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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., Comment: accepted by MICCAI 2024

Remote physiological measurement (RPM) is an essential tool for healthcare monitoring as it enables the measurement of physiological signs, e.g., heart rate, in a remote setting via physical wearables. Recently, with facial videos, we have seen rapid advancements in video-based RPMs. However, adopting facial videos for RPM in the clinical setting largely depends on the accuracy and robustness (work across patient populations). Fortunately, the capability of the state-of-the-art transformer architecture in general (natural) video understanding has resulted in marked improvements and has been translated to facial understanding, including RPM. However, existing RPM methods usually need RPM-specific modules, e.g., temporal difference convolution and handcrafted feature maps. Although these customized modules can increase accuracy, they are not demonstrated for their robustness across datasets. Further, due to their customization of the transformer architecture, they cannot use the advancements made in general video transformers (GVT). In this study, we interrogate the GVT architecture and empirically analyze how the training designs, i.e., data pre-processing and network configurations, affect the model performance applied to RPM. Based on the structure of video transformers, we propose to configure its spatiotemporal hierarchy to align with the dense temporal information needed in RPM for signal feature extraction. We define several practical guidelines and gradually adapt GVTs for RPM without introducing RPM-specific modules. Our experiments demonstrate favorable results to existing RPM-specific module counterparts. We conducted extensive experiments with five datasets using intra-dataset and cross-dataset settings. We highlight that the proposed guidelines GVT2RPM can be generalized to any video transformers and is robust to various datasets., Comment: Code is available at https://github.com/Dylan-H-Wang/facial-ai

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., Comment: Accepted at CVPR2024 as Oral Presentation && Best Paper Candidate

With increasing reliance on medical imaging in clinical practices, automated report generation from medical images is in great demand. Existing report generation methods typically adopt an encoder-decoder deep learning framework to build a uni-directional image-to-report mapping. However, such a framework ignores the bi-directional mutual associations between images and reports, thus incurring difficulties in associating the intrinsic medical meanings between them. Recent generative representation learning methods have demonstrated the benefits of dual-modal learning from both image and text modalities. However, these methods exhibit two major drawbacks for medical report generation: 1) they tend to capture morphological information and have difficulties in capturing subtle pathological semantic information, and 2) they predict masked text rely on both unmasked images and text, inevitably degrading performance when inference is based solely on images. In this study, we propose a new report generation framework with dual-modal dynamic traceback learning (DTrace) to overcome the two identified drawbacks and enable dual-modal learning for medical report generation. To achieve this, our DTrace introduces a traceback mechanism to control the semantic validity of generated content via self-assessment. Further, our DTrace introduces a dynamic learning strategy to adapt to various proportions of image and text input, enabling report generation without reliance on textual input during inference. Extensive experiments on two well-benchmarked datasets (IU-Xray and MIMIC-CXR) show that our DTrace outperforms state-of-the-art medical report generation methods.

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 four public benchmark datasets on four downstream tasks, including segmentation, zero-shot classification, supervised 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., Comment: 11 pages, 5 figures. Under review

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.

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., Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

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., Comment: Under Review

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., Comment: Early Accepted at International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023)

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., Comment: Accepted at International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023)

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., Comment: Under Review

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.

Supervised deep learning methods have achieved considerable success in medical image analysis, owing to the availability of large-scale and well-annotated datasets. However, creating such datasets for whole slide images (WSIs) in histopathology is a challenging task due to their gigapixel size. In recent years, self-supervised learning (SSL) has emerged as an alternative solution to reduce the annotation overheads in WSIs, as it does not require labels for training. These SSL approaches, however, are not designed for handling multi-resolution WSIs, which limits their performance in learning discriminative image features. In this paper, we propose a Dual-branch SSL Framework for WSI tumour segmentation (DSF-WSI) that can effectively learn image features from multi-resolution WSIs. Our DSF-WSI connected two branches and jointly learnt low and high resolution WSIs in a self-supervised manner. Moreover, we introduced a novel Context-Target Fusion Module (CTFM) and a masked jigsaw pretext task to align the learnt multi-resolution features. Furthermore, we designed a Dense SimSiam Learning (DSL) strategy to maximise the similarity of different views of WSIs, enabling the learnt representations to be more efficient and discriminative. We evaluated our method using two public datasets on breast and liver cancer segmentation tasks. The experiment results demonstrated that our DSF-WSI can effectively extract robust and efficient representations, which we validated through subsequent fine-tuning and semi-supervised settings. Our proposed method achieved better accuracy than other state-of-the-art approaches. Code is available at https://github.com/Dylan-H-Wang/dsf-wsi.

Over the last decade, supervised deep learning on manually annotated big data has been progressing significantly on computer vision tasks. But the application of deep learning in medical image analysis was limited by the scarcity of high-quality annotated medical imaging data. An emerging solution is self-supervised learning (SSL), among which contrastive SSL is the most successful approach to rivalling or outperforming supervised learning. This review investigates several state-of-the-art contrastive SSL algorithms originally on natural images as well as their adaptations for medical images, and concludes by discussing recent advances, current limitations, and future directions in applying contrastive SSL in the medical domain., Comment: Article links: https://link.springer.com/article/10.1007/s11633-022-1406-4

Motion artifacts compromise the quality of magnetic resonance imaging (MRI) and pose challenges to achieving diagnostic outcomes and image-guided therapies. In recent years, supervised deep learning approaches have emerged as successful solutions for motion artifact reduction (MAR). One disadvantage of these methods is their dependency on acquiring paired sets of motion artifact-corrupted (MA-corrupted) and motion artifact-free (MA-free) MR images for training purposes. Obtaining such image pairs is difficult and therefore limits the application of supervised training. In this paper, we propose a novel UNsupervised Abnormality Extraction Network (UNAEN) to alleviate this problem. Our network is capable of working with unpaired MA-corrupted and MA-free images. It converts the MA-corrupted images to MA-reduced images by extracting abnormalities from the MA-corrupted images using a proposed artifact extractor, which intercepts the residual artifact maps from the MA-corrupted MR images explicitly, and a reconstructor to restore the original input from the MA-reduced images. The performance of UNAEN was assessed by experimenting with various publicly available MRI datasets and comparing them with state-of-the-art methods. The quantitative evaluation demonstrates the superiority of UNAEN over alternative MAR methods and visually exhibits fewer residual artifacts. Our results substantiate the potential of UNAEN as a promising solution applicable in real-world clinical environments, with the capability to enhance diagnostic accuracy and facilitate image-guided therapies. Our codes are publicly available at https://github.com/YuSheng-Zhou/UNAEN., Comment: Accepted by IEEE Journal of Biomedical and Health Informatics

Prostate cancer (PCa) is one of the most prevalent cancers in men and many people around the world die from clinically significant PCa (csPCa). Early diagnosis of csPCa in bi-parametric MRI (bpMRI), which is non-invasive, cost-effective, and more efficient compared to multiparametric MRI (mpMRI), can contribute to precision care for PCa. The rapid rise in artificial intelligence (AI) algorithms are enabling unprecedented improvements in providing decision support systems that can aid in csPCa diagnosis and understanding. However, existing state of the art AI algorithms which are based on deep learning technology are often limited to 2D images that fails to capture inter-slice correlations in 3D volumetric images. The use of 3D convolutional neural networks (CNNs) partly overcomes this limitation, but it does not adapt to the anisotropy of images, resulting in sub-optimal semantic representation and poor generalization. Furthermore, due to the limitation of the amount of labelled data of bpMRI and the difficulty of labelling, existing CNNs are built on relatively small datasets, leading to a poor performance. To address the limitations identified above, we propose a new Zonal-aware Self-supervised Mesh Network (Z-SSMNet) that adaptatively fuses multiple 2D, 2.5D and 3D CNNs to effectively balance representation for sparse inter-slice information and dense intra-slice information in bpMRI. A self-supervised learning (SSL) technique is further introduced to pre-train our network using unlabelled data to learn the generalizable image features. Furthermore, we constrained our network to understand the zonal specific domain knowledge to improve the diagnosis precision of csPCa. Experiments on the PI-CAI Challenge dataset demonstrate our proposed method achieves better performance for csPCa detection and diagnosis in bpMRI., Comment: 8 pages, 1 figure, PI-CAI challenge

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)., Comment: Brain Tumor Sequence Registration challenge (BraTS-Reg 2022)

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., Comment: HEad and neCK TumOR segmentation and outcome prediction challenge (HECKTOR 2022)

[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., Comment: EMBC 2023

Multi-modality Fluorodeoxyglucose (FDG) positron emission tomography / computed tomography (PET/CT) has been routinely used in the assessment of common cancers, such as lung cancer, lymphoma, and melanoma. This is mainly attributed to the fact that PET/CT combines the high sensitivity for tumor detection of PET and anatomical information from CT. In PET/CT image assessment, automatic tumor segmentation is an important step, and in recent years, deep learning based methods have become the state-of-the-art. Unfortunately, existing methods tend to over-segment the tumor regions and include regions such as the normal high uptake organs, inflammation, and other infections. In this study, we introduce a false positive reduction network to overcome this limitation. We firstly introduced a self-supervised pre-trained global segmentation module to coarsely delineate the candidate tumor regions using a self-supervised pre-trained encoder. The candidate tumor regions were then refined by removing false positives via a local refinement module. Our experiments with the MICCAI 2022 Automated Lesion Segmentation in Whole-Body FDG-PET/CT (AutoPET) challenge dataset showed that our method achieved a dice score of 0.9324 with the preliminary testing data and was ranked 1st place in dice on the leaderboard. Our method was also ranked in the top 7 methods on the final testing data, the final ranking will be announced during the 2022 MICCAI AutoPET workshop. Our code is available at: https://github.com/YigePeng/AutoPET_False_Positive_Reduction., Comment: Pre-print paper for 2022 MICCAI AutoPET Challenge

Transfer function (TF) plays a key role for the generation of direct volume rendering (DVR), by enabling accurate identification of structures of interest (SOIs) interactively as well as ensuring appropriate visibility of them. Attempts at mitigating the repetitive manual process of TF design have led to approaches that make use of a knowledge database consisting of pre-designed TFs by domain experts. In these approaches, a user navigates the knowledge database to find the most suitable pre-designed TF for their input volume to visualize the SOIs. Although these approaches potentially reduce the workload to generate the TFs, they, however, require manual TF navigation of the knowledge database, as well as the likely fine tuning of the selected TF to suit the input. In this work, we propose a TF design approach where we introduce a new content-based retrieval (CBR) to automatically navigate the knowledge database. Instead of pre-designed TFs, our knowledge database contains image volumes with SOI labels. Given an input image volume, our CBR approach retrieves relevant image volumes (with SOI labels) from the knowledge database; the retrieved labels are then used to generate and optimize TFs of the input. This approach does not need any manual TF navigation and fine tuning. For improving SOI retrieval performance, we propose a two-stage CBR scheme to enable the use of local intensity and regional deep image feature representations in a complementary manner. We demonstrate the capabilities of our approach with comparison to a conventional CBR approach in visualization, where an intensity profile matching algorithm is used, and also with potential use-cases in medical image volume visualization where DVR plays an indispensable role for different clinical usages., Comment: submitted to Computer Graphics Forum for review

Deformable image registration is a crucial step in medical image analysis for finding a non-linear spatial transformation between a pair of fixed and moving images. Deep registration methods based on Convolutional Neural Networks (CNNs) have been widely used as they can perform image registration in a fast and end-to-end manner. However, these methods usually have limited performance for image pairs with large deformations. Recently, iterative deep registration methods have been used to alleviate this limitation, where the transformations are iteratively learned in a coarse-to-fine manner. However, iterative methods inevitably prolong the registration runtime, and tend to learn separate image features for each iteration, which hinders the features from being leveraged to facilitate the registration at later iterations. In this study, we propose a Non-Iterative Coarse-to-finE registration Network (NICE-Net) for deformable image registration. In the NICE-Net, we propose: (i) a Single-pass Deep Cumulative Learning (SDCL) decoder that can cumulatively learn coarse-to-fine transformations within a single pass (iteration) of the network, and (ii) a Selectively-propagated Feature Learning (SFL) encoder that can learn common image features for the whole coarse-to-fine registration process and selectively propagate the features as needed. Extensive experiments on six public datasets of 3D brain Magnetic Resonance Imaging (MRI) show that our proposed NICE-Net can outperform state-of-the-art iterative deep registration methods while only requiring similar runtime to non-iterative methods., Comment: Accepted at International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022)

High-resolution (HR) magnetic resonance imaging is critical in aiding doctors in their diagnoses and image-guided treatments. However, acquiring HR images can be time-consuming and costly. Consequently, deep learning-based super-resolution reconstruction (SRR) has emerged as a promising solution for generating super-resolution (SR) images from low-resolution (LR) images. Unfortunately, training such neural networks requires aligned authentic HR and LR image pairs, which are challenging to obtain due to patient movements during and between image acquisitions. While rigid movements of hard tissues can be corrected with image registration, aligning deformed soft tissues is complex, making it impractical to train neural networks with authentic HR and LR image pairs. Previous studies have focused on SRR using authentic HR images and down-sampled synthetic LR images. However, the difference in degradation representations between synthetic and authentic LR images suppresses the quality of SR images reconstructed from authentic LR images. To address this issue, we propose a novel Unsupervised Degradation Adaptation Network (UDEAN). Our network consists of a degradation learning network and an SRR network. The degradation learning network downsamples the HR images using the degradation representation learned from the misaligned or unpaired LR images. The SRR network then learns the mapping from the down-sampled HR images to the original ones. Experimental results show that our method outperforms state-of-the-art networks and is a promising solution to the challenges in clinical settings., Comment: Accepted by IEEE Transactions on Artificial Intelligence

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks., Comment: Accepted @ ACL2022 Workshop: The First Workshop on Efficient Benchmarking in NLP

Mixed reality head-mounted displays (mxdR-HMD) have the potential to visualize volumetric medical imaging data in holograms to provide a true sense of volumetric depth. An effective user interface, however, has yet to be thoroughly studied. Tangible user interfaces (TUIs) enable a tactile interaction with a hologram through an object. The object has physical properties indicating how it might be used with multiple degrees-of-freedom. We propose a TUI using a planar object (PO) for the holographic medical volume visualization and exploration. We refer to it as mxdR hologram slicer (mxdR-HS). Users can slice the hologram to examine particular regions of interest (ROIs) and intermix complementary data and annotations. The mxdR-HS introduces a novel real-time ad-hoc marker-less PO tracking method that works with any PO where corners are visible. The aim of mxdR-HS is to maintain minimum computational latency while preserving practical tracking accuracy to enable seamless TUI integration in the commercial mxdR-HMD, which has limited computational resources. We implemented the mxdR-HS on a commercial Microsoft HoloLens with a built-in depth camera. Our experimental results showed our mxdR-HS had a superior computational latency but marginally lower tracking accuracy than two marker-based tracking methods and resulted in enhanced computational latency and tracking accuracy than 10 marker-less tracking methods. Our mxdR-HS, in a medical environment, can be suggested as a visual guide to display complex volumetric medical imaging data., Comment: 17 pages

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.

Motion estimation is a fundamental step in dynamic medical image processing for the assessment of target organ anatomy and function. However, existing image-based motion estimation methods, which optimize the motion field by evaluating the local image similarity, are prone to produce implausible estimation, especially in the presence of large motion. In this study, we provide a novel motion estimation framework of Dense-Sparse-Dense (DSD), which comprises two stages. In the first stage, we process the raw dense image to extract sparse landmarks to represent the target organ anatomical topology and discard the redundant information that is unnecessary for motion estimation. For this purpose, we introduce an unsupervised 3D landmark detection network to extract spatially sparse but representative landmarks for the target organ motion estimation. In the second stage, we derive the sparse motion displacement from the extracted sparse landmarks of two images of different time points. Then, we present a motion reconstruction network to construct the motion field by projecting the sparse landmarks displacement back into the dense image domain. Furthermore, we employ the estimated motion field from our two-stage DSD framework as initialization and boost the motion estimation quality in light-weight yet effective iterative optimization. We evaluate our method on two dynamic medical imaging tasks to model cardiac motion and lung respiratory motion, respectively. Our method has produced superior motion estimation accuracy compared to existing comparative methods. Besides, the extensive experimental results demonstrate that our solution can extract well representative anatomical landmarks without any requirement of manual annotation. Our code is publicly available online., Comment: accepted by IEEE Transactions on Cybernetics

Nasopharyngeal Carcinoma (NPC) is a malignant epithelial cancer arising from the nasopharynx. Survival prediction is a major concern for NPC patients, as it provides early prognostic information to plan treatments. Recently, deep survival models based on deep learning have demonstrated the potential to outperform traditional radiomics-based survival prediction models. Deep survival models usually use image patches covering the whole target regions (e.g., nasopharynx for NPC) or containing only segmented tumor regions as the input. However, the models using the whole target regions will also include non-relevant background information, while the models using segmented tumor regions will disregard potentially prognostic information existing out of primary tumors (e.g., local lymph node metastasis and adjacent tissue invasion). In this study, we propose a 3D end-to-end Deep Multi-Task Survival model (DeepMTS) for joint survival prediction and tumor segmentation in advanced NPC from pretreatment PET/CT. Our novelty is the introduction of a hard-sharing segmentation backbone to guide the extraction of local features related to the primary tumors, which reduces the interference from non-relevant background information. In addition, we also introduce a cascaded survival network to capture the prognostic information existing out of primary tumors and further leverage the global tumor information (e.g., tumor size, shape, and locations) derived from the segmentation backbone. Our experiments with two clinical datasets demonstrate that our DeepMTS can consistently outperform traditional radiomics-based survival prediction models and existing deep survival models., Comment: Accepted at IEEE Journal of Biomedical and Health Informatics (JBHI)

Recent advances in supervised deep learning methods are enabling remote measurements of photoplethysmography-based physiological signals using facial videos. The performance of these supervised methods, however, are dependent on the availability of large labelled data. Contrastive learning as a self-supervised method has recently achieved state-of-the-art performances in learning representative data features by maximising mutual information between different augmented views. However, existing data augmentation techniques for contrastive learning are not designed to learn physiological signals from videos and often fail when there are complicated noise and subtle and periodic colour or shape variations between video frames. To address these problems, we present a novel self-supervised spatiotemporal learning framework for remote physiological signal representation learning, where there is a lack of labelled training data. Firstly, we propose a landmark-based spatial augmentation that splits the face into several informative parts based on the Shafer dichromatic reflection model to characterise subtle skin colour fluctuations. We also formulate a sparsity-based temporal augmentation exploiting Nyquist-Shannon sampling theorem to effectively capture periodic temporal changes by modelling physiological signal features. Furthermore, we introduce a constrained spatiotemporal loss which generates pseudo-labels for augmented video clips. It is used to regulate the training process and handle complicated noise. We evaluated our framework on 3 public datasets and demonstrated superior performances than other self-supervised methods and achieved competitive accuracy compared to the state-of-the-art supervised methods., Comment: Accepted as AAAI22 paper. Code: https://github.com/Dylan-H-Wang/SLF-RPM

The segmentation of medical images is a fundamental step in automated clinical decision support systems. Existing medical image segmentation methods based on supervised deep learning, however, remain problematic because of their reliance on large amounts of labelled training data. Although medical imaging data repositories continue to expand, there has not been a commensurate increase in the amount of annotated data. Hence, we propose a new spatial guided self-supervised clustering network (SGSCN) for medical image segmentation, where we introduce multiple loss functions designed to aid in grouping image pixels that are spatially connected and have similar feature representations. It iteratively learns feature representations and clustering assignment of each pixel in an end-to-end fashion from a single image. We also propose a context-based consistency loss that better delineates the shape and boundaries of image regions. It enforces all the pixels belonging to a cluster to be spatially close to the cluster centre. We evaluated our method on 2 public medical image datasets and compared it to existing conventional and self-supervised clustering methods. Experimental results show that our method was most accurate for medical image segmentation., Comment: Accepted at Medical Image Computing and Computer Assisted Interventions (MICCAI) 2021

The availability of biomedical text data and advances in natural language processing (NLP) have made new applications in biomedical NLP possible. Language models trained or fine tuned using domain specific corpora can outperform general models, but work to date in biomedical NLP has been limited in terms of corpora and tasks. We present BioALBERT, a domain-specific adaptation of A Lite Bidirectional Encoder Representations from Transformers (ALBERT), trained on biomedical (PubMed and PubMed Central) and clinical (MIMIC-III) corpora and fine tuned for 6 different tasks across 20 benchmark datasets. Experiments show that BioALBERT outperforms the state of the art on named entity recognition (+11.09% BLURB score improvement), relation extraction (+0.80% BLURB score), sentence similarity (+1.05% BLURB score), document classification (+0.62% F1-score), and question answering (+2.83% BLURB score). It represents a new state of the art in 17 out of 20 benchmark datasets. By making BioALBERT models and data available, our aim is to help the biomedical NLP community avoid computational costs of training and establish a new set of baselines for future efforts across a broad range of biomedical NLP tasks.

Vaccines are an important public health measure, but vaccine hesitancy and refusal can create clusters of low vaccine coverage and reduce the effectiveness of vaccination programs. Social media provides an opportunity to estimate emerging risks to vaccine acceptance by including geographical location and detailing vaccine-related concerns. Methods for classifying social media posts, such as vaccine-related tweets, use language models (LMs) trained on general domain text. However, challenges to measuring vaccine sentiment at scale arise from the absence of tonal stress and gestural cues and may not always have additional information about the user, e.g., past tweets or social connections. Another challenge in LMs is the lack of commonsense knowledge that are apparent in users metadata, i.e., emoticons, positive and negative words etc. In this study, to classify vaccine sentiment tweets with limited information, we present a novel end-to-end framework consisting of interconnected components that use domain-specific LM trained on vaccine-related tweets and models commonsense knowledge into a bidirectional gated recurrent network (CK-BiGRU) with context-aware attention. We further leverage syntactical, user metadata and sentiment information to capture the sentiment of a tweet. We experimented using two popular vaccine-related Twitter datasets and demonstrate that our proposed approach outperforms state-of-the-art models in identifying pro-vaccine, anti-vaccine and neutral tweets., Comment: Accepted in International Joint Conference on Neural Networks (IJCNN) 2021

Sequential whole-body 18F-Fluorodeoxyglucose (FDG) positron emission tomography (PET) scans are regarded as the imaging modality of choice for the assessment of treatment response in the lymphomas because they detect treatment response when there may not be changes on anatomical imaging. Any computerized analysis of lymphomas in whole-body PET requires automatic segmentation of the studies so that sites of disease can be quantitatively monitored over time. State-of-the-art PET image segmentation methods are based on convolutional neural networks (CNNs) given their ability to leverage annotated datasets to derive high-level features about the disease process. Such methods, however, focus on PET images from a single time-point and discard information from other scans or are targeted towards specific organs and cannot cater for the multiple structures in whole-body PET images. In this study, we propose a spatio-temporal 'dual-stream' neural network (ST-DSNN) to segment sequential whole-body PET scans. Our ST-DSNN learns and accumulates image features from the PET images done over time. The accumulated image features are used to enhance the organs / structures that are consistent over time to allow easier identification of sites of active lymphoma. Our results show that our method outperforms the state-of-the-art PET image segmentation methods., Comment: 16 pages

Distant metastases (DM) refer to the dissemination of tumors, usually, beyond the organ where the tumor originated. They are the leading cause of death in patients with soft-tissue sarcomas (STSs). Positron emission tomography-computed tomography (PET-CT) is regarded as the imaging modality of choice for the management of STSs. It is difficult to determine from imaging studies which STS patients will develop metastases. 'Radiomics' refers to the extraction and analysis of quantitative features from medical images and it has been employed to help identify such tumors. The state-of-the-art in radiomics is based on convolutional neural networks (CNNs). Most CNNs are designed for single-modality imaging data (CT or PET alone) and do not exploit the information embedded in PET-CT where there is a combination of an anatomical and functional imaging modality. Furthermore, most radiomic methods rely on manual input from imaging specialists for tumor delineation, definition and selection of radiomic features. This approach, however, may not be scalable to tumors with complex boundaries and where there are multiple other sites of disease. We outline a new 3D CNN to help predict DM in STS patients from PET-CT data. The 3D CNN uses a constrained feature learning module and a hierarchical multi-modality feature learning module that leverages the complementary information from the modalities to focus on semantically important regions. Our results on a public PET-CT dataset of STS patients show that multi-modal information improves the ability to identify those patients who develop DM. Further our method outperformed all other related state-of-the-art methods., Comment: Under Review