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Direct assembly of genome signals from nanopore sequencing
Karmazinová, Inna ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
The aim of this bachelor thesis is to search for overlaps between signals from nanopore sequencing using MinION device version R9. The theoretical part deals with methods used for genome assembly - greedy algorithm, overlap-layout-consensus (OLC) and de Bruijn graphs. Oxford Nanopore Technologies introduced the MinION device, which simplifies sequencing using the current change, which occurs while the DNA is passing through the nanopore. The error rate of the device is still high, the accuracy problem occurs during the base-calling. Using the difference signal, possibly also the dynamic time warping, it is possible to find overlaps between the individual signals. Signal analysis and genome assembly using the MinION signal could provide better accuracy.
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Dynamic Programming in Biosignal Processing
Procházka, Petr ; Kolářová, Jana (referee) ; Klimek, Martin (advisor)
Bachelor thesis describes the dynamic time warping method (DTW), which is used for extrasystoles detection in ECG signales. Several methods for extracting a reference cycle are described in this paper. These methods are applied either to whole heart cycles or just to QRS complexes. Afterwards these methods are compared with results of cluster analysis.
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Identification of persons via voice imprint
Mekyska, Jiří ; Atassi, Hicham (referee) ; Smékal, Zdeněk (advisor)
This work deals with the text-dependent speaker recognition in systems, where just a few training samples exist. For the purpose of this recognition, the voice imprint based on different features (e.g. MFCC, PLP, ACW etc.) is proposed. At the beginning, there is described the way, how the speech signal is produced. Some speech characteristics important for speaker recognition are also mentioned. The next part of work deals with the speech signal analysis. There is mentioned the preprocessing and also the feature extraction methods. The following part describes the process of speaker recognition and mentions the evaluation of the used methods: speaker identification and verification. Last theoretically based part of work deals with the classifiers which are suitable for the text-dependent recognition. The classifiers based on fractional distances, dynamic time warping, dispersion matching and vector quantization are mentioned. This work continues by design and realization of system, which evaluates all described classifiers for voice imprint based on different features.
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Automatic speech recordings segmentation tool
Santa, Roman ; Zvončák, Vojtěch (referee) ; Kováč, Daniel (advisor)
Nástroj pre automatickú segmentáciu spracováva nahrávky reči a extrahuje hovorené slovo z nahrávok. Je dôležité, aby pokročilá analýza pracovala iba s rečovými časťami z nahrávky. Nástroj na segmentáciu má ulahčiť spracovanie nahrávok pre analýzu rozdielov medzi hláskami pacientov s parkinsonovou chorobou a tými zdravými. Cieľ tejto práce je navrhnúť a otestovať detektory reči s Google WebRTC detektorom a vybrať ten najvhodnejší detektor reči s minimálnym počtom chýb. Ďalej, vytvoriť nástroj na segmentáciu nahrávok a otestovať rozpoznávanie reči pomocou dynamic time warping. Bola použitá databáza poskytnutá laboratóriom pre analýzu mozgových ochorení. Obsahuje české a maďarské nahrávky s rovnakým počtom mužských a ženských pacientov a aj rovnakým počtom zdravých pacientov a pacientov s parkinsonovou chorobou. Najlepšie výsledky v testoch dosiahol detektor na základe energie reči. Nebol zistený žiaden rozdiel v presnosti detektoru pri spracovaní mužských a ženských nahrávok alebo nahrávok zdravých či chorých pacientov. Nahrávky s nízkym odstupom signálu od šumu boli náročnejšie na spracovanie s frekvenciou chýb od 12%. Na základe výsledkov, bol navrhnutý nový detektor pre spracovanie úplnej nahrávky. Na záver bol testovaný algoritmus pre rozpoznávanie podobnosti reči na základe melovských kepstrálnych koeficientov.
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Recognition methods for biosignals
Juračka, Zdeněk ; Vítek, Martin (referee) ; Kolářová, Jana (advisor)
The thesis is focused on the recognition methods study used in one-dimensional signal processing. A lot of recognition methods exist, this thesis briefly describes the principle of some of them, e.g. artificial neural networks, fuzzy systems, expert systems and decision trees. Dynamic time warping (DTW) method has been chosen for signal processing available from UBMI database. DTW can be used as a non-linear signal processing method. The result of this method is to determine the similarity of two compared signals on the basis of their distance calculation. One of the reasons for choosing this method was the possibility of various length signal processing. The principle of the method as well as the calculation of the distance between two input data sequences is described in the thesis. DTW path finding method is also mentioned. The method was applied on randomly selected numbers and a set of simulated signals. The method was applied to ECG and action potential signals recorded on the isolated rabbit heart. DTW was used to evaluate shape changes of these signals in repeated phases of the experiment known as ischemia and reperfusion. Selected cardiac cycles were detected and included into different experiment phases on the basis of calculated distance results using DTW. Sensitivity was selected as an evaluative criterion of this classification method. It reached a value of 65%. DTW algorithm was further tested on the selected cardiac cycle mapping to the corresponding minute record in the selected experiment phase. It reached a sensitivity of 68.3%. The motion artifact appearance was monitored using DTW on AP signals. The method functioned more precisely on signals measured in ischemia phases. Along with the above mentioned, the thesis discusses all aspects of heart electrical manifestation activities called as ECG signals and action potentials, such as origin, propagation, recording, post-processing and measuring out.
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A tool for simultaneous playback of multiple composition interpretations
Švejcar, Michael ; Ištvánek, Matěj (referee) ; Miklánek, Štěpán (advisor)
The purpose of this Bachelor’s thesis was to create a piece of software which enables the user to simultaneously play back multiple interpretations of a musical piece and switch between them instantaneously. This was achieved using the App Designer in the MATLAB environment, which is intended for developing applications with graphical user interface. The key to the development of the application was especially the use of available toolboxes and algorithms for computing chromagrams and multiscale dynamic time warping. The final IntSwitcher player enables the user to load two recordings of interpretations of one song. Chromagrams which characterize the individual recordings in terms of tonal development over time are first calculated from the input files. After that, the multiscale dynamic time warping method is applied on the chromagrams, which outputs the warping path. The warping path in this case is a matrix, in which musically corresponding samples of loaded audio files are assigned together with the resolution of 50 ms. From this, the corresponding time position of currently inactive track is computed along with its slider position. If the user switches the currently played recording, the second track starts playing in the same part of composition, even if that part is at a different time in each of the individual recordings. The final software is an appropriate tool for studying differences between various interpretations of the same musical piece.
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Dynamic time warping in biosignal processing
Novobilský, Petr ; Provazník, Ivo (referee) ; Kolářová, Jana (advisor)
The thesis deals with one of the non-linear methods for signal processing - dynamic time warping (DTW). The method observes shape changes, which should be used in biomedical signals processing. The thesis involves the method description and consecution for finding DTW optimal way. The method is applied on the number series in the edutainment program, on the group of simulated signals and real electrocardiograms (ECG). ECG recordings were gained by performing experiments on the Masaryk University and their aim was clarifying the influence of voltage-sensitive dye on the heart tissue. One-lead ECG was described in time domain, frequency domain, time-frequency domain and subsequently remitted to DTW algorithm. The method outcomes evaluates the diversity rate of ECG signals obtained in each experiment stages. During the data evaluation were followed up the changes in process of the tension-sensible paint application and the stage of scouring toward control. The difference of elaborating signals group was verified in the time domain (37,5 %), in the frequency domain (75 %) and in the time-frequency domain (25 %). However, due to the small data group was not possible to explicitly approve the activity of voltage-sensitive dye on the heart tissue and to determinate limiting value of minimum algorithm way DTW for each heart round electrocardiogram classification. In the more data group analysis it is supposed to manifest the trend of growth heart round ECG differences in the stage of staining toward the stage of scouring.
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Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
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System for finding duplicate recordings based on audio information
Švejcar, Michael ; Miklánek, Štěpán (referee) ; Ištvánek, Matěj (advisor)
This diploma thesis discusses different methods of detecting duplicates in a music file database. The problem at hand is that files containing the same recording may differ in sound quality, applause at the end of a performance and other such parameters. The aim of this thesis is to design and implement a system that identifies duplicate recordings and provides an output file for the comparison. The system needs to not be affected by the mentioned parameters but precise enough to prevent matching non-identical recordings. The system is realized using the Python programming language, freely available libraries for computing chroma features, Image Hashing technique and multiple variants of the dynamic time warping algorithm. Three comparison methods were implemented in the system, differing in precision and computation complexity. The methods were then tested on a prepared dataset and four preset precision options were created. The final system seems very precise and insusceptible to detecting recordings that are very similar but not identical as duplicates, for example in case of different interpretations of the same musical piece.
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System for finding duplicate recordings based on audio information
Švejcar, Michael ; Miklánek, Štěpán (referee) ; Ištvánek, Matěj (advisor)
This diploma thesis discusses different methods of detecting duplicates in a music file database. The problem at hand is that files containing the same recording may differ in sound quality, applause at the end of a performance and other such parameters. The aim of this thesis is to design and implement a system that identifies duplicate recordings and provides an output file for the comparison. The system needs to not be affected by the mentioned parameters but precise enough to prevent matching non-identical recordings. The system is realized using the Python programming language, freely available libraries for computing chroma features, Image Hashing technique and multiple variants of the dynamic time warping algorithm. Three comparison methods were implemented in the system, differing in precision and computation complexity. The methods were then tested on a prepared dataset and four preset precision options were created. The final system seems very precise and insusceptible to detecting recordings that are very similar but not identical as duplicates, for example in case of different interpretations of the same musical piece.
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