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arXiv 2021年

作者： Chatterjee, Soumick Breitkopf, Mario Sarasaen, Chompunuch Yassin, Hadya Rose, Georg Nürnberger, Andreas Speck, Oliver Faculty of Computer Science Otto von Guericke University Magdeburg Germany Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Germany Otto von Guericke University Magdeburg Biomedical Magnetic Resonance Germany Research Campus Stimulate Otto von Guericke University Magdeburg Germany Institute for Medical Engineering Otto von Guericke University Magdeburg Germany German Center for Neurodegenerative Disease Magdeburg Germany Center for Behavioral Brain Sciences Magdeburg Germany Leibniz Institute for Neurobiology Magdeburg Germany

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990±0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968±0.005) and 17 for radially (0.962±0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects. Copyright © 2021, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Fine-tuning deep learning model parameters for improved super-resolution of dynamic MRI with prior-knowledge

arXiv

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arXiv 2021年

作者： Sarasaen, Chompunuch Chatterjee, Soumick Breitkopf, Mario Rose, Georg Nürnberger, Andreas Speck, Oliver Biomedical Magnetic Resonance Otto von Guericke University Magdeburg Germany Institute for Medical Engineering Otto von Guericke University Magdeburg Germany Research Campus Stimulate Otto von Guericke University Magdeburg Germany Faculty of Computer Science Otto von Guericke University Magdeburg Germany Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Germany German Center for Neurodegenerative Disease Magdeburg Germany Center for Behavioral Brain Sciences Magdeburg Germany Leibniz Institute for Neurobiology Magdeburg Germany

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. A U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25% of the k-space) before and after fine-tuning were 0.939 ± 0.008 and 0.957 ± 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors. Copyright © 2021, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Anomaly detection on attributed networks via contrastive self-supervised learning

arXiv

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arXiv 2021年

作者： Liu, Yixin Li, Zhao Pan, Shirui Gong, Chen Zhou, Chuan Karypis, George The Department of Data Science and AI Faculty of Information Technology Monash University ClaytonVIC3800 Australia The Alibaba Group Hangzhou310000 China The PCA Laboratory Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology Nanjing210094 China The Department of Computing The Hong Kong Polytechnic University Hong Kong The Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100093 China The Department of Computer Science and Engineering University of Minnesota MinneapolisMN55455 United States

Anomaly detection on attributed networks attracts considerable research interests due to wide applications of attributed networks in modeling a wide range of complex systems. Recently, the deep learning-based anomaly detection methods have shown promising results over shallow approaches, especially on networks with high-dimensional attributes and complex structures. However, existing approaches, which employ graph autoencoder as their backbone, do not fully exploit the rich information of the network, resulting in suboptimal performance. Furthermore, these methods do not directly target anomaly detection in their learning objective and fail to scale to large networks due to the full graph training mechanism. To overcome these limitations, in this paper, we present a novel Contrastive self-supervised Learning framework for Anomaly detection on attributed networks (CoLA for abbreviation). Our framework fully exploits the local information from network data by sampling a novel type of contrastive instance pair, which can capture the relationship between each node and its neighboring substructure in an unsupervised way. Meanwhile, a well-designed graph neural network-based contrastive learning model is proposed to learn informative embedding from high-dimensional attributes and local structure and measure the agreement of each instance pairs with its outputted scores. The multi-round predicted scores by the contrastive learning model are further used to evaluate the abnormality of each node with statistical estimation. In this way, the learning model is trained by a specific anomaly detection-aware target. Furthermore, since the input of the graph neural network module is batches of instance pairs instead of the full network, our framework can adapt to large networks flexibly. Experimental results show that our proposed framework outperforms the state-of-the-art baseline methods on all seven benchmark datasets. © 2021, CC BY.

关键词： Anomaly detection

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Mutual Consistency Learning for Semi-supervised Medical Image Segmentation

arXiv

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arXiv 2021年

作者： Wu, Yicheng Ge, Zongyuan Zhang, Donghao Xu, Minfeng Zhang, Lei Xia, Yong Cai, Jianfei Department of Data Science & AI Faculty of Information Technology Monash University MelbourneVIC3800 Australia Monash-Airdoc Research Monash University MelbourneVIC3800 Australia Monash Medical AI Monash eResearch Centre MelbourneVIC3800 Australia DAMO Academy Alibaba Group Hangzhou311121 China National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology School of Computer Science and Engineering Northwestern Polytechnical University Xi'an710072 China

In this paper, we propose a novel mutual consistency network (MC-Net+) to effectively exploit the unlabeled data for semi-supervised medical image segmentation. The MC-Net+ model is motivated by the observation that deep models trained with limited annotations are prone to output highly uncertain and easily mis-classified predictions in the ambiguous regions (e.g., adhesive edges or thin branches) for medical image segmentation. Leveraging these challenging samples can make the semi-supervised segmentation model training more effective. Therefore, our proposed MC-Net+ model consists of two new designs. First, the model contains one shared encoder and multiple slightly different decoders (i.e., using different up-sampling strategies). The statistical discrepancy of multiple decoders' outputs is computed to denote the model's uncertainty, which indicates the unlabeled hard regions. Second, we apply a novel mutual consistency constraint between one decoder's probability output and other decoders' soft pseudo labels. In this way, we minimize the discrepancy of multiple outputs (i.e., the model uncertainty) during training and force the model to generate invariant results in such challenging regions, aiming at regularizing the model training. We compared the segmentation results of our MC-Net+ model with five state-of-the-art semi-supervised approaches on three public medical datasets. Extension experiments with two standard semi-supervised settings demonstrate the superior performance of our model over other methods, which sets a new state of the art for semi-supervised medical image segmentation. Our code is released publicly at https://***/ycwu1997/MC-Net. © 2021, CC BY-NC-SA.

关键词： Image segmentation

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TUdataset: A collection of benchmark datasets for learning with graphs

arXiv

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arXiv 2020年

作者： Morris, Christopher Kriege, Nils M. Bause, Franka Kersting, Kristian Mutzel, Petra Neumann, Marion CERC in Data Science for Real-Time Decision-Making Poly-technique MontrÃl’al Faculty of Computer Science University of Vienna Department of Computer Science TU Dortmund University Machine Learning Group TU Darmstadt Department of Computer Science University of Bonn Department of Computer Science and Engineering Washington University in St. Louis

Recently, there has been an increasing interest in (supervised) learning with graph data, especially using graph neural networks. However, the development of meaningful benchmark datasets and standardized evaluation procedures is lagging, consequently hindering advancements in this area. To address this, we introduce the TUdataSET for graph classification and regression. The collection consists of over 120 datasets of varying sizes from a wide range of applications. We provide Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools. Here, we give an overview of the datasets, standardized evaluation procedures, and provide baseline experiments. All datasets are available at ***. The experiments are fully reproducible from the code available at ***/chrsmrrs/tudataset. Copyright © 2020, The Authors. All rights reserved.

关键词： Graph neural networks

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Design of a Domain-Specific Metamodel for Industrial Business Process Management

Design of a Domain-Specific Metamodel for Industrial Busines...

引用

IIAI International Conference on Advanced Applied Informatics (IIAIAAI)

作者： Wilfrid Utz Faculty of Computer Science Research Group Knowledge Engineering University of Vienna Vienna Austria

ISBN: (纸本)9781728126289

Enterprises operate in fast-changing environments nowadays and experience the continuous need to adapt to changing circumstances and new strategical and technological developments. This observation impacts how enterprise information systems are analysed, designed, implemented and used. Focusing on the analysis and design phases, conceptual modelling methods in the field of enterprise architecture management experience a continuous evolution in research and practice. Existing methods are re-purposed for specific requirements, new methods are developed/evaluated in concrete industrial settings and coupling/integration techniques support holistic viewpoints. Nevertheless, current practices in the design and enactment of such methods, and more specifically their metamodels, are inefficient with respect to agile and iterative considerations. Within this paper, a novel design approach for modelling method engineering is discussed that builds on the notion of meta-models as conceptual structures. Syntactic and semantic operation on these structures aim to facilitate the design process following the design science research methodology. The approach is evaluated by introducing a case developed as part of the European research project GO0D MAN. In the context of the project an enterprise architecture metamodel has been designed, developed and deployed that supports an integrated viewpoint of conceptual model artefacts coupled with operational data visualisations to assess the effectiveness of design decisions.

关键词： Enterprise architecture management Modelling Metamodelling Conceptual structure Conceptual Architecture Modeling Industrial enterprises Construction management Business process management METHODS engineering Process management Enterprise information system design phases meta-models design process Walker-A Motif design theory Metamodels Companies

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2021 BEETL Competition: Advancing Transfer Learning for Subject Independence & Heterogenous EEG data Sets 35

2021 BEETL Competition: Advancing Transfer Learning for Subj...

引用

35th Conference on Neural Information Processing Systems - Competitions and Demonstrations, NeurIPS 2021

作者： Wei, Xiaoxi Aldo Faisal, A. Grosse-Wentrup, Moritz Gramfort, Alexandre Chevallier, Sylvain Jayaram, Vinay Jeunet, Camille Bakas, Stylianos Ludwig, Siegfried Barmpas, Konstantinos Bahri, Mehdi Panagakis, Yannis Laskaris, Nikolaos Adamos, Dimitrios A. Zafeiriou, Stefanos Duong, William C. Gordon, Stephen M. Lawhern, Vernon J. Śliwowski, Maciej Rouanne, Vincent Tempczyk, Piotr Brain and Behaviour Lab Imperial College London United Kingdom Institute of Artificial and Human Intelligence University of Bayreuth Germany Faculty of Computer Science CogSciHub Data Science@Univie University of Vienna Austria Universite Paris-Saclay Inria CEA Palaiseau France LISV UVSQ Université Paris-Saclay France Reality Labs United States University of Bordeaux France Cogitat Ltd. United Kingdom Intelligent Behaviour Understanding Group Imperial College London United Kingdom Aristotle University of Thessaloniki Greece National and Kapodistrian University of Athens Greece DCS Corporation AlexandriaVA United States Human Research and Engineering Directorate DEVCOM Army Research Laboratory Aberdeen Proving GroundMD United States Univ. Grenoble Alpes CEA LETI Clinatec GrenobleF-38000 France Université Paris-Saclay CEA List PalaiseauF-91120 France Warsaw Poland deeptale.ai Poland

Transfer learning and meta-learning offer some of the most promising avenues to unlock the scalability of healthcare and consumer technologies driven by biosignal data. This is because regular machine learning methods cannot generalise well across human subjects and handle learning from different, heterogeneously collected data sets, thus limiting the scale of training data available. On the other hand, the many developments in transfer- and meta-learning fields would benefit significantly from a real-world benchmark with immediate practical application. Therefore, we pick electroencephalography (EEG) as an exemplar for all the things that make biosignal data analysis a hard problem. We design two transfer learning challenges around a. clinical diagnostics and b. neurotechnology. These two challenges are designed to probe algorithmic performance with all the challenges of biosignal data, such as low signal-to-noise ratios, major variability among subjects, differences in the data recording sessions and techniques, and even between the specific BCI tasks recorded in the dataset. Task 1 is centred on the field of medical diagnostics, addressing automatic sleep stage annotation across subjects. Task 2 is centred on Brain-computer Interfacing (BCI), addressing motor imagery decoding across both subjects and data sets. The successful 2021 BEETL competition with its over 30 competing teams and its 3 winning entries brought attention to the potential of deep transfer learning and combinations of set theory and conventional machine learning techniques to overcome the challenges. The results set a new state-of-the-art for the real-world BEETL benchmarks. © 2022 X. Wei et al.

关键词： Electroencephalography

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Sinogram upsampling using Primal-Dual UNet for undersampled CT and radial MRI reconstruction

arXiv

引用

arXiv 2021年

作者： Ernst, Philipp Chatterjee, Soumick Rose, Georg Speck, Oliver Nürnberger, Andreas Faculty of Computer Science Otto von Guericke University Magdeburg Germany Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Germany Biomedical Magnetic Resonance Otto von Guericke University Magdeburg Germany Otto von Guericke University Research Campus STIMULATE Magdeburg Germany Genomics Research Centre Human Technopole Milan Italy Institute for Medical Engineering Otto von Guericke University Magdeburg Germany German Centre for Neurodegenerative Disease Magdeburg Germany Centre for Behavioural Brain Sciences Magdeburg Germany

Computed tomography (CT) and magnetic resonance imaging (MRI) are two widely used clinical imaging modalities for noninvasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932±0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919±0.016. Furthermore, the proposed model resulted in 0.903±0.019 and 0.957±0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively-statistically significant improvements over the original model, which resulted in 0.867±0.025 and 0.949±0.025. Finally, this paper shows that the proposed network not only improves the overall image quality, but also improves the image quality for the regions-of-interest: liver, kidneys, and spleen;as well

关键词： Image reconstruction

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Retrospective motion correction of MR images using prior-assisted deep learning

arXiv

引用

arXiv 2020年

作者： Chatterjee, Soumick Sciarra, Alessandro Dünnwald, Max Oeltze-Jafra, Steffen Nürnberger, Andreas Speck, Oliver Department of Biomedical Magnetic Resonance Data and Knowledge Engineering Group Faculty of Computer Science Otto-von-Guericke Univeristy Magdeburg Germany MedDigit Department of Neurology Medical Faculty University Hopspital Department of Biomedical Magnetic Resonance Otto-von-Guericke Univeristy Magdeburg Germany MedDigit Department of Neurology Medical Faculty University Hopspital Faculty of Computer Science Otto-von-Guericke Univeristy Magdeburg Germany MedDigit Department of Neurology Medical Faculty University Hopspital German Centre for Neurodegenerative Diseases Center for Behavioral Brain Sciences Magdeburg Germany Data and Knowledge Engineering Group Faculty of Computer Science Otto-von-Guericke Univeristy Center for Behavioral Brain Sciences Magdeburg Germany Department of Biomedical Magnetic Resonance Otto-von-Guericke Univeristy German Centre for Neurodegenerative Diseases Leibniz Institute for Neurobiology Center for Behavioral Brain Sciences Magdeburg Germany

In MRI, motion artefacts are among the most common types of artefacts. They can degrade images and render them unusable for accurate diagnosis. Traditional methods, such as prospective or retrospective motion correction, have been proposed to avoid or alleviate motion artefacts. Recently, several other methods based on deep learning approaches have been proposed to solve this problem. This work proposes to enhance the performance of existing deep learning models by the inclusion of additional information present as image priors. The proposed approach has shown promising results and will be further investigated for clinical validity. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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An AO-ADMM approach to constraining PARAFAC2 on all modes

arXiv

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arXiv 2021年

作者： Roald, Marie Schenker, Carla Calhoun, Vince D. Adalı, Tülay Bro, Rasmus Cohen, Jeremy E. Acar, Evrim Department of Data Science and Knowledge Discovery Simula Metropolitan Center for Digital Engineering Oslo Norway Faculty of Technology Art and Design Oslo Metropolitan University Oslo Norway Department of Psychology Georgia State University AtlantaGA United States Department of Computer Science and Electrical Engineering UMBC BaltimoreMD United States Department of Food Science University of Copenhagen Copenhagen Denmark Univ Lyon INSA-Lyon UCBL UJM-Saint Etienne CNRS Inserm CREATIS UMR 5220 U1206 VilleurbanneF-69100 France

Analyzing multi-way measurements with variations across one mode of the dataset is a challenge in various fields including data mining, neuroscience and chemometrics. For example, measurements may evolve over time or have unaligned time profiles. The PARAFAC2 model has been successfully used to analyze such data by allowing the underlying factor matrices in one mode (i.e., the evolving mode) to change across slices. The traditional approach to fit a PARAFAC2 model is to use an alternating least squares-based algorithm, which handles the constant cross-product constraint of the PARAFAC2 model by implicitly estimating the evolving factor matrices. This approach makes imposing regularization on these factor matrices challenging. There is currently no algorithm to flexibly impose such regularization with general penalty functions and hard constraints. In order to address this challenge and to avoid the implicit estimation, in this paper, we propose an algorithm for fitting PARAFAC2 based on alternating optimization with the alternating direction method of multipliers (AO-ADMM). With numerical experiments on simulated data, we show that the proposed PARAFAC2 AO-ADMM approach allows for flexible constraints, recovers the underlying patterns accurately, and is computationally efficient compared to the state-of-the-art. We also apply our model to two real-world datasets from neuroscience and chemometrics, and show that constraining the evolving mode improves the interpretability of the extracted *** Codes 15A69, 90C26 © 2021, CC BY.

关键词： Matrix algebra

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