Dinggang Shen

Zhengliang Liu, Yue Huang, Xiaowei Yu et al.

The digitization of healthcare has facilitated the sharing and re-using of medical data but has also raised concerns about confidentiality and privacy. HIPAA (Health Insurance Portability and Accountability Act) mandates removing re-identifying information before the dissemination of medical records. Thus, effective and efficient solutions for de-identifying medical data, especially those in free-text forms, are highly needed. While various computer-assisted de-identification methods, including both rule-based and learning-based, have been developed and used in prior practice, such solutions still lack generalizability or need to be fine-tuned according to different scenarios, significantly imposing restrictions in wider use. The advancement of large language models (LLM), such as ChatGPT and GPT-4, have shown great potential in processing text data in the medical domain with zero-shot in-context learning, especially in the task of privacy protection, as these models can identify confidential information by their powerful named entity recognition (NER) capability. In this work, we developed a novel GPT4-enabled de-identification framework (``DeID-GPT") to automatically identify and remove the identifying information. Compared to existing commonly used medical text data de-identification methods, our developed DeID-GPT showed the highest accuracy and remarkable reliability in masking private information from the unstructured medical text while preserving the original structure and meaning of the text. This study is one of the earliest to utilize ChatGPT and GPT-4 for medical text data processing and de-identification, which provides insights for further research and solution development on the use of LLMs such as ChatGPT/GPT-4 in healthcare. Codes and benchmarking data information are available at https://github.com/yhydhx/ChatGPT-API.

Zhengliang Liu, Aoxiao Zhong, Yiwei Li et al.

We introduce Radiology-GPT, a large language model for radiology. Using an instruction tuning approach on an extensive dataset of radiology domain knowledge, Radiology-GPT demonstrates superior performance compared to general language models such as StableLM, Dolly and LLaMA. It exhibits significant versatility in radiological diagnosis, research, and communication. This work serves as a catalyst for future developments in clinical NLP. The successful implementation of Radiology-GPT is indicative of the potential of localizing generative large language models, specifically tailored for distinctive medical specialties, while ensuring adherence to privacy standards such as HIPAA. The prospect of developing individualized, large-scale language models that cater to specific needs of various hospitals presents a promising direction. The fusion of conversational competence and domain-specific knowledge in these models is set to foster future development in healthcare AI. A demo of Radiology-GPT is available at https://huggingface.co/spaces/allen-eric/radiology-gpt.

Yue Zhao, Lingming Zhang, Yang Liu et al.

Precise segmentation of teeth from intra-oral scanner images is an essential task in computer-aided orthodontic surgical planning. The state-of-the-art deep learning-based methods often simply concatenate the raw geometric attributes (i.e., coordinates and normal vectors) of mesh cells to train a single-stream network for automatic intra-oral scanner image segmentation. However, since different raw attributes reveal completely different geometric information, the naive concatenation of different raw attributes at the (low-level) input stage may bring unnecessary confusion in describing and differentiating between mesh cells, thus hampering the learning of high-level geometric representations for the segmentation task. To address this issue, we design a two-stream graph convolutional network (i.e., TSGCN), which can effectively handle inter-view confusion between different raw attributes to more effectively fuse their complementary information and learn discriminative multi-view geometric representations. Specifically, our TSGCN adopts two input-specific graph-learning streams to extract complementary high-level geometric representations from coordinates and normal vectors, respectively. Then, these single-view representations are further fused by a self-attention module to adaptively balance the contributions of different views in learning more discriminative multi-view representations for accurate and fully automatic tooth segmentation. We have evaluated our TSGCN on a real-patient dataset of dental (mesh) models acquired by 3D intraoral scanners. Experimental results show that our TSGCN significantly outperforms state-of-the-art methods in 3D tooth (surface) segmentation. Github: https://github.com/ZhangLingMing1/TSGCNet.

Honglin Xiong, Sheng Wang, Yitao Zhu et al.

The recent progress of large language models (LLMs), including ChatGPT and GPT-4, in comprehending and responding to human instructions has been remarkable. Nevertheless, these models typically perform better in English and have not been explicitly trained for the medical domain, resulting in suboptimal precision in diagnoses, drug recommendations, and other medical advice. Additionally, training and deploying a dialogue model is still believed to be impossible for hospitals, hindering the promotion of LLMs. To tackle these challenges, we have collected databases of medical dialogues in Chinese with ChatGPT's help and adopted several techniques to train an easy-deploy LLM. Remarkably, we were able to fine-tune the ChatGLM-6B on a single A100 80G in 13 hours, which means having a healthcare-purpose LLM can be very affordable. DoctorGLM is currently an early-stage engineering attempt and contain various mistakes. We are sharing it with the broader community to invite feedback and suggestions to improve its healthcare-focused capabilities: https://github.com/xionghonglin/DoctorGLM.

Mianxin Liu, Han Zhang, Feng Shi et al. · tsinghua

Functional connectivity network (FCN) data from functional magnetic resonance imaging (fMRI) is increasingly used for the diagnoses of brain disorders. However, state-of-the-art studies used to build the FCN using a single brain parcellation atlas at a certain spatial scale, which largely neglected functional interactions across different spatial scales in hierarchical manners. In this study, we propose a novel framework to perform multiscale FCN analysis for brain disorder diagnosis. We first use a set of well-defined multiscale atlases to compute multiscale FCNs. Then, we utilize biologically meaningful brain hierarchical relationships among the regions in multiscale atlases to perform nodal pooling across multiple spatial scales, namely "Atlas-guided Pooling". Accordingly, we propose a Multiscale-Atlases-based Hierarchical Graph Convolutional Network (MAHGCN), built on the stacked layers of graph convolution and the atlas-guided pooling, for a comprehensive extraction of diagnostic information from multiscale FCNs. Experiments on neuroimaging data from 1792 subjects demonstrate the effectiveness of our proposed method in the diagnoses of Alzheimer's disease (AD), the prodromal stage of AD (i.e., mild cognitive impairment [MCI]), as well as autism spectrum disorder (ASD), with accuracy of 88.9%, 78.6%, and 72.7% respectively. All results show significant advantages of our proposed method over other competing methods. This study not only demonstrates the feasibility of brain disorder diagnosis using resting-state fMRI empowered by deep learning, but also highlights that the functional interactions in the multiscale brain hierarchy are worth being explored and integrated into deep learning network architectures for better understanding the neuropathology of brain disorders.

Honglin Xiong, Yuxian Tang, Feng Li et al.

Motion artifacts in magnetic resonance imaging (MRI) degrade diagnostic reliability. Existing deep learning methods are typically contrast-specific and fail to generalize across diverse modalities and artifact severities. We propose a unified framework combining parameter-informed contrast disentanglement with severity-aware adaptive correction. ScanCLIP, pretrained on over 30,000 MRI text-image pairs, derives contrast embeddings from acquisition parameters to disentangle contrast style from anatomical content, yielding contrast-free features. A Vision Transformer then estimates motion severity and routes features through a Mixture-of-Experts network, enabling targeted artifact correction. A dual-pathway decoder reconstructs both the clean image and residual artifact map, enforcing image-space consistency. On IXI and HCP benchmarks, our method improves PSNR by 0.75 dB and SSIM by up to 0.0279 over state-of-the-art approaches, with larger gains at higher artifact severities. It further demonstrates robust zero-shot generalization on real-world clinical data acquired with unseen scanning parameters, where existing methods either fail to remove artifacts or introduce additional distortions.

Zeyu Han, Yuhan Wang, Luping Zhou et al.

To obtain high-quality positron emission tomography (PET) scans while reducing radiation exposure to the human body, various approaches have been proposed to reconstruct standard-dose PET (SPET) images from low-dose PET (LPET) images. One widely adopted technique is the generative adversarial networks (GANs), yet recently, diffusion probabilistic models (DPMs) have emerged as a compelling alternative due to their improved sample quality and higher log-likelihood scores compared to GANs. Despite this, DPMs suffer from two major drawbacks in real clinical settings, i.e., the computationally expensive sampling process and the insufficient preservation of correspondence between the conditioning LPET image and the reconstructed PET (RPET) image. To address the above limitations, this paper presents a coarse-to-fine PET reconstruction framework that consists of a coarse prediction module (CPM) and an iterative refinement module (IRM). The CPM generates a coarse PET image via a deterministic process, and the IRM samples the residual iteratively. By delegating most of the computational overhead to the CPM, the overall sampling speed of our method can be significantly improved. Furthermore, two additional strategies, i.e., an auxiliary guidance strategy and a contrastive diffusion strategy, are proposed and integrated into the reconstruction process, which can enhance the correspondence between the LPET image and the RPET image, further improving clinical reliability. Extensive experiments on two human brain PET datasets demonstrate that our method outperforms the state-of-the-art PET reconstruction methods. The source code is available at \url{https://github.com/Show-han/PET-Reconstruction}.

Yiqing Shen, Yulin Luo, Dinggang Shen et al.

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.

Haixing Dai, Zhengliang Liu, Wenxiong Liao et al.

Text data augmentation is an effective strategy for overcoming the challenge of limited sample sizes in many natural language processing (NLP) tasks. This challenge is especially prominent in the few-shot learning scenario, where the data in the target domain is generally much scarcer and of lowered quality. A natural and widely-used strategy to mitigate such challenges is to perform data augmentation to better capture the data invariance and increase the sample size. However, current text data augmentation methods either can't ensure the correct labeling of the generated data (lacking faithfulness) or can't ensure sufficient diversity in the generated data (lacking compactness), or both. Inspired by the recent success of large language models, especially the development of ChatGPT, which demonstrated improved language comprehension abilities, in this work, we propose a text data augmentation approach based on ChatGPT (named AugGPT). AugGPT rephrases each sentence in the training samples into multiple conceptually similar but semantically different samples. The augmented samples can then be used in downstream model training. Experiment results on few-shot learning text classification tasks show the superior performance of the proposed AugGPT approach over state-of-the-art text data augmentation methods in terms of testing accuracy and distribution of the augmented samples.

Hao Hou, Jun Xu, Yingkun Hou et al.

Real-world face super-resolution (SR) is a highly ill-posed image restoration task. The fully-cycled Cycle-GAN architecture is widely employed to achieve promising performance on face SR, but prone to produce artifacts upon challenging cases in real-world scenarios, since joint participation in the same degradation branch will impact final performance due to huge domain gap between real-world and synthetic LR ones obtained by generators. To better exploit the powerful generative capability of GAN for real-world face SR, in this paper, we establish two independent degradation branches in the forward and backward cycle-consistent reconstruction processes, respectively, while the two processes share the same restoration branch. Our Semi-Cycled Generative Adversarial Networks (SCGAN) is able to alleviate the adverse effects of the domain gap between the real-world LR face images and the synthetic LR ones, and to achieve accurate and robust face SR performance by the shared restoration branch regularized by both the forward and backward cycle-consistent learning processes. Experiments on two synthetic and two real-world datasets demonstrate that, our SCGAN outperforms the state-of-the-art methods on recovering the face structures/details and quantitative metrics for real-world face SR. The code will be publicly released at https://github.com/HaoHou-98/SCGAN.

Sheng Wang, Xi Ouyang, Tianming Liu et al.

When deep neural network (DNN) was first introduced to the medical image analysis community, researchers were impressed by its performance. However, it is evident now that a large number of manually labeled data is often a must to train a properly functioning DNN. This demand for supervision data and labels is a major bottleneck in current medical image analysis, since collecting a large number of annotations from experienced experts can be time-consuming and expensive. In this paper, we demonstrate that the eye movement of radiologists reading medical images can be a new form of supervision to train the DNN-based computer-aided diagnosis (CAD) system. Particularly, we record the tracks of the radiologists' gaze when they are reading images. The gaze information is processed and then used to supervise the DNN's attention via an Attention Consistency module. To the best of our knowledge, the above pipeline is among the earliest efforts to leverage expert eye movement for deep-learning-based CAD. We have conducted extensive experiments on knee X-ray images for osteoarthritis assessment. The results show that our method can achieve considerable improvement in diagnosis performance, with the help of gaze supervision.

Yonghao Li, Tao Zhou, Kelei He et al.

Cross-modality magnetic resonance (MR) image synthesis can be used to generate missing modalities from given ones. Existing (supervised learning) methods often require a large number of paired multi-modal data to train an effective synthesis model. However, it is often challenging to obtain sufficient paired data for supervised training. In reality, we often have a small number of paired data while a large number of unpaired data. To take advantage of both paired and unpaired data, in this paper, we propose a Multi-scale Transformer Network (MT-Net) with edge-aware pre-training for cross-modality MR image synthesis. Specifically, an Edge-preserving Masked AutoEncoder (Edge-MAE) is first pre-trained in a self-supervised manner to simultaneously perform 1) image imputation for randomly masked patches in each image and 2) whole edge map estimation, which effectively learns both contextual and structural information. Besides, a novel patch-wise loss is proposed to enhance the performance of Edge-MAE by treating different masked patches differently according to the difficulties of their respective imputations. Based on this proposed pre-training, in the subsequent fine-tuning stage, a Dual-scale Selective Fusion (DSF) module is designed (in our MT-Net) to synthesize missing-modality images by integrating multi-scale features extracted from the encoder of the pre-trained Edge-MAE. Further, this pre-trained encoder is also employed to extract high-level features from the synthesized image and corresponding ground-truth image, which are required to be similar (consistent) in the training. Experimental results show that our MT-Net achieves comparable performance to the competing methods even using $70\%$ of all available paired data. Our code will be publicly available at https://github.com/lyhkevin/MT-Net.

Jiaqi Wang, Zhengliang Liu, Lin Zhao et al.

Visual prompt engineering is a fundamental technology in the field of visual and image Artificial General Intelligence, serving as a key component for achieving zero-shot capabilities. As the development of large vision models progresses, the importance of prompt engineering becomes increasingly evident. Designing suitable prompts for specific visual tasks has emerged as a meaningful research direction. This review aims to summarize the methods employed in the computer vision domain for large vision models and visual prompt engineering, exploring the latest advancements in visual prompt engineering. We present influential large models in the visual domain and a range of prompt engineering methods employed on these models. It is our hope that this review provides a comprehensive and systematic description of prompt engineering methods based on large visual models, offering valuable insights for future researchers in their exploration of this field.

Zhengliang Liu, Yiwei Li, Peng Shu et al.

This paper introduces Radiology-Llama2, a large language model specialized for radiology through a process known as instruction tuning. Radiology-Llama2 is based on the Llama2 architecture and further trained on a large dataset of radiology reports to generate coherent and clinically useful impressions from radiological findings. Quantitative evaluations using ROUGE metrics on the MIMIC-CXR and OpenI datasets demonstrate that Radiology-Llama2 achieves state-of-the-art performance compared to other generative language models, with a Rouge-1 score of 0.4834 on MIMIC-CXR and 0.4185 on OpenI. Additional assessments by radiology experts highlight the model's strengths in understandability, coherence, relevance, conciseness, and clinical utility. The work illustrates the potential of localized language models designed and tuned for specialized domains like radiology. When properly evaluated and deployed, such models can transform fields like radiology by automating rote tasks and enhancing human expertise.

Xiang Li, Lin Zhao, Lu Zhang et al.

Large-scale Artificial General Intelligence (AGI) models, including Large Language Models (LLMs) such as ChatGPT/GPT-4, have achieved unprecedented success in a variety of general domain tasks. Yet, when applied directly to specialized domains like medical imaging, which require in-depth expertise, these models face notable challenges arising from the medical field's inherent complexities and unique characteristics. In this review, we delve into the potential applications of AGI models in medical imaging and healthcare, with a primary focus on LLMs, Large Vision Models, and Large Multimodal Models. We provide a thorough overview of the key features and enabling techniques of LLMs and AGI, and further examine the roadmaps guiding the evolution and implementation of AGI models in the medical sector, summarizing their present applications, potentialities, and associated challenges. In addition, we highlight potential future research directions, offering a holistic view on upcoming ventures. This comprehensive review aims to offer insights into the future implications of AGI in medical imaging, healthcare, and beyond.

Lei Zhou, Yuzhong Zhang, Jiadong Zhang et al.

Automated breast tumor segmentation on the basis of dynamic contrast-enhancement magnetic resonance imaging (DCE-MRI) has shown great promise in clinical practice, particularly for identifying the presence of breast disease. However, accurate segmentation of breast tumor is a challenging task, often necessitating the development of complex networks. To strike an optimal trade-off between computational costs and segmentation performance, we propose a hybrid network via the combination of convolution neural network (CNN) and transformer layers. Specifically, the hybrid network consists of a encoder-decoder architecture by stacking convolution and decovolution layers. Effective 3D transformer layers are then implemented after the encoder subnetworks, to capture global dependencies between the bottleneck features. To improve the efficiency of hybrid network, two parallel encoder subnetworks are designed for the decoder and the transformer layers, respectively. To further enhance the discriminative capability of hybrid network, a prototype learning guided prediction module is proposed, where the category-specified prototypical features are calculated through on-line clustering. All learned prototypical features are finally combined with the features from decoder for tumor mask prediction. The experimental results on private and public DCE-MRI datasets demonstrate that the proposed hybrid network achieves superior performance than the state-of-the-art (SOTA) methods, while maintaining balance between segmentation accuracy and computation cost. Moreover, we demonstrate that automatically generated tumor masks can be effectively applied to identify HER2-positive subtype from HER2-negative subtype with the similar accuracy to the analysis based on manual tumor segmentation. The source code is available at https://github.com/ZhouL-lab/PLHN.

Jiaqi Wang, Enze Shi, Sigang Yu et al.

Prompt engineering is a critical technique in the field of natural language processing that involves designing and optimizing the prompts used to input information into models, aiming to enhance their performance on specific tasks. With the recent advancements in large language models, prompt engineering has shown significant superiority across various domains and has become increasingly important in the healthcare domain. However, there is a lack of comprehensive reviews specifically focusing on prompt engineering in the medical field. This review will introduce the latest advances in prompt engineering in the field of natural language processing for the medical field. First, we will provide the development of prompt engineering and emphasize its significant contributions to healthcare natural language processing applications such as question-answering systems, text summarization, and machine translation. With the continuous improvement of general large language models, the importance of prompt engineering in the healthcare domain is becoming increasingly prominent. The aim of this article is to provide useful resources and bridges for healthcare natural language processing researchers to better explore the application of prompt engineering in this field. We hope that this review can provide new ideas and inspire for research and application in medical natural language processing.

Lei Ma, Jingyang Zhang, Ke Deng et al.

Dental template and parametric dental models are important tools for various applications in digital dentistry. However, constructing an unbiased dental template and accurate parametric dental models remains a challenging task due to the complex anatomical and morphological dental structures and also low volume ratio of the teeth. In this study, we develop an unbiased dental template by constructing an accurate dental atlas from CBCT images with guidance of teeth segmentation. First, to address the challenges, we propose to enhance the CBCT images and their segmentation images, including image cropping, image masking and segmentation intensity reassigning. Then, we further use the segmentation images to perform co-registration with the CBCT images to generate an accurate dental atlas, from which an unbiased dental template can be generated. By leveraging the unbiased dental template, we construct parametric dental models by estimating point-to-point correspondences between the dental models and employing Principal Component Analysis to determine shape subspaces of the parametric dental models. A total of 159 CBCT images of real subjects are collected to perform the constructions. Experimental results demonstrate effectiveness of our proposed method in constructing unbiased dental template and parametric dental model. The developed dental template and parametric dental models are available at https://github.com/Marvin0724/Teeth_template.

Han Wu, Jiadong Zhang, Yu Fang et al.

Accurately localizing and identifying vertebrae from CT images is crucial for various clinical applications. However, most existing efforts are performed on 3D with cropping patch operation, suffering from the large computation costs and limited global information. In this paper, we propose a multi-view vertebra localization and identification from CT images, converting the 3D problem into a 2D localization and identification task on different views. Without the limitation of the 3D cropped patch, our method can learn the multi-view global information naturally. Moreover, to better capture the anatomical structure information from different view perspectives, a multi-view contrastive learning strategy is developed to pre-train the backbone. Additionally, we further propose a Sequence Loss to maintain the sequential structure embedded along the vertebrae. Evaluation results demonstrate that, with only two 2D networks, our method can localize and identify vertebrae in CT images accurately, and outperforms the state-of-the-art methods consistently. Our code is available at https://github.com/ShanghaiTech-IMPACT/Multi-View-Vertebra-Localization-and-Identification-from-CT-Images.

Chong Ma, Zihao Wu, Jiaqi Wang et al.

The 'Impression' section of a radiology report is a critical basis for communication between radiologists and other physicians, and it is typically written by radiologists based on the 'Findings' section. However, writing numerous impressions can be laborious and error-prone for radiologists. Although recent studies have achieved promising results in automatic impression generation using large-scale medical text data for pre-training and fine-tuning pre-trained language models, such models often require substantial amounts of medical text data and have poor generalization performance. While large language models (LLMs) like ChatGPT have shown strong generalization capabilities and performance, their performance in specific domains, such as radiology, remains under-investigated and potentially limited. To address this limitation, we propose ImpressionGPT, which leverages the in-context learning capability of LLMs by constructing dynamic contexts using domain-specific, individualized data. This dynamic prompt approach enables the model to learn contextual knowledge from semantically similar examples from existing data. Additionally, we design an iterative optimization algorithm that performs automatic evaluation on the generated impression results and composes the corresponding instruction prompts to further optimize the model. The proposed ImpressionGPT model achieves state-of-the-art performance on both MIMIC-CXR and OpenI datasets without requiring additional training data or fine-tuning the LLMs. This work presents a paradigm for localizing LLMs that can be applied in a wide range of similar application scenarios, bridging the gap between general-purpose LLMs and the specific language processing needs of various domains.

Lin Zhao, Lu Zhang, Zihao Wu et al.

Artificial General Intelligence (AGI) has been a long-standing goal of humanity, with the aim of creating machines capable of performing any intellectual task that humans can do. To achieve this, AGI researchers draw inspiration from the human brain and seek to replicate its principles in intelligent machines. Brain-inspired artificial intelligence is a field that has emerged from this endeavor, combining insights from neuroscience, psychology, and computer science to develop more efficient and powerful AI systems. In this article, we provide a comprehensive overview of brain-inspired AI from the perspective of AGI. We begin with the current progress in brain-inspired AI and its extensive connection with AGI. We then cover the important characteristics for both human intelligence and AGI (e.g., scaling, multimodality, and reasoning). We discuss important technologies toward achieving AGI in current AI systems, such as in-context learning and prompt tuning. We also investigate the evolution of AGI systems from both algorithmic and infrastructural perspectives. Finally, we explore the limitations and future of AGI.

Zhengliang Liu, Tianyang Zhong, Yiwei Li et al.

The rise of large language models (LLMs) has marked a pivotal shift in the field of natural language processing (NLP). LLMs have revolutionized a multitude of domains, and they have made a significant impact in the medical field. Large language models are now more abundant than ever, and many of these models exhibit bilingual capabilities, proficient in both English and Chinese. However, a comprehensive evaluation of these models remains to be conducted. This lack of assessment is especially apparent within the context of radiology NLP. This study seeks to bridge this gap by critically evaluating thirty two LLMs in interpreting radiology reports, a crucial component of radiology NLP. Specifically, the ability to derive impressions from radiologic findings is assessed. The outcomes of this evaluation provide key insights into the performance, strengths, and weaknesses of these LLMs, informing their practical applications within the medical domain.

Jingyang Zhang, Peng Xue, Ran Gu et al.

In clinical practice, a segmentation network is often required to continually learn on a sequential data stream from multiple sites rather than a consolidated set, due to the storage cost and privacy restriction. However, during the continual learning process, existing methods are usually restricted in either network memorizability on previous sites or generalizability on unseen sites. This paper aims to tackle the challenging problem of Synchronous Memorizability and Generalizability (SMG) and to simultaneously improve performance on both previous and unseen sites, with a novel proposed SMG-learning framework. First, we propose a Synchronous Gradient Alignment (SGA) objective, which not only promotes the network memorizability by enforcing coordinated optimization for a small exemplar set from previous sites (called replay buffer), but also enhances the generalizability by facilitating site-invariance under simulated domain shift. Second, to simplify the optimization of SGA objective, we design a Dual-Meta algorithm that approximates the SGA objective as dual meta-objectives for optimization without expensive computation overhead. Third, for efficient rehearsal, we configure the replay buffer comprehensively considering additional inter-site diversity to reduce redundancy. Experiments on prostate MRI data sequentially acquired from six institutes demonstrate that our method can simultaneously achieve higher memorizability and generalizability over state-of-the-art methods. Code is available at https://github.com/jingyzhang/SMG-Learning.

Zihao Wu, Lu Zhang, Chao Cao et al.

Recently, ChatGPT and GPT-4 have emerged and gained immense global attention due to their unparalleled performance in language processing. Despite demonstrating impressive capability in various open-domain tasks, their adequacy in highly specific fields like radiology remains untested. Radiology presents unique linguistic phenomena distinct from open-domain data due to its specificity and complexity. Assessing the performance of large language models (LLMs) in such specific domains is crucial not only for a thorough evaluation of their overall performance but also for providing valuable insights into future model design directions: whether model design should be generic or domain-specific. To this end, in this study, we evaluate the performance of ChatGPT/GPT-4 on a radiology NLI task and compare it to other models fine-tuned specifically on task-related data samples. We also conduct a comprehensive investigation on ChatGPT/GPT-4's reasoning ability by introducing varying levels of inference difficulty. Our results show that 1) GPT-4 outperforms ChatGPT in the radiology NLI task; 2) other specifically fine-tuned models require significant amounts of data samples to achieve comparable performance to ChatGPT/GPT-4. These findings demonstrate that constructing a generic model that is capable of solving various tasks across different domains is feasible.

Sheng Wang, Zihao Zhao, Xi Ouyang et al.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Zhenxiang Xiao, Yuzhong Chen, Lu Zhang et al.

Prompts have been proven to play a crucial role in large language models, and in recent years, vision models have also been using prompts to improve scalability for multiple downstream tasks. In this paper, we focus on adapting prompt design based on instruction tuning into a visual transformer model for image classification which we called Instruction-ViT. The key idea is to implement multi-modal prompts (text or image prompt) related to category information to guide the fine-tuning of the model. Based on the experiments of several image captionining tasks, the performance and domain adaptability were improved. Our work provided an innovative strategy to fuse multi-modal prompts with better performance and faster adaptability for visual classification models.

Chong Ma, Lin Zhao, Yuzhong Chen et al.

Learning harmful shortcuts such as spurious correlations and biases prevents deep neural networks from learning the meaningful and useful representations, thus jeopardizing the generalizability and interpretability of the learned representation. The situation becomes even more serious in medical imaging, where the clinical data (e.g., MR images with pathology) are limited and scarce while the reliability, generalizability and transparency of the learned model are highly required. To address this problem, we propose to infuse human experts' intelligence and domain knowledge into the training of deep neural networks. The core idea is that we infuse the visual attention information from expert radiologists to proactively guide the deep model to focus on regions with potential pathology and avoid being trapped in learning harmful shortcuts. To do so, we propose a novel eye-gaze-guided vision transformer (EG-ViT) for diagnosis with limited medical image data. We mask the input image patches that are out of the radiologists' interest and add an additional residual connection in the last encoder layer of EG-ViT to maintain the correlations of all patches. The experiments on two public datasets of INbreast and SIIM-ACR demonstrate our EG-ViT model can effectively learn/transfer experts' domain knowledge and achieve much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the EG-ViT model's interpretability. In general, EG-ViT takes the advantages of both human expert's prior knowledge and the power of deep neural networks. This work opens new avenues for advancing current artificial intelligence paradigms by infusing human intelligence.

Tianyang Zhong, Zhengliang Liu, Yi Pan et al.

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

Tianyang Zhong, Yaonai Wei, Li Yang et al.

Large language models (LLMs) such as ChatGPT have recently demonstrated significant potential in mathematical abilities, providing valuable reasoning paradigm consistent with human natural language. However, LLMs currently have difficulty in bridging perception, language understanding and reasoning capabilities due to incompatibility of the underlying information flow among them, making it challenging to accomplish tasks autonomously. On the other hand, abductive learning (ABL) frameworks for integrating the two abilities of perception and reasoning has seen significant success in inverse decipherment of incomplete facts, but it is limited by the lack of semantic understanding of logical reasoning rules and the dependence on complicated domain knowledge representation. This paper presents a novel method (ChatABL) for integrating LLMs into the ABL framework, aiming at unifying the three abilities in a more user-friendly and understandable manner. The proposed method uses the strengths of LLMs' understanding and logical reasoning to correct the incomplete logical facts for optimizing the performance of perceptual module, by summarizing and reorganizing reasoning rules represented in natural language format. Similarly, perceptual module provides necessary reasoning examples for LLMs in natural language format. The variable-length handwritten equation deciphering task, an abstract expression of the Mayan calendar decoding, is used as a testbed to demonstrate that ChatABL has reasoning ability beyond most existing state-of-the-art methods, which has been well supported by comparative studies. To our best knowledge, the proposed ChatABL is the first attempt to explore a new pattern for further approaching human-level cognitive ability via natural language interaction with ChatGPT.

Jiaqi Wang, Hanqi Jiang, Yiheng Liu et al.

In an era defined by the explosive growth of data and rapid technological advancements, Multimodal Large Language Models (MLLMs) stand at the forefront of artificial intelligence (AI) systems. Designed to seamlessly integrate diverse data types-including text, images, videos, audio, and physiological sequences-MLLMs address the complexities of real-world applications far beyond the capabilities of single-modality systems. In this paper, we systematically sort out the applications of MLLM in multimodal tasks such as natural language, vision, and audio. We also provide a comparative analysis of the focus of different MLLMs in the tasks, and provide insights into the shortcomings of current MLLMs, and suggest potential directions for future research. Through these discussions, this paper hopes to provide valuable insights for the further development and application of MLLM.

Chong Ma, Lin Zhao, Yuzhong Chen et al.

Shortcut learning is common but harmful to deep learning models, leading to degenerated feature representations and consequently jeopardizing the model's generalizability and interpretability. However, shortcut learning in the widely used Vision Transformer framework is largely unknown. Meanwhile, introducing domain-specific knowledge is a major approach to rectifying the shortcuts, which are predominated by background related factors. For example, in the medical imaging field, eye-gaze data from radiologists is an effective human visual prior knowledge that has the great potential to guide the deep learning models to focus on meaningful foreground regions of interest. However, obtaining eye-gaze data is time-consuming, labor-intensive and sometimes even not practical. In this work, we propose a novel and effective saliency-guided vision transformer (SGT) model to rectify shortcut learning in ViT with the absence of eye-gaze data. Specifically, a computational visual saliency model is adopted to predict saliency maps for input image samples. Then, the saliency maps are used to distil the most informative image patches. In the proposed SGT, the self-attention among image patches focus only on the distilled informative ones. Considering this distill operation may lead to global information lost, we further introduce, in the last encoder layer, a residual connection that captures the self-attention across all the image patches. The experiment results on four independent public datasets show that our SGT framework can effectively learn and leverage human prior knowledge without eye gaze data and achieves much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the interpretability of the ViT model, demonstrating the promise of transferring human prior knowledge derived visual saliency in rectifying shortcut learning

Chenfan Xu, Zhentao Liu, Yuan Liu et al.

Orthodontic treatment usually requires regular face-to-face examinations to monitor dental conditions of the patients. When in-person diagnosis is not feasible, an alternative is to utilize five intra-oral photographs for remote dental monitoring. However, it lacks of 3D information, and how to reconstruct 3D dental models from such sparse view photographs is a challenging problem. In this study, we propose a 3D teeth reconstruction framework, named TeethDreamer, aiming to restore the shape and position of the upper and lower teeth. Given five intra-oral photographs, our approach first leverages a large diffusion model's prior knowledge to generate novel multi-view images with known poses to address sparse inputs and then reconstructs high-quality 3D teeth models by neural surface reconstruction. To ensure the 3D consistency across generated views, we integrate a 3D-aware feature attention mechanism in the reverse diffusion process. Moreover, a geometry-aware normal loss is incorporated into the teeth reconstruction process to enhance geometry accuracy. Extensive experiments demonstrate the superiority of our method over current state-of-the-arts, giving the potential to monitor orthodontic treatment remotely. Our code is available at https://github.com/ShanghaiTech-IMPACT/TeethDreamer

Zhenrong Shen, Xi Ouyang, Bin Xiao et al.

Lung nodule detection in chest X-ray (CXR) images is common to early screening of lung cancers. Deep-learning-based Computer-Assisted Diagnosis (CAD) systems can support radiologists for nodule screening in CXR. However, it requires large-scale and diverse medical data with high-quality annotations to train such robust and accurate CADs. To alleviate the limited availability of such datasets, lung nodule synthesis methods are proposed for the sake of data augmentation. Nevertheless, previous methods lack the ability to generate nodules that are realistic with the size attribute desired by the detector. To address this issue, we introduce a novel lung nodule synthesis framework in this paper, which decomposes nodule attributes into three main aspects including shape, size, and texture, respectively. A GAN-based Shape Generator firstly models nodule shapes by generating diverse shape masks. The following Size Modulation then enables quantitative control on the diameters of the generated nodule shapes in pixel-level granularity. A coarse-to-fine gated convolutional Texture Generator finally synthesizes visually plausible nodule textures conditioned on the modulated shape masks. Moreover, we propose to synthesize nodule CXR images by controlling the disentangled nodule attributes for data augmentation, in order to better compensate for the nodules that are easily missed in the detection task. Our experiments demonstrate the enhanced image quality, diversity, and controllability of the proposed lung nodule synthesis framework. We also validate the effectiveness of our data augmentation on greatly improving nodule detection performance.

Tianyang Zhong, Wei Zhao, Yutong Zhang et al.

Radiology report generation, as a key step in medical image analysis, is critical to the quantitative analysis of clinically informed decision-making levels. However, complex and diverse radiology reports with cross-source heterogeneity pose a huge generalizability challenge to the current methods under massive data volume, mainly because the style and normativity of radiology reports are obviously distinctive among institutions, body regions inspected and radiologists. Recently, the advent of large language models (LLM) offers great potential for recognizing signs of health conditions. To resolve the above problem, we collaborate with the Second Xiangya Hospital in China and propose ChatRadio-Valuer based on the LLM, a tailored model for automatic radiology report generation that learns generalizable representations and provides a basis pattern for model adaptation in sophisticated analysts' cases. Specifically, ChatRadio-Valuer is trained based on the radiology reports from a single institution by means of supervised fine-tuning, and then adapted to disease diagnosis tasks for human multi-system evaluation (i.e., chest, abdomen, muscle-skeleton, head, and maxillofacial $\&$ neck) from six different institutions in clinical-level events. The clinical dataset utilized in this study encompasses a remarkable total of \textbf{332,673} observations. From the comprehensive results on engineering indicators, clinical efficacy and deployment cost metrics, it can be shown that ChatRadio-Valuer consistently outperforms state-of-the-art models, especially ChatGPT (GPT-3.5-Turbo) and GPT-4 et al., in terms of the diseases diagnosis from radiology reports. ChatRadio-Valuer provides an effective avenue to boost model generalization performance and alleviate the annotation workload of experts to enable the promotion of clinical AI applications in radiology reports.

Mancheng Meng, Ziyan Wu, Terrence Chen et al.

Predicting the future trajectory of a person remains a challenging problem, due to randomness and subjectivity of human movement. However, the moving patterns of human in a constrained scenario typically conform to a limited number of regularities to a certain extent, because of the scenario restrictions and person-person or person-object interactivity. Thus, an individual person in this scenario should follow one of the regularities as well. In other words, a person's subsequent trajectory has likely been traveled by others. Based on this hypothesis, we propose to forecast a person's future trajectory by learning from the implicit scene regularities. We call the regularities, inherently derived from the past dynamics of the people and the environment in the scene, scene history. We categorize scene history information into two types: historical group trajectory and individual-surroundings interaction. To exploit these two types of information for trajectory prediction, we propose a novel framework Scene History Excavating Network (SHENet), where the scene history is leveraged in a simple yet effective approach. In particular, we design two components: the group trajectory bank module to extract representative group trajectories as the candidate for future path, and the cross-modal interaction module to model the interaction between individual past trajectory and its surroundings for trajectory refinement. In addition, to mitigate the uncertainty in ground-truth trajectory, caused by the aforementioned randomness and subjectivity of human movement, we propose to include smoothness into the training process and evaluation metrics. We conduct extensive evaluations to validate the efficacy of our proposed framework on ETH, UCY, as well as a new, challenging benchmark dataset PAV, demonstrating superior performance compared to state-of-the-art methods.

Zhengliang Liu, Hanqi Jiang, Tianyang Zhong et al.

In this paper, we present a large-scale evaluation probing GPT-4V's capabilities and limitations for biomedical image analysis. GPT-4V represents a breakthrough in artificial general intelligence (AGI) for computer vision, with applications in the biomedical domain. We assess GPT-4V's performance across 16 medical imaging categories, including radiology, oncology, ophthalmology, pathology, and more. Tasks include modality recognition, anatomy localization, disease diagnosis, report generation, and lesion detection. The extensive experiments provide insights into GPT-4V's strengths and weaknesses. Results show GPT-4V's proficiency in modality and anatomy recognition but difficulty with disease diagnosis and localization. GPT-4V excels at diagnostic report generation, indicating strong image captioning skills. While promising for biomedical imaging AI, GPT-4V requires further enhancement and validation before clinical deployment. We emphasize responsible development and testing for trustworthy integration of biomedical AGI. This rigorous evaluation of GPT-4V on diverse medical images advances understanding of multimodal large language models (LLMs) and guides future work toward impactful healthcare applications.

Xiangxi Meng, Yuning Gu, Yongsheng Pan et al.

Multi-modal medical image completion has been extensively applied to alleviate the missing modality issue in a wealth of multi-modal diagnostic tasks. However, for most existing synthesis methods, their inferences of missing modalities can collapse into a deterministic mapping from the available ones, ignoring the uncertainties inherent in the cross-modal relationships. Here, we propose the Unified Multi-Modal Conditional Score-based Generative Model (UMM-CSGM) to take advantage of Score-based Generative Model (SGM) in modeling and stochastically sampling a target probability distribution, and further extend SGM to cross-modal conditional synthesis for various missing-modality configurations in a unified framework. Specifically, UMM-CSGM employs a novel multi-in multi-out Conditional Score Network (mm-CSN) to learn a comprehensive set of cross-modal conditional distributions via conditional diffusion and reverse generation in the complete modality space. In this way, the generation process can be accurately conditioned by all available information, and can fit all possible configurations of missing modalities in a single network. Experiments on BraTS19 dataset show that the UMM-CSGM can more reliably synthesize the heterogeneous enhancement and irregular area in tumor-induced lesions for any missing modalities.

Ruiyang Zhao, Zhao He, Tao Wang et al.

Interventional magnetic resonance imaging (i-MRI) for surgical guidance could help visualize the interventional process such as deep brain stimulation (DBS), improving the surgery performance and patient outcome. Different from retrospective reconstruction in conventional dynamic imaging, i-MRI for DBS has to acquire and reconstruct the interventional images sequentially online. Here we proposed a convolutional long short-term memory (Conv-LSTM) based recurrent neural network (RNN), or ConvLR, to reconstruct interventional images with golden-angle radial sampling. By using an initializer and Conv-LSTM blocks, the priors from the pre-operative reference image and intra-operative frames were exploited for reconstructing the current frame. Data consistency for radial sampling was implemented by a soft-projection method. To improve the reconstruction accuracy, an adversarial learning strategy was adopted. A set of interventional images based on the pre-operative and post-operative MR images were simulated for algorithm validation. Results showed with only 10 radial spokes, ConvLR provided the best performance compared with state-of-the-art methods, giving an acceleration up to 40 folds. The proposed algorithm has the potential to achieve real-time i-MRI for DBS and can be used for general purpose MR-guided intervention.

Jiaqi Cui, Pinxian Zeng, Xinyi Zeng et al.

To obtain high-quality positron emission tomography (PET) images while minimizing radiation exposure, various methods have been proposed for reconstructing standard-dose PET (SPET) images from low-dose PET (LPET) sinograms directly. However, current methods often neglect boundaries during sinogram-to-image reconstruction, resulting in high-frequency distortion in the frequency domain and diminished or fuzzy edges in the reconstructed images. Furthermore, the convolutional architectures, which are commonly used, lack the ability to model long-range non-local interactions, potentially leading to inaccurate representations of global structures. To alleviate these problems, we propose a transformer-based model that unites triple domains of sinogram, image, and frequency for direct PET reconstruction, namely TriDo-Former. Specifically, the TriDo-Former consists of two cascaded networks, i.e., a sinogram enhancement transformer (SE-Former) for denoising the input LPET sinograms and a spatial-spectral reconstruction transformer (SSR-Former) for reconstructing SPET images from the denoised sinograms. Different from the vanilla transformer that splits an image into 2D patches, based specifically on the PET imaging mechanism, our SE-Former divides the sinogram into 1D projection view angles to maintain its inner-structure while denoising, preventing the noise in the sinogram from prorogating into the image domain. Moreover, to mitigate high-frequency distortion and improve reconstruction details, we integrate global frequency parsers (GFPs) into SSR-Former. The GFP serves as a learnable frequency filter that globally adjusts the frequency components in the frequency domain, enforcing the network to restore high-frequency details resembling real SPET images. Validations on a clinical dataset demonstrate that our TriDo-Former outperforms the state-of-the-art methods qualitatively and quantitatively.

Yu Fang, Lanzhuju Mei, Changjian Li et al.

Cone beam computed tomography (CBCT) has been widely used in clinical practice, especially in dental clinics, while the radiation dose of X-rays when capturing has been a long concern in CBCT imaging. Several research works have been proposed to reconstruct high-quality CBCT images from sparse-view 2D projections, but the current state-of-the-arts suffer from artifacts and the lack of fine details. In this paper, we propose SNAF for sparse-view CBCT reconstruction by learning the neural attenuation fields, where we have invented a novel view augmentation strategy to overcome the challenges introduced by insufficient data from sparse input views. Our approach achieves superior performance in terms of high reconstruction quality (30+ PSNR) with only 20 input views (25 times fewer than clinical collections), which outperforms the state-of-the-arts. We have further conducted comprehensive experiments and ablation analysis to validate the effectiveness of our approach.

Lin Teng, Zihao Zhao, Jiawei Huang et al.

Automatic and accurate segmentation of brain MR images throughout the human lifespan into tissue and structure is crucial for understanding brain development and diagnosing diseases. However, challenges arise from the intricate variations in brain appearance due to rapid early brain development, aging, and disorders, compounded by the limited availability of manually-labeled datasets. In response, we present a two-step segmentation framework employing Knowledge-Guided Prompt Learning (KGPL) for brain MRI. Specifically, we first pre-train segmentation models on large-scale datasets with sub-optimal labels, followed by the incorporation of knowledge-driven embeddings learned from image-text alignment into the models. The introduction of knowledge-wise prompts captures semantic relationships between anatomical variability and biological processes, enabling models to learn structural feature embeddings across diverse age groups. Experimental findings demonstrate the superiority and robustness of our proposed method, particularly noticeable when employing Swin UNETR as the backbone. Our approach achieves average DSC values of 95.17% and 94.19% for brain tissue and structure segmentation, respectively. Our code is available at https://github.com/TL9792/KGPL.

Peng Xue, Jingyang Zhang, Lei Ma et al.

Image registration of liver dynamic contrast-enhanced computed tomography (DCE-CT) is crucial for diagnosis and image-guided surgical planning of liver cancer. However, intensity variations due to the flow of contrast agents combined with complex spatial motion induced by respiration brings great challenge to existing intensity-based registration methods. To address these problems, we propose a novel structure-aware registration method by incorporating structural information of related organs with segmentation-guided deep registration network. Existing segmentation-guided registration methods only focus on volumetric registration inside the paired organ segmentations, ignoring the inherent attributes of their anatomical structures. In addition, such paired organ segmentations are not always available in DCE-CT images due to the flow of contrast agents. Different from existing segmentation-guided registration methods, our proposed method extracts structural information in hierarchical geometric perspectives of line and surface. Then, according to the extracted structural information, structure-aware constraints are constructed and imposed on the forward and backward deformation field simultaneously. In this way, all available organ segmentations, including unpaired ones, can be fully utilized to avoid the side effect of contrast agent and preserve the topology of organs during registration. Extensive experiments on an in-house liver DCE-CT dataset and a public LiTS dataset show that our proposed method can achieve higher registration accuracy and preserve anatomical structure more effectively than state-of-the-art methods.

Yutong Zhang, Yi Pan, Tianyang Zhong et al.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Yitao Zhu, Zhenrong Shen, Zihao Zhao et al.

The common practice in developing computer-aided diagnosis (CAD) models based on transformer architectures usually involves fine-tuning from ImageNet pre-trained weights. However, with recent advances in large-scale pre-training and the practice of scaling laws, Vision Transformers (ViT) have become much larger and less accessible to medical imaging communities. Additionally, in real-world scenarios, the deployments of multiple CAD models can be troublesome due to problems such as limited storage space and time-consuming model switching. To address these challenges, we propose a new method MeLo (Medical image Low-rank adaptation), which enables the development of a single CAD model for multiple clinical tasks in a lightweight manner. It adopts low-rank adaptation instead of resource-demanding fine-tuning. By fixing the weight of ViT models and only adding small low-rank plug-ins, we achieve competitive results on various diagnosis tasks across different imaging modalities using only a few trainable parameters. Specifically, our proposed method achieves comparable performance to fully fine-tuned ViT models on four distinct medical imaging datasets using about 0.17% trainable parameters. Moreover, MeLo adds only about 0.5MB of storage space and allows for extremely fast model switching in deployment and inference. Our source code and pre-trained weights are available on our website (https://absterzhu.github.io/melo.github.io/).

Zhentao Liu, Yu Fang, Changjian Li et al.

Cone Beam Computed Tomography (CBCT) plays a vital role in clinical imaging. Traditional methods typically require hundreds of 2D X-ray projections to reconstruct a high-quality 3D CBCT image, leading to considerable radiation exposure. This has led to a growing interest in sparse-view CBCT reconstruction to reduce radiation doses. While recent advances, including deep learning and neural rendering algorithms, have made strides in this area, these methods either produce unsatisfactory results or suffer from time inefficiency of individual optimization. In this paper, we introduce a novel geometry-aware encoder-decoder framework to solve this problem. Our framework starts by encoding multi-view 2D features from various 2D X-ray projections with a 2D CNN encoder. Leveraging the geometry of CBCT scanning, it then back-projects the multi-view 2D features into the 3D space to formulate a comprehensive volumetric feature map, followed by a 3D CNN decoder to recover 3D CBCT image. Importantly, our approach respects the geometric relationship between 3D CBCT image and its 2D X-ray projections during feature back projection stage, and enjoys the prior knowledge learned from the data population. This ensures its adaptability in dealing with extremly sparse view inputs without individual training, such as scenarios with only 5 or 10 X-ray projections. Extensive evaluations on two simulated datasets and one real-world dataset demonstrate exceptional reconstruction quality and time efficiency of our method.

Lin Zhao, Xiao Chen, Eric Z. Chen et al.

Multi-contrast Magnetic Resonance Imaging (MRI) generates multiple medical images with rich and complementary information for routine clinical use; however, it suffers from a long acquisition time. Recent works for accelerating MRI, mainly designed for single contrast, may not be optimal for multi-contrast scenario since the inherent correlations among the multi-contrast images are not exploited. In addition, independent reconstruction of each contrast usually does not translate to optimal performance of downstream tasks. Motivated by these aspects, in this paper we design an end-to-end framework for accelerating multi-contrast MRI which simultaneously optimizes the entire MR imaging workflow including sampling, reconstruction and downstream tasks to achieve the best overall outcomes. The proposed framework consists of a sampling mask generator for each image contrast and a reconstructor exploiting the inter-contrast correlations with a recurrent structure which enables the information sharing in a holistic way. The sampling mask generator and the reconstructor are trained jointly across the multiple image contrasts. The acceleration ratio of each image contrast is also learnable and can be driven by a downstream task performance. We validate our approach on a multi-contrast brain dataset and a multi-contrast knee dataset. Experiments show that (1) our framework consistently outperforms the baselines designed for single contrast on both datasets; (2) our newly designed recurrent reconstruction network effectively improves the reconstruction quality for multi-contrast images; (3) the learnable acceleration ratio improves the downstream task performance significantly. Overall, this work has potentials to open up new avenues for optimizing the entire multi-contrast MR imaging workflow.

Chenyu Xue, Fan Wang, Yuanzhuo Zhu et al.

Deploying reliable deep learning techniques in interdisciplinary applications needs learned models to output accurate and (even more importantly) explainable predictions. Existing approaches typically explicate network outputs in a post-hoc fashion, under an implicit assumption that faithful explanations come from accurate predictions/classifications. We have an opposite claim that explanations boost (or even determine) classification. That is, end-to-end learning of explanation factors to augment discriminative representation extraction could be a more intuitive strategy to inversely assure fine-grained explainability, e.g., in those neuroimaging and neuroscience studies with high-dimensional data containing noisy, redundant, and task-irrelevant information. In this paper, we propose such an explainable geometric deep network dubbed as NeuroExplainer, with applications to uncover altered infant cortical development patterns associated with preterm birth. Given fundamental cortical attributes as network input, our NeuroExplainer adopts a hierarchical attention-decoding framework to learn fine-grained attentions and respective discriminative representations to accurately recognize preterm infants from term-born infants at term-equivalent age. NeuroExplainer learns the hierarchical attention-decoding modules under subject-level weak supervision coupled with targeted regularizers deduced from domain knowledge regarding brain development. These prior-guided constraints implicitly maximizes the explainability metrics (i.e., fidelity, sparsity, and stability) in network training, driving the learned network to output detailed explanations and accurate classifications. Experimental results on the public dHCP benchmark suggest that NeuroExplainer led to quantitatively reliable explanation results that are qualitatively consistent with representative neuroimaging studies.

Mianxin Liu, Jingyang Zhang, Yao Wang et al.

Brain disorders in the early and late life of humans potentially share pathological alterations in brain functions. However, the key evidence from neuroimaging data for pathological commonness remains unrevealed. To explore this hypothesis, we build a deep learning model, using multi-site functional magnetic resonance imaging data (N=4,410, 6 sites), for classifying 5 different brain disorders from healthy controls, with a set of common features. Our model achieves 62.6(1.9)% overall classification accuracy on data from the 6 investigated sites and detects a set of commonly affected functional subnetworks at different spatial scales, including default mode, executive control, visual, and limbic networks. In the deep-layer feature representation for individual data, we observe young and aging patients with disorders are continuously distributed, which is in line with the clinical concept of the "spectrum of disorders". The revealed spectrum underlying early- and late-life brain disorders promotes the understanding of disorder comorbidities in the lifespan.

Caiwen Jiang, Yuzhen Ding, Mi Jia et al.

Proton therapy offers superior organ-at-risk sparing but is highly sensitive to anatomical changes, making accurate deformable image registration (DIR) across longitudinal CT scans essential. Conventional DIR methods are often too slow for emerging online adaptive workflows, while existing deep learning-based approaches are primarily designed for generic benchmarks and underutilize clinically relevant information beyond images. To address this gap, we propose a clinically scalable coarse-to-fine deformable registration framework that integrates multimodal information from the proton radiotherapy workflow to accommodate diverse clinical scenarios. The model employs dual CNN-based encoders for hierarchical feature extraction and a transformer-based decoder to progressively refine deformation fields. Beyond CT intensities, clinically critical priors, including target and organ-at-risk contours, dose distributions, and treatment planning text, are incorporated through anatomy- and risk-guided attention, text-conditioned feature modulation, and foreground-aware optimization, enabling anatomically focused and clinically informed deformation estimation. We evaluate the proposed framework on a large-scale proton therapy DIR dataset comprising 1,222 paired planning and repeat CT scans across multiple anatomical regions and disease types. Extensive experiments demonstrate consistent improvements over state-of-the-art methods, enabling fast and robust clinically meaningful registration.

Lei Ma, Peng Xue, Yuning Gu et al.

In recent years, the demand for dental implants has surged, driven by their high success rates and esthetic advantages. However, accurate prediction of missing teeth for precise digital implant planning remains a challenge due to the intricate nature of dental structures and the variability in tooth loss patterns. This study presents a novel framework for accurate prediction of missing teeth in different patterns, facilitating digital implant planning. The proposed framework begins by estimating point-to-point correspondence among a dataset of dental mesh models reconstructed from CBCT images of healthy subjects. Subsequently, tooth dictionaries are constructed for each tooth type, encoding their position and shape information based on the established point-to-point correspondence. To predict missing teeth in a given dental mesh model, sparse coefficients are learned by sparsely representing adjacent teeth of the missing teeth using the corresponding tooth dictionaries. These coefficients are then applied to the dictionaries of the missing teeth to generate accurate predictions of their positions and shapes. The evaluation results on real subjects shows that our proposed framework achieves an average prediction error of 1.04mm for predictions of single missing tooth and an average prediction error of 1.33mm for the prediction of 14 missing teeth, which demonstrates its capability of accurately predicting missing teeth in various patterns. By accurately predicting missing teeth, dental professionals can improve the planning and placement of dental implants, leading to better esthetic and functional outcomes for patients undergoing dental implant procedures.