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Papers by Katarína Bachratá

Mathematics, Jul 13, 2023

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Communications - Scientific letters of the University of Zilina, 2009

Symmetry

RBC (Red Blood Cell) membrane is a highly elastic structure, and proper modelling of this elastic... more RBC (Red Blood Cell) membrane is a highly elastic structure, and proper modelling of this elasticity is essential for biomedical applications that involve computational experiments with blood flow. In this work, we present a new method for estimating one of the key parameters of red blood cell elasticity, which uses a neural network trained on the simulation outputs. We test classic LSTM (Long-Short Term Memory) architecture for the time series regression task, and we also experiment with novel CNN-LSTM (Convolutional Neural Network) architecture. We paid special attention to investigating the impact of the way the three-dimensional training data are reduced to their two-dimensional projections. Such a comparison is possible thanks to working with simulation outputs that are equivalently defined for all dimensions and their combinations. The obtained results can be used as recommendations for an appropriate way to record real experiments for which the reduced dimension of the acquir...

2014 ELEKTRO, 2014

The complex problem of simulating the attributes and abilities of microfluidic chambers can be di... more The complex problem of simulating the attributes and abilities of microfluidic chambers can be divided into several interconnected areas like modelling the flow through chambers of various shapes, elastic models of particles, the interaction of fluid flow and the particles, modelling the adhesion on the surface of the devices, estimating the necessary degree of accuracy of utilized models, mastering and realization of computing-intensive simulations. In contrary to detailed results in each of this specific areas, in this paper we are going to outline the overall picture of our research, as well as of other research we know of, in the way we have become acquainted with it in the course of the past few years.

2011 9th International Conference on Emerging eLearning Technologies and Applications (ICETA), 2011

The problems in the e-learning course market (for example their low sales compared to mobile appl... more The problems in the e-learning course market (for example their low sales compared to mobile applications) show that besides the development of new technologies, it is necessary to also pay attention to other factors that affect the creation of meaningful courses. These factors are the content of said courses, as well as their real applications as related to their didactic and educational aims. Furthermore, attention has to be paid to the administration and maintenance of courses and the training of educators in their proper use. In this article we aim to show the risks of over-dependence on ICT technologies in the teaching of mathematics, and suggest who should be preparing meaningful e-learning courses.

2019 17th International Conference on Emerging eLearning Technologies and Applications (ICETA), 2019

We describe a variant of the well-known educational card game “Set”. A web-based interface is int... more We describe a variant of the well-known educational card game “Set”. A web-based interface is introduced for real-time evaluation of the game. We discuss the advantages of this approach, which may be used for various other games.

The methods that are explained in this textbook (based on linear spaces) are not better than thos... more The methods that are explained in this textbook (based on linear spaces) are not better than those a human would use for the analysis of a small amount of data based on experience. However, today it is necessary to constantly analyze a very large number of processes, often in unfavourable conditions and with a short reaction time. In these conditions it is better to use computers instead of humans for the analysis of processes. Such discrete methods of analysis are are contained in this book.

2012 IEEE 10th International Conference on Emerging eLearning Technologies and Applications (ICETA), 2012

In an Economic Statistics course, we were faced with the challenge of forming mathematical thinki... more In an Economic Statistics course, we were faced with the challenge of forming mathematical thinking in students with often strongly negative attitudes towards mathematics. We had to contend with a reduced number of hours compared to courses in the previous accreditation. For instruction, we chose the creation of simple statistical models in a spreadsheet application, which could be created even without understanding how and why a theory works. Theoretical justification and the derivation of models was required of only the best students.

Human Mutation, 2015

Although most of the pertinent data on the sequence-directed processes leading to genome rearrang... more Although most of the pertinent data on the sequence-directed processes leading to genome rearrangements (GRs) have come from studies on somatic tissues, little is known about GRs in the germ line of patients with hereditary disorders. This study aims at identifying DNA motifs and higher order structures of genome architecture, which can result in losses and gains of genetic material in the germ line. We first identified candidate motifs by studying 112 pathogenic germ-line GRs in hereditary colorectal cancer patients, and subsequently created an algorithm, termed recombination type ratio, which correctly predicts the propensity of rearrangements with respect to homologous versus nonhomologous recombination events.

tts.kis.fri.utc.sk

... do radu )()( ) t t k k k Φ ∑ = ∞ −∞ ξ ξ c x ... [4] JAKAB, F., ANDRÉ, M.: Measuring and Evalu... more ... do radu )()( ) t t k k k Φ ∑ = ∞ −∞ ξ ξ c x ... [4] JAKAB, F., ANDRÉ, M.: Measuring and Evaluation of QoS Parameters in IP Networks, V. Doktorandská konferencia a tudentská vedecká odborná súťa TU v Koiciach, Koice, 13.5.2004, pp. 119-120, ISBN 80-968395-9-4 ...

Quality of Service (QoS) in IP multimedia converged networks which provides different serving lev... more Quality of Service (QoS) in IP multimedia converged networks which provides different serving levels of different traffic flows is a crucial issue. The token bucket mechanism is one of core QoS concept whose well understanding is required and improve modelling and implementation techniques required in such multimedia networks. This paper describes and defines two basic network elements- a work conserving link and a token bucket. We define two different types of a token bucket and we show that both of them can be transformed into some work conserving link. Transformation means that the work conserving link allows input unit to pass if and only if the token bucket would allow input unit to pass.

Simulation of microfluidic devices is a great tool for optimizing these devices. For the developm... more Simulation of microfluidic devices is a great tool for optimizing these devices. For the development of simulation models, it is necessary to ensure a sufficient degree of simulation accuracy. Accuracy is ensured by measuring appropriate values that tell us about the course of the simulation and can also be measured in a real experiment. Measured values will simplify the real situation so that we can develop the model for a specific purpose and measure the values that are relevant to the research. In this article we present the approach in which the data we have gained from simulation are used to improve the quality of data processing from video from a real experiment.

Computer simulations of a blood flow in microfluidic devices are an important tool to make their ... more Computer simulations of a blood flow in microfluidic devices are an important tool to make their development and optimization more efficient. These simulations quickly become limited by their computational complexity. Analysis of large output data by machine learning methods is a possible solution of this problem. We apply deep learning methods in this paper, namely we use convolutional neural networks (CNNs) for description and prediction of the red blood cells’ trajectory, which is crucial in modeling of a blood flow. We evaluated several types of CNN architectures, formats of theirs input data and the learning methods on simulation data inspired by a real experiment. The results we obtained establish a starting point for further use of deep learning methods in reducing computational demand of microfluid device simulations.

2019 International Conference on Information and Digital Technologies (IDT), 2019

Understanding the biophysical properties of cells is one of the highly researched areas in recent... more Understanding the biophysical properties of cells is one of the highly researched areas in recent years. There are many examples of the usefulness of this knowledge, such as [1], where the deformability of cells is used as a marker for distinguishing malignant cells. Thus the motivation to model elastic cells with a nucleus is quite strong and we are currently working on a computational model of a cell with a nucleus. In order to obtain a working model, one must take several steps. Among them is the calibration process. For this step, we chose biological experiment where cells are stretched using optical traps. Using this method, the cell is stretched more linearly then in experiments with holders, such as silica beads, attached to the cell. That and the fact that this method was used on circulating tumour cells (CTC) are the reasons we chose this particular experiment. In this work, we focus on the simulation of the optical stretcher and its validation for our further work. We firs...

In this article we will give brief overview of elastic parameter of our red blood cell (RBC) mode... more In this article we will give brief overview of elastic parameter of our red blood cell (RBC) model. Next we will discuss the importance of calibration of these parameters to get behaviour close to the behaviour of the actual RBC. For this purpose we used a widely known experiment where RBC are stretched by attaching silica beads to their membrane and applying force to these beads. The main focus of this article is how to model this stretching process and more precisely, how to choose between several options available to simulate the optical tweezers stretching. We compared three approaches - “points”, “hat” and “ring”, and based on simulation results selected the “ring” approach. Afterwards we computed working “rings” for different cell discretizations.