THE OPEN SOURCE MATLAB TOOLBOX Gait-CAD

AND ITS APPLICATION TO BIOELECTRIC SIGNAL PROCESSING

R. Mikut, O. Burmeister, S. Braun, M. Reischl
Institute for Applied Computer Science, Forschungszentrum Karlsruhe GmbH, Germany
E-Mail ralf.mikut@iai.fzk.de

Abstract In this paper, the open source Matlab toolbox analysis of time series and features, especially for classifi-
Gait-CAD is presented. This toolbox is designed for the cation, but also for regression problems. Our intention is
visualization and analysis of time series and single features the design of an open platform as a framework for the
with a special focus to classification problems. The aim is development and improvement of data mining methods.
to provide an open platform for the development and im-
provement of data mining methods and the application to Methods
various medical and technical problems.
The toolbox Gait-CAD bases on Matlab (tested for the
Keywords Data Mining, Tools, Neuroprostheses
versions 5.3 and 2007b). The decision to a Matlab-based
solution was made to use the wide mathematical function-
Introduction ality of this package provided by The Mathworks Inc. A
In many applications, large data sets of time series and main disadvantage is the need for a MATLAB license.
single features are recorded. An at least semi-automatic The toolbox is operated by a graphical user interface
search for unknown or partially known relations requires (GUI) with menu items and control elements like popup
the use of data mining methods [1]. In the last years, a huge lists, checkboxes, and edit elements (Figure 1). This en-
number of potentially useful methods and software tools ables inexperienced users to work with the toolbox. How-
have been proposed including methods for feature extrac- ever, the implemented algorithms work independently
tion, classification, and regression. from the GUI. Thus, the Matlab-typical way of program-
Many existing software tools are very powerful, but they ming using a command prompt and variables is possible.
cover only a very limited subset of implemented methods. Furthermore, an automation and batch standardization of
However, the coupling between different necessary proc- analyzes is possible by designing individual macros. More
essing steps (as e.g. feature extraction from time series and details for the handling are explained in a comprehensible
classification) is rather weak. This leads often to the reim- PDF handbook.
plementation of existing methods or a stepwise transfer of
partial results between different tools.
Some tools are focused on a script-based processing result-
ing in problems for a transfer to other applications due to a
time-consuming manual adaptation of implemented algo-
rithms. A generally accepted tool platform does not exist at
the moment.
These facts make a fast comparison of new developed
methods against a broader set of existing methods very
time consuming. As a consequence, the new methods will
only be compared with a small number of concurrent ap-
proaches - a broad comparison is not feasible.
In our opinion, an ideal data mining tool
• has to contain various data mining methods from
feature extraction to classification and regression us-
ing statistical approaches up to newer approaches
from computational intelligence,
• has to be free and open source to guarantee a wide Figure 1: Gait-CAD screenshot
acceptance in the scientific community and the fast in-
tegration of new methods, Gait-CAD is an open source software. The German version
• needs to be modular with well documented interfaces is available since November 2006, the English one since
to integrate various methods useful for highly special- January 2008 It is licensed under the conditions of the
ized application domains, and GNU General Public License (GNU-GPL) of The Free
• has to support a GUI based exploration of the data set Software Foundation. The download is possible using the
as well as a highly automated script based processing downloading section at
of routine operations.
This paper presents the Matlab toolbox Gait-CAD as a first http://www.iai.fzk.de/projekte/biosignal/index.html.
step in this direction. It is focused on the visualization and
To use the toolbox for the design of a data mining algo-
rithm, a training data set is required. This data set is nor-
mally given by a binary Matlab project file, containing
matrices and vectors with predefined structures and names.
This data set is normally given by a binary Matlab project
file, containing matrices with given names. Additionally,
the user is able to add own textual identifiers and further
information to the matrices and structures. Missing infor-
mation is compensated by standard values and identifiers.
The import of data from text files (single files or complete
directories, single features or time series) is possible.
The training data set is organized with n = 1, ..., N data
points, each containing
• sz time series (described by a matrix with the dimen-
sion sz × K, with K - number of sample points),
• s single features (vector with the dimension s)
• sy discrete output variables (vector with the dimension
sy).
The management of multiple output variables (i.e. diagno-
ses with respect to diseases in medical applications, deci-
sions for therapies, qualitative evaluations of therapy suc-
cesses, gender, age-groups etc.) for each data point allows
a flexible selection of multiple classification problems.
Additionally, input and output variables may be switched
depending on the problem.
Gait-CAD implements the standardized data mining
process proposed by [2]. The main components are shown
in Figure 2. Gait-CAD permits a comfortable handling of
numerous algorithms for the
• selection of data points (e.g. detection of outliers,
discarding of incomplete data points and features, se-
lection of parts of data sets),
• feature extraction (e.g. spectrograms, FFT analysis,
correlation analysis, linear filtering, calculation of ex-
trema, mean values, fuzzification etc.),
• evaluation and selection of features and time series
(e.g. multivariate analysis of variances, t-test, informa-
tion measures, regression analysis),
• feature aggregation (e.g. discriminant analysis, princi-
pal component analysis - PCA, independent compo-
nent analysis - ICA),
• supervised and unsupervised classification (e.g. deci-
sion trees, cluster algorithms, Bayes classifier, artifi-
cial neural networks (ANN), nearest neighbour algo-
rithms, support vector machines - SVM, fuzzy sys-
tems), and
• validation strategies (e.g. cross-validation, bootstrap).
Additionally, there are various possibilities to visualize
results, automatically log results and process steps in text
and LaTeX files, rename variables etc.
For some functions, Gait-CAD uses additional commercial
Matlab toolboxes (e.g. Signal, Statistics, Neural Network,
and Wavelet toolbox from the MathWorks, Inc.) or freely
available GNU-GPL toolboxes. But most of the self-
implemented functions require only a standard Matlab
installation.
The feature extraction is realized with plugins. Plugins
are single Matlab functions called plugin_*.m, which are
included in a special directory or in the working directory.
Database
Problem formulation
(verbalized)
Collecting Problem formulation
training data set (formalized)
Evaluation
measures
Validation
strategies
Visualization
Data point Feature Feature Feature Classification/
selection extraction selection aggregation Regression
Design of a data mining method (Gait-CAD)
Figure 2: Design process of a data mining algorithm [2]
They generate
• new time series from one (e.g. by low-pass or high-
pass filtering, segmentation) or more (e.g. minimum,
mean or maximum value) existing time series, or
• new single features from one time series in a pre-
defined segment (e.g. mean value for the complete
time series or the first 50% of sampling points). The
segment can be defined by a special file or interac-
tively by selecting a region of interest.
Gait-CAD contains a large number of pre-defined plugins
and segments. The structure allows a user-defined expan-
sion with special feature types for each specific application
field.
Macros are recorded sequences of clicked menu items and
control elements. The main advantages are an automation
of long sequences of operations (e.g. for the use in different
projects) and the opportunity for the integration of user-
defined functions. A manual modification is possible due
to its textual Matlab syntax.
Application-specific extension packages can be easily
integrated into the graphical user interface. Gait-CAD
contains templates for new menu items and control ele-
ments as a starting point for a manual modification. It
allows the integration of own functions using any parame-
ter from the control elements or available variables. An
example is a special package for electroneurography pro-
vided by the University of Freiburg. It contains the algo-
rithms described in [3].
Results
In many clinical applications, the available data set con-
tains time series of recorded bioelectric signals such as
muscle, nerve, or brain signals.
The automatic design of data mining solutions offers an
objective and reliable method for the generation of hy-
potheses for clinical trials, the data-based design of clinical
decision support systems for diagnosis and therapy plan-
ning, and the adaptation of medical devices to individual
patients.
An example for the latter task is the detection of user inten-
tions from brain, nerve or muscle signals or the informa-
tion processing of nerve signals from natural limbs for
neuroprostheses (Figure 3).
 Intentions Neural Interface
Central
Data
Nervous
System
Sensor analysis
Control
Pattern
Stimu-
Stimu-
lator
lator
Pattern
generator
generator
Data
analysis
Feedback
Figure 3: Interface for the design of neuroprostheses [4]
Table 1: Examples for recent applications of Gait-CAD to
bioelectric signals (EMG: electromyography, ENG: elec-
troneurography, EEG: electroencephalography, ECoG:
electrocorticography)
Applications
Hand prosthesis control [5]
Detection of mechanical stimuli from nerve
signals with cuff electrodes [6]
Detection of artefacts from Function Electri-
cal Stimulation (FES) [7]
Analysis of Central Pattern Generators [8]
Design algorithms for Brain Computer
Interfaces [5, 9]
Gait analysis [10]
Data analysis plays a key role in this concept for the data-
based detection of human intentions from bioelectric sig-
nals and for the use of biosensors. Gait-CAD has supported
these steps for a number of different scenarios:
For the first task, Brain Computer Interfaces are often
controlled by imagined movements. The brain signals can
be recorded by surface (EEG) or invasive (ECoG) elec-
trode arrays resulting in a set of time series. The data min-
ing task consists of the extraction new time series (e.g. by
bandpass filters) and a classification to differentiate the
movement intentions. In addition, an analysis of the local
and temporal information content is useful to understand
the processes [9]. Hand prostheses are usually controlled
by muscle signals originating from two electrodes. Here,
classification problems exist for the switching between
different grasp types [5].
For future neuroprostheses, a scenario including functional
electro stimulation and a recording of afferent nerve signals
induced by mechanical stimuli is intended. The nerve
signals are recorded by cuff electrodes. Here, very high
sampling frequencies (50 kHz) are necessary to extract
useful information. The problem is the detection and local-
ization of mechanical stimuli by a classification task [6].
Besides these applications, Gait-CAD is now used in many
medical, biological, and technical application scenarios.
From a data mining point of view, these very different
applications can be unified and the synergies can be used
with the presented platform.
Discussion
The aim of Gait-CAD is to provide an interface to apply
and compare data mining methods. Its architecture allows
to enlarge the toolbox by further algorithms. Everyone is
invited to support the further development of Gait-CAD.
Interface
Artificial Acknowledgements
Protheses
Software
Interface Thanks to all the busy programmers, developers of algo-
Software
rithms, and testers, especially to Tobias Loose, and Sebas-
Stimu- Natural
lator Limbs tian Gollmer. The support by the Deutsche Forschungsge-
Sensor meinschaft (German research association) within the pro-
ject "Diagnosis support in gait analysis" and the Cooperate
Research Center "Humanoid Robots" was a great help to
build the basis for the further development of the toolbox.
References
[1] Fayyad, U.; Piatetsky-Shapiro, G.; Smyth, P.: From
Data Mining to Knowledge Discovery in Databases.
Signals AI Magazine, Vol. 17, pp. 37–54, 1996.
EMG [2] Mikut, R.; Reischl, M.; Burmeister, O.; Loose, T.:
ENG Data Mining in Medical Time Series. Biomediz-
inische Technik, vol. 51, pp. 288–293, 2006.
EMG, [3] Krüger, T. B.; Levchuk, O.; Stieglitz, T.: Decoding of
ENG Neural Signals with MATLAB - Onset Detection and
EMG Classification as a Guided Tool. Biomedizinische
EEG, Technik, vol. 52, Ergänzungsband, 2007
ECoG [4] Mikut, R.; Krüger, T.; Reischl, M.; Burmeister, O.;
EMG Rupp, R.; Stieglitz, T.: Regelungs- und Steuerungs-
konzepte für Neuroprothesen am Beispiel der oberen
Extremitäten. at - Automatisierungstechnik, vol. 54,
pp. 523–536, 2006.
[5] Reischl, M.: Ein Verfahren zum automatischen
Entwurf von Mensch-Maschine-Schnittstellen am
Beispiel myoelektrischer Handprothesen. Disserta-
tion, Universität Karlsruhe, Universitätsverlag
Karlsruhe. 2006.
[6] Krüger, T.; Reischl, M.; Lago, N.; Burmeister, O.;
Mikut, R.; Ruff, R.; Hoffmann, K.-P.; Navarro, X.;
Stieglitz, T.: Analysis of Microelectrode-Signals in
the Peripheral Nervous System, In-Vivo and Post-
Processing. In: Proc., Mikrosystemtechnik Kongress
Deutschland, pp. 69–72. Freiburg: VDE-Verlag.
2005.
[7] Rohm, M.: Evaluierung und Inbetriebnahme von
Sensorkonzepten für die Steuerung von funktionellen
Orthesen der oberen Extremität. Diplomarbeit, Uni-
versität Darmstadt, Forschungszentrum Karlsruhe.
2008.
[8] Chen, Y.: A Concept for the Application of Neural
Oscillators and Spinal Reflexes to Humanoid Robots
and Neuroprostheses. Diplomarbeit, Universität
Karlsruhe (TH), in preparation, 2008.
[9] Burmeister, O.; Reischl, M.; Mikut, R.: Application
of Time-Variant Classifiers to Invasively Recorded
Signals from Brain and Peripheral Nerve. Biomediz-
inische Technik, vol. 52, Ergänzungsband, 2007.
[10] Wolf, S.; Loose, T.; Schablowski, M.; Döderlein, L.;
Rupp, R.; Gerner, H. J.; Bretthauer, G.; Mikut, R.:
Automated feature assessment in instrumented gait
analysis. Gait & Posture, 23 (3), S. 331-338; 2006