Pathology-genomic fusion via biologically informed cross-modality graph learning for survival analysis

The diagnosis and prognosis of cancer are typically based on multi-modal clinical data, including histology images and genomic data, due to the complex pathogenesis and high heterogeneity. Despite the advancements in digital pathology and high-throughput genome sequencing, establishing effective multi-modal fusion models for survival prediction and revealing the potential association between histopathology and transcriptomics remains challenging. In this paper, we propose Pathology-Genome Heterogeneous Graph (PGHG) that integrates whole slide images (WSI) and bulk RNA-Seq expression data with heterogeneous graph neural network for cancer survival analysis. The PGHG consists of biological knowledge-guided representation learning network and pathology-genome heterogeneous graph. The representation learning network utilizes the biological prior knowledge of intra-modal and inter-modal data associations to guide the feature extraction. The node features of each modality are updated through attention-based graph learning strategy. Unimodal features and bi-modal fused features are extracted via attention pooling module and then used for survival prediction. We evaluate the model on low-grade gliomas, glioblastoma, and kidney renal papillary cell carcinoma datasets from the Cancer Genome Atlas (TCGA) and the First Affiliated Hospital of Zhengzhou University (FAHZU). Extensive experimental results demonstrate that the proposed method outperforms both unimodal and other multi-modal fusion models. For demonstrating the model interpretability, we also visualize the attention heatmap of pathological images and utilize integrated gradient algorithm to identify important tissue structure, biological pathways and key genes.

Swin-UMamba: Mamba-based UNet with ImageNet-based pretraining

Accurate medical image segmentation demands the integration of multi-scale information, spanning from local features to global dependencies. However, it is challenging for existing methods to model long-range global information, where convolutional neural networks (CNNs) are constrained by their local receptive fields, and vision transformers (ViTs) suffer from high quadratic complexity of their attention mechanism. Recently, Mamba-based models have gained great attention for their impressive ability in long sequence modeling. Several studies have demonstrated that these models can outperform popular vision models in various tasks, offering higher accuracy, lower memory consumption, and less computational burden. However, existing Mamba-based models are mostly trained from scratch and do not explore the power of pretraining, which has been proven to be quite effective for data-efficient medical image analysis. This paper introduces a novel Mamba-based model, Swin-UMamba, designed specifically for medical image segmentation tasks, leveraging the advantages of ImageNet-based pretraining. Our experimental results reveal the vital role of ImageNet-based training in enhancing the performance of Mamba-based models. Swin-UMamba demonstrates superior performance with a large margin compared to CNNs, ViTs, and latest Mamba-based models. Notably, on AbdomenMRI, Encoscopy, and Microscopy datasets, Swin-UMamba outperforms its closest counterpart U-Mamba by an average score of 3.58%. The code and models of Swin-UMamba are publicly available at: https://github.com/JiarunLiu/Swin-UMamba

Improving Medical Report Generation with Adapter Tuning and Knowledge Enhancement in Vision-Language Foundation Models

Medical report generation demands automatic creation of coherent and precise descriptions for medical images. However, the scarcity of labelled medical image-report pairs poses formidable challenges in developing large-scale neural networks capable of harnessing the potential of artificial intelligence, exemplified by large language models. This study builds upon the state-of-the-art vision-language pre-training and fine-tuning approach, BLIP-2, to customize general large-scale foundation models. Integrating adapter tuning and a medical knowledge enhancement loss, our model significantly improves accuracy and coherence. Validation on the dataset of ImageCLEFmedical 2023 demonstrates our model's prowess, achieving the best-averaged results against several state-of-the-art methods. Significant improvements in ROUGE and CIDEr underscore our method's efficacy, highlighting promising outcomes for the rapid medical-domain adaptation of the vision-language foundation models in addressing challenges posed by data scarcity.

Score-based Diffusion Models With Self-supervised Learning For Accelerated 3D Multi-contrast Cardiac Magnetic Resonance Imaging

Long scan time significantly hinders the widespread applications of three-dimensional multi-contrast cardiac magnetic resonance (3D-MC-CMR) imaging. This study aims to accelerate 3D-MC-CMR acquisition by a novel method based on score-based diffusion models with self-supervised learning. Specifically, we first establish a mapping between the undersampled k-space measurements and the MR images, utilizing a self-supervised Bayesian reconstruction network. Secondly, we develop a joint score-based diffusion model on 3D-MC-CMR images to capture their inherent distribution. The 3D-MC-CMR images are finally reconstructed using the conditioned Langenvin Markov chain Monte Carlo sampling. This approach enables accurate reconstruction without fully sampled training data. Its performance was tested on the dataset acquired by a 3D joint myocardial T1 and T1rho mapping sequence. The T1 and T1rho maps were estimated via a dictionary matching method from the reconstructed images. Experimental results show that the proposed method outperforms traditional compressed sensing and existing self-supervised deep learning MRI reconstruction methods. It also achieves high quality T1 and T1rho parametric maps close to the reference maps obtained by traditional mapping sequences, even at a high acceleration rate of 14.

Model-driven CT reconstruction algorithm for nano-resolution X-ray phase contrast imaging

The limited imaging performance of low-density objects in a zone plate based nano-resolution hard X-ray computed tomography (CT) system can be significantly improved by accessing the phase information. To do so, a grating-based Lau interferometer needs to be integrated. However, the nano-resolution phase contrast CT, denoted as nPCT, reconstructed from such an interferometer system may suffer resolution loss due to the strong signal diffraction. Aimed at performing accurate nPCT image reconstruction directly from these diffracted projections, a new model-driven nPCT image reconstruction algorithm is developed. First, the diffraction procedure is mathematically modeled into a matrix B, from which the projections without signal splitting can be generated invertedly. Second, a penalized weighed least-square model with total variation (PWLS-TV) is employed to denoise these projections. Finally, nPCT images with high resolution and high accuracy are reconstructed using the filtered-back-projection (FBP) method. Numerical simulations demonstrate that this algorithm is able to deal with diffracted projections having any splitting distances. Interestingly, results reveal that nPCT images with higher signal-to-noise-ratio (SNR) can be reconstructed from projections with larger signal splittings. In conclusion, a novel model-driven nPCT image reconstruction algorithm with high accuracy and robustness is verified for the Lau interferometer based hard X-ray nPCT imaging system.

Self-Supervised Federated Learning for Fast MR Imaging

Federated learning (FL) based magnetic resonance (MR) image reconstruction can facilitate learning valuable priors from multi-site institutions without violating patient's privacy for accelerating MR imaging. However, existing methods rely on fully sampled data for collaborative training of the model. The client that only possesses undersampled data can neither participate in FL nor benefit from other clients. Furthermore, heterogeneous data distributions hinder FL from training an effective deep learning reconstruction model and thus cause performance degradation. To address these issues, we propose a Self-Supervised Federated Learning method (SSFedMRI). SSFedMRI explores the physics-based contrastive reconstruction networks in each client to realize cross-site collaborative training in the absence of fully sampled data. Furthermore, a personalized soft update scheme is designed to simultaneously capture the global shared representations among different centers and maintain the specific data distribution of each client. The proposed method is evaluated on four datasets and compared to the latest state-of-the-art approaches. Experimental results demonstrate that SSFedMRI possesses strong capability in reconstructing accurate MR images both visually and quantitatively on both in-distribution and out-of-distribution datasets.

Model-based Federated Learning for Accurate MR Image Reconstruction from Undersampled k-space Data

Deep learning-based methods have achieved encouraging performances in the field of magnetic resonance (MR) image reconstruction. Nevertheless, to properly learn a powerful and robust model, these methods generally require large quantities of data, the collection of which from multiple centers may cause ethical and data privacy violation issues. Lately, federated learning has served as a promising solution to exploit multi-center data while getting rid of the data transfer between institutions. However, high heterogeneity exists in the data from different centers, and existing federated learning methods tend to use average aggregation methods to combine the client's information, which limits the performance and generalization capability of the trained models. In this paper, we propose a Model-based Federated learning framework (ModFed). ModFed has three major contributions: 1) Different from the existing data-driven federated learning methods, model-driven neural networks are designed to relieve each client's dependency on large data; 2) An adaptive dynamic aggregation scheme is proposed to address the data heterogeneity issue and improve the generalization capability and robustness the trained neural network models; 3) A spatial Laplacian attention mechanism and a personalized client-side loss regularization are introduced to capture the detailed information for accurate image reconstruction. ModFed is evaluated on three in-vivo datasets. Experimental results show that ModFed has strong capability in improving image reconstruction quality and enforcing model generalization capability when compared to the other five state-of-the-art federated learning approaches. Codes will be made available at https://github.com/ternencewu123/ModFed.

SPIRiT-Diffusion: Self-Consistency Driven Diffusion Model for Accelerated MRI

Diffusion models are a leading method for image generation and have been successfully applied in magnetic resonance imaging (MRI) reconstruction. Current diffusion-based reconstruction methods rely on coil sensitivity maps (CSM) to reconstruct multi-coil data. However, it is difficult to accurately estimate CSMs in practice use, resulting in degradation of the reconstruction quality. To address this issue, we propose a self-consistency-driven diffusion model inspired by the iterative self-consistent parallel imaging (SPIRiT), namely SPIRiT-Diffusion. Specifically, the iterative solver of the self-consistent term in SPIRiT is utilized to design a novel stochastic differential equation (SDE) for diffusion process. Then $\textit{k}$-space data can be interpolated directly during the reverse diffusion process, instead of using CSM to separate and combine individual coil images. This method indicates that the optimization model can be used to design SDE in diffusion models, driving the diffusion process strongly conforming with the physics involved in the optimization model, dubbed model-driven diffusion. The proposed SPIRiT-Diffusion method was evaluated on a 3D joint Intracranial and Carotid Vessel Wall imaging dataset. The results demonstrate that it outperforms the CSM-based reconstruction methods, and achieves high reconstruction quality at a high acceleration rate of 10.

SPIRiT-Diffusion: SPIRiT-driven Score-Based Generative Modeling for Vessel Wall imaging

Diffusion model is the most advanced method in image generation and has been successfully applied to MRI reconstruction. However, the existing methods do not consider the characteristics of multi-coil acquisition of MRI data. Therefore, we give a new diffusion model, called SPIRiT-Diffusion, based on the SPIRiT iterative reconstruction algorithm. Specifically, SPIRiT-Diffusion characterizes the prior distribution of coil-by-coil images by score matching and characterizes the k-space redundant prior between coils based on self-consistency. With sufficient prior constraint utilized, we achieve superior reconstruction results on the joint Intracranial and Carotid Vessel Wall imaging dataset.

Iterative Data Refinement for Self-Supervised MR Image Reconstruction

Magnetic Resonance Imaging (MRI) has become an important technique in the clinic for the visualization, detection, and diagnosis of various diseases. However, one bottleneck limitation of MRI is the relatively slow data acquisition process. Fast MRI based on k-space undersampling and high-quality image reconstruction has been widely utilized, and many deep learning-based methods have been developed in recent years. Although promising results have been achieved, most existing methods require fully-sampled reference data for training the deep learning models. Unfortunately, fully-sampled MRI data are difficult if not impossible to obtain in real-world applications. To address this issue, we propose a data refinement framework for self-supervised MR image reconstruction. Specifically, we first analyze the reason of the performance gap between self-supervised and supervised methods and identify that the bias in the training datasets between the two is one major factor. Then, we design an effective self-supervised training data refinement method to reduce this data bias. With the data refinement, an enhanced self-supervised MR image reconstruction framework is developed to prompt accurate MR imaging. We evaluate our method on an in-vivo MRI dataset. Experimental results show that without utilizing any fully sampled MRI data, our self-supervised framework possesses strong capabilities in capturing image details and structures at high acceleration factors.