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Deformable 3D/3D CT-to-digital-tomosynthesis image registration in image-guided bronchoscopy interventions

Computers in Biology and Medicine 2024年 171卷 108199-108199页

作者： Saad, Fatima Frysch, Robert Saalfeld, Sylvia Kellnberger, Stephan Schulz, Jessica Fahrig, Rebecca Bhadra, Krish Nürnberger, Andreas Rose, Georg Institute for Medical Engineering Otto-von-Guericke University Magdeburg Germany Forschungscampus STIMULATE Otto-von-Guericke University Magdeburg Germany Department of Simulation and Graphics Otto-von-Guericke University Magdeburg Germany Siemens Healthcare GmbH Forchheim Germany CHI Memorial Rees Skillern Cancer Institute Chattanooga United States Data and Knowledge Engineering Group Faculty of Computer Science Otto-von-Guericke University Magdeburg Germany

Traditional navigational bronchoscopy procedures rely on preprocedural computed tomography (CT) and intraoperative chest radiography and cone-beam CT (CBCT) to biopsy peripheral lung lesions. This navigational approach is challenging due to the projective nature of radiography, and the high radiation dose, long imaging time, and large footprints of CBCT. Digital tomosynthesis (DTS) is considered an attractive alternative combining the advantages of radiography and CBCT. Only the depth resolution cannot match a full CBCT image due to the limited angle acquisition. To address this issue, preoperative CT is a good auxiliary in guiding bronchoscopy interventions. Nevertheless, CT-to-body divergence caused by anatomic changes and respiratory motion, hinders the effective use of CT imaging. To mitigate CT-to-body divergence, we propose a novel deformable 3D/3D CT-to-DTS registration algorithm employing a multistage, multiresolution approach and using affine and elastic B-spline transformation models with bone and lung mask images. A multiresolution strategy with a Gaussian image pyramid and a multigrid strategy within the B-spline model are applied. The normalized correlation coefficient is included in the cost function for the affine model and a multimetric weighted cost function is used for the B-spline model, with weights determined heuristically. Tested on simulated and real patient bronchoscopy data, the algorithm yields promising results. Assessed qualitatively by visual inspection and quantitatively by computing the Dice coefficient (DC) and the average symmetric surface distance (ASSD), the algorithm achieves mean DC of 0.82±0.05 and 0.74±0.05, and mean ASSD of 0.65±0.29mm and 0.93±0.43mm for simulated and real data, respectively. This algorithm lays the groundwork for CT-aided intraoperative DTS imaging in image-guided bronchoscopy interventions with future studies focusing on automated metric weight setting. © 2024

关键词： Image registration

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Complex Network for Complex Problems: A comparative study of CNN and Complex-valued CNN

arXiv

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arXiv 2023年

作者： Chatterjee, Soumick Tummala, Pavan 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 German Center for Neurodegenerative Disease Magdeburg Germany Center for Behavioral Brain Sciences Magdeburg Germany

Neural networks, especially convolutional neural networks (CNN), are one of the most common tools these days used in computer vision. Most of these networks work with real-valued data using real-valued features. Complex-valued convolutional neural networks (CV-CNN) can preserve the algebraic structure of complex-valued input data and have the potential to learn more complex relationships between the input and the ground-truth. Although some comparisons of CNNs and CV-CNNs for different tasks have been performed in the past, a large-scale investigation comparing different models operating on different tasks has not been conducted. Furthermore, because complex features contain both real and imaginary components, CV-CNNs have double the number of trainable parameters as real-valued CNNs in terms of the actual number of trainable parameters. Whether or not the improvements in performance with CV-CNN observed in the past have been because of the complex features or just because of having double the number of trainable parameters has not yet been explored. This paper presents a comparative study of CNN, CNNx2 (CNN with double the number of trainable parameters as the CNN), and CV-CNN. The experiments were performed using seven models for two different tasks - brain tumour classification and segmentation in brain MRIs. The results have revealed that the CV-CNN models outperformed the CNN and CNNx2 models. Copyright © 2023, The Authors. All rights reserved.

关键词： Image segmentation

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data Augmentation Approach for Language Identification in Imbalanced Bilingual Code-Mixed Social Media datasets

Data Augmentation Approach for Language Identification in Im...

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IEEE International Conference on Artificial Intelligence in engineering and Technology (IICAIET)

作者： Mohd Suhairi Md Suhaimin Mohd Hanafi Ahmad Hijazi Ervin Gubin Moung Mohd Azwan Mohamad Hamza Data Technology and Applications Research Group Faculty of Computing and Informatics Universiti Malaysia Sabah Sabah Malaysia Polytechnic and Community College Education Department Ministry of Higher Education Malaysia Putrajaya Malaysia Faculty of Computing and Informatics Creative Advanced Machine Intelligence Research Centre Universiti Malaysia Sabah Sabah Malaysia Knowledge Engineering & Computational Linguistic (KECL) Research Group Universiti Malaysia Pahang Pahang Malaysia

Addressing the problem of language identification in code-mixed datasets poses notable challenges due to data scarcity and high confusability in bilingual contexts. These challenges are further amplified by the associated imbalance and noise characteristic of social media data, complicating efforts to optimize performance. This paper introduces an augmentation approach designed to enhance language identification in bilingual code-mixed social media data. By incorporating reverse translation, semantic similarity, and sampling techniques alongside customized reprocessing strategies, our approach offers a comprehensive solution to these complex issues. To evaluate the effectiveness of the proposed approach, experiments were conducted on language identification at both the sentence and word levels. The results demonstrated the potential of the approach in optimizing language identification performance, offering a compelling combination of generation techniques for addressing the challenges of language identification in code-mixed data.

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Self-optimization in distributed manufacturing systems using Modular State-based Stackelberg Games

arXiv

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arXiv 2024年

作者： Yuwono, Steve Hussain, Ahmar Kamal Schwung, Dorothea Schwung, Andreas Department of Automation Technology and Learning Systems South Westphalia University of Applied Sciences Lübecker Ring 2 Soest59494 Germany Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Universitätsplatz 2 Magdeburg39106 Germany Department of Artificial Intelligence and Data Science in Automation Technology Hochschule Düsseldorf University of Applied Sciences Münsterstraße 156 Düsseldorf40476 Germany

In this study, we introduce Modular State-based Stackelberg Games (Mod-SbSG), a novel game structure developed for distributed self-learning in modular manufacturing systems. Mod-SbSG enhances cooperative decision-making among self-learning agents within production systems by integrating State-based Potential Games (SbPG) with Stackelberg games. This hierarchical structure assigns more important modules of the manufacturing system a first-mover advantage, while less important modules respond optimally to the leaders' decisions. This decision-making process differs from typical multi-agent learning algorithms in manufacturing systems, where decisions are made simultaneously. We provide convergence guarantees for the novel game structure and design learning algorithms to account for the hierarchical game structure. We further analyse the effects of single-leader/multiple-follower and multiple-leader/multiple-follower scenarios within a Mod-SbSG. To assess its effectiveness, we implement and test Mod-SbSG in an industrial control setting using two laboratory-scale testbeds featuring sequential and serial-parallel processes. The proposed approach delivers promising results compared to the vanilla SbPG, which reduces overflow by 97.1%, and in some cases, prevents overflow entirely. Additionally, it decreases power consumption by 5-13% while satisfying the production demand, which significantly improves potential (global objective) values. © 2024, CC BY-NC-ND.

关键词： Reinforcement learning

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Unboxing the black-box of deep learning based reconstruction of undersampled MRIs 4

Unboxing the black-box of deep learning based reconstruction...

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4th Italian Workshop on Explainable Artificial Intelligence, XAI.it 2023

作者： Chatterjee, Soumick Das, Arnab Khatun, Rupali Nürnberger, Andreas Genomics Research Centre Human Technopole Milan Italy Faculty of Computer Science Otto von Guericke University Magdeburg Magdeburg Germany Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Magdeburg Germany German Research Centre for Artificial Intelligence Kaiserslautern Germany Translational Radiobiology Department of Radiation Oncology Universitätsklinikum Erlangen Erlangen Germany Department of Radiation Oncology Universitätsklinikum Erlangen Friedrich-Alexnder-Universität Erlangen-Nürnberg Erlangen Germany Comprehensive Cancer Centre Erlangen-EMN Erlangen Germany Centre for Behavioural Brain Sciences Magdeburg Germany

Deep learning has emerged as a very important area of research and has shown immense potential in solving different kinds of problem, including in the medical field. For tasks like undersampled MRI reconstruction - the process of speeding up MRI acquisition with the help of undersampling, deep learning has shown its dominance over the years. But one of the major problems with deep learning is trust: Complex reasonings done by these models appear black-box to the users. Therefore, to build trust and better acceptability, it is important to open up this black-box nature of these models. For classification models, several approaches have been proposed. Nevertheless, for models dealing with inverse problems, like the reconstruction of the undersampled MRIs, it is more challenging as the output of the model has the same number of output pixels as the input, making the interpretability of such models more complex. This research explores different methods to understand the working mechanism of a deep learning model for the task of undersampled MRI reconstruction. © 2023 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).

关键词： Inverse problems

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Advances in Machine Learning for the Behavioral Sciences

arXiv

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arXiv 2019年

作者： Kliegr, Tomáš Bahník, Štěpán Fürnkranz, Johannes Department of Information and Knowledge Engineering Faculty of Informatics and Statistics University of Economics Prague Czech Republic Department of Management Faculty of Business Administration University of Economics Prague Czech Republic Computational Data Analytics Group Department of Computer Science Johannes Kepler Universität Linz Altenbergerstraße 66B Linz4040 Austria

The areas of machine learning and knowledge discovery in databases have considerably matured in recent years. In this article, we briefly review recent developments as well as classical algorithms that stood the test of time. Our goal is to provide a general introduction into different tasks such as learning from tabular data, behavioral data, or textual data, with a particular focus on actual and potential applications in behavioral sciences. The supplemental appendix to the article also provides practical guidance for using the methods by pointing the reader to proven software implementations. The focus is on R, but we also cover some libraries in other programming languages as well as systems with easy-to-use graphical interfaces. Copyright © 2019, The Authors. All rights reserved.

关键词： data mining

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Weakly-supervised segmentation using inherently-explainable classification models and their application to brain tumour classification

arXiv

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arXiv 2022年

作者： Chatterjee, Soumick Yassin, Hadya Dubost, Florian Nürnberger, Andreas Speck, Oliver Data and Knowledge Engineering Group Faculty of Computer Science Otto von Guericke University Magdeburg Germany Biomedical Magnetic Resonance Faculty of Nature Sciences Otto von Guericke University Magdeburg Germany Genomics Research Centre Human Technopole Milan Italy Institute for Medical Engineering Faculty of Electrical Engineering and Information Technology Otto von Guericke University Magdeburg Germany Department of Biomedical Data Science Stanford University StanfordCA United States Centre for Behavioural Brain Sciences Magdeburg Germany German Centre for Neurodegenerative Disease Magdeburg Germany

Deep learning models have shown their potential in recent years for several applications. However, most of the models are opaque in nature and difficult to trust due to their complex reasoning - commonly known as the black-box problem. Some fields, such as medicine, require a high degree of transparency to accept and adopt such technologies. Consequently, there is a movement towards creating explainable/interpretable models or applying post-hoc explainability/interpretability methods on classifiers to build trust in deep learning models. Moreover, deep learning methods can be used for segmentation tasks, which typically require hard-to-obtain, time-consuming manually-annotated segmentation labels for training. This paper introduces three inherently-explainable classifiers to tackle both of these problems as one. The localisation heatmaps provided by the networks - representing the models' focus areas and being used in classification decision-making - can be directly interpreted, without requiring any post-hoc methods to derive information for model explanation. The models are trained by using the input image and only the classification labels as groundtruth in a supervised fashion - without using any information about the location of the region of interest (i.e. the segmentation labels), making the segmentation training of the models weakly-supervised through classification labels. The final segmentation of the regions of interest is obtained by thresholding these heatmaps. The models were employed for the task of multi-class brain tumour classification using two different datasets, resulting in the best F1-score of 0.93 for the supervised classification task while securing a median Dice score of 0.67 ± 0.08 for the weakly-supervised segmentation task. Furthermore, the obtained accuracy on a subset of tumour-only images outperformed the state-of-the-art glioma tumour grading binary classifiers with the best model achieving 98.7% accuracy. Copyright © 2022, The Autho

关键词： Magnetic resonance imaging

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Robust and Fast Measure of Information via Low-rank Representation

arXiv

引用

arXiv 2022年

作者： Dong, Yuxin Gong, Tieliang Yu, Shujian Chen, Hong Li, Chen School of Computer Science and Technology Xi’an Jiaotong University Xi’an710049 China Shaanxi Provincial Key Laboratory of Big Data Knowledge Engineering Ministry of Education Xi’an710049 China Machine Learning Group UiT - The Arctic University of Norway Norway College of Science Huazhong Agriculture University Wuhan430070 China Engineering Research Center of Intelligent Technology for Agriculture Ministry of Education Wuhan430070 China

The matrix-based Rényi’s entropy allows us to directly quantify information measures from given data, without explicit estimation of the underlying probability distribution. This intriguing property makes it widely applied in statistical inference and machine learning tasks. However, this information theoretical quantity is not robust against noise in the data, and is computationally prohibitive in large-scale applications. To address these issues, we propose a novel measure of information, termed low-rank matrix-based Rényi’s entropy, based on low-rank representations of infinitely divisible kernel matrices. The proposed entropy functional inherits the specialty of of the original definition to directly quantify information from data, but enjoys additional advantages including robustness and effective calculation. Specifically, our low-rank variant is more sensitive to informative perturbations induced by changes in underlying distributions, while being insensitive to uninformative ones caused by noises. Moreover, low-rank Rényi’s entropy can be efficiently approximated by random projection and Lanczos iteration techniques, reducing the overall complexity from O(n3) to O(n2s) or even O(ns2), where n is the number of data samples and s n. We conduct large-scale experiments to evaluate the effectiveness of this new information measure, demonstrating superior results compared to matrix-based Rényi’s entropy in terms of both performance and computational efficiency. Copyright © 2022, The Authors. All rights reserved.

关键词： Entropy

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Upgraded W-net with attention gates and its application in unsupervised 3D liver segmentation

arXiv

引用

arXiv 2020年

作者： Mitta, Dhanunjaya Chatterjee, Soumick 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 German Center for Neurodegenerative Disease Magdeburg Germany Center for Behavioral Brain Sciences Magdeburg Germany Leibniz Institute for Neurobiology Magdeburg Germany

Segmentation of biomedical images can assist radiologists to make a better diagnosis and take decisions faster by helping in the detection of abnormalities, such as tumors. Manual or semi-automated segmentation, however, can be a time-consuming task. Most deep learning based automated segmentation methods are supervised and rely on manually segmented ground-truth. A possible solution for the problem would be an unsupervised deep learning based approach for automated segmentation, which this research work tries to address. We use a W-Net architecture and modified it, such that it can be applied to 3D volumes. In addition, to suppress noise in the segmentation we added attention gates to the skip connections. The loss for the segmentation output was calculated using soft N-Cuts and for the reconstruction output using SSIM. Conditional Random Fields were used as a post-processing step to fine-tune the results. The proposed method has shown promising results, with a dice coefficient of 0.88 for the liver segmentation compared against manual segmentation. Copyright © 2020, The Authors. All rights reserved.

关键词： Diagnosis

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Reading-strategy Inspired Visual Representation Learning for Text-to-Video Retrieval

arXiv

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arXiv 2022年

作者： Dong, Jianfeng Wang, Yabing Chen, Xianke Qu, Xiaoye Li, Xirong He, Yuan Wang, Xun The College of Computer and Information Engineering Zhejiang Gongshang University Hangzhou310035 China The State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China The School of Electronic Information and Communications Huazhong University of Science and Technology Hubei430074 China The Key Lab of Data Engineering and Knowledge Engineering Renmin University of China The AIMC Lab. School of Information Renmin University of China Beijing100872 China The Alibaba Group Beijing100102 China

This paper aims for the task of text-to-video retrieval, where given a query in the form of a natural-language sentence, it is asked to retrieve videos which are semantically relevant to the given query, from a great number of unlabeled videos. The success of this task depends on cross-modal representation learning that projects both videos and sentences into common spaces for semantic similarity computation. In this work, we concentrate on video representation learning, an essential component for text-to-video retrieval. Inspired by the reading strategy of humans, we propose a Reading-strategy Inspired Visual Representation Learning (RIVRL) to represent videos, which consists of two branches: a previewing branch and an intensive-reading branch. The previewing branch is designed to briefly capture the overview information of videos, while the intensive-reading branch is designed to obtain more in-depth information. Moreover, the intensive-reading branch is aware of the video overview captured by the previewing branch. Such holistic information is found to be useful for the intensive-reading branch to extract more fine-grained features. Extensive experiments on three datasets are conducted, where our model RIVRL achieves a new state-of-the-art on TGIF and VATEX. Moreover, on MSR-VTT, our model using two video features shows comparable performance to the state-of-the-art using seven video features and even outperforms models pre-trained on the large-scale HowTo100M dataset. Code is available at https://***/LiJiaBei-7/rivrl. © 2022, CC BY.

关键词： Video recording

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