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155 results on '"Fujarewicz, Krzysztof"'

1. Towards the use of multiple ROIs for radiomics-based survival modelling: finding a strategy of aggregating lesions

Author

Wilk, Agata Małgorzata, Swierniak, Andrzej, d'Amico, Andrea, Suwiński, Rafał, Fujarewicz, Krzysztof, and Borys, Damian

Subjects
Statistics - Applications
Abstract

The main objective of this work is to explore the possibility of incorporating radiomic information from multiple lesions into survival models. We hypothesise that when more lesions are present, their inclusion can improve model performance, and we aim to find an optimal strategy for using multiple distinct regions in modelling. The idea of using multiple regions of interest (ROIs) to extract radiomic features for predictive models has been implemented in many recent works. However, in almost all studies, analogous regions were segmented according to particular criteria for all patients -- for example, the primary tumour and peritumoral area, or subregions of the primary tumour. They can be included in a model in a straightforward way as additional features. A more interesting scenario occurs when multiple distinct ROIs are present, such as multiple lesions in a regionally disseminated cancer. Since the number of such regions may differ between patients, their inclusion in a model is non-trivial and requires additional processing steps. We proposed several methods of handling multiple ROIs representing either ROI or risk aggregation strategy, compared them to a published one, and evaluated their performance in different classes of survival models in a Monte Carlo Cross-Validation scheme. We demonstrated the effectiveness of the methods using a cohort of 115 non-small cell lung cancer patients, for whom we predicted the metastasis risk based on features extracted from PET images in original resolution or interpolated to CT image resolution. For both feature sets, incorporating all available lesions, as opposed to a singular ROI representing the primary tumour, allowed for considerable improvement of predictive ability regardless of the model., Comment: To be submitted to Computerized Medical Imaging and Graphics

Published
2024

3. Improving the Predictive Ability of Radiomics-Based Regression Survival Models Through Incorporating Multiple Regions of Interest

Author

Wilk, Agata Małgorzata, Kozłowska, Emilia, Borys, Damian, D’Amico, Andrea, Gorczewska, Izabela, Debosz-Suwińska, Iwona, Gałecki, Seweryn, Fujarewicz, Krzysztof, Suwiński, Rafał, Świerniak, Andrzej, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Strumiłło, Paweł, editor, Klepaczko, Artur, editor, Strzelecki, Michał, editor, and Bociąga, Dorota, editor

Published
2024
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4. Improving the Predictive Ability of Radiomics-Based Regression Survival Models Through Incorporating Multiple Regions of Interest

Author

Wilk, Agata Małgorzata, primary, Kozłowska, Emilia, additional, Borys, Damian, additional, D’Amico, Andrea, additional, Gorczewska, Izabela, additional, Debosz-Suwińska, Iwona, additional, Gałecki, Seweryn, additional, Fujarewicz, Krzysztof, additional, Suwiński, Rafał, additional, and Świerniak, Andrzej, additional

Published
2023
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5. Potential of Radiomics Features for Predicting Time to Metastasis in NSCLC

Author

Wilk, Agata, Borys, Damian, Fujarewicz, Krzysztof, d’Amico, Andrea, Suwiński, Rafał, Świerniak, Andrzej, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Nguyen, Ngoc Thanh, editor, Tran, Tien Khoa, editor, Tukayev, Ualsher, editor, Hong, Tzung-Pei, editor, Trawiński, Bogdan, editor, and Szczerbicki, Edward, editor

Published
2022
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6. Machine Learning Approach to Predict Metastasis in Lung Cancer Based on Radiomic Features

Author

Fujarewicz, Krzysztof, Wilk, Agata, Borys, Damian, d’Amico, Andrea, Suwiński, Rafał, Świerniak, Andrzej, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Nguyen, Ngoc Thanh, editor, Tran, Tien Khoa, editor, Tukayev, Ualsher, editor, Hong, Tzung-Pei, editor, Trawiński, Bogdan, editor, and Szczerbicki, Edward, editor

Published
2022
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7. Finding the Time-Dependent Virus Transmission Intensity via Gradient Method and Adjoint Sensitivity Analysis

Author

Łakomiec, Krzysztof, Wilk, Agata, Psiuk-Maksymowicz, Krzysztof, Fujarewicz, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Pietka, Ewa, editor, Badura, Pawel, editor, Kawa, Jacek, editor, and Wieclawek, Wojciech, editor

Published
2022
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9. Biological Models’ Parameter Estimation Based on Discrete Measurements and Adjoint Sensitivity Analysis

Author

Fujarewicz, Krzysztof, Łakomiec, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Bartoszewicz, Andrzej, editor, and Kabziński, Jacek, editor

Published
2020
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10. BioTest - Remote Platform for Hypothesis Testing and Analysis of Biomedical Data

Author

Psiuk-Maksymowicz, Krzysztof, Jaksik, Roman, Placzek, Aleksander, Gruca, Aleksandra, Student, Sebastian, Borys, Damian, Mrozek, Dariusz, Fujarewicz, Krzysztof, Swierniak, Andrzej, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Korbicz, Józef, editor, Maniewski, Roman, editor, Patan, Krzysztof, editor, and Kowal, Marek, editor

Published
2020
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11. On Stability of Feature Selection Based on MALDI Mass Spectrometry Imaging Data and Simulated Biopsy

Author

Wilk, Agata, Gawin, Marta, Frątczak, Katarzyna, Widłak, Piotr, Fujarewicz, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Korbicz, Józef, editor, Maniewski, Roman, editor, Patan, Krzysztof, editor, and Kowal, Marek, editor

Published
2020
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12. Towards Personalized Radio-Chemotherapy – Learning from Clinical Data vs. Model Optimization

Author

Świerniak, Andrzej, Śmieja, Jarosław, Fujarewicz, Krzysztof, Suwiński, Rafał, 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, Nguyen, Ngoc Thanh, editor, Jearanaitanakij, Kietikul, editor, Selamat, Ali, editor, Trawiński, Bogdan, editor, and Chittayasothorn, Suphamit, editor

Published
2020
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15. The Role of Different TET Proteins in Cytosine Demethylation Revealed by Mathematical Modeling.

Author

Kurasz, Karolina, Rzeszowska-Wolny, Joanna, Oliński, Ryszard, Foksiński, Marek, and Fujarewicz, Krzysztof

Subjects
DEMETHYLATION, MATHEMATICAL models, PROTEINS, CYTOSINE, DEOXYCYTIDINE, CELL lines
Abstract

In living cells, some reactions can be conducted by more than one enzyme and sometimes it is difficult to establish which enzyme is responsible. Such is the case with proteins from the TET family, capable of converting 5-methyl-2'-deoxycytidine (5- m d C ) in DNA to 5-(hydroxymethyl)-2'-deoxycytidine (5- h m d C ) and further to 5-formyl-2'-deoxycytidine (5- f d C ) and 5-carboxy-2'-deoxycytidine (5- c a d C ). The estimation of the efficiency of particular TETs in particular oxidative reactions and different cell types is important but experimentally difficult. Here, we propose an approach with mathematical modeling in which methylation and known deoxycytidine modification pathways are presented by 343 possible model versions with assumed different combinations of TET1, 2, and 3 activities in different pathways. Model parameters were calculated on the basis of 5- m d C , 5- h m d C , 5- f d C , 5- c a d C , and 5- h m d U levels experimentally assessed in five human cultured cell lines and previously published. Selection of the model versions that give in simulations the best average fit to experimental data suggested that not all TET proteins participate in all modification reactions and that TET3 activity may be especially important in the reaction of 5- f d C removal. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Sensitivity Analysis of Biomedical Models Using Green’s Function

Author

Łakomiec, Krzysztof, Kurasz, Karolina, Fujarewicz, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Pietka, Ewa, editor, Badura, Pawel, editor, Kawa, Jacek, editor, and Wieclawek, Wojciech, editor

Published
2019
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17. Classification System for Multi-class Biomedical Data that Allows Different Data Fusion Strategies

Author

Student, Sebastian, Łakomiec, Krzysztof, Płuciennik, Alicja, Bensz, Wojciech, Fujarewicz, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Pietka, Ewa, editor, Badura, Pawel, editor, Kawa, Jacek, editor, and Wieclawek, Wojciech, editor

Published
2019
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18. Integration Strategies of Cross-Platform Microarray Data Sets in Multiclass Classification Problem

Author

Student, Sebastian, Płuciennik, Alicja, Łakomiec, Krzysztof, Wilk, Agata, Bensz, Wojciech, Fujarewicz, Krzysztof, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Misra, Sanjay, editor, Gervasi, Osvaldo, editor, Murgante, Beniamino, editor, Stankova, Elena, editor, Korkhov, Vladimir, editor, Torre, Carmelo, editor, Rocha, Ana Maria A.C., editor, Taniar, David, editor, Apduhan, Bernady O., editor, and Tarantino, Eufemia, editor

Published
2019
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19. Detection of Genetic Aberrations in Cancer Driving Signaling Pathways Based on Joint Analysis of Heterogeneous Genomics Data

Author

Jaksik, Roman, Fujarewicz, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Rocha, Álvaro, editor, and Guarda, Teresa, editor

Published
2018
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20. Comparing Different Data Fusion Strategies for Cancer Classification

Author

Pojda, Katarzyna, Jakubczak, Michał, Student, Sebastian, Świerniak, Andrzej, Fujarewicz, Krzysztof, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Rocha, Álvaro, editor, and Guarda, Teresa, editor

Published
2018
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21. Feature Selection Based on Logistic Regression for 2-Class Classification of Multidimensional Molecular Data

Author

Student, Sebastian, Płuciennik, Alicja, Jakubczak, Michał, Fujarewicz, Krzysztof, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Agre, Gennady, editor, van Genabith, Josef, editor, and Declerck, Thierry, editor

Published
2018
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23. Scalability of a Genomic Data Analysis in the BioTest Platform

Author

Psiuk-Maksymowicz, Krzysztof, Mrozek, Dariusz, Jaksik, Roman, Borys, Damian, Fujarewicz, Krzysztof, Swierniak, Andrzej, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Nguyen, Ngoc Thanh, editor, Tojo, Satoshi, editor, Nguyen, Le Minh, editor, and Trawiński, Bogdan, editor

Published
2017
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24. Large-Scale Data Classification System Based on Galaxy Server and Protected from Information Leak

Author

Fujarewicz, Krzysztof, Student, Sebastian, Zielański, Tomasz, Jakubczak, Michał, Pieter, Justyna, Pojda, Katarzyna, Świerniak, Andrzej, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Nguyen, Ngoc Thanh, editor, Tojo, Satoshi, editor, Nguyen, Le Minh, editor, and Trawiński, Bogdan, editor

Published
2017
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27. A Holistic Approach to Testing Biomedical Hypotheses and Analysis of Biomedical Data

Author

Psiuk-Maksymowicz, Krzysztof, Płaczek, Aleksander, Jaksik, Roman, Student, Sebastian, Borys, Damian, Mrozek, Dariusz, Fujarewicz, Krzysztof, Świerniak, Andrzej, Diniz Junqueira Barbosa, Simone, Series editor, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kara, Orhun, Series editor, Liu, Ting, Series editor, Kotenko, Igor, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Kozielski, Stanisław, editor, Mrozek, Dariusz, editor, Kasprowski, Paweł, editor, Małysiak-Mrozek, Bożena, editor, and Kostrzewa, Daniel, editor

Published
2016
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28. Integrated System Supporting Research on Environment Related Cancers

Author

Bensz, Wojciech, Borys, Damian, Fujarewicz, Krzysztof, Herok, Kinga, Jaksik, Roman, Krasucki, Marcin, Kurczyk, Agata, Matusik, Kamil, Mrozek, Dariusz, Ochab, Magdalena, Pacholczyk, Marcin, Pieter, Justyna, Puszynski, Krzysztof, Psiuk-Maksymowicz, Krzysztof, Student, Sebastian, Swierniak, Andrzej, Smieja, Jaroslaw, Kacprzyk, Janusz, Series editor, Król, Dariusz, editor, Madeyski, Lech, editor, and Nguyen, Ngoc Thanh, editor

Published
2016
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48. Generalized Backpropagation through Time for Continuous Time Neural Networks and Discrete Time Measurements

Author

Fujarewicz, Krzysztof, Galuszka, Adam, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Rutkowski, Leszek, editor, Siekmann, Jörg H., editor, Tadeusiewicz, Ryszard, editor, and Zadeh, Lotfi A., editor

Published
2004
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50. Integrated System Supporting Research on Environment Related Cancers

Author

Bensz, Wojciech, primary, Borys, Damian, additional, Fujarewicz, Krzysztof, additional, Herok, Kinga, additional, Jaksik, Roman, additional, Krasucki, Marcin, additional, Kurczyk, Agata, additional, Matusik, Kamil, additional, Mrozek, Dariusz, additional, Ochab, Magdalena, additional, Pacholczyk, Marcin, additional, Pieter, Justyna, additional, Puszynski, Krzysztof, additional, Psiuk-Maksymowicz, Krzysztof, additional, Student, Sebastian, additional, Swierniak, Andrzej, additional, and Smieja, Jaroslaw, additional

Published
2016
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