Despite standardization efforts there is still no widely used standard format for storing electro... more Despite standardization efforts there is still no widely used standard format for storing electrophysiological data. This standard is necessary for effective collaboration between scientists. This work deals with adjustments of existing general data/metadata model for electrophysiological experiments and proposal/implementation of HDF data format for their storage.
Abnormal functional connectivity (FC) has been commonly observed during alcohol use disorder (AUD... more Abnormal functional connectivity (FC) has been commonly observed during alcohol use disorder (AUD). In this work, FC analysis has been performed by incorporating EEG-based graph-theoretic analysis and a machine learning (ML) framework. Brain FC was quantified with synchronization likelihood (SL). Undirected graphs for each channel pair were constructed involving the SL measures. Furthermore, the graph-based features such as minimum spanning tree, distances between nodes, and maximum flow between the graph nodes were computed, termed as EEG data matrix. The matrix was used as input data to the ML framework to classify the study participants. The ML framework was validated with data acquired from 30 AUD patients and an age-matched group of 30 healthy controls. In this study, the classifiers such as SVM (accuracy = 98.7%), Naive Bayes (accuracy = 88.6%), and logistic regression (accuracy = 89%) have shown promising discrimination results. The method was compared with two existing metho...
With increasing amounts of experimental data, openness, fairness, and reproducibility of scientif... more With increasing amounts of experimental data, openness, fairness, and reproducibility of scientific experimental work have become important factors for researchers, journals and funding bodies. However, these kinds of challenges are not easily and directly achievable. The goal of this paper is to contribute to these efforts by introducing advances in building more mature lifecycle of electroencephalography/event-related potential data. The progressive data standardization initiatives, data formats, and trends in using machine and deep learning methods for processing of domain data are described and discussed. An open processing workflow based on the analysis of current software tools for preprocessing, processing and classification of electroencephalography/event-related potential data is proposed, implemented and verified on a publicly
The P3 (or P300) event-related brain potential is thought to reflect brain electric activity rela... more The P3 (or P300) event-related brain potential is thought to reflect brain electric activity related to cognitive processes. It is widely used not only in psychological research and clinical diagnosis but also in the brain computer interface (BCI) systems. To elicit the P3 component the oddball stimulation protocol is often used. In this paper, design of simple visual odd-ball protocol stimulator, which generates stimuli with predefined parameters, is described. The stimulator also generates additional signals for synchronization with EEG recording computer. Application of the stimulator in experimental work is also presented here.
Deep learning has emerged as a new branch of machine learning in recent years. Some of the relate... more Deep learning has emerged as a new branch of machine learning in recent years. Some of the related algorithms have been reported to beat state-of-the-art approaches in many applications. The main aim of this paper is to verify one of the deep learning algorithms, specifically a stacked autoencoder, to detect the P300 component. This component, as a specific brain response, is widely used in the systems based on brain-computer interface. A simple brain-computer interface experiment more than 200 school-age participants was performed to obtain large datasets containing the P300 component. After feature extraction the collected data were split into the training and testing sets. State-of-the art BCI classifiers (such as LDA, SVM, or Bayesian LDA) were applied to the data and then compared with the results of stacked autoencoders.
2012 5th International Conference on BioMedical Engineering and Informatics
ABSTRACT EEG/ERP (electroencephalography, event related potential) laboratories produce experimen... more ABSTRACT EEG/ERP (electroencephalography, event related potential) laboratories produce experimental data and metadata. Large amounts of data and various data formats lead to incompatible results and difficult communication among laboratories. Authors' research group has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP research. In addition, a module integrated within the EEG/ERP Portal allowing to process experimental data using analytic tools is developed. An integration of the EEG/ERP Portal with other systems is ensured using web services.
Introduction Navigated transcranial magnetic stimulation (nTMS) is non invasive method to map the... more Introduction Navigated transcranial magnetic stimulation (nTMS) is non invasive method to map the motor cortex including primary motor cortex (PrG - precentral gyrus) and premotor areas (PMa). This study aimed to investigate whether tumorous brain lesion induce a change in motor cortex localization or organisation investigated by nTMS. Methods We enrolled 10 patients with intraaxial motor tumor (gliomas). All patients underwent preoperative navigational MRI folowed by nTMS. Both lesional and non lesional hemispheres were stimulated. MEPs were recorded by EMG. The measured muscle was APB. MEPs latency for each positive stimulation point was measured. The surface of positive stimulation areas on the cortex were calculated for both hemispheres and results were compared. Results The positive MEPs responses were registered from PrG as well as from PMa with different latencies. There were mosaic distribution of short and long latencies of MEPs responses without dependence on the location in the PrG or PMa in both hemispheres. The positive motor area distributions were significantly larger from lesional than for non lesional hemisphere for both PrG and PMa areas (PrG lesional vs. non lesional surface = 947 mm2 vs. 393 mm2, PMa lesional vs. non lesional surface = 620 mm2 vs. 545 mm2). Conclusion The intraaxial motor eloquent tumors induce changes in motor cortex. The motor areas spread widely in the anterior-posterior direction in lesional hemisphere. The localisation short latencies found in PMa suggesting for detection of primary motor areas outside the PrG. This study was supported by the Charles University Research Fund Progress Q 39.
Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies, 2017
Unwillingness of many people to assume responsibilities for a personal health, fitness and wellne... more Unwillingness of many people to assume responsibilities for a personal health, fitness and wellness seems to be widespread. This can be partially remedied by individualized exercise and wellness program that integrates the basic knowledge domains: lifestyle, sports and fitness, and nutrition and personal/environmental health. However, collection, management and analysis of data and metadata related to these domains is demanding and time consuming task. Moreover, the appropriate annotation of raw data is crucial for their next processing. To promote such a program a software infrastructure for collection, storage, management, analysis and interpretation of health related data and metadata has been proposed and part of this infrastructure has been developed and tested outside laboratory conditions. This software prototype allows experimenters to collect various heterogeneous health related data in a highly organized and efficient way. Data are then evaluated and users can view relevant information related to their health and fitness.
ABSTRACT The paper deals with the help system as a part of dialogue grammar based development env... more ABSTRACT The paper deals with the help system as a part of dialogue grammar based development environment. This programming environment is intended especially for visually impaired programmers. The generation of help dialogues according to language grammar is described. Different levels of the help system are widely discussed and specific examples for C/C++ language are presented. The final part of the paper is devoted to possible improvements in the current help system.
ABSTRACT This paper deals with adaptation of typical dialogue manager structure to dialogue syste... more ABSTRACT This paper deals with adaptation of typical dialogue manager structure to dialogue system for blind and purblind programmers within the framework of the project: “Dialog System for Support of Visually Impaired Programmers”. The main goal of this project is to develop a dialogue system allowing generating, editing and debugging of source code. The dialogue is based on the natural speech communication, supported by the speech recognition system and speech synthesis considering the large extent prosodic aspects of the Czech language.
Despite standardization efforts there is still no widely used standard format for storing electro... more Despite standardization efforts there is still no widely used standard format for storing electrophysiological data. This standard is necessary for effective collaboration between scientists. This work deals with adjustments of existing general data/metadata model for electrophysiological experiments and proposal/implementation of HDF data format for their storage.
Abnormal functional connectivity (FC) has been commonly observed during alcohol use disorder (AUD... more Abnormal functional connectivity (FC) has been commonly observed during alcohol use disorder (AUD). In this work, FC analysis has been performed by incorporating EEG-based graph-theoretic analysis and a machine learning (ML) framework. Brain FC was quantified with synchronization likelihood (SL). Undirected graphs for each channel pair were constructed involving the SL measures. Furthermore, the graph-based features such as minimum spanning tree, distances between nodes, and maximum flow between the graph nodes were computed, termed as EEG data matrix. The matrix was used as input data to the ML framework to classify the study participants. The ML framework was validated with data acquired from 30 AUD patients and an age-matched group of 30 healthy controls. In this study, the classifiers such as SVM (accuracy = 98.7%), Naive Bayes (accuracy = 88.6%), and logistic regression (accuracy = 89%) have shown promising discrimination results. The method was compared with two existing metho...
With increasing amounts of experimental data, openness, fairness, and reproducibility of scientif... more With increasing amounts of experimental data, openness, fairness, and reproducibility of scientific experimental work have become important factors for researchers, journals and funding bodies. However, these kinds of challenges are not easily and directly achievable. The goal of this paper is to contribute to these efforts by introducing advances in building more mature lifecycle of electroencephalography/event-related potential data. The progressive data standardization initiatives, data formats, and trends in using machine and deep learning methods for processing of domain data are described and discussed. An open processing workflow based on the analysis of current software tools for preprocessing, processing and classification of electroencephalography/event-related potential data is proposed, implemented and verified on a publicly
The P3 (or P300) event-related brain potential is thought to reflect brain electric activity rela... more The P3 (or P300) event-related brain potential is thought to reflect brain electric activity related to cognitive processes. It is widely used not only in psychological research and clinical diagnosis but also in the brain computer interface (BCI) systems. To elicit the P3 component the oddball stimulation protocol is often used. In this paper, design of simple visual odd-ball protocol stimulator, which generates stimuli with predefined parameters, is described. The stimulator also generates additional signals for synchronization with EEG recording computer. Application of the stimulator in experimental work is also presented here.
Deep learning has emerged as a new branch of machine learning in recent years. Some of the relate... more Deep learning has emerged as a new branch of machine learning in recent years. Some of the related algorithms have been reported to beat state-of-the-art approaches in many applications. The main aim of this paper is to verify one of the deep learning algorithms, specifically a stacked autoencoder, to detect the P300 component. This component, as a specific brain response, is widely used in the systems based on brain-computer interface. A simple brain-computer interface experiment more than 200 school-age participants was performed to obtain large datasets containing the P300 component. After feature extraction the collected data were split into the training and testing sets. State-of-the art BCI classifiers (such as LDA, SVM, or Bayesian LDA) were applied to the data and then compared with the results of stacked autoencoders.
2012 5th International Conference on BioMedical Engineering and Informatics
ABSTRACT EEG/ERP (electroencephalography, event related potential) laboratories produce experimen... more ABSTRACT EEG/ERP (electroencephalography, event related potential) laboratories produce experimental data and metadata. Large amounts of data and various data formats lead to incompatible results and difficult communication among laboratories. Authors' research group has contributed to the building of a neuroinformatics infrastructure by developing and integrating data management and analytic tools for EEG/ERP research. In addition, a module integrated within the EEG/ERP Portal allowing to process experimental data using analytic tools is developed. An integration of the EEG/ERP Portal with other systems is ensured using web services.
Introduction Navigated transcranial magnetic stimulation (nTMS) is non invasive method to map the... more Introduction Navigated transcranial magnetic stimulation (nTMS) is non invasive method to map the motor cortex including primary motor cortex (PrG - precentral gyrus) and premotor areas (PMa). This study aimed to investigate whether tumorous brain lesion induce a change in motor cortex localization or organisation investigated by nTMS. Methods We enrolled 10 patients with intraaxial motor tumor (gliomas). All patients underwent preoperative navigational MRI folowed by nTMS. Both lesional and non lesional hemispheres were stimulated. MEPs were recorded by EMG. The measured muscle was APB. MEPs latency for each positive stimulation point was measured. The surface of positive stimulation areas on the cortex were calculated for both hemispheres and results were compared. Results The positive MEPs responses were registered from PrG as well as from PMa with different latencies. There were mosaic distribution of short and long latencies of MEPs responses without dependence on the location in the PrG or PMa in both hemispheres. The positive motor area distributions were significantly larger from lesional than for non lesional hemisphere for both PrG and PMa areas (PrG lesional vs. non lesional surface = 947 mm2 vs. 393 mm2, PMa lesional vs. non lesional surface = 620 mm2 vs. 545 mm2). Conclusion The intraaxial motor eloquent tumors induce changes in motor cortex. The motor areas spread widely in the anterior-posterior direction in lesional hemisphere. The localisation short latencies found in PMa suggesting for detection of primary motor areas outside the PrG. This study was supported by the Charles University Research Fund Progress Q 39.
Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies, 2017
Unwillingness of many people to assume responsibilities for a personal health, fitness and wellne... more Unwillingness of many people to assume responsibilities for a personal health, fitness and wellness seems to be widespread. This can be partially remedied by individualized exercise and wellness program that integrates the basic knowledge domains: lifestyle, sports and fitness, and nutrition and personal/environmental health. However, collection, management and analysis of data and metadata related to these domains is demanding and time consuming task. Moreover, the appropriate annotation of raw data is crucial for their next processing. To promote such a program a software infrastructure for collection, storage, management, analysis and interpretation of health related data and metadata has been proposed and part of this infrastructure has been developed and tested outside laboratory conditions. This software prototype allows experimenters to collect various heterogeneous health related data in a highly organized and efficient way. Data are then evaluated and users can view relevant information related to their health and fitness.
ABSTRACT The paper deals with the help system as a part of dialogue grammar based development env... more ABSTRACT The paper deals with the help system as a part of dialogue grammar based development environment. This programming environment is intended especially for visually impaired programmers. The generation of help dialogues according to language grammar is described. Different levels of the help system are widely discussed and specific examples for C/C++ language are presented. The final part of the paper is devoted to possible improvements in the current help system.
ABSTRACT This paper deals with adaptation of typical dialogue manager structure to dialogue syste... more ABSTRACT This paper deals with adaptation of typical dialogue manager structure to dialogue system for blind and purblind programmers within the framework of the project: “Dialog System for Support of Visually Impaired Programmers”. The main goal of this project is to develop a dialogue system allowing generating, editing and debugging of source code. The dialogue is based on the natural speech communication, supported by the speech recognition system and speech synthesis considering the large extent prosodic aspects of the Czech language.
Uploads