Lipei Zhang

Yanteng Zhang, Qizhi Teng, Xiaohai He et al. · salesforce

Structural MRI and PET imaging play an important role in the diagnosis of Alzheimer's disease (AD), showing the morphological changes and glucose metabolism changes in the brain respectively. The manifestations in the brain image of some cognitive impairment patients are relatively inconspicuous, for example, it still has difficulties in achieving accurate diagnosis through sMRI in clinical practice. With the emergence of deep learning, convolutional neural network (CNN) has become a valuable method in AD-aided diagnosis, but some CNN methods cannot effectively learn the features of brain image, making the diagnosis of AD still presents some challenges. In this work, we propose an end-to-end 3D CNN framework for AD diagnosis based on ResNet, which integrates multi-layer features obtained under the effect of the attention mechanism to better capture subtle differences in brain images. The attention maps showed our model can focus on key brain regions related to the disease diagnosis. Our method was verified in ablation experiments with two modality images on 792 subjects from the ADNI database, where AD diagnostic accuracies of 89.71% and 91.18% were achieved based on sMRI and PET respectively, and also outperformed some state-of-the-art methods.

Yiran Wei, Xi Chen, Lei Zhu et al.

The isocitrate dehydrogenase (IDH) gene mutation is an essential biomarker for the diagnosis and prognosis of glioma. It is promising to better predict glioma genotype by integrating focal tumor image and geometric features with brain network features derived from MRI. Convolutions neural networks show reasonable performance in predicting IDH mutation, which, however, cannot learn from non-Euclidean data, e.g., geometric and network data. In this study, we propose a multi-modal learning framework using three separate encoders to extract features of focal tumor image, tumor geometrics and global brain networks. To mitigate the limited availability of diffusion MRI, we develop a self-supervised approach to generate brain networks from anatomical multi-sequence MRI. Moreover, to extract tumor-related features from the brain network, we design a hierarchical attention module for the brain network encoder. Further, we design a bi-level multi-modal contrastive loss to align the multi-modal features and tackle the domain gap at the focal tumor and global brain. Finally, we propose a weighted population graph to integrate the multi-modal features for genotype prediction. Experimental results on the testing set show that the proposed model outperforms the baseline deep learning models. The ablation experiments validate the performance of different components of the framework. The visualized interpretation corresponds to clinical knowledge with further validation. In conclusion, the proposed learning framework provides a novel approach for predicting the genotype of glioma.

Lipei Zhang, Yiran Wei, Ying Fu et al.

Whole slide images (WSI) provide valuable phenotypic information for histological assessment and malignancy grading of tumors. The WSI-based grading promises to provide rapid diagnostic support and facilitate digital health. Currently, the most commonly used WSIs are derived from formalin-fixed paraffin-embedded (FFPE) and Frozen section. The majority of automatic tumor grading models are developed based on FFPE sections, which could be affected by the artifacts introduced by tissue processing. The frozen section exists problems such as low quality that might influence training within single modality as well. To overcome this problem in a single modal training and achieve better multi-modal and discriminative representation disentanglement in brain tumor, we propose a mutual contrastive low-rank learning (MCL) scheme to integrate FFPE and frozen sections for glioma grading. We first design a mutual learning scheme to jointly optimize the model training based on FFPE and frozen sections. In this proposed scheme, we design a normalized modality contrastive loss (NMC-loss), which could promote to disentangle multi-modality complementary representation of FFPE and frozen sections from the same patient. To reduce intra-class variance, and increase inter-class margin at intra- and inter-patient levels, we conduct a low-rank (LR) loss. Our experiments show that the proposed scheme achieves better performance than the model trained based on each single modality or mixed modalities and even improves the feature extraction in classical attention-based multiple instances learning methods (MIL). The combination of NMC-loss and low-rank loss outperforms other typical contrastive loss functions.

Sergio Calvo-Ordonez, Chun-Wun Cheng, Jiahao Huang et al.

Diffusion Probabilistic Models stand as a critical tool in generative modelling, enabling the generation of complex data distributions. This family of generative models yields record-breaking performance in tasks such as image synthesis, video generation, and molecule design. Despite their capabilities, their efficiency, especially in the reverse process, remains a challenge due to slow convergence rates and high computational costs. In this paper, we introduce an approach that leverages continuous dynamical systems to design a novel denoising network for diffusion models that is more parameter-efficient, exhibits faster convergence, and demonstrates increased noise robustness. Experimenting with Denoising Diffusion Probabilistic Models (DDPMs), our framework operates with approximately a quarter of the parameters, and $\sim$ 30\% of the Floating Point Operations (FLOPs) compared to standard U-Nets in DDPMs. Furthermore, our model is notably faster in inference than the baseline when measured in fair and equal conditions. We also provide a mathematical intuition as to why our proposed reverse process is faster as well as a mathematical discussion of the empirical tradeoffs in the denoising downstream task. Finally, we argue that our method is compatible with existing performance enhancement techniques, enabling further improvements in efficiency, quality, and speed.

Yanqi Cheng, Lipei Zhang, Zhenda Shen et al.

The utilisation of Plug-and-Play (PnP) priors in inverse problems has become increasingly prominent in recent years. This preference is based on the mathematical equivalence between the general proximal operator and the regularised denoiser, facilitating the adaptation of various off-the-shelf denoiser priors to a wide range of inverse problems. However, existing PnP models predominantly rely on pre-trained denoisers using large datasets. In this work, we introduce Single-Shot PnP methods (SS-PnP), shifting the focus to solving inverse problems with minimal data. First, we integrate Single-Shot proximal denoisers into iterative methods, enabling training with single instances. Second, we propose implicit neural priors based on a novel function that preserves relevant frequencies to capture fine details while avoiding the issue of vanishing gradients. We demonstrate, through extensive numerical and visual experiments, that our method leads to better approximations.

Yanteng Zhang, Songheng Li, Zeyu Shen et al.

Large-scale brain imaging datasets provide unprecedented opportunities for developing domain foundation models through pretraining. However, unlike natural image datasets in computer vision, these neuroimaging data often exhibit high heterogeneity in quality, ranging from well-structured scans to severely distorted or incomplete brain volumes. This raises a fundamental question: can noise or low-quality scans contribute meaningfully to pretraining, or do they instead hinder model learning? In this study, we systematically explore the role of data quality level in pretraining and its impact on downstream tasks. Specifically, we perform pretraining on datasets with different quality levels and perform fine-tuning for brain age prediction on external cohorts. Our results show significant performance differences across quality levels, revealing both opportunities and limitations. We further discuss the gap between computer vision practices and clinical neuroimaging standards, emphasizing the necessity of domain-aware curation to ensure trusted and generalizable domain-specific foundation models.

Lipei Zhang, Aozhi Liu, Jing Xiao et al.

A number of methods based on deep learning have been applied to medical image segmentation and have achieved state-of-the-art performance. Due to the importance of chest x-ray data in studying COVID-19, there is a demand for state-of-the-art models capable of precisely segmenting soft tissue on the chest x-rays. The dataset for exploring best segmentation model is from Montgomery and Shenzhen hospital which had opened in 2014. The most famous technique is U-Net which has been used to many medical datasets including the Chest X-rays. However, most variant U-Nets mainly focus on extraction of contextual information and skip connections. There is still a large space for improving extraction of spatial features. In this paper, we propose a dual encoder fusion U-Net framework for Chest X-rays based on Inception Convolutional Neural Network with dilation, Densely Connected Recurrent Convolutional Neural Network, which is named DEFU-Net. The densely connected recurrent path extends the network deeper for facilitating contextual feature extraction. In order to increase the width of network and enrich representation of features, the inception blocks with dilation are adopted. The inception blocks can capture globally and locally spatial information from various receptive fields. At the same time, the two paths are fused by summing features, thus preserving the contextual and spatial information for decoding part. This multi-learning-scale model is benefiting in Chest X-ray dataset from two different manufacturers (Montgomery and Shenzhen hospital). The DEFU-Net achieves the better performance than basic U-Net, residual U-Net, BCDU-Net, R2U-Net and attention R2U-Net. This model has proved the feasibility for mixed dataset and approaches state-of-the-art. The source code for this proposed framework is public https://github.com/uceclz0/DEFU-Net.

Amer Essakine, Yanqi Cheng, Chun-Wun Cheng et al.

Implicit Neural Representations (INRs) have emerged as a paradigm in knowledge representation, offering exceptional flexibility and performance across a diverse range of applications. INRs leverage multilayer perceptrons (MLPs) to model data as continuous implicit functions, providing critical advantages such as resolution independence, memory efficiency, and generalisation beyond discretised data structures. Their ability to solve complex inverse problems makes them particularly effective for tasks including audio reconstruction, image representation, 3D object reconstruction, and high-dimensional data synthesis. This survey provides a comprehensive review of state-of-the-art INR methods, introducing a clear taxonomy that categorises them into four key areas: activation functions, position encoding, combined strategies, and network structure optimisation. We rigorously analyse their critical properties, such as full differentiability, smoothness, compactness, and adaptability to varying resolutions while also examining their strengths and limitations in addressing locality biases and capturing fine details. Our experimental comparison offers new insights into the trade-offs between different approaches, showcasing the capabilities and challenges of the latest INR techniques across various tasks. In addition to identifying areas where current methods excel, we highlight key limitations and potential avenues for improvement, such as developing more expressive activation functions, enhancing positional encoding mechanisms, and improving scalability for complex, high-dimensional data. This survey serves as a roadmap for researchers, offering practical guidance for future exploration in the field of INRs. We aim to foster new methodologies by outlining promising research directions for INRs and applications.

Zhenxuan Zhang, Lipei Zhang, Yanqi Cheng et al.

In motion-robust magnetic resonance imaging (MRI), slice-to-volume reconstruction is critical for recovering anatomically consistent 3D brain volumes from 2D slices, especially under accelerated acquisitions or patient motion. However, this task remains challenging due to hierarchical structural disruptions. It includes local detail loss from k-space undersampling, global structural aliasing caused by motion, and volumetric anisotropy. Therefore, we propose a progressive refinement implicit neural representation (PR-INR) framework. Our PR-INR unifies motion correction, structural refinement, and volumetric synthesis within a geometry-aware coordinate space. Specifically, a motion-aware diffusion module is first employed to generate coarse volumetric reconstructions that suppress motion artifacts and preserve global anatomical structures. Then, we introduce an implicit detail restoration module that performs residual refinement by aligning spatial coordinates with visual features. It corrects local structures and enhances boundary precision. Further, a voxel continuous-aware representation module represents the image as a continuous function over 3D coordinates. It enables accurate inter-slice completion and high-frequency detail recovery. We evaluate PR-INR on five public MRI datasets under various motion conditions (3% and 5% displacement), undersampling rates (4x and 8x) and slice resolutions (scale = 5). Experimental results demonstrate that PR-INR outperforms state-of-the-art methods in both quantitative reconstruction metrics and visual quality. It further shows generalization and robustness across diverse unseen domains.

Zhongying Deng, Haoyu Wang, Ziyan Huang et al.

Brain diseases, such as Alzheimer's disease and brain tumors, present profound challenges due to their complexity and societal impact. Recent advancements in brain foundation models have shown significant promise in addressing a range of brain-related tasks. However, current brain foundation models are limited by task and data homogeneity, restricted generalization beyond segmentation or classification, and inefficient adaptation to diverse clinical tasks. In this work, we propose SAM-Brain3D, a brain-specific foundation model trained on over 66,000 brain image-label pairs across 14 MRI sub-modalities, and Hypergraph Dynamic Adapter (HyDA), a lightweight adapter for efficient and effective downstream adaptation. SAM-Brain3D captures detailed brain-specific anatomical and modality priors for segmenting diverse brain targets and broader downstream tasks. HyDA leverages hypergraphs to fuse complementary multi-modal data and dynamically generate patient-specific convolutional kernels for multi-scale feature fusion and personalized patient-wise adaptation. Together, our framework excels across a broad spectrum of brain disease segmentation and classification tasks. Extensive experiments demonstrate that our method consistently outperforms existing state-of-the-art approaches, offering a new paradigm for brain disease analysis through multi-modal, multi-scale, and dynamic foundation modeling.

Lipei Zhang, Yanqi Cheng, Lihao Liu et al.

Recent advances in deep learning have significantly improved brain tumour segmentation techniques; however, the results still lack confidence and robustness as they solely consider image data without biophysical priors or pathological information. Integrating biophysics-informed regularisation is one effective way to change this situation, as it provides an prior regularisation for automated end-to-end learning. In this paper, we propose a novel approach that designs brain tumour growth Partial Differential Equation (PDE) models as a regularisation with deep learning, operational with any network model. Our method introduces tumour growth PDE models directly into the segmentation process, improving accuracy and robustness, especially in data-scarce scenarios. This system estimates tumour cell density using a periodic activation function. By effectively integrating this estimation with biophysical models, we achieve better capture of tumour characteristics. This approach not only aligns the segmentation closer to actual biological behaviour but also strengthens the model's performance under limited data conditions. We demonstrate the effectiveness of our framework through extensive experiments on the BraTS 2023 dataset, showcasing significant improvements in both precision and reliability of tumour segmentation.

Guanwen Qiu, Xiaobing Yu, Baolin Sun et al.

Using histopathological images to automatically classify cancer is a difficult task for accurately detecting cancer, especially to identify metastatic cancer in small image patches obtained from larger digital pathology scans. Computer diagnosis technology has attracted wide attention from researchers. In this paper, we propose a noval method which combines the deep learning algorithm in image classification, the DenseNet169 framework and Rectified Adam optimization algorithm. The connectivity pattern of DenseNet is direct connections from any layer to all consecutive layers, which can effectively improve the information flow between different layers. With the fact that RAdam is not easy to fall into a local optimal solution, and it can converge quickly in model training. The experimental results shows that our model achieves superior performance over the other classical convolutional neural networks approaches, such as Vgg19, Resnet34, Resnet50. In particular, the Auc-Roc score of our DenseNet169 model is 1.77% higher than Vgg19 model, and the Accuracy score is 1.50% higher. Moreover, we also study the relationship between loss value and batches processed during the training stage and validation stage, and obtain some important and interesting findings.

Aozhi Liu, Lipei Zhang, Yaqi Mei et al.

One of the challenges of the Optical Music Recognition task is to transcript the symbols of the camera-captured images into digital music notations. Previous end-to-end model which was developed as a Convolutional Recurrent Neural Network does not explore sufficient contextual information from full scales and there is still a large room for improvement. We propose an innovative framework that combines a block of Residual Recurrent Convolutional Neural Network with a recurrent Encoder-Decoder network to map a sequence of monophonic music symbols corresponding to the notations present in the image. The Residual Recurrent Convolutional block can improve the ability of the model to enrich the context information. The experiment results are benchmarked against a publicly available dataset called CAMERA-PRIMUS, which demonstrates that our approach surpass the state-of-the-art end-to-end method using Convolutional Recurrent Neural Network.