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

To obtain high-quality positron emission tomography (PET) scans while reducing radiation exposure to the human body, various approaches have been proposed to reconstruct standard-dose PET (SPET) images from low-dose PET (LPET) images. One widely adopted technique is the generative adversarial networks (GANs), yet recently, diffusion probabilistic models (DPMs) have emerged as a compelling alternative due to their improved sample quality and higher log-likelihood scores compared to GANs. Despite this, DPMs suffer from two major drawbacks in real clinical settings, i.e., the computationally expensive sampling process and the insufficient preservation of correspondence between the conditioning LPET image and the reconstructed PET (RPET) image. To address the above limitations, this paper presents a coarse-to-fine PET reconstruction framework that consists of a coarse prediction module (CPM) and an iterative refinement module (IRM). The CPM generates a coarse PET image via a deterministic process, and the IRM samples the residual iteratively. By delegating most of the computational overhead to the CPM, the overall sampling speed of our method can be significantly improved. Furthermore, two additional strategies, i.e., an auxiliary guidance strategy and a contrastive diffusion strategy, are proposed and integrated into the reconstruction process, which can enhance the correspondence between the LPET image and the RPET image, further improving clinical reliability. Extensive experiments on two human brain PET datasets demonstrate that our method outperforms the state-of-the-art PET reconstruction methods. The source code is available at \url{https://github.com/Show-han/PET-Reconstruction}.Comment: Accepted and presented in MICCAI 2023. To be published in Proceeding

A Review on Low-Dose Emission Tomography Post-Reconstruction Denoising with Neural Network Approaches.

Low-dose emission tomography (ET) plays a crucial role in medical imaging, enabling the acquisition of functional information for various biological processes while minimizing the patient dose. However, the inherent randomness in the photon counting process is a source of noise which is amplified in low-dose ET. This review article provides an overview of existing post-processing techniques, with an emphasis on deep neural network (NN) approaches. Furthermore, we explore future directions in the field of NN-based low-dose ET. This comprehensive examination sheds light on the potential of deep learning in enhancing the quality and resolution of low-dose ET images, ultimately advancing the field of medical imaging

A Review on Low-Dose Emission Tomography Post-Reconstruction Denoising with Neural Network Approaches

Low-dose emission tomography (ET) plays a crucial role in medical imaging, enabling the acquisition of functional information for various biological processes while minimizing the patient dose. However, the inherent randomness in the photon counting process is a source of noise which is amplified in low-dose ET. This review article provides an overview of existing post-processing techniques, with an emphasis on deep neural network (NN) approaches. Furthermore, we explore future directions in the field of NN-based low-dose ET. This comprehensive examination sheds light on the potential of deep learning in enhancing the quality and resolution of low-dose ET images, ultimately advancing the field of medical imaging.Comment: 16 pages, 6 figure

Data synthesis and adversarial networks: A review and meta-analysis in cancer imaging

Despite technological and medical advances, the detection, interpretation, and treatment of cancer based on imaging data continue to pose significant challenges. These include inter-observer variability, class imbalance, dataset shifts, inter- and intra-tumour heterogeneity, malignancy determination, and treatment effect uncertainty. Given the recent advancements in image synthesis, Generative Adversarial Networks (GANs), and adversarial training, we assess the potential of these technologies to address a number of key challenges of cancer imaging. We categorise these challenges into (a) data scarcity and imbalance, (b) data access and privacy, (c) data annotation and segmentation, (d) cancer detection and diagnosis, and (e) tumour profiling, treatment planning and monitoring. Based on our analysis of 164 publications that apply adversarial training techniques in the context of cancer imaging, we highlight multiple underexplored solutions with research potential. We further contribute the Synthesis Study Trustworthiness Test (SynTRUST), a meta-analysis framework for assessing the validation rigour of medical image synthesis studies. SynTRUST is based on 26 concrete measures of thoroughness, reproducibility, usefulness, scalability, and tenability. Based on SynTRUST, we analyse 16 of the most promising cancer imaging challenge solutions and observe a high validation rigour in general, but also several desirable improvements. With this work, we strive to bridge the gap between the needs of the clinical cancer imaging community and the current and prospective research on data synthesis and adversarial networks in the artificial intelligence community

Locality and compositionality in representation learning for complex visual tasks

L'utilisation d'architectures neuronales profondes associée à des innovations spécifiques telles que les méthodes adversarielles, l’entraînement préalable sur de grands ensembles de données et l'estimation de l'information mutuelle a permis, ces dernières années, de progresser rapidement dans de nombreuses tâches de vision par ordinateur complexes telles que la classification d'images de catégories préalablement inconnues (apprentissage zéro-coups), la génération de scènes ou la classification multimodale. Malgré ces progrès, il n’est pas certain que les méthodes actuelles d’apprentissage de représentations suffiront à atteindre une performance équivalente au niveau humain sur des tâches visuelles arbitraires et, de fait, cela pose des questions quant à la direction de la recherche future. Dans cette thèse, nous nous concentrerons sur deux aspects des représentations qui semblent nécessaires pour atteindre de bonnes performances en aval pour l'apprentissage des représentations : la localité et la compositionalité. La localité peut être comprise comme la capacité d'une représentation à retenir des informations locales. Ceci sera pertinent dans de nombreux cas, et bénéficiera particulièrement à la vision informatique, domaine dans lequel les images naturelles comportent intrinsèquement des informations locales, par exemple des parties pertinentes d’une image, des objets multiples présents dans une scène... D'autre part, une représentation compositionnelle peut être comprise comme une représentation qui résulte d'une combinaison de parties plus simples. Les réseaux neuronaux convolutionnels sont intrinsèquement compositionnels, et de nombreuses images complexes peuvent être considérées comme la composition de sous-composantes pertinentes : les objets et attributs individuels dans une scène, les attributs sémantiques dans l'apprentissage zéro-coups en sont deux exemples. Nous pensons que ces deux propriétés détiennent la clé pour concevoir de meilleures méthodes d'apprentissage de représentations. Dans cette thèse, nous présentons trois articles traitant de la localité et/ou de la compositionnalité, et de leur application à l'apprentissage de représentations pour des tâches visuelles complexes. Dans le premier article, nous introduisons des méthodes de mesure de la localité et de la compositionnalité pour les représentations d'images, et nous démontrons que les représentations locales et compositionnelles sont plus performantes dans l'apprentissage zéro-coups. Nous utilisons également ces deux notions comme base pour concevoir un nouvel algorithme d'apprentissage des représentations qui atteint des performances de pointe dans notre cadre expérimental, une variante de l'apprentissage "zéro-coups" plus difficile où les informations externes, par exemple un pré-entraînement sur d'autres ensembles de données d'images, ne sont pas autorisées. Dans le deuxième article, nous montrons qu'en encourageant un générateur à conserver des informations locales au niveau de l'objet, à l'aide d'un module dit de similarité de graphes de scène, nous pouvons améliorer les performances de génération de scènes. Ce modèle met également en évidence l'importance de la composition, car de nombreux composants fonctionnent individuellement sur chaque objet présent. Pour démontrer pleinement la portée de notre approche, nous effectuons une analyse détaillée et proposons un nouveau cadre pour évaluer les modèles de génération de scènes. Enfin, dans le troisième article, nous montrons qu'en encourageant une forte information mutuelle entre les représentations multimodales locales et globales des images médicales en 2D et 3D, nous pouvons améliorer la classification et la segmentation des images. Ce cadre général peut être appliqué à une grande variété de contextes et démontre les avantages non seulement de la localité, mais aussi de la compositionnalité, car les représentations multimodales sont combinées pour obtenir une représentation plus générale.The use of deep neural architectures coupled with specific innovations such as adversarial methods, pre-training on large datasets and mutual information estimation has in recent years allowed rapid progress in many complex vision tasks such as zero-shot learning, scene generation, or multi-modal classification. Despite such progress, it is still not clear if current representation learning methods will be enough to attain human-level performance on arbitrary visual tasks, and if not, what direction should future research take. In this thesis, we will focus on two aspects of representations that seem necessary to achieve good downstream performance for representation learning: locality and compositionality. Locality can be understood as a representation's ability to retain local information. This will be relevant in many cases, and will specifically benefit computer vision where natural images inherently feature local information, i.e. relevant patches of an image, multiple objects present in a scene... On the other hand, a compositional representation can be understood as one that arises from a combination of simpler parts. Convolutional neural networks are inherently compositional, and many complex images can be seen as composition of relevant sub-components: individual objects and attributes in a scene, semantic attributes in zero-shot learning are two examples. We believe both properties hold the key to designing better representation learning methods. In this thesis, we present 3 articles dealing with locality and/or compositionality, and their application to representation learning for complex visual tasks. In the first article, we introduce ways of measuring locality and compositionality for image representations, and demonstrate that local and compositional representations perform better at zero-shot learning. We also use these two notions as the basis for designing class-matching deep info-max, a novel representation learning algorithm that achieves state-of-the-art performance on our proposed "Zero-shot from scratch" setting, a harder zero-shot setting where external information, e.g. pre-training on other image datasets is not allowed. In the second article, we show that by encouraging a generator to retain local object-level information, using a scene-graph similarity module, we can improve scene generation performance. This model also showcases the importance of compositionality as many components operate individually on each object present. To fully demonstrate the reach of our approach, we perform detailed analysis, and propose a new framework to evaluate scene generation models. Finally, in the third article, we show that encouraging high mutual information between local and global multi-modal representations of 2D and 3D medical images can lead to improvements in image classification and segmentation. This general framework can be applied to a wide variety of settings, and demonstrates the benefits of not only locality, but also of compositionality as multi-modal representations are combined to obtain a more general one

Multi-scale Transformer Network with Edge-aware Pre-training for Cross-Modality MR Image Synthesis

Cross-modality magnetic resonance (MR) image synthesis can be used to generate missing modalities from given ones. Existing (supervised learning) methods often require a large number of paired multi-modal data to train an effective synthesis model. However, it is often challenging to obtain sufficient paired data for supervised training. In reality, we often have a small number of paired data while a large number of unpaired data. To take advantage of both paired and unpaired data, in this paper, we propose a Multi-scale Transformer Network (MT-Net) with edge-aware pre-training for cross-modality MR image synthesis. Specifically, an Edge-preserving Masked AutoEncoder (Edge-MAE) is first pre-trained in a self-supervised manner to simultaneously perform 1) image imputation for randomly masked patches in each image and 2) whole edge map estimation, which effectively learns both contextual and structural information. Besides, a novel patch-wise loss is proposed to enhance the performance of Edge-MAE by treating different masked patches differently according to the difficulties of their respective imputations. Based on this proposed pre-training, in the subsequent fine-tuning stage, a Dual-scale Selective Fusion (DSF) module is designed (in our MT-Net) to synthesize missing-modality images by integrating multi-scale features extracted from the encoder of the pre-trained Edge-MAE. Further, this pre-trained encoder is also employed to extract high-level features from the synthesized image and corresponding ground-truth image, which are required to be similar (consistent) in the training. Experimental results show that our MT-Net achieves comparable performance to the competing methods even using $70\%$ of all available paired data. Our code will be publicly available at https://github.com/lyhkevin/MT-Net.Comment: 13 pages, 15 figure

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

A cross-scanner and cross-tracer deep learning method for the recovery of standard-dose imaging quality from low-dose PET

PURPOSE: A critical bottleneck for the credibility of artificial intelligence (AI) is replicating the results in the diversity of clinical practice. We aimed to develop an AI that can be independently applied to recover high-quality imaging from low-dose scans on different scanners and tracers. METHODS: Brain [(18)F]FDG PET imaging of 237 patients scanned with one scanner was used for the development of AI technology. The developed algorithm was then tested on [(18)F]FDG PET images of 45 patients scanned with three different scanners, [(18)F]FET PET images of 18 patients scanned with two different scanners, as well as [(18)F]Florbetapir images of 10 patients. A conditional generative adversarial network (GAN) was customized for cross-scanner and cross-tracer optimization. Three nuclear medicine physicians independently assessed the utility of the results in a clinical setting. RESULTS: The improvement achieved by AI recovery significantly correlated with the baseline image quality indicated by structural similarity index measurement (SSIM) (r = −0.71, p < 0.05) and normalized dose acquisition (r = −0.60, p < 0.05). Our cross-scanner and cross-tracer AI methodology showed utility based on both physical and clinical image assessment (p < 0.05). CONCLUSION: The deep learning development for extensible application on unknown scanners and tracers may improve the trustworthiness and clinical acceptability of AI-based dose reduction. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00259-021-05644-1