparse-view CT reconstruction. A DDPM network based on patches extracted from fully sampled projection data is trained and then used to inpaint down-sampled projection data. The network does not require paired full-sampled and down-sampled data, enabling unsupervised learning. Since the data processing is patch-based, the deep learning workflow can be distributed in parallel, overcoming the memory problem of large-scale data. Our experiments show that the proposed method can effectively suppress few-view artifacts while faithfully preserving textural details.

Dennis Hein, Afshin Bozorgpour, Dorit Merhof et al.

Physics-inspired Generative Models (GMs), in particular Diffusion Models (DMs) and Poisson Flow Models (PFMs), enhance Bayesian methods and promise great utility in medical imaging. This review examines the transformative role of such generative methods. First, a variety of physics-inspired GMs, including Denoising Diffusion Probabilistic Models (DDPMs), Score-based Diffusion Models (SDMs), and Poisson Flow Generative Models (PFGMs and PFGM++), are revisited, with an emphasis on their accuracy, robustness as well as acceleration. Then, major applications of physics-inspired GMs in medical imaging are presented, comprising image reconstruction, image generation, and image analysis. Finally, future research directions are brainstormed, including unification of physics-inspired GMs, integration with Vision-Language Models (VLMs), and potential novel applications of GMs. Since the development of generative methods has been rapid, this review will hopefully give peers and learners a timely snapshot of this new family of physics-driven generative models and help capitalize their enormous potential for medical imaging.

Zihan Liu, Ge Wang, Jiaqi Wang et al.

Peptides are formed by the dehydration condensation of multiple amino acids. The primary structure of a peptide can be represented either as an amino acid sequence or as a molecular graph consisting of atoms and chemical bonds. Previous studies have indicated that deep learning routes specific to sequential and graphical peptide forms exhibit comparable performance on downstream tasks. Despite the fact that these models learn representations of the same modality of peptides, we find that they explain their predictions differently. Considering sequential and graphical models as two experts making inferences from different perspectives, we work on fusing expert knowledge to enrich the learned representations for improving the discriminative performance. To achieve this, we propose a peptide co-modeling method, RepCon, which employs a contrastive learning-based framework to enhance the mutual information of representations from decoupled sequential and graphical end-to-end models. It considers representations from the sequential encoder and the graphical encoder for the same peptide sample as a positive pair and learns to enhance the consistency of representations between positive sample pairs and to repel representations between negative pairs. Empirical studies of RepCon and other co-modeling methods are conducted on open-source discriminative datasets, including aggregation propensity, retention time, antimicrobial peptide prediction, and family classification from Peptide Database. Our results demonstrate the superiority of the co-modeling approach over independent modeling, as well as the superiority of RepCon over other methods under the co-modeling framework. In addition, the attribution on RepCon further corroborates the validity of the approach at the level of model explanation.

Wenjun Xia, Yongyi Shi, Chuang Niu et al.

Computed tomography (CT) involves a patient's exposure to ionizing radiation. To reduce the radiation dose, we can either lower the X-ray photon count or down-sample projection views. However, either of the ways often compromises image quality. To address this challenge, here we introduce an iterative reconstruction algorithm regularized by a diffusion prior. Drawing on the exceptional imaging prowess of the denoising diffusion probabilistic model (DDPM), we merge it with a reconstruction procedure that prioritizes data fidelity. This fusion capitalizes on the merits of both techniques, delivering exceptional reconstruction results in an unsupervised framework. To further enhance the efficiency of the reconstruction process, we incorporate the Nesterov momentum acceleration technique. This enhancement facilitates superior diffusion sampling in fewer steps. As demonstrated in our experiments, our method offers a potential pathway to high-definition CT image reconstruction with minimized radiation.

Huidong Xie, Bo Zhou, Xiongchao Chen et al.

Cardiovascular disease (CVD) is the leading cause of death worldwide, and myocardial perfusion imaging using SPECT has been widely used in the diagnosis of CVDs. The GE 530/570c dedicated cardiac SPECT scanners adopt a stationary geometry to simultaneously acquire 19 projections to increase sensitivity and achieve dynamic imaging. However, the limited amount of angular sampling negatively affects image quality. Deep learning methods can be implemented to produce higher-quality images from stationary data. This is essentially a few-view imaging problem. In this work, we propose a novel 3D transformer-based dual-domain network, called TIP-Net, for high-quality 3D cardiac SPECT image reconstructions. Our method aims to first reconstruct 3D cardiac SPECT images directly from projection data without the iterative reconstruction process by proposing a customized projection-to-image domain transformer. Then, given its reconstruction output and the original few-view reconstruction, we further refine the reconstruction using an image-domain reconstruction network. Validated by cardiac catheterization images, diagnostic interpretations from nuclear cardiologists, and defect size quantified by an FDA 510(k)-cleared clinical software, our method produced images with higher cardiac defect contrast on human studies compared with previous baseline methods, potentially enabling high-quality defect visualization using stationary few-view dedicated cardiac SPECT scanners.

Chuang Niu, Ge Wang

Early detection of lung nodules with computed tomography (CT) is critical for the longer survival of lung cancer patients and better quality of life. Computer-aided detection/diagnosis (CAD) is proven valuable as a second or concurrent reader in this context. However, accurate detection of lung nodules remains a challenge for such CAD systems and even radiologists due to not only the variability in size, location, and appearance of lung nodules but also the complexity of lung structures. This leads to a high false-positive rate with CAD, compromising its clinical efficacy. Motivated by recent computer vision techniques, here we present a self-supervised region-based 3D transformer model to identify lung nodules among a set of candidate regions. Specifically, a 3D vision transformer (ViT) is developed that divides a CT image volume into a sequence of non-overlap cubes, extracts embedding features from each cube with an embedding layer, and analyzes all embedding features with a self-attention mechanism for the prediction. To effectively train the transformer model on a relatively small dataset, the region-based contrastive learning method is used to boost the performance by pre-training the 3D transformer with public CT images. Our experiments show that the proposed method can significantly improve the performance of lung nodule screening in comparison with the commonly used 3D convolutional neural networks.

Chi Ding, Qingchao Zhang, Ge Wang et al.

We propose a novel Learned Alternating Minimization Algorithm (LAMA) for dual-domain sparse-view CT image reconstruction. LAMA is naturally induced by a variational model for CT reconstruction with learnable nonsmooth nonconvex regularizers, which are parameterized as composite functions of deep networks in both image and sinogram domains. To minimize the objective of the model, we incorporate the smoothing technique and residual learning architecture into the design of LAMA. We show that LAMA substantially reduces network complexity, improves memory efficiency and reconstruction accuracy, and is provably convergent for reliable reconstructions. Extensive numerical experiments demonstrate that LAMA outperforms existing methods by a wide margin on multiple benchmark CT datasets.

Chuang Niu, Giridhar Dasegowda, Pingkun Yan et al.

Although radiographs are the most frequently used worldwide due to their cost-effectiveness and widespread accessibility, the structural superposition along the x-ray paths often renders suspicious or concerning lung nodules difficult to detect. In this study, we apply "X-ray dissectography" to dissect lungs digitally from a few radiographic projections, suppress the interference of irrelevant structures, and improve lung nodule detectability. For this purpose, a collaborative detection network is designed to localize lung nodules in 2D dissected projections and 3D physical space. Our experimental results show that our approach can significantly improve the average precision by 20+% in comparison with the common baseline that detects lung nodules from original projections using a popular detection network. Potentially, this approach could help re-design the current X-ray imaging protocols and workflows and improve the diagnostic performance of chest radiographs in lung diseases.

Soham Bhosale, Arjun Krishna, Ge Wang et al.

Medical Image Segmentation is a useful application for medical image analysis including detecting diseases and abnormalities in imaging modalities such as MRI, CT etc. Deep learning has proven to be promising for this task but usually has a low accuracy because of the lack of appropriate publicly available annotated or segmented medical datasets. In addition, the datasets that are available may have a different texture because of different dosage values or scanner properties than the images that need to be segmented. This paper presents a StyleGAN-driven approach for segmenting publicly available large medical datasets by using readily available extremely small annotated datasets in similar modalities. The approach involves augmenting the small segmented dataset and eliminating texture differences between the two datasets. The dataset is augmented by being passed through six different StyleGANs that are trained on six different style images taken from the large non-annotated dataset we want to segment. Specifically, style transfer is used to augment the training dataset. The annotations of the training dataset are hence combined with the textures of the non-annotated dataset to generate new anatomically sound images. The augmented dataset is then used to train a U-Net segmentation network which displays a significant improvement in the segmentation accuracy in segmenting the large non-annotated dataset.

Qing Lyu, Ge Wang

MRI and CT are most widely used medical imaging modalities. It is often necessary to acquire multi-modality images for diagnosis and treatment such as radiotherapy planning. However, multi-modality imaging is not only costly but also introduces misalignment between MRI and CT images. To address this challenge, computational conversion is a viable approach between MRI and CT images, especially from MRI to CT images. In this paper, we propose to use an emerging deep learning framework called diffusion and score-matching models in this context. Specifically, we adapt denoising diffusion probabilistic and score-matching models, use four different sampling strategies, and compare their performance metrics with that using a convolutional neural network and a generative adversarial network model. Our results show that the diffusion and score-matching models generate better synthetic CT images than the CNN and GAN models. Furthermore, we investigate the uncertainties associated with the diffusion and score-matching networks using the Monte-Carlo method, and improve the results by averaging their Monte-Carlo outputs. Our study suggests that diffusion and score-matching models are powerful to generate high quality images conditioned on an image obtained using a complementary imaging modality, analytically rigorous with clear explainability, and highly competitive with CNNs and GANs for image synthesis.

Yongyi Shi, Wenjun Xia, Ge Wang et al.

Lowering radiation dose per view and utilizing sparse views per scan are two common CT scan modes, albeit often leading to distorted images characterized by noise and streak artifacts. Blind image quality assessment (BIQA) strives to evaluate perceptual quality in alignment with what radiologists perceive, which plays an important role in advancing low-dose CT reconstruction techniques. An intriguing direction involves developing BIQA methods that mimic the operational characteristic of the human visual system (HVS). The internal generative mechanism (IGM) theory reveals that the HVS actively deduces primary content to enhance comprehension. In this study, we introduce an innovative BIQA metric that emulates the active inference process of IGM. Initially, an active inference module, implemented as a denoising diffusion probabilistic model (DDPM), is constructed to anticipate the primary content. Then, the dissimilarity map is derived by assessing the interrelation between the distorted image and its primary content. Subsequently, the distorted image and dissimilarity map are combined into a multi-channel image, which is inputted into a transformer-based image quality evaluator. Remarkably, by exclusively utilizing this transformer-based quality evaluator, we won the second place in the MICCAI 2023 low-dose computed tomography perceptual image quality assessment grand challenge. Leveraging the DDPM-derived primary content, our approach further improves the performance on the challenge dataset.

Zihan Liu, Ge Wang, Yun Luo et al.

Recent research has revealed that Graph Neural Networks (GNNs) are susceptible to adversarial attacks targeting the graph structure. A malicious attacker can manipulate a limited number of edges, given the training labels, to impair the victim model's performance. Previous empirical studies indicate that gradient-based attackers tend to add edges rather than remove them. In this paper, we present a theoretical demonstration revealing that attackers tend to increase inter-class edges due to the message passing mechanism of GNNs, which explains some previous empirical observations. By connecting dissimilar nodes, attackers can more effectively corrupt node features, making such attacks more advantageous. However, we demonstrate that the inherent smoothness of GNN's message passing tends to blur node dissimilarity in the feature space, leading to the loss of crucial information during the forward process. To address this issue, we propose a novel surrogate model with multi-level propagation that preserves the node dissimilarity information. This model parallelizes the propagation of unaggregated raw features and multi-hop aggregated features, while introducing batch normalization to enhance the dissimilarity in node representations and counteract the smoothness resulting from topological aggregation. Our experiments show significant improvement with our approach.Furthermore, both theoretical and experimental evidence suggest that adding inter-class edges constitutes an easily observable attack pattern. We propose an innovative attack loss that balances attack effectiveness and imperceptibility, sacrificing some attack effectiveness to attain greater imperceptibility. We also provide experiments to validate the compromise performance achieved through this attack loss.

Wenjun Xia, Hsin Wu Tseng, Chuang Niu et al.

Breast cancer is the most prevalent cancer among women worldwide, and early detection is crucial for reducing its mortality rate and improving quality of life. Dedicated breast computed tomography (CT) scanners offer better image quality than mammography and tomosynthesis in general but at higher radiation dose. To enable breast CT for cancer screening, the challenge is to minimize the radiation dose without compromising image quality, according to the ALARA principle (as low as reasonably achievable). Over the past years, deep learning has shown remarkable successes in various tasks, including low-dose CT especially few-view CT. Currently, the diffusion model presents the state of the art for CT reconstruction. To develop the first diffusion model-based breast CT reconstruction method, here we report innovations to address the large memory requirement for breast cone-beam CT reconstruction and high computational cost of the diffusion model. Specifically, in this study we transform the cutting-edge Denoising Diffusion Probabilistic Model (DDPM) into a parallel framework for sub-volume-based sparse-view breast CT image reconstruction in projection and image domains. This novel approach involves the concurrent training of two distinct DDPM models dedicated to processing projection and image data synergistically in the dual domains. Our experimental findings reveal that this method delivers competitive reconstruction performance at half to one-third of the standard radiation doses. This advancement demonstrates an exciting potential of diffusion-type models for volumetric breast reconstruction at high-resolution with much-reduced radiation dose and as such hopefully redefines breast cancer screening and diagnosis.

Xinrui Song, Jiajin Zhang, Pingkun Yan et al.

The integration of artificial intelligence (AI) chatbots into higher education marks a shift towards a new generation of pedagogical tools, mirroring the arrival of milestones like the internet. With the launch of ChatGPT-4 Turbo in November 2023, we developed a ChatGPT-based teaching application (https://chat.openai.com/g/g-1imx1py4K-chatge-medical-imaging) and integrated it into our undergraduate medical imaging course in the Spring 2024 semester. This study investigates the use of ChatGPT throughout a semester-long trial, providing insights into students' engagement, perception, and the overall educational effectiveness of the technology. We systematically collected and analyzed data concerning students' interaction with ChatGPT, focusing on their attitudes, concerns, and usage patterns. The findings indicate that ChatGPT offers significant advantages such as improved information access and increased interactivity, but its adoption is accompanied by concerns about the accuracy of the information provided and the necessity for well-defined guidelines to optimize its use.

Rodrigo de Barros Vimieiro, Chuang Niu, Hongming Shan et al.

Digital breast tomosynthesis (DBT) exams should utilize the lowest possible radiation dose while maintaining sufficiently good image quality for accurate medical diagnosis. In this work, we propose a convolution neural network (CNN) to restore low-dose (LD) DBT projections to achieve an image quality equivalent to a standard full-dose (FD) acquisition. The proposed network architecture benefits from priors in terms of layers that were inspired by traditional model-based (MB) restoration methods, considering a model-based deep learning approach, where the network is trained to operate in the variance stabilization transformation (VST) domain. To accurately control the network operation point, in terms of noise and blur of the restored image, we propose a loss function that minimizes the bias and matches residual noise between the input and the output. The training dataset was composed of clinical data acquired at the standard FD and low-dose pairs obtained by the injection of quantum noise. The network was tested using real DBT projections acquired with a physical anthropomorphic breast phantom. The proposed network achieved superior results in terms of the mean normalized squared error (MNSE), training time and noise spatial correlation compared with networks trained with traditional data-driven methods. The proposed approach can be extended for other medical imaging application that requires LD acquisitions.

Wenjun Xia, Qing Lyu, Ge Wang

Low-dose computed tomography (LDCT) is an important topic in the field of radiology over the past decades. LDCT reduces ionizing radiation-induced patient health risks but it also results in a low signal-to-noise ratio (SNR) and a potential compromise in the diagnostic performance. In this paper, to improve the LDCT denoising performance, we introduce the conditional denoising diffusion probabilistic model (DDPM) and show encouraging results with a high computational efficiency. Specifically, given the high sampling cost of the original DDPM model, we adapt the fast ordinary differential equation (ODE) solver for a much-improved sampling efficiency. The experiments show that the accelerated DDPM can achieve 20x speedup without compromising image quality.

Chuang Niu, Ge Wang

Self-supervised representation learning maps high-dimensional data into a meaningful embedding space, where samples of similar semantic contents are close to each other. Most of the recent representation learning methods maximize cosine similarity or minimize the distance between the embedding features of different views from the same sample usually on the $l2$ normalized unit hypersphere. To prevent the trivial solutions that all samples have the same embedding feature, various techniques have been developed, such as contrastive learning, stop gradient, variance and covariance regularization, etc. In this study, we propose MUlti-Segmental Informational Coding (MUSIC) for self-supervised representation learning. MUSIC divides the embedding feature into multiple segments that discriminatively partition samples into different semantic clusters and different segments focus on different partition principles. Information theory measurements are directly used to optimize MUSIC and theoretically guarantee trivial solutions are avoided. MUSIC does not depend on commonly used techniques, such as memory bank or large batches, asymmetry networks, gradient stopping, momentum weight updating, etc, making the training framework flexible. Our experiments demonstrate that MUSIC achieves better results than most related Barlow Twins and VICReg methods on ImageNet classification with linear probing, and requires neither deep projectors nor large feature dimensions. Code will be made available.

Chuang Niu, Ge Wang

Minimum redundancy among different elements of an embedding in a latent space is a fundamental requirement or major preference in representation learning to capture intrinsic informational structures. Current self-supervised learning methods minimize a pair-wise covariance matrix to reduce the feature redundancy and produce promising results. However, such representation features of multiple variables may contain the redundancy among more than two feature variables that cannot be minimized via the pairwise regularization. Here we propose the High-Order Mixed-Moment-based Embedding (HOME) strategy to reduce the redundancy between any sets of feature variables, which is to our best knowledge the first attempt to utilize high-order statistics/information in this context. Multivariate mutual information is minimum if and only if multiple variables are mutually independent, which suggests the necessary conditions of factorized mixed moments among multiple variables. Based on these statistical and information theoretic principles, our general HOME framework is presented for self-supervised representation learning. Our initial experiments show that a simple version in the form of a three-order HOME scheme already significantly outperforms the current two-order baseline method (i.e., Barlow Twins) in terms of the linear evaluation on representation features.

Fenglei Fan, Juntong Fan, Dayang Wang et al.

The rapid growth of large models' size has far outpaced that of computing resources. To bridge this gap, encouraged by the parsimonious relationship between genotype and phenotype in the brain's growth and development, we propose the so-called Hyper-Compression that turns the model compression into the issue of parameter representation via a hyperfunction. Specifically, it is known that the trajectory of some low-dimensional dynamic systems can fill the high-dimensional space eventually. Thus, Hyper-Compression, using these dynamic systems as the hyperfunctions, represents the parameters of the target network by their corresponding composition number or trajectory length. This suggests a novel mechanism for model compression, substantially different from the existing pruning, quantization, distillation, and decomposition. Along this direction, we methodologically identify a suitable dynamic system with the irrational winding as the hyperfunction and theoretically derive its associated error bound. Next, guided by our theoretical insights, we propose several engineering twists to make the Hyper-Compression pragmatic and effective. Lastly, systematic and comprehensive experiments on \textcolor{black}{NLP models such as LLaMA and Qwen series and vision models} confirm that Hyper-Compression enjoys the following \textbf{PNAS} merits: 1) \textbf{P}referable compression ratio; 2) \textbf{N}o post-hoc retraining; 3) \textbf{A}ffordable inference time; and 4) \textbf{S}hort compression time. It compresses LLaMA2-7B in an hour and achieves close-to-int4-quantization performance, without retraining and with a performance drop of less than 1\%. We have open-sourced our code in https://github.com/Juntongkuki/Hyper-Compression.git for free download and evaluation.

Chuang Niu, Christopher Wiedeman, Mengzhou Li et al.

This study aims to improve photon counting CT (PCCT) image resolution using denoising diffusion probabilistic models (DDPM). Although DDPMs have shown superior performance when applied to various computer vision tasks, their effectiveness has yet to be translated to high dimensional CT super-resolution. To train DDPMs in a conditional sampling manner, we first leverage CatSim to simulate realistic lower resolution PCCT images from high-resolution CT scans. Since maximizing DDPM performance is time-consuming for both inference and training, especially on high-dimensional PCCT data, we explore both 2D and 3D networks for conditional DDPM and apply methods to accelerate training. In particular, we decompose the 3D task into efficient 2D DDPMs and design a joint 2D inference in the reverse diffusion process that synergizes 2D results of all three dimensions to make the final 3D prediction. Experimental results show that our DDPM achieves improved results versus baseline reference models in recovering high-frequency structures, suggesting that a framework based on realistic simulation and DDPM shows promise for improving PCCT resolution.

Md Selim, Jie Zhang, Faraneh Fathi et al.

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

Zhihao Chen, Tao Chen, Chenhui Wang et al.

While various deep learning methods were proposed for low-dose computed tomography (CT) denoising, they often suffer from over-smoothing, blurring, and lack of explainability. To alleviate these issues, we propose a plug-and-play Language-Engaged Dual-space Alignment loss (LEDA) to optimize low-dose CT denoising models. Our idea is to leverage large language models (LLMs) to align denoised CT and normal dose CT images in both the continuous perceptual space and discrete semantic space, which is the first LLM-based scheme for low-dose CT denoising. LEDA involves two steps: the first is to pretrain an LLM-guided CT autoencoder, which can encode a CT image into continuous high-level features and quantize them into a token space to produce semantic tokens derived from the LLM's vocabulary; and the second is to minimize the discrepancy between the denoised CT images and normal dose CT in terms of both encoded high-level features and quantized token embeddings derived by the LLM-guided CT autoencoder. Extensive experimental results on two public LDCT denoising datasets demonstrate that our LEDA can enhance existing denoising models in terms of quantitative metrics and qualitative evaluation, and also provide explainability through language-level image understanding. Source code is available at https://github.com/hao1635/LEDA.

Arjun Krishna, Ge Wang, Klaus Mueller

Medical imaging applications are highly specialized in terms of human anatomy, pathology, and imaging domains. Therefore, annotated training datasets for training deep learning applications in medical imaging not only need to be highly accurate but also diverse and large enough to encompass almost all plausible examples with respect to those specifications. We argue that achieving this goal can be facilitated through a controlled generation framework for synthetic images with annotations, requiring multiple conditional specifications as input to provide control. We employ a Denoising Diffusion Probabilistic Model (DDPM) to train a large-scale generative model in the lung CT domain and expand upon a classifier-free sampling strategy to showcase one such generation framework. We show that our approach can produce annotated lung CT images that can faithfully represent anatomy, convincingly fooling experts into perceiving them as real. Our experiments demonstrate that controlled generative frameworks of this nature can surpass nearly every state-of-the-art image generative model in achieving anatomical consistency in generated medical images when trained on comparable large medical datasets.

Aiyue Chen, Bin Dong, Jingru Li et al.

Video generation using diffusion models is highly computationally intensive, with 3D attention in Diffusion Transformer (DiT) models accounting for over 80\% of the total computational resources. In this work, we introduce {\bf RainFusion}, a novel training-free sparse attention method that exploits inherent sparsity nature in visual data to accelerate attention computation while preserving video quality. Specifically, we identify three unique sparse patterns in video generation attention calculations--Spatial Pattern, Temporal Pattern and Textural Pattern. The sparse pattern for each attention head is determined online with negligible overhead (\textasciitilde\,0.2\%) with our proposed {\bf ARM} (Adaptive Recognition Module) during inference. Our proposed {\bf RainFusion} is a plug-and-play method, that can be seamlessly integrated into state-of-the-art 3D-attention video generation models without additional training or calibration. We evaluate our method on leading open-sourced models including HunyuanVideo, OpenSoraPlan-1.2 and CogVideoX-5B, demonstrating its broad applicability and effectiveness. Experimental results show that RainFusion achieves over {\bf 2\(\times\)} speedup in attention computation while maintaining video quality, with only a minimal impact on VBench scores (-0.2\%).

Yuanlin Yang, Quanjian Song, Zhexian Gao et al.

Diffusion models have emerged as the dominant paradigm for style transfer, but their text-driven mechanism is hindered by a core limitation: it treats textual descriptions as uniform, monolithic guidance. This limitation overlooks the semantic gap between the non-spatial nature of textual descriptions and the spatially-aware attributes of visual style, often leading to the loss of semantic structure and fine-grained details during stylization. In this paper, we propose StyDeco, an unsupervised framework that resolves this limitation by learning text representations specifically tailored for the style transfer task. Our framework first employs Prior-Guided Data Distillation (PGD), a strategy designed to distill stylistic knowledge without human supervision. It leverages a powerful frozen generative model to automatically synthesize pseudo-paired data. Subsequently, we introduce Contrastive Semantic Decoupling (CSD), a task-specific objective that adapts a text encoder using domain-specific weights. CSD performs a two-class clustering in the semantic space, encouraging source and target representations to form distinct clusters. Extensive experiments on three classic benchmarks demonstrate that our framework outperforms several existing approaches in both stylistic fidelity and structural preservation, highlighting its effectiveness in style transfer with semantic preservation. In addition, our framework supports a unique de-stylization process, further demonstrating its extensibility. Our code is vailable at https://github.com/QuanjianSong/StyDeco.

Jun Xia, Lirong Wu, Ge Wang et al.

Contrastive Learning (CL) has emerged as a dominant technique for unsupervised representation learning which embeds augmented versions of the anchor close to each other (positive samples) and pushes the embeddings of other samples (negatives) apart. As revealed in recent studies, CL can benefit from hard negatives (negatives that are most similar to the anchor). However, we observe limited benefits when we adopt existing hard negative mining techniques of other domains in Graph Contrastive Learning (GCL). We perform both experimental and theoretical analysis on this phenomenon and find it can be attributed to the message passing of Graph Neural Networks (GNNs). Unlike CL in other domains, most hard negatives are potentially false negatives (negatives that share the same class with the anchor) if they are selected merely according to the similarities between anchor and themselves, which will undesirably push away the samples of the same class. To remedy this deficiency, we propose an effective method, dubbed \textbf{ProGCL}, to estimate the probability of a negative being true one, which constitutes a more suitable measure for negatives' hardness together with similarity. Additionally, we devise two schemes (i.e., \textbf{ProGCL-weight} and \textbf{ProGCL-mix}) to boost the performance of GCL. Extensive experiments demonstrate that ProGCL brings notable and consistent improvements over base GCL methods and yields multiple state-of-the-art results on several unsupervised benchmarks or even exceeds the performance of supervised ones. Also, ProGCL is readily pluggable into various negatives-based GCL methods for performance improvement. We release the code at \textcolor{magenta}{\url{https://github.com/junxia97/ProGCL}}.

Xinrui Song, Hengtao Guo, Xuanang Xu et al.

Prostate cancer biopsy benefits from accurate fusion of transrectal ultrasound (TRUS) and magnetic resonance (MR) images. In the past few years, convolutional neural networks (CNNs) have been proved powerful in extracting image features crucial for image registration. However, challenging applications and recent advances in computer vision suggest that CNNs are quite limited in its ability to understand spatial correspondence between features, a task in which the self-attention mechanism excels. This paper aims to develop a self-attention mechanism specifically for cross-modal image registration. Our proposed cross-modal attention block effectively maps each of the features in one volume to all features in the corresponding volume. Our experimental results demonstrate that a CNN network designed with the cross-modal attention block embedded outperforms an advanced CNN network 10 times of its size. We also incorporated visualization techniques to improve the interpretability of our network. The source code of our work is available at https://github.com/DIAL-RPI/Attention-Reg .

Chuang Niu, Hongming Shan, Ge Wang

The similarity among samples and the discrepancy between clusters are two crucial aspects of image clustering. However, current deep clustering methods suffer from the inaccurate estimation of either feature similarity or semantic discrepancy. In this paper, we present a Semantic Pseudo-labeling-based Image ClustEring (SPICE) framework, which divides the clustering network into a feature model for measuring the instance-level similarity and a clustering head for identifying the cluster-level discrepancy. We design two semantics-aware pseudo-labeling algorithms, prototype pseudo-labeling, and reliable pseudo-labeling, which enable accurate and reliable self-supervision over clustering. Without using any ground-truth label, we optimize the clustering network in three stages: 1) train the feature model through contrastive learning to measure the instance similarity, 2) train the clustering head with the prototype pseudo-labeling algorithm to identify cluster semantics, and 3) jointly train the feature model and clustering head with the reliable pseudo-labeling algorithm to improve the clustering performance. Extensive experimental results demonstrate that SPICE achieves significant improvements (~10%) over existing methods and establishes the new state-of-the-art clustering results on six image benchmark datasets in terms of three popular metrics. Importantly, SPICE significantly reduces the gap between unsupervised and fully-supervised classification; e.g., there is only a 2% (91.8% vs 93.8%) accuracy difference on CIFAR-10. Our code has been made publically available at https://github.com/niuchuangnn/SPICE.

Hanqing Chao, Xi Fang, Jiajin Zhang et al.

While image analysis of chest computed tomography (CT) for COVID-19 diagnosis has been intensively studied, little work has been performed for image-based patient outcome prediction. Management of high-risk patients with early intervention is a key to lower the fatality rate of COVID-19 pneumonia, as a majority of patients recover naturally. Therefore, an accurate prediction of disease progression with baseline imaging at the time of the initial presentation can help in patient management. In lieu of only size and volume information of pulmonary abnormalities and features through deep learning based image segmentation, here we combine radiomics of lung opacities and non-imaging features from demographic data, vital signs, and laboratory findings to predict need for intensive care unit (ICU) admission. To our knowledge, this is the first study that uses holistic information of a patient including both imaging and non-imaging data for outcome prediction. The proposed methods were thoroughly evaluated on datasets separately collected from three hospitals, one in the United States, one in Iran, and another in Italy, with a total 295 patients with reverse transcription polymerase chain reaction (RT-PCR) assay positive COVID-19 pneumonia. Our experimental results demonstrate that adding non-imaging features can significantly improve the performance of prediction to achieve AUC up to 0.884 and sensitivity as high as 96.1%, which can be valuable to provide clinical decision support in managing COVID-19 patients. Our methods may also be applied to other lung diseases including but not limited to community acquired pneumonia. The source code of our work is available at https://github.com/DIAL-RPI/COVID19-ICUPrediction.

Chuang Niu, Jun Zhang, Ge Wang et al.

We propose a self-supervised Gaussian ATtention network for image Clustering (GATCluster). Rather than extracting intermediate features first and then performing the traditional clustering algorithm, GATCluster directly outputs semantic cluster labels without further post-processing. Theoretically, we give a Label Feature Theorem to guarantee the learned features are one-hot encoded vectors, and the trivial solutions are avoided. To train the GATCluster in a completely unsupervised manner, we design four self-learning tasks with the constraints of transformation invariance, separability maximization, entropy analysis, and attention mapping. Specifically, the transformation invariance and separability maximization tasks learn the relationships between sample pairs. The entropy analysis task aims to avoid trivial solutions. To capture the object-oriented semantics, we design a self-supervised attention mechanism that includes a parameterized attention module and a soft-attention loss. All the guiding signals for clustering are self-generated during the training process. Moreover, we develop a two-step learning algorithm that is memory-efficient for clustering large-size images. Extensive experiments demonstrate the superiority of our proposed method in comparison with the state-of-the-art image clustering benchmarks. Our code has been made publicly available at https://github.com/niuchuangnn/GATCluster.

Huidong Xie, Hongming Shan, Wenxiang Cong et al.

Breast CT provides image volumes with isotropic resolution in high contrast, enabling detection of small calcification (down to a few hundred microns in size) and subtle density differences. Since breast is sensitive to x-ray radiation, dose reduction of breast CT is an important topic, and for this purpose, few-view scanning is a main approach. In this article, we propose a Deep Efficient End-to-end Reconstruction (DEER) network for few-view breast CT image reconstruction. The major merits of our network include high dose efficiency, excellent image quality, and low model complexity. By the design, the proposed network can learn the reconstruction process with as few as O(N) parameters, where N is the side length of an image to be reconstructed, which represents orders of magnitude improvements relative to the state-of-the-art deep-learning-based reconstruction methods that map raw data to tomographic images directly. Also, validated on a cone-beam breast CT dataset prepared by Koning Corporation on a commercial scanner, our method demonstrates a competitive performance over the state-of-the-art reconstruction networks in terms of image quality. The source code of this paper is available at: https://github.com/HuidongXie/DEER.

Zhihao Chen, Bin Hu, Chuang Niu et al.

Large language models (LLMs), such as ChatGPT, have demonstrated impressive capabilities in various tasks and attracted an increasing interest as a natural language interface across many domains. Recently, large vision-language models (VLMs) like BLIP-2 and GPT-4 have been intensively investigated, which learn rich vision-language correlation from image-text pairs. However, despite these developments, the application of LLMs and VLMs in image quality assessment (IQA), particularly in medical imaging, remains to be explored, which is valuable for objective performance evaluation and potential supplement or even replacement of radiologists' opinions. To this end, this paper introduces IQAGPT, an innovative image quality assessment system integrating an image quality captioning VLM with ChatGPT for generating quality scores and textual reports. First, we build a CT-IQA dataset for training and evaluation, comprising 1,000 CT slices with diverse quality levels professionally annotated. To better leverage the capabilities of LLMs, we convert annotated quality scores into semantically rich text descriptions using a prompt template. Second, we fine-tune the image quality captioning VLM on the CT-IQA dataset to generate quality descriptions. The captioning model fuses the image and text features through cross-modal attention. Third, based on the quality descriptions, users can talk with ChatGPT to rate image quality scores or produce a radiological quality report. Our preliminary results demonstrate the feasibility of assessing image quality with large models. Remarkably, our IQAGPT outperforms GPT-4 and CLIP-IQA, as well as the multi-task classification and regression models that solely rely on images.

Dennis Hein, Staffan Holmin, Timothy Szczykutowicz et al.

Diffusion and Poisson flow models have shown impressive performance in a wide range of generative tasks, including low-dose CT image denoising. However, one limitation in general, and for clinical applications in particular, is slow sampling. Due to their iterative nature, the number of function evaluations (NFE) required is usually on the order of $10-10^3$, both for conditional and unconditional generation. In this paper, we present posterior sampling Poisson flow generative models (PPFM), a novel image denoising technique for low-dose and photon-counting CT that produces excellent image quality whilst keeping NFE=1. Updating the training and sampling processes of Poisson flow generative models (PFGM)++, we learn a conditional generator which defines a trajectory between the prior noise distribution and the posterior distribution of interest. We additionally hijack and regularize the sampling process to achieve NFE=1. Our results shed light on the benefits of the PFGM++ framework compared to diffusion models. In addition, PPFM is shown to perform favorably compared to current state-of-the-art diffusion-style models with NFE=1, consistency models, as well as popular deep learning and non-deep learning-based image denoising techniques, on clinical low-dose CT images and clinical images from a prototype photon-counting CT system.

Xiang Liu, Zhe Su, Yongyi Shi et al.

Recently, topological deep learning (TDL), which integrates algebraic topology with deep neural networks, has achieved tremendous success in processing point-cloud data, emerging as a promising paradigm in data science. However, TDL has not been developed for data on differentiable manifolds, including images, due to the challenges posed by differential topology. We address this challenge by introducing manifold topological deep learning (MTDL) for the first time. To highlight the power of Hodge theory rooted in differential topology, we consider a simple convolutional neural network (CNN) in MTDL. In this novel framework, original images are represented as smooth manifolds with vector fields that are decomposed into three orthogonal components based on Hodge theory. These components are then concatenated to form an input image for the CNN architecture. The performance of MTDL is evaluated using the MedMNIST v2 benchmark database, which comprises 717,287 biomedical images from eleven 2D and six 3D datasets. MTDL significantly outperforms other competing methods, extending TDL to a wide range of data on smooth manifolds.

Dennis Hein, Grant Stevens, Adam Wang et al.

X-ray computed tomography (CT) is widely used for medical diagnosis and treatment planning; however, concerns about ionizing radiation exposure drive efforts to optimize image quality at lower doses. This study introduces Poisson Flow Consistency Models (PFCM), a novel family of deep generative models that combines the robustness of PFGM++ with the efficient single-step sampling of consistency models. PFCM are derived by generalizing consistency distillation to PFGM++ through a change-of-variables and an updated noise distribution. As a distilled version of PFGM++, PFCM inherit the ability to trade off robustness for rigidity via the hyperparameter $D \in (0,\infty)$. A fact that we exploit to adapt this novel generative model for the task of low-dose CT image denoising, via a ``task-specific'' sampler that ``hijacks'' the generative process by replacing an intermediate state with the low-dose CT image. While this ``hijacking'' introduces a severe mismatch -- the noise characteristics of low-dose CT images are different from that of intermediate states in the Poisson flow process -- we show that the inherent robustness of PFCM at small $D$ effectively mitigates this issue. The resulting sampler achieves excellent performance in terms of LPIPS, SSIM, and PSNR on the Mayo low-dose CT dataset. By contrast, an analogous sampler based on standard consistency models is found to be significantly less robust under the same conditions, highlighting the importance of a tunable $D$ afforded by our novel framework. To highlight generalizability, we show effective denoising of clinical images from a prototype photon-counting system reconstructed using a sharper kernel and at a range of energy levels.

Tai An, Ruwu Cai, Yanzhe Zhang et al.

In the era of large language models (LLMs), N:M sparsity has emerged as a structured compression technique critical for accelerating inference. While prior work has primarily focused on weight sparsity, it often suffers from significant accuracy degradation. Activation sparsity, though promising, is typically training-dependent and faces challenges in generalization. To address these limitations, we introduce Amber Pruner, a training-free N:M activation sparsity method designed specifically for the prefill stage, targeting the acceleration of linear projection layers in LLMs. Extensive experiments across multiple models and sparsity ratios (2:4, 4:8, and 8:16) demonstrate that Amber Pruner can effectively sparsify and accelerate more than 55% of linear computations without requiring model retraining. To further enhance generality and efficiency, we propose Outstanding-sparse, a unified framework that integrates Amber Pruner with post-training W8A8 quantization. Our approach preserves strong performance across a range of downstream tasks, with notable advantages in generative tasks. This work pioneers a new frontier in activation sparsity, providing foundational insights that are poised to guide the co-evolution of algorithms and architectures in the design of next-generation AI systems.

Poorya Aghaomidi, Ge Wang

Accurate sleep stage classification is essential for understanding sleep disorders and improving overall health. This study proposes a novel three-stage approach for sleep stage classification using ECG signals, offering a more accessible alternative to traditional methods that often rely on complex modalities like EEG. In Stages 1 and 2, we initialize the weights of two networks, which are then integrated in Stage 3 for comprehensive classification. In the first phase, we estimate key features using Feature Imitating Networks (FINs) to achieve higher accuracy and faster convergence. The second phase focuses on identifying the N1 sleep stage through the time-frequency representation of ECG signals. Finally, the third phase integrates models from the previous stages and employs a Kolmogorov-Arnold Network (KAN) to classify five distinct sleep stages. Additionally, data augmentation techniques, particularly SMOTE, are used in enhancing classification capabilities for underrepresented stages like N1. Our results demonstrate significant improvements in the classification performance, with an overall accuracy of 80.79% an overall kappa of 0.73. The model achieves specific accuracies of 86.70% for Wake, 60.36% for N1, 83.89% for N2, 84.85% for N3, and 87.16% for REM. This study emphasizes the importance of weight initialization and data augmentation in optimizing sleep stage classification with ECG signals.