Predicting Infant Brain Connectivity with Federated Multi-Trajectory GNNs using Scarce Data

The understanding of the convoluted evolution of infant brain networks during the first postnatal year is pivotal for identifying the dynamics of early brain connectivity development. Existing deep learning solutions suffer from three major limitations. First, they cannot generalize to multi-trajectory prediction tasks, where each graph trajectory corresponds to a particular imaging modality or connectivity type (e.g., T1-w MRI). Second, existing models require extensive training datasets to achieve satisfactory performance which are often challenging to obtain. Third, they do not efficiently utilize incomplete time series data. To address these limitations, we introduce FedGmTE-Net++, a federated graph-based multi-trajectory evolution network. Using the power of federation, we aggregate local learnings among diverse hospitals with limited datasets. As a result, we enhance the performance of each hospital's local generative model, while preserving data privacy. The three key innovations of FedGmTE-Net++ are: (i) presenting the first federated learning framework specifically designed for brain multi-trajectory evolution prediction in a data-scarce environment, (ii) incorporating an auxiliary regularizer in the local objective function to exploit all the longitudinal brain connectivity within the evolution trajectory and maximize data utilization, (iii) introducing a two-step imputation process, comprising a preliminary KNN-based precompletion followed by an imputation refinement step that employs regressors to improve similarity scores and refine imputations. Our comprehensive experimental results showed the outperformance of FedGmTE-Net++ in brain multi-trajectory prediction from a single baseline graph in comparison with benchmark methods.

CLIP in Medical Imaging: A Comprehensive Survey

Contrastive Language-Image Pre-training (CLIP), a simple yet effective pre-training paradigm, successfully introduces text supervision to vision models. It has shown promising results across various tasks, attributable to its generalizability and interpretability. The use of CLIP has recently gained increasing interest in the medical imaging domain, serving both as a pre-training paradigm for aligning medical vision and language, and as a critical component in diverse clinical tasks. With the aim of facilitating a deeper understanding of this promising direction, this survey offers an in-depth exploration of the CLIP paradigm within the domain of medical imaging, regarding both refined CLIP pre-training and CLIP-driven applications. In this study, We (1) start with a brief introduction to the fundamentals of CLIP methodology. (2) Then, we investigate the adaptation of CLIP pre-training in the medical domain, focusing on how to optimize CLIP given characteristics of medical images and reports. (3) Furthermore, we explore the practical utilization of CLIP pre-trained models in various tasks, including classification, dense prediction, and cross-modal tasks. (4) Finally, we discuss existing limitations of CLIP in the context of medical imaging and propose forward-looking directions to address the demands of medical imaging domain. We expect that this comprehensive survey will provide researchers in the field of medical image analysis with a holistic understanding of the CLIP paradigm and its potential implications. The project page can be found on https://github.com/zhaozh10/Awesome-CLIP-in-Medical-Imaging.

Mining Gaze for Contrastive Learning toward Computer-Assisted Diagnosis

Obtaining large-scale radiology reports can be difficult for medical images due to various reasons, limiting the effectiveness of contrastive pre-training in the medical image domain and underscoring the need for alternative methods. In this paper, we propose eye-tracking as an alternative to text reports, as it allows for the passive collection of gaze signals without disturbing radiologist's routine diagnosis process. By tracking the gaze of radiologists as they read and diagnose medical images, we can understand their visual attention and clinical reasoning. When a radiologist has similar gazes for two medical images, it may indicate semantic similarity for diagnosis, and these images should be treated as positive pairs when pre-training a computer-assisted diagnosis (CAD) network through contrastive learning. Accordingly, we introduce the Medical contrastive Gaze Image Pre-training (McGIP) as a plug-and-play module for contrastive learning frameworks. McGIP uses radiologist's gaze to guide contrastive pre-training. We evaluate our method using two representative types of medical images and two common types of gaze data. The experimental results demonstrate the practicality of McGIP, indicating its high potential for various clinical scenarios and applications.

MARformer: An Efficient Metal Artifact Reduction Transformer for Dental CBCT Images

Cone Beam Computed Tomography (CBCT) plays a key role in dental diagnosis and surgery. However, the metal teeth implants could bring annoying metal artifacts during the CBCT imaging process, interfering diagnosis and downstream processing such as tooth segmentation. In this paper, we develop an efficient Transformer to perform metal artifacts reduction (MAR) from dental CBCT images. The proposed MAR Transformer (MARformer) reduces computation complexity in the multihead self-attention by a new Dimension-Reduced Self-Attention (DRSA) module, based on that the CBCT images have globally similar structure. A Patch-wise Perceptive Feed Forward Network (P2FFN) is also proposed to perceive local image information for fine-grained restoration. Experimental results on CBCT images with synthetic and real-world metal artifacts show that our MARformer is efficient and outperforms previous MAR methods and two restoration Transformers.

MeLo: Low-rank Adaptation is Better than Fine-tuning for Medical Image Diagnosis

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/).

3D Structure-guided Network for Tooth Alignment in 2D Photograph

Orthodontics focuses on rectifying misaligned teeth (i.e., malocclusions), affecting both masticatory function and aesthetics. However, orthodontic treatment often involves complex, lengthy procedures. As such, generating a 2D photograph depicting aligned teeth prior to orthodontic treatment is crucial for effective dentist-patient communication and, more importantly, for encouraging patients to accept orthodontic intervention. In this paper, we propose a 3D structure-guided tooth alignment network that takes 2D photographs as input (e.g., photos captured by smartphones) and aligns the teeth within the 2D image space to generate an orthodontic comparison photograph featuring aesthetically pleasing, aligned teeth. Notably, while the process operates within a 2D image space, our method employs 3D intra-oral scanning models collected in clinics to learn about orthodontic treatment, i.e., projecting the pre- and post-orthodontic 3D tooth structures onto 2D tooth contours, followed by a diffusion model to learn the mapping relationship. Ultimately, the aligned tooth contours are leveraged to guide the generation of a 2D photograph with aesthetically pleasing, aligned teeth and realistic textures. We evaluate our network on various facial photographs, demonstrating its exceptional performance and strong applicability within the orthodontic industry.

ChatRadio-Valuer: A Chat Large Language Model for Generalizable Radiology Report Generation Based on Multi-institution and Multi-system Data

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.

Radiology-Llama2: Best-in-Class Large Language Model for Radiology

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.

Contrastive Diffusion Model with Auxiliary Guidance for Coarse-to-Fine PET Reconstruction

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}.

Tissue Segmentation of Thick-Slice Fetal Brain MR Scans with Guidance from High-Quality Isotropic Volumes

Accurate tissue segmentation of thick-slice fetal brain magnetic resonance (MR) scans is crucial for both reconstruction of isotropic brain MR volumes and the quantification of fetal brain development. However, this task is challenging due to the use of thick-slice scans in clinically-acquired fetal brain data. To address this issue, we propose to leverage high-quality isotropic fetal brain MR volumes (and also their corresponding annotations) as guidance for segmentation of thick-slice scans. Due to existence of significant domain gap between high-quality isotropic volume (i.e., source data) and thick-slice scans (i.e., target data), we employ a domain adaptation technique to achieve the associated knowledge transfer (from high-quality <source> volumes to thick-slice <target> scans). Specifically, we first register the available high-quality isotropic fetal brain MR volumes across different gestational weeks to construct longitudinally-complete source data. To capture domain-invariant information, we then perform Fourier decomposition to extract image content and style codes. Finally, we propose a novel Cycle-Consistent Domain Adaptation Network (C2DA-Net) to efficiently transfer the knowledge learned from high-quality isotropic volumes for accurate tissue segmentation of thick-slice scans. Our C2DA-Net can fully utilize a small set of annotated isotropic volumes to guide tissue segmentation on unannotated thick-slice scans. Extensive experiments on a large-scale dataset of 372 clinically acquired thick-slice MR scans demonstrate that our C2DA-Net achieves much better performance than cutting-edge methods quantitatively and qualitatively.