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24 results on '"Gazda, Matej"'

1. Generative Adversarial Networks in Ultrasound Imaging: Extending Field of View Beyond Conventional Limits

Author

Gazda, Matej, Kadoury, Samuel, Gazda, Jakub, and Drotar, Peter

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition
Abstract

Transthoracic Echocardiography (TTE) is a fundamental, non-invasive diagnostic tool in cardiovascular medicine, enabling detailed visualization of cardiac structures crucial for diagnosing various heart conditions. Despite its widespread use, TTE ultrasound imaging faces inherent limitations, notably the trade-off between field of view (FoV) and resolution. This paper introduces a novel application of conditional Generative Adversarial Networks (cGANs), specifically designed to extend the FoV in TTE ultrasound imaging while maintaining high resolution. Our proposed cGAN architecture, termed echoGAN, demonstrates the capability to generate realistic anatomical structures through outpainting, effectively broadening the viewable area in medical imaging. This advancement has the potential to enhance both automatic and manual ultrasound navigation, offering a more comprehensive view that could significantly reduce the learning curve associated with ultrasound imaging and aid in more accurate diagnoses. The results confirm that echoGAN reliably reproduce detailed cardiac features, thereby promising a significant step forward in the field of non-invasive cardiac naviagation and diagnostics.

Published
2024

2. End-to-end Deformable Attention Graph Neural Network for Single-view Liver Mesh Reconstruction

Author

Gazda, Matej, Drotar, Peter, Romaguera, Liset Vazquez, and Kadoury, Samuel

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence
Abstract

Intensity modulated radiotherapy (IMRT) is one of the most common modalities for treating cancer patients. One of the biggest challenges is precise treatment delivery that accounts for varying motion patterns originating from free-breathing. Currently, image-guided solutions for IMRT is limited to 2D guidance due to the complexity of 3D tracking solutions. We propose a novel end-to-end attention graph neural network model that generates in real-time a triangular shape of the liver based on a reference segmentation obtained at the preoperative phase and a 2D MRI coronal slice taken during the treatment. Graph neural networks work directly with graph data and can capture hidden patterns in non-Euclidean domains. Furthermore, contrary to existing methods, it produces the shape entirely in a mesh structure and correctly infers mesh shape and position based on a surrogate image. We define two on-the-fly approaches to make the correspondence of liver mesh vertices with 2D images obtained during treatment. Furthermore, we introduce a novel task-specific identity loss to constrain the deformation of the liver in the graph neural network to limit phenomenons such as flying vertices or mesh holes. The proposed method achieves results with an average error of 3.06 +- 0.7 mm and Chamfer distance with L2 norm of 63.14 +- 27.28., Comment: Copyright 2023 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works

Published
2023

3. Biomedical image analysis competitions: The state of current participation practice

Author

Eisenmann, Matthias, Reinke, Annika, Weru, Vivienn, Tizabi, Minu Dietlinde, Isensee, Fabian, Adler, Tim J., Godau, Patrick, Cheplygina, Veronika, Kozubek, Michal, Ali, Sharib, Gupta, Anubha, Kybic, Jan, Noble, Alison, de Solórzano, Carlos Ortiz, Pachade, Samiksha, Petitjean, Caroline, Sage, Daniel, Wei, Donglai, Wilden, Elizabeth, Alapatt, Deepak, Andrearczyk, Vincent, Baid, Ujjwal, Bakas, Spyridon, Balu, Niranjan, Bano, Sophia, Bawa, Vivek Singh, Bernal, Jorge, Bodenstedt, Sebastian, Casella, Alessandro, Choi, Jinwook, Commowick, Olivier, Daum, Marie, Depeursinge, Adrien, Dorent, Reuben, Egger, Jan, Eichhorn, Hannah, Engelhardt, Sandy, Ganz, Melanie, Girard, Gabriel, Hansen, Lasse, Heinrich, Mattias, Heller, Nicholas, Hering, Alessa, Huaulmé, Arnaud, Kim, Hyunjeong, Landman, Bennett, Li, Hongwei Bran, Li, Jianning, Ma, Jun, Martel, Anne, Martín-Isla, Carlos, Menze, Bjoern, Nwoye, Chinedu Innocent, Oreiller, Valentin, Padoy, Nicolas, Pati, Sarthak, Payette, Kelly, Sudre, Carole, van Wijnen, Kimberlin, Vardazaryan, Armine, Vercauteren, Tom, Wagner, Martin, Wang, Chuanbo, Yap, Moi Hoon, Yu, Zeyun, Yuan, Chun, Zenk, Maximilian, Zia, Aneeq, Zimmerer, David, Bao, Rina, Choi, Chanyeol, Cohen, Andrew, Dzyubachyk, Oleh, Galdran, Adrian, Gan, Tianyuan, Guo, Tianqi, Gupta, Pradyumna, Haithami, Mahmood, Ho, Edward, Jang, Ikbeom, Li, Zhili, Luo, Zhengbo, Lux, Filip, Makrogiannis, Sokratis, Müller, Dominik, Oh, Young-tack, Pang, Subeen, Pape, Constantin, Polat, Gorkem, Reed, Charlotte Rosalie, Ryu, Kanghyun, Scherr, Tim, Thambawita, Vajira, Wang, Haoyu, Wang, Xinliang, Xu, Kele, Yeh, Hung, Yeo, Doyeob, Yuan, Yixuan, Zeng, Yan, Zhao, Xin, Abbing, Julian, Adam, Jannes, Adluru, Nagesh, Agethen, Niklas, Ahmed, Salman, Khalil, Yasmina Al, Alenyà, Mireia, Alhoniemi, Esa, An, Chengyang, Anwar, Talha, Arega, Tewodros Weldebirhan, Avisdris, Netanell, Aydogan, Dogu Baran, Bai, Yingbin, Calisto, Maria Baldeon, Basaran, Berke Doga, Beetz, Marcel, Bian, Cheng, Bian, Hao, Blansit, Kevin, Bloch, Louise, Bohnsack, Robert, Bosticardo, Sara, Breen, Jack, Brudfors, Mikael, Brüngel, Raphael, Cabezas, Mariano, Cacciola, Alberto, Chen, Zhiwei, Chen, Yucong, Chen, Daniel Tianming, Cho, Minjeong, Choi, Min-Kook, Xie, Chuantao Xie Chuantao, Cobzas, Dana, Cohen-Adad, Julien, Acero, Jorge Corral, Das, Sujit Kumar, de Oliveira, Marcela, Deng, Hanqiu, Dong, Guiming, Doorenbos, Lars, Efird, Cory, Escalera, Sergio, Fan, Di, Serj, Mehdi Fatan, Fenneteau, Alexandre, Fidon, Lucas, Filipiak, Patryk, Finzel, René, Freitas, Nuno R., Friedrich, Christoph M., Fulton, Mitchell, Gaida, Finn, Galati, Francesco, Galazis, Christoforos, Gan, Chang Hee, Gao, Zheyao, Gao, Shengbo, Gazda, Matej, Gerats, Beerend, Getty, Neil, Gibicar, Adam, Gifford, Ryan, Gohil, Sajan, Grammatikopoulou, Maria, Grzech, Daniel, Güley, Orhun, Günnemann, Timo, Guo, Chunxu, Guy, Sylvain, Ha, Heonjin, Han, Luyi, Han, Il Song, Hatamizadeh, Ali, He, Tian, Heo, Jimin, Hitziger, Sebastian, Hong, SeulGi, Hong, SeungBum, Huang, Rian, Huang, Ziyan, Huellebrand, Markus, Huschauer, Stephan, Hussain, Mustaffa, Inubushi, Tomoo, Polat, Ece Isik, Jafaritadi, Mojtaba, Jeong, SeongHun, Jian, Bailiang, Jiang, Yuanhong, Jiang, Zhifan, Jin, Yueming, Joshi, Smriti, Kadkhodamohammadi, Abdolrahim, Kamraoui, Reda Abdellah, Kang, Inha, Kang, Junghwa, Karimi, Davood, Khademi, April, Khan, Muhammad Irfan, Khan, Suleiman A., Khantwal, Rishab, Kim, Kwang-Ju, Kline, Timothy, Kondo, Satoshi, Kontio, Elina, Krenzer, Adrian, Kroviakov, Artem, Kuijf, Hugo, Kumar, Satyadwyoom, La Rosa, Francesco, Lad, Abhi, Lee, Doohee, Lee, Minho, Lena, Chiara, Li, Hao, Li, Ling, Li, Xingyu, Liao, Fuyuan, Liao, KuanLun, Oliveira, Arlindo Limede, Lin, Chaonan, Lin, Shan, Linardos, Akis, Linguraru, Marius George, Liu, Han, Liu, Tao, Liu, Di, Liu, Yanling, Lourenço-Silva, João, Lu, Jingpei, Lu, Jiangshan, Luengo, Imanol, Lund, Christina B., Luu, Huan Minh, Lv, Yi, Macar, Uzay, Maechler, Leon, L., Sina Mansour, Marshall, Kenji, Mazher, Moona, McKinley, Richard, Medela, Alfonso, Meissen, Felix, Meng, Mingyuan, Miller, Dylan, Mirjahanmardi, Seyed Hossein, Mishra, Arnab, Mitha, Samir, Mohy-ud-Din, Hassan, Mok, Tony Chi Wing, Murugesan, Gowtham Krishnan, Karthik, Enamundram Naga, Nalawade, Sahil, Nalepa, Jakub, Naser, Mohamed, Nateghi, Ramin, Naveed, Hammad, Nguyen, Quang-Minh, Quoc, Cuong Nguyen, Nichyporuk, Brennan, Oliveira, Bruno, Owen, David, Pal, Jimut Bahan, Pan, Junwen, Pan, Wentao, Pang, Winnie, Park, Bogyu, Pawar, Vivek, Pawar, Kamlesh, Peven, Michael, Philipp, Lena, Pieciak, Tomasz, Plotka, Szymon, Plutat, Marcel, Pourakpour, Fattaneh, Preložnik, Domen, Punithakumar, Kumaradevan, Qayyum, Abdul, Queirós, Sandro, Rahmim, Arman, Razavi, Salar, Ren, Jintao, Rezaei, Mina, Rico, Jonathan Adam, Rieu, ZunHyan, Rink, Markus, Roth, Johannes, Ruiz-Gonzalez, Yusely, Saeed, Numan, Saha, Anindo, Salem, Mostafa, Sanchez-Matilla, Ricardo, Schilling, Kurt, Shao, Wei, Shen, Zhiqiang, Shi, Ruize, Shi, Pengcheng, Sobotka, Daniel, Soulier, Théodore, Fadida, Bella Specktor, Stoyanov, Danail, Mun, Timothy Sum Hon, Sun, Xiaowu, Tao, Rong, Thaler, Franz, Théberge, Antoine, Thielke, Felix, Torres, Helena, Wahid, Kareem A., Wang, Jiacheng, Wang, YiFei, Wang, Wei, Wang, Xiong, Wen, Jianhui, Wen, Ning, Wodzinski, Marek, Wu, Ye, Xia, Fangfang, Xiang, Tianqi, Xiaofei, Chen, Xu, Lizhan, Xue, Tingting, Yang, Yuxuan, Yang, Lin, Yao, Kai, Yao, Huifeng, Yazdani, Amirsaeed, Yip, Michael, Yoo, Hwanseung, Yousefirizi, Fereshteh, Yu, Shunkai, Yu, Lei, Zamora, Jonathan, Zeineldin, Ramy Ashraf, Zeng, Dewen, Zhang, Jianpeng, Zhang, Bokai, Zhang, Jiapeng, Zhang, Fan, Zhang, Huahong, Zhao, Zhongchen, Zhao, Zixuan, Zhao, Jiachen, Zhao, Can, Zheng, Qingshuo, Zhi, Yuheng, Zhou, Ziqi, Zou, Baosheng, Maier-Hein, Klaus, Jäger, Paul F., Kopp-Schneider, Annette, and Maier-Hein, Lena

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Published
2022

4. Self-supervised deep convolutional neural network for chest X-ray classification

Author

Gazda, Matej, Gazda, Jakub, Plavka, Jan, and Drotar, Peter

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Neural and Evolutionary Computing
Abstract

Chest radiography is a relatively cheap, widely available medical procedure that conveys key information for making diagnostic decisions. Chest X-rays are almost always used in the diagnosis of respiratory diseases such as pneumonia or the recent COVID-19. In this paper, we propose a self-supervised deep neural network that is pretrained on an unlabeled chest X-ray dataset. The learned representations are transferred to downstream task - the classification of respiratory diseases. The results obtained on four public datasets show that our approach yields competitive results without requiring large amounts of labeled training data., Comment: The work was published by IEEE Access. DOI: 10.1109/ACCESS.2021.3125324

Published
2021
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6. Mixup Augmentation for Kidney and Kidney Tumor Segmentation

Author

Gazda, Matej, Bugata, Peter, Gazda, Jakub, Hubacek, David, Hresko, David Jozef, Drotar, Peter, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Heller, Nicholas, editor, Isensee, Fabian, editor, Trofimova, Darya, editor, Tejpaul, Resha, editor, Papanikolopoulos, Nikolaos, editor, and Weight, Christopher, editor

Published
2022
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7. Brief Overview of Neural Networks for Medical Applications

Author

Hireš Máté, Bugata Peter, Gazda Matej, Hreško Dávid J., Kanász Róbert, Vavrek Lukáš, and Drotár Peter

Subjects
neural network, convolutional neural network, image segmentation, ecg, u-net, lstm, medical imaging, Electrical engineering. Electronics. Nuclear engineering, TK1-9971
Abstract

Neural networks experienced great deal of success in many domains of machine intelligence. In tasks such as object detection, speech recognition or natural language processing is performance of neural networks close to that of human. This allows penetration of neural networks in many domains. The medicine is one of the domains that can successfully harvest methodological advances in neural networks. Medical personnel has to deal with huge amount of data that are used for patients’ diagnosis, monitoring and treatment. Application of neural networks in diagnosis and decision support systems have proven to add more objectivity to diagnosis, allow for quicker and more accurate decision and provide more personalized treatment. In this brief review we describe several main architectures of neural networks together with their applications. We provide description of convolutional neural networks, auto-encoders and recurrent neural networks together with their applications such as medical image segmentation, processing of electrocardiogram for arrhythmia detection and many others.

Published
2022
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13. Comparison of CNN-Learned vs. Handcrafted Features for Detection of Parkinson’s Disease Dysgraphia in a Multilingual Dataset

Author

Galáž, Zoltán, Drotár, Peter, Mekyska, Jiří, Gazda, Matej, Mucha, Ján, Zvončák, Vojtěch, Smékal, Zdeněk, Faúndez Zanuy, Marcos, Castrillon, Reinel, Orozco-Arroyave, Juan Rafael, Rapcsak, Steven Z., Kincses, Tamás, Brabenec, Luboš, Rektorová, Irena, Galáž, Zoltán, Drotár, Peter, Mekyska, Jiří, Gazda, Matej, Mucha, Ján, Zvončák, Vojtěch, Smékal, Zdeněk, Faúndez Zanuy, Marcos, Castrillon, Reinel, Orozco-Arroyave, Juan Rafael, Rapcsak, Steven Z., Kincses, Tamás, Brabenec, Luboš, and Rektorová, Irena

Abstract

Parkinson’s disease dysgraphia (PDYS), one of the earliest signs of Parkinson’s disease (PD), has been researched as a promising biomarker of PD and as the target of a noninvasive and inexpensive approach to monitoring the progress of the disease. However, although several approaches to supportive PDYS diagnosis have been proposed (mainly based on handcrafted features (HF) extracted from online handwriting or the utilization of deep neural networks), it remains unclear which approach provides the highest discrimination power and how these approaches can be transferred between different datasets and languages. This study aims to compare classification performance based on two types of features: features automatically extracted by a pretrained convolutional neural network (CNN) and HF designed by human experts. Both approaches are evaluated on a multilingual dataset collected from 143 PD patients and 151 healthy controls in the Czech Republic, United States, Colombia, and Hungary. The subjects performed the spiral drawing task (SDT; a language-independent task) and the sentence writing task (SWT; a language-dependent task). Models based on logistic regression and gradient boosting were trained in several scenarios, specifically single language (SL), leave one language out (LOLO), and all languages combined (ALC). We found that the HF slightly outperformed the CNN-extracted features in all considered evaluation scenarios for the SWT. In detail, the following balanced accuracy (BACC) scores were achieved: SL—0.65 (HF), 0.58 (CNN); LOLO—0.65 (HF), 0.57 (CNN); and ALC—0.69 (HF), 0.66 (CNN). However, in the case of the SDT, features extracted by a CNN provided competitive results: SL—0.66 (HF), 0.62 (CNN); LOLO—0.56 (HF), 0.54 (CNN); and ALC—0.60 (HF), 0.60 (CNN). In summary, regarding the SWT, the HF outperformed the CNN-extracted features over 6%(mean BACC of 0.66 for HF, and 0.60 for CNN). In the case of the SDT, both feature sets provided almost identical classificatio

Published
2022

14. Comparison of CNN-Learned vs. Handcrafted Features for Detection of Parkinson's Disease Dysgraphia in a Multilingual Dataset

Author

Galaz, Zoltan, primary, Drotar, Peter, additional, Mekyska, Jiri, additional, Gazda, Matej, additional, Mucha, Jan, additional, Zvoncak, Vojtech, additional, Smekal, Zdenek, additional, Faundez-Zanuy, Marcos, additional, Castrillon, Reinel, additional, Orozco-Arroyave, Juan Rafael, additional, Rapcsak, Steven, additional, Kincses, Tamas, additional, Brabenec, Lubos, additional, and Rektorova, Irena, additional

Published
2022
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20. External Validation of UDCA Response Score in Slovak and Croatian Patients with Primary Biliary Cholangitis

Author

Gazda, Jakub, primary, Janicko, Martin, additional, Drazilova, Sylvia, additional, Grgurevic, Ivica, additional, Kanizaj, Tajana Filipec, additional, Koller, Tomas, additional, Bodorovska, Beatrica, additional, Mijic, Maja, additional, Mikolasevic, Ivana, additional, Stromar, Ivana Knezevic, additional, Kucinsky, Branislav, additional, Gazda, Matej, additional, and Jarcuska, Peter, additional

Published
2021
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21. BRIEF OVERVIEW OF NEURAL NETWORKS FOR MEDICAL APPLICATIONS.

Author

HIREŠ, Máté, BUGATA, Peter, GAZDA, Matej, HREŠKO, Dávid J., KAŃASZ, Róbert, VAVREK, Lukáš, and DROTÁR, Peter

Subjects
RECURRENT neural networks, ARTIFICIAL intelligence, NATURAL language processing, MEDICAL personnel, AUTOMATIC speech recognition, DECISION support systems, CONVOLUTIONAL neural networks
Abstract

Neural networks experienced great deal of success in many domains of machine intelligence. In tasks such as object detection, speech recognition or natural language processing is performance of neural networks close to that of human. This allows penetration of neural networks in many domains. The medicine is one of the domains that can successfully harvest methodological advances in neural networks. Medical personnel has to deal with huge amount of data that are used for patients' diagnosis, monitoring and treatment. Application of neural networks in diagnosis and decision support systems have proven to add more objectivity to diagnosis, allow for quicker and more accurate decision and provide more personalized treatment. In this brief review we describe several main architectures of neural networks together with their applications. We provide description of convolutional neural networks, auto-encoders and recurrent neural networks together with their applications such as medical image segmentation, processing of electrocardiogram for arrhythmia detection and many others. [ABSTRACT FROM AUTHOR]

Published
2022
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23. CONTROLLABLE AND TOLERABLE GENERALIZED EIGENVECTORS OF INTERVAL MAX-PLUS MATRICES.

Author

GAZDA, MATEJ and PLAVKA, JÁN

Subjects
MATRICES (Mathematics), ALGEBRA, EIGENVECTORS
Abstract

By max-plus algebra we mean the set of reals R equipped with the operations a = b = maxfa; bg and ab =a+b for a;b2R: A vector x is said to be a generalized eigenvector of max-plus matrices A; B 2 R(m; n) if A x = = B x for some = 2 R. The investigation of properties of generalized eigenvectors is important for the applications. The values of vector or matrix inputs in practice are usually not exact numbers and they can be rather considered as values in some intervals. In this paper the properties of matrices and vectors with inexact (interval) entries are studied and complete solutions of the controllable, the tolerable and the strong generalized eigenproblem in max-plus algebra are presented. As a consequence of the obtained results, efficient algorithms for checking equivalent conditions are introduced. [ABSTRACT FROM AUTHOR]

Published
2021
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