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mse - calculates multiscale entropy (MSE) of one or multiple data sets


mse [ option ... ]


This program reads data (a column of numbers in text form) from its standard input (or optionally from a list of input files; see the -F option below), creates a set of coarse-grained series with a user-selected range of scales, and calculates sample entropy (SampEn) for each coarse-grained series. The user may specify the pattern length (m) and the similarity criterion (r) for the SampEn calculations, and may select any contiguous subset of the input data. The program can also iterate over a set of user-specified m and r values. If multiple data sets are provided, these calculations are performed separately for each data set, and then the mean and sample deviation of these SampEn values at each scale are calculated. The results are written to the standard output.

Options are:

-a dn
Set the scale increment to dn (1-40; default: 1).
-b dm
Set the m increment to dm (1-10; default: 1).
-c dr
Set the scale increment to dr (>0; default: 0.05).
-F listfile
Read and process up to 100 data sets from the files named in listfile (a text file containing a column of file names). The output includes results for each file, followed by means and sample deviations of the per-file results.
-i n
Begin the analysis with row n of (each) data set. Rows are numbered beginning with 0; by default, analysis begins with row 0.
-I n
Stop the analysis with row n of (each) data set. By default, analysis ends at row 39999, or at the end of the data set if there are fewer rows.
-m n
Set the minimum m (pattern length for SampEn) to n (1-10; default: 2).
-M n
Set the maximum m to n (1-10; default: 2).
-n n
Set the maximum scale for coarse-graining to n (1-40; default: 20).
-r n
Set the minimum r (similarity criterion for SampEn) to n (>0; default: 0.15).
-R n
Set the maximum m to n (>0; default: 0.15).


To obtain MSE results with default settings for the first 40,000 RR intervals in record nsr047 of the Normal Sinus Rhythm RR Interval Database (nsr2db), use this command:
ann2rr -r nsr2db/nsr047 -a ecg -A -i s4 | mse

(ann2rr(1) reads the ecg annotations for the record, calculates the RR intervals, and writes them to its standard output, which is connected to mse's standard input. mse reads the intervals and calculates SampEn for scales 1 through 20, for m = 2 and r = 0.15.)

For additional examples illustrating the use of mse's options, see the tutorial at


Madalena Costa (


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