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Papers by Andrzej Swierniak

Research paper thumbnail of Chamonix, France BIOTECHNO 2014 Editors BIOTECHNO 2014 Committee BIOTECHNO Advisory Chairs BIOTECHNO 2014 Technical Program Committee

in Chamonix, France, covered these three main areas: bioinformatics, biomedical technologies, and... more in Chamonix, France, covered these three main areas: bioinformatics, biomedical technologies, and biocomputing. Bioinformatics deals with the system-level study of complex interactions in biosystems providing a quantitative systemic approach to understand them and appropriate tool support and concepts to model them. Understanding and modeling biosystems requires simulation of biological behaviors and functions. Bioinformatics itself constitutes a vast area of research and specialization, as many classical domains such as databases, modeling, and regular expressions are used to represent, store, retrieve and process a huge volume of knowledge. There are challenging aspects concerning biocomputation technologies, bioinformatics mechanisms dealing with chemoinformatics, bioimaging, and neuroinformatics. Biotechnology is defined as the industrial use of living organisms or biological techniques developed through basic research. Bio-oriented technologies became very popular in various re...

Research paper thumbnail of Multilayer Evolutionary Games – A New Tool for Modelling Cancer Cell Heterogeneity

Research paper thumbnail of The Stochastic Mathematical Model Predicts Angio-Therapy Could Delay the Emergence of Metastases in Lung Cancer

Biocybernetics and Biomedical Engineering – Current Trends and Challenges, 2021

Research paper thumbnail of Robust Stabilization of Fault Tolerant Decentralized Linear Systems

IFAC Proceedings Volumes, 1998

Research paper thumbnail of Intelligent Information and Database Systems

Lecture Notes in Computer Science, 2010

Research paper thumbnail of Fuzzy controllers design via fixed point theorem

Fuzzy Sets and Systems, 1986

Abstract We present a possibility of fuzzy systems design basing on a special fixed point theorem... more Abstract We present a possibility of fuzzy systems design basing on a special fixed point theorem. We consider systems described by input-output models with fuzzy uncertainty. A control objective is to reach the desired output neighborhood.

Research paper thumbnail of Radiation Induced Bystander Effects in Human Lymphoblastoid Cells

Research paper thumbnail of Optimization of Antiangiogenic Therapy as Optimal Control Problem

Research paper thumbnail of Association between patient-and tumor-related factors and the gene expression profile of papillary thyroid cancer

Research paper thumbnail of Different Models of Chemotherapy Taking Into Account Drug Resistance Stemming from Gene Amplification

International Journal of Applied Mathematics and Computer Science, 2003

Research paper thumbnail of System Modeling and Machine Learning in Prediction of Metastases in Lung Cancer

Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies

Research paper thumbnail of Potential of Radiomics Features for Predicting Time to Metastasis in NSCLC

Lecture Notes in Computer Science, 2022

Research paper thumbnail of Comparing Different Data Fusion Strategies for Cancer Classification

Proceedings of the International Conference on Information Technology & Systems (ICITS 2018), 2018

Automatic cancer diagnosis can be performed based on different types of data sets. Some of them a... more Automatic cancer diagnosis can be performed based on different types of data sets. Some of them are microarray data, clinical trial data and cytopathological data. Usually class prediction is done by chosen classification method, for example a machine learning algorithm, and uses only one type of the available data. In this work an additional predictive value of a fusion of these three types of data is examined. To perform such research, authors upgrade and use their recently developed Spicy system. Different data fusion strategies have been tested on thyroid cancer data set. The workflow that has been created and the new module of a data fusion implemented in the Spicy system allows to qualify fusion of microarray data, clinical trials data and information about the Bethesda system class as a valuable method of prediction the thyroid nodule malignancy.

Research paper thumbnail of Modelling of cell aging - system theoretic approach

Journal of Medical Informatics and Technologies, 2001

Research paper thumbnail of W co grają komórki rakowe

Przegląd Elektrotechniczny, 2010

Research paper thumbnail of Modeling and Optimization of Radio-Chemotherapy

Advances in Intelligent Systems and Computing, 2019

Pre- or post-operational chemo-radiotherapy have become one of the standard adjuvant therapies in... more Pre- or post-operational chemo-radiotherapy have become one of the standard adjuvant therapies in recent years. Though both chemo- and radiotherapy protocols are standardized, the question about the order in which they should be applied, or concurrency, remains an open question. In this work we attempt to answer it with mathematical modeling and optimization of two-dimensional control that represents therapy in a control-theory based approach. In order to address this problem, two issues are discussed. First, two different ways of modeling tumor growth under therapy are compared. For each of them, the necessary conditions for optimal control representing the therapy are presented and discussed. Then, Kaplan-Meier survival curves are compared for standard therapy protocols used in clinics and different approaches to model tumor growth. Finally, a framework for analysis of treatment efficacy is presented, in which optimization and survival analysis are used sequentially.

Research paper thumbnail of Molecular markers to differentiate between pancreatic cancer and normal pancreas/chronic pancreatitis: Gene expression profiling study

Journal of Clinical Oncology, 2007

21150 Background: The aim of the study was to analyze the gene expression profile of pancreatic c... more 21150 Background: The aim of the study was to analyze the gene expression profile of pancreatic cancer by multivariate methods of class prediction. Methods: The snap-frozen or RNA-later preserved samples of 18 pancreatic adenocarcinomas, 9 chronic pancreatitis cases and 6 specimens collected from microscopically unchanged pancreas (N/CP) were analyzed by HG-U133 Plus 2.0 oligonucleotide microarrays (Affymetrix). The obtained dataset was pre-processed using GC-RMA method, gene selection was carried out both by class comparison methods (Welch test with Benjamini-Hochberg correction, False Discovery Rate FDR<5%) and by our own algorithms of class prediction, based on Support Vector Machines technique (Recurrent Feature Replacement and Bootstrap-Based Feature Ranking). Real- time quantitative PCR (Q-PCR) was carried out on Applied Biosystems 7900 HT machine, with Universal Probe Library (Roche) fluorescent probes and normalization by three reference genes index (geNorm, Vandesompele ...

Research paper thumbnail of Optimal Control in a Model of Chemotherapy-induced Radiosensilisation

Mathematica Applicanda, 2019

Research paper thumbnail of Development of a population of cancer cells: Observation and modeling by a Mixed Spatial Evolutionary Games approach

Journal of theoretical biology, Sep 20, 2016

Living cells, like whole living organisms during evolution, communicate with their neighbors, int... more Living cells, like whole living organisms during evolution, communicate with their neighbors, interact with the environment, divide, change their phenotypes, and eventually die. The development of specific ways of communication (through signaling molecules and receptors) allows some cellular subpopulations to survive better, to coordinate their physiological status, and during embryonal development to create tissues and organs or in some conditions to become tumors. Populations of cells cultured in vitro interact similarly, also competing for space and nutrients and stimulating each other to better survive or to die. The results of these intercellular interactions of different types seem to be good examples of biological evolutionary games, and have been the subjects of simulations by the methods of evolutionary game theory where individual cells are treated as players. Here we present examples of intercellular contacts in a population of living human cancer HeLa cells cultured in v...

Research paper thumbnail of A Holistic Approach to Testing Biomedical Hypotheses and Analysis of Biomedical Data

Communications in Computer and Information Science, 2016

Testing biomedical hypotheses is performed based on advanced and usually many-step analysis of bi... more Testing biomedical hypotheses is performed based on advanced and usually many-step analysis of biomedical data. This requires sophisticated analytical methods and data structures that allow to store intermediate results, which are needed in the subsequent steps. However, biomedical data, especially reference data, often change in time and new analytical methods are created every year. This causes the necessity to repeat the iterative analyses with new methods and new reference data sets, which in turn causes frequent changes of the underlying data structures. Such instability of data structures can be mitigated by the use of the idea of data lake, instead of traditional database systems.

Research paper thumbnail of Chamonix, France BIOTECHNO 2014 Editors BIOTECHNO 2014 Committee BIOTECHNO Advisory Chairs BIOTECHNO 2014 Technical Program Committee

in Chamonix, France, covered these three main areas: bioinformatics, biomedical technologies, and... more in Chamonix, France, covered these three main areas: bioinformatics, biomedical technologies, and biocomputing. Bioinformatics deals with the system-level study of complex interactions in biosystems providing a quantitative systemic approach to understand them and appropriate tool support and concepts to model them. Understanding and modeling biosystems requires simulation of biological behaviors and functions. Bioinformatics itself constitutes a vast area of research and specialization, as many classical domains such as databases, modeling, and regular expressions are used to represent, store, retrieve and process a huge volume of knowledge. There are challenging aspects concerning biocomputation technologies, bioinformatics mechanisms dealing with chemoinformatics, bioimaging, and neuroinformatics. Biotechnology is defined as the industrial use of living organisms or biological techniques developed through basic research. Bio-oriented technologies became very popular in various re...

Research paper thumbnail of Multilayer Evolutionary Games – A New Tool for Modelling Cancer Cell Heterogeneity

Research paper thumbnail of The Stochastic Mathematical Model Predicts Angio-Therapy Could Delay the Emergence of Metastases in Lung Cancer

Biocybernetics and Biomedical Engineering – Current Trends and Challenges, 2021

Research paper thumbnail of Robust Stabilization of Fault Tolerant Decentralized Linear Systems

IFAC Proceedings Volumes, 1998

Research paper thumbnail of Intelligent Information and Database Systems

Lecture Notes in Computer Science, 2010

Research paper thumbnail of Fuzzy controllers design via fixed point theorem

Fuzzy Sets and Systems, 1986

Abstract We present a possibility of fuzzy systems design basing on a special fixed point theorem... more Abstract We present a possibility of fuzzy systems design basing on a special fixed point theorem. We consider systems described by input-output models with fuzzy uncertainty. A control objective is to reach the desired output neighborhood.

Research paper thumbnail of Radiation Induced Bystander Effects in Human Lymphoblastoid Cells

Research paper thumbnail of Optimization of Antiangiogenic Therapy as Optimal Control Problem

Research paper thumbnail of Association between patient-and tumor-related factors and the gene expression profile of papillary thyroid cancer

Research paper thumbnail of Different Models of Chemotherapy Taking Into Account Drug Resistance Stemming from Gene Amplification

International Journal of Applied Mathematics and Computer Science, 2003

Research paper thumbnail of System Modeling and Machine Learning in Prediction of Metastases in Lung Cancer

Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies

Research paper thumbnail of Potential of Radiomics Features for Predicting Time to Metastasis in NSCLC

Lecture Notes in Computer Science, 2022

Research paper thumbnail of Comparing Different Data Fusion Strategies for Cancer Classification

Proceedings of the International Conference on Information Technology & Systems (ICITS 2018), 2018

Automatic cancer diagnosis can be performed based on different types of data sets. Some of them a... more Automatic cancer diagnosis can be performed based on different types of data sets. Some of them are microarray data, clinical trial data and cytopathological data. Usually class prediction is done by chosen classification method, for example a machine learning algorithm, and uses only one type of the available data. In this work an additional predictive value of a fusion of these three types of data is examined. To perform such research, authors upgrade and use their recently developed Spicy system. Different data fusion strategies have been tested on thyroid cancer data set. The workflow that has been created and the new module of a data fusion implemented in the Spicy system allows to qualify fusion of microarray data, clinical trials data and information about the Bethesda system class as a valuable method of prediction the thyroid nodule malignancy.

Research paper thumbnail of Modelling of cell aging - system theoretic approach

Journal of Medical Informatics and Technologies, 2001

Research paper thumbnail of W co grają komórki rakowe

Przegląd Elektrotechniczny, 2010

Research paper thumbnail of Modeling and Optimization of Radio-Chemotherapy

Advances in Intelligent Systems and Computing, 2019

Pre- or post-operational chemo-radiotherapy have become one of the standard adjuvant therapies in... more Pre- or post-operational chemo-radiotherapy have become one of the standard adjuvant therapies in recent years. Though both chemo- and radiotherapy protocols are standardized, the question about the order in which they should be applied, or concurrency, remains an open question. In this work we attempt to answer it with mathematical modeling and optimization of two-dimensional control that represents therapy in a control-theory based approach. In order to address this problem, two issues are discussed. First, two different ways of modeling tumor growth under therapy are compared. For each of them, the necessary conditions for optimal control representing the therapy are presented and discussed. Then, Kaplan-Meier survival curves are compared for standard therapy protocols used in clinics and different approaches to model tumor growth. Finally, a framework for analysis of treatment efficacy is presented, in which optimization and survival analysis are used sequentially.

Research paper thumbnail of Molecular markers to differentiate between pancreatic cancer and normal pancreas/chronic pancreatitis: Gene expression profiling study

Journal of Clinical Oncology, 2007

21150 Background: The aim of the study was to analyze the gene expression profile of pancreatic c... more 21150 Background: The aim of the study was to analyze the gene expression profile of pancreatic cancer by multivariate methods of class prediction. Methods: The snap-frozen or RNA-later preserved samples of 18 pancreatic adenocarcinomas, 9 chronic pancreatitis cases and 6 specimens collected from microscopically unchanged pancreas (N/CP) were analyzed by HG-U133 Plus 2.0 oligonucleotide microarrays (Affymetrix). The obtained dataset was pre-processed using GC-RMA method, gene selection was carried out both by class comparison methods (Welch test with Benjamini-Hochberg correction, False Discovery Rate FDR<5%) and by our own algorithms of class prediction, based on Support Vector Machines technique (Recurrent Feature Replacement and Bootstrap-Based Feature Ranking). Real- time quantitative PCR (Q-PCR) was carried out on Applied Biosystems 7900 HT machine, with Universal Probe Library (Roche) fluorescent probes and normalization by three reference genes index (geNorm, Vandesompele ...

Research paper thumbnail of Optimal Control in a Model of Chemotherapy-induced Radiosensilisation

Mathematica Applicanda, 2019

Research paper thumbnail of Development of a population of cancer cells: Observation and modeling by a Mixed Spatial Evolutionary Games approach

Journal of theoretical biology, Sep 20, 2016

Living cells, like whole living organisms during evolution, communicate with their neighbors, int... more Living cells, like whole living organisms during evolution, communicate with their neighbors, interact with the environment, divide, change their phenotypes, and eventually die. The development of specific ways of communication (through signaling molecules and receptors) allows some cellular subpopulations to survive better, to coordinate their physiological status, and during embryonal development to create tissues and organs or in some conditions to become tumors. Populations of cells cultured in vitro interact similarly, also competing for space and nutrients and stimulating each other to better survive or to die. The results of these intercellular interactions of different types seem to be good examples of biological evolutionary games, and have been the subjects of simulations by the methods of evolutionary game theory where individual cells are treated as players. Here we present examples of intercellular contacts in a population of living human cancer HeLa cells cultured in v...

Research paper thumbnail of A Holistic Approach to Testing Biomedical Hypotheses and Analysis of Biomedical Data

Communications in Computer and Information Science, 2016

Testing biomedical hypotheses is performed based on advanced and usually many-step analysis of bi... more Testing biomedical hypotheses is performed based on advanced and usually many-step analysis of biomedical data. This requires sophisticated analytical methods and data structures that allow to store intermediate results, which are needed in the subsequent steps. However, biomedical data, especially reference data, often change in time and new analytical methods are created every year. This causes the necessity to repeat the iterative analyses with new methods and new reference data sets, which in turn causes frequent changes of the underlying data structures. Such instability of data structures can be mitigated by the use of the idea of data lake, instead of traditional database systems.