arXiv subjects

Lei Bi

Publications and source records attributed to Lei Bi.

At least 37 records · Page 2Linked to original sources

arXiv2024

Automatic Left Ventricular Cavity Segmentation via Deep Spatial Sequential Network in 4D Computed Tomography Studies

Automated segmentation of left ventricular cavity (LVC) in temporal cardiac image sequences (multiple time points) is a fundamental requirement for quantitative analysis of its structural and functional changes. Deep learning based methods for the segmentation of LVC are the state of the art; however, these methods are generally formulated to work on single time points, and fails to exploit the complementary information from the temporal image sequences that can aid in segmentation accuracy and consistency among the images across the time points. Furthermore, these segmentation methods perform poorly in segmenting the end-systole (ES) phase images, where the left ventricle deforms to the smallest irregular shape, and the boundary between the blood chamber and myocardium becomes inconspicuous. To overcome these limitations, we propose a new method to automatically segment temporal cardiac images where we introduce a spatial sequential (SS) network to learn the deformation and motion characteristics of the LVC in an unsupervised manner; these characteristics were then integrated with sequential context information derived from bi-directional learning (BL) where both chronological and reverse-chronological directions of the image sequence were used. Our experimental results on a cardiac computed tomography (CT) dataset demonstrated that our spatial-sequential network with bi-directional learning (SS-BL) method outperformed existing methods for LVC segmentation. Our method was also applied to MRI cardiac dataset and the results demonstrated the generalizability of our method.

eess.IV↗

arXiv2024

Hyper-Fusion Network for Semi-Automatic Segmentation of Skin Lesions

Automatic skin lesion segmentation methods based on fully convolutional networks (FCNs) are regarded as the state-of-the-art for accuracy. When there are, however, insufficient training data to cover all the variations in skin lesions, where lesions from different patients may have major differences in size/shape/texture, these methods failed to segment the lesions that have image characteristics, which are less common in the training datasets. FCN-based semi-automatic segmentation methods, which fuse user-inputs with high-level semantic image features derived from FCNs offer an ideal complement to overcome limitations of automatic segmentation methods. These semi-automatic methods rely on the automated state-of-the-art FCNs coupled with user-inputs for refinements, and therefore being able to tackle challenging skin lesions. However, there are a limited number of FCN-based semi-automatic segmentation methods and all these methods focused on early-fusion, where the first few convolutional layers are used to fuse image features and user-inputs and then derive fused image features for segmentation. For early-fusion based methods, because the user-input information can be lost after the first few convolutional layers, consequently, the user-input information will have limited guidance and constraint in segmenting the challenging skin lesions with inhomogeneous textures and fuzzy boundaries. Hence, in this work, we introduce a hyper-fusion network (HFN) to fuse the extracted user-inputs and image features over multiple stages. We separately extract complementary features which then allows for an iterative use of user-inputs along all the fusion stages to refine the segmentation. We evaluated our HFN on ISIC 2017, ISIC 2016 and PH2 datasets, and our results show that the HFN is more accurate and generalizable than the state-of-the-art methods.

cs.CV↗

arXiv2024

3DPX: Single Panoramic X-ray Analysis Guided by 3D Oral Structure Reconstruction

Panoramic X-ray (PX) is a prevalent modality in dentistry practice owing to its wide availability and low cost. However, as a 2D projection of a 3D structure, PX suffers from anatomical information loss and PX diagnosis is limited compared to that with 3D imaging modalities. 2D-to-3D reconstruction methods have been explored for the ability to synthesize the absent 3D anatomical information from 2D PX for use in PX image analysis. However, there are challenges in leveraging such 3D synthesized reconstructions. First, inferring 3D depth from 2D images remains a challenging task with limited accuracy. The second challenge is the joint analysis of 2D PX with its 3D synthesized counterpart, with the aim to maximize the 2D-3D synergy while minimizing the errors arising from the synthesized image. In this study, we propose a new method termed 3DPX - PX image analysis guided by 2D-to-3D reconstruction, to overcome these challenges. 3DPX consists of (i) a novel progressive reconstruction network to improve 2D-to-3D reconstruction and, (ii) a contrastive-guided bidirectional multimodality alignment module for 3D-guided 2D PX classification and segmentation tasks. The reconstruction network progressively reconstructs 3D images with knowledge imposed on the intermediate reconstructions at multiple pyramid levels and incorporates Multilayer Perceptrons to improve semantic understanding. The downstream networks leverage the reconstructed images as 3D anatomical guidance to the PX analysis through feature alignment, which increases the 2D-3D synergy with bidirectional feature projection and decease the impact of potential errors with contrastive guidance. Extensive experiments on two oral datasets involving 464 studies demonstrate that 3DPX outperforms the state-of-the-art methods in various tasks including 2D-to-3D reconstruction, PX classification and lesion segmentation.

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arXiv2024

3DPX: Progressive 2D-to-3D Oral Image Reconstruction with Hybrid MLP-CNN Networks

Panoramic X-ray (PX) is a prevalent modality in dental practice for its wide availability and low cost. However, as a 2D projection image, PX does not contain 3D anatomical information, and therefore has limited use in dental applications that can benefit from 3D information, e.g., tooth angular misa-lignment detection and classification. Reconstructing 3D structures directly from 2D PX has recently been explored to address limitations with existing methods primarily reliant on Convolutional Neural Networks (CNNs) for direct 2D-to-3D mapping. These methods, however, are unable to correctly infer depth-axis spatial information. In addition, they are limited by the in-trinsic locality of convolution operations, as the convolution kernels only capture the information of immediate neighborhood pixels. In this study, we propose a progressive hybrid Multilayer Perceptron (MLP)-CNN pyra-mid network (3DPX) for 2D-to-3D oral PX reconstruction. We introduce a progressive reconstruction strategy, where 3D images are progressively re-constructed in the 3DPX with guidance imposed on the intermediate recon-struction result at each pyramid level. Further, motivated by the recent ad-vancement of MLPs that show promise in capturing fine-grained long-range dependency, our 3DPX integrates MLPs and CNNs to improve the semantic understanding during reconstruction. Extensive experiments on two large datasets involving 464 studies demonstrate that our 3DPX outperforms state-of-the-art 2D-to-3D oral reconstruction methods, including standalone MLP and transformers, in reconstruction quality, and also im-proves the performance of downstream angular misalignment classification tasks.

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arXiv2024

Correlation-aware Coarse-to-fine MLPs for Deformable Medical Image Registration

Deformable image registration is a fundamental step for medical image analysis. Recently, transformers have been used for registration and outperformed Convolutional Neural Networks (CNNs). Transformers can capture long-range dependence among image features, which have been shown beneficial for registration. However, due to the high computation/memory loads of self-attention, transformers are typically used at downsampled feature resolutions and cannot capture fine-grained long-range dependence at the full image resolution. This limits deformable registration as it necessitates precise dense correspondence between each image pixel. Multi-layer Perceptrons (MLPs) without self-attention are efficient in computation/memory usage, enabling the feasibility of capturing fine-grained long-range dependence at full resolution. Nevertheless, MLPs have not been extensively explored for image registration and are lacking the consideration of inductive bias crucial for medical registration tasks. In this study, we propose the first correlation-aware MLP-based registration network (CorrMLP) for deformable medical image registration. Our CorrMLP introduces a correlation-aware multi-window MLP block in a novel coarse-to-fine registration architecture, which captures fine-grained multi-range dependence to perform correlation-aware coarse-to-fine registration. Extensive experiments with seven public medical datasets show that our CorrMLP outperforms state-of-the-art deformable registration methods.

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arXiv2024

Enhancing medical vision-language contrastive learning via inter-matching relation modelling

Medical image representations can be learned through medical vision-language contrastive learning (mVLCL) where medical imaging reports are used as weak supervision through image-text alignment. These learned image representations can be transferred to and benefit various downstream medical vision tasks such as disease classification and segmentation. Recent mVLCL methods attempt to align image sub-regions and the report keywords as local-matchings. However, these methods aggregate all local-matchings via simple pooling operations while ignoring the inherent relations between them. These methods therefore fail to reason between local-matchings that are semantically related, e.g., local-matchings that correspond to the disease word and the location word (semantic-relations), and also fail to differentiate such clinically important local-matchings from others that correspond to less meaningful words, e.g., conjunction words (importance-relations). Hence, we propose a mVLCL method that models the inter-matching relations between local-matchings via a relation-enhanced contrastive learning framework (RECLF). In RECLF, we introduce a semantic-relation reasoning module (SRM) and an importance-relation reasoning module (IRM) to enable more fine-grained report supervision for image representation learning. We evaluated our method using six public benchmark datasets on four downstream tasks, including segmentation, zero-shot classification, linear classification, and cross-modal retrieval. Our results demonstrated the superiority of our RECLF over the state-of-the-art mVLCL methods with consistent improvements across single-modal and cross-modal tasks. These results suggest that our RECLF, by modelling the inter-matching relations, can learn improved medical image representations with better generalization capabilities.

cs.CV↗

arXiv2023

Full-resolution MLPs Empower Medical Dense Prediction

Dense prediction is a fundamental requirement for many medical vision tasks such as medical image restoration, registration, and segmentation. The most popular vision model, Convolutional Neural Networks (CNNs), has reached bottlenecks due to the intrinsic locality of convolution operations. Recently, transformers have been widely adopted for dense prediction for their capability to capture long-range visual dependence. However, due to the high computational complexity and large memory consumption of self-attention operations, transformers are usually used at downsampled feature resolutions. Such usage cannot effectively leverage the tissue-level textural information available only at the full image resolution. This textural information is crucial for medical dense prediction as it can differentiate the subtle human anatomy in medical images. In this study, we hypothesize that Multi-layer Perceptrons (MLPs) are superior alternatives to transformers in medical dense prediction where tissue-level details dominate the performance, as MLPs enable long-range dependence at the full image resolution. To validate our hypothesis, we develop a full-resolution hierarchical MLP framework that uses MLPs beginning from the full image resolution. We evaluate this framework with various MLP blocks on a wide range of medical dense prediction tasks including restoration, registration, and segmentation. Extensive experiments on six public well-benchmarked datasets show that, by simply using MLPs at full resolution, our framework outperforms its CNN and transformer counterparts and achieves state-of-the-art performance on various medical dense prediction tasks.

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arXiv2023

Self-Supervised Multi-Modality Learning for Multi-Label Skin Lesion Classification

The clinical diagnosis of skin lesion involves the analysis of dermoscopic and clinical modalities. Dermoscopic images provide a detailed view of the surface structures whereas clinical images offer a complementary macroscopic information. The visual diagnosis of melanoma is also based on seven-point checklist which involves identifying different visual attributes. Recently, supervised learning approaches such as convolutional neural networks (CNNs) have shown great performances using both dermoscopic and clinical modalities (Multi-modality). The seven different visual attributes in the checklist are also used to further improve the the diagnosis. The performances of these approaches, however, are still reliant on the availability of large-scaled labeled data. The acquisition of annotated dataset is an expensive and time-consuming task, more so with annotating multi-attributes. To overcome this limitation, we propose a self-supervised learning (SSL) algorithm for multi-modality skin lesion classification. Our algorithm enables the multi-modality learning by maximizing the similarities between paired dermoscopic and clinical images from different views. In addition, we generate surrogate pseudo-multi-labels that represent seven attributes via clustering analysis. We also propose a label-relation-aware module to refine each pseudo-label embedding and capture the interrelationships between pseudo-multi-labels. We validated the effectiveness of our algorithm using well-benchmarked seven-point skin lesion dataset. Our results show that our algorithm achieved better performances than other state-of-the-art SSL counterparts.

cs.CV↗

arXiv2023

PET Synthesis via Self-supervised Adaptive Residual Estimation Generative Adversarial Network

Positron emission tomography (PET) is a widely used, highly sensitive molecular imaging in clinical diagnosis. There is interest in reducing the radiation exposure from PET but also maintaining adequate image quality. Recent methods using convolutional neural networks (CNNs) to generate synthesized high-quality PET images from low-dose counterparts have been reported to be state-of-the-art for low-to-high image recovery methods. However, these methods are prone to exhibiting discrepancies in texture and structure between synthesized and real images. Furthermore, the distribution shift between low-dose PET and standard PET has not been fully investigated. To address these issues, we developed a self-supervised adaptive residual estimation generative adversarial network (SS-AEGAN). We introduce (1) An adaptive residual estimation mapping mechanism, AE-Net, designed to dynamically rectify the preliminary synthesized PET images by taking the residual map between the low-dose PET and synthesized output as the input, and (2) A self-supervised pre-training strategy to enhance the feature representation of the coarse generator. Our experiments with a public benchmark dataset of total-body PET images show that SS-AEGAN consistently outperformed the state-of-the-art synthesis methods with various dose reduction factors.

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arXiv2023

AutoFuse: Automatic Fusion Networks for Deformable Medical Image Registration

Deformable image registration aims to find a dense non-linear spatial correspondence between a pair of images, which is a crucial step for many medical tasks such as tumor growth monitoring and population analysis. Recently, Deep Neural Networks (DNNs) have been widely recognized for their ability to perform fast end-to-end registration. However, DNN-based registration needs to explore the spatial information of each image and fuse this information to characterize spatial correspondence. This raises an essential question: what is the optimal fusion strategy to characterize spatial correspondence? Existing fusion strategies (e.g., early fusion, late fusion) were empirically designed to fuse information by manually defined prior knowledge, which inevitably constrains the registration performance within the limits of empirical designs. In this study, we depart from existing empirically-designed fusion strategies and develop a data-driven fusion strategy for deformable image registration. To achieve this, we propose an Automatic Fusion network (AutoFuse) that provides flexibility to fuse information at many potential locations within the network. A Fusion Gate (FG) module is also proposed to control how to fuse information at each potential network location based on training data. Our AutoFuse can automatically optimize its fusion strategy during training and can be generalizable to both unsupervised registration (without any labels) and semi-supervised registration (with weak labels provided for partial training data). Extensive experiments on two well-benchmarked medical registration tasks (inter- and intra-patient registration) with eight public datasets show that our AutoFuse outperforms state-of-the-art unsupervised and semi-supervised registration methods.

eess.IV↗

arXiv2023

Merging-Diverging Hybrid Transformer Networks for Survival Prediction in Head and Neck Cancer

Survival prediction is crucial for cancer patients as it provides early prognostic information for treatment planning. Recently, deep survival models based on deep learning and medical images have shown promising performance for survival prediction. However, existing deep survival models are not well developed in utilizing multi-modality images (e.g., PET-CT) and in extracting region-specific information (e.g., the prognostic information in Primary Tumor (PT) and Metastatic Lymph Node (MLN) regions). In view of this, we propose a merging-diverging learning framework for survival prediction from multi-modality images. This framework has a merging encoder to fuse multi-modality information and a diverging decoder to extract region-specific information. In the merging encoder, we propose a Hybrid Parallel Cross-Attention (HPCA) block to effectively fuse multi-modality features via parallel convolutional layers and cross-attention transformers. In the diverging decoder, we propose a Region-specific Attention Gate (RAG) block to screen out the features related to lesion regions. Our framework is demonstrated on survival prediction from PET-CT images in Head and Neck (H&N) cancer, by designing an X-shape merging-diverging hybrid transformer network (named XSurv). Our XSurv combines the complementary information in PET and CT images and extracts the region-specific prognostic information in PT and MLN regions. Extensive experiments on the public dataset of HEad and neCK TumOR segmentation and outcome prediction challenge (HECKTOR 2022) demonstrate that our XSurv outperforms state-of-the-art survival prediction methods.

eess.IV↗

arXiv2023

Non-iterative Coarse-to-fine Transformer Networks for Joint Affine and Deformable Image Registration

Image registration is a fundamental requirement for medical image analysis. Deep registration methods based on deep learning have been widely recognized for their capabilities to perform fast end-to-end registration. Many deep registration methods achieved state-of-the-art performance by performing coarse-to-fine registration, where multiple registration steps were iterated with cascaded networks. Recently, Non-Iterative Coarse-to-finE (NICE) registration methods have been proposed to perform coarse-to-fine registration in a single network and showed advantages in both registration accuracy and runtime. However, existing NICE registration methods mainly focus on deformable registration, while affine registration, a common prerequisite, is still reliant on time-consuming traditional optimization-based methods or extra affine registration networks. In addition, existing NICE registration methods are limited by the intrinsic locality of convolution operations. Transformers may address this limitation for their capabilities to capture long-range dependency, but the benefits of using transformers for NICE registration have not been explored. In this study, we propose a Non-Iterative Coarse-to-finE Transformer network (NICE-Trans) for image registration. Our NICE-Trans is the first deep registration method that (i) performs joint affine and deformable coarse-to-fine registration within a single network, and (ii) embeds transformers into a NICE registration framework to model long-range relevance between images. Extensive experiments with seven public datasets show that our NICE-Trans outperforms state-of-the-art registration methods on both registration accuracy and runtime.

cs.CV↗

arXiv2023

AdaMSS: Adaptive Multi-Modality Segmentation-to-Survival Learning for Survival Outcome Prediction from PET/CT Images

Survival prediction is a major concern for cancer management. Deep survival models based on deep learning have been widely adopted to perform end-to-end survival prediction from medical images. Recent deep survival models achieved promising performance by jointly performing tumor segmentation with survival prediction, where the models were guided to extract tumor-related information through Multi-Task Learning (MTL). However, these deep survival models have difficulties in exploring out-of-tumor prognostic information. In addition, existing deep survival models are unable to effectively leverage multi-modality images. Empirically-designed fusion strategies were commonly adopted to fuse multi-modality information via task-specific manually-designed networks, thus limiting the adaptability to different scenarios. In this study, we propose an Adaptive Multi-modality Segmentation-to-Survival model (AdaMSS) for survival prediction from PET/CT images. Instead of adopting MTL, we propose a novel Segmentation-to-Survival Learning (SSL) strategy, where our AdaMSS is trained for tumor segmentation and survival prediction sequentially in two stages. This strategy enables the AdaMSS to focus on tumor regions in the first stage and gradually expand its focus to include other prognosis-related regions in the second stage. We also propose a data-driven strategy to fuse multi-modality information, which realizes adaptive optimization of fusion strategies based on training data during training. With the SSL and data-driven fusion strategies, our AdaMSS is designed as an adaptive model that can self-adapt its focus regions and fusion strategy for different training stages. Extensive experiments with two large clinical datasets show that our AdaMSS outperforms state-of-the-art survival prediction methods.

eess.IV↗

arXiv2023

CG-3DSRGAN: A classification guided 3D generative adversarial network for image quality recovery from low-dose PET images

Positron emission tomography (PET) is the most sensitive molecular imaging modality routinely applied in our modern healthcare. High radioactivity caused by the injected tracer dose is a major concern in PET imaging and limits its clinical applications. However, reducing the dose leads to inadequate image quality for diagnostic practice. Motivated by the need to produce high quality images with minimum low-dose, Convolutional Neural Networks (CNNs) based methods have been developed for high quality PET synthesis from its low-dose counterparts. Previous CNNs-based studies usually directly map low-dose PET into features space without consideration of different dose reduction level. In this study, a novel approach named CG-3DSRGAN (Classification-Guided Generative Adversarial Network with Super Resolution Refinement) is presented. Specifically, a multi-tasking coarse generator, guided by a classification head, allows for a more comprehensive understanding of the noise-level features present in the low-dose data, resulting in improved image synthesis. Moreover, to recover spatial details of standard PET, an auxiliary super resolution network - Contextual-Net - is proposed as a second-stage training to narrow the gap between coarse prediction and standard PET. We compared our method to the state-of-the-art methods on whole-body PET with different dose reduction factors (DRFs). Experiments demonstrate our method can outperform others on all DRF.

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arXiv2022

Brain Tumor Sequence Registration with Non-iterative Coarse-to-fine Networks and Dual Deep Supervision

In this study, we focus on brain tumor sequence registration between pre-operative and follow-up Magnetic Resonance Imaging (MRI) scans of brain glioma patients, in the context of Brain Tumor Sequence Registration challenge (BraTS-Reg 2022). Brain tumor registration is a fundamental requirement in brain image analysis for quantifying tumor changes. This is a challenging task due to large deformations and missing correspondences between pre-operative and follow-up scans. For this task, we adopt our recently proposed Non-Iterative Coarse-to-finE registration Networks (NICE-Net) - a deep learning-based method for coarse-to-fine registering images with large deformations. To overcome missing correspondences, we extend the NICE-Net by introducing dual deep supervision, where a deep self-supervised loss based on image similarity and a deep weakly-supervised loss based on manually annotated landmarks are deeply embedded into the NICE-Net. At the BraTS-Reg 2022, our method achieved a competitive result on the validation set (mean absolute error: 3.387) and placed 4th in the final testing phase (Score: 0.3544).

cs.CV↗

arXiv2022

Radiomics-enhanced Deep Multi-task Learning for Outcome Prediction in Head and Neck Cancer

Outcome prediction is crucial for head and neck cancer patients as it can provide prognostic information for early treatment planning. Radiomics methods have been widely used for outcome prediction from medical images. However, these methods are limited by their reliance on intractable manual segmentation of tumor regions. Recently, deep learning methods have been proposed to perform end-to-end outcome prediction so as to remove the reliance on manual segmentation. Unfortunately, without segmentation masks, these methods will take the whole image as input, such that makes them difficult to focus on tumor regions and potentially unable to fully leverage the prognostic information within the tumor regions. In this study, we propose a radiomics-enhanced deep multi-task framework for outcome prediction from PET/CT images, in the context of HEad and neCK TumOR segmentation and outcome prediction challenge (HECKTOR 2022). In our framework, our novelty is to incorporate radiomics as an enhancement to our recently proposed Deep Multi-task Survival model (DeepMTS). The DeepMTS jointly learns to predict the survival risk scores of patients and the segmentation masks of tumor regions. Radiomics features are extracted from the predicted tumor regions and combined with the predicted survival risk scores for final outcome prediction, through which the prognostic information in tumor regions can be further leveraged. Our method achieved a C-index of 0.681 on the testing set, placing the 2nd on the leaderboard with only 0.00068 lower in C-index than the 1st place.

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arXiv2022

Hyper-Connected Transformer Network for Multi-Modality PET-CT Segmentation

[18F]-Fluorodeoxyglucose (FDG) positron emission tomography - computed tomography (PET-CT) has become the imaging modality of choice for diagnosing many cancers. Co-learning complementary PET-CT imaging features is a fundamental requirement for automatic tumor segmentation and for developing computer aided cancer diagnosis systems. In this study, we propose a hyper-connected transformer (HCT) network that integrates a transformer network (TN) with a hyper connected fusion for multi-modality PET-CT images. The TN was leveraged for its ability to provide global dependencies in image feature learning, which was achieved by using image patch embeddings with a self-attention mechanism to capture image-wide contextual information. We extended the single-modality definition of TN with multiple TN based branches to separately extract image features. We also introduced a hyper connected fusion to fuse the contextual and complementary image features across multiple transformers in an iterative manner. Our results with two clinical datasets show that HCT achieved better performance in segmentation accuracy when compared to the existing methods.

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arXiv2022

Topology-enabled highly efficient beam combination

Beam combination with high efficiency is desirable to overcome the power limit of single electromagnetic sources, enabling long-distance optical communication and high-power laser. The efficiency of coherent beam combination is severely limited by the phase correlation between different input light beams. Here, we theoretically proposed and experimentally demonstrated a new mechanism for beam combining, the topology-enabled beam combination (TEBC), from multiple spatial channels with high efficiency based on a unidirectional topological edge state. We show that the topologically protected power orthogonal excitation arising from both the unidirectional edge states and the energy conservation ensures -0.31dB (93%) efficiency experimentally for a multi-channel combination of coherent microwaves at 9.1-9.3 GHz. Moreover, we demonstrate broadband, phase insensitive, and high-efficiency beam combination using the TEBC mechanism with one single topological photonic crystal device, which significantly reduces the device footprint and design complexity. Our scheme transcends the limits of the required phase correlations in the scenario of coherent beam combination and the number of combined channels in the scenario of incoherent beam combination.

physics.optics↗