mbiases - compute
a new set of value for the matrices A[][] and PI[].
SYNOPSIS
-
mbiases
{-i <input compiled matrices file>}
{-f <biases list file>}
{-o <output compiled matrices file>}
DESCRIPTION
mbiases takes a list of biases for tag transitions and compute a
new set of value for the matrices A[][] and PI[].
OPTIONS
-
mbiases supports the following options:
-
-i Input Matrices file
-
The matrices file created by the mtrain program (compiled form)
(default: MM).
-
-f Biases list file
-
This file indicates the preferences for transitions biases to be used to
reajust the values in the A[][] and PI[] matrices. See the format below
(default: biases.lst).
-
-o Output compiled file
-
The output matrices file (default: MM.new).
-
-v version.
FORMAT
| Biases file |
| AJ0 |
NN1 |
+4 |
|
NN2 |
+4 |
|
VVB |
-4 |
|
VVZ |
-4 |
| AT0 |
NN1 |
=.5 |
|
NN2 |
=.2 |
|
VVB |
=.3 |
|
!OTHER |
=0 |
| !PI |
PRP |
+4 |
|
NN1 |
+1 |
|
!OTHER |
-2 |
| ..... |
The formalism indicates that the transition probability between the first
state and the second state will be decreased (increased), if the rate (third
column) is negative (positive). The flag !PI appearing in the first
column indicates that the values concern the matrix PI, i.e. the initial
state.
The Rate indicated in the third column can range from the value [-10..+10].
This takes into account the standard deviation of the state and computes
a linear function to increase or decrease the different values.
| DT |
!OTHER |
+1 |
|
|
|
| !PI |
WP |
+2 |
|
DT |
-4 |
|
!OTHER |
=0 |
The numerical stability is always re-calculated.
COMMAND EXAMPLES
> mbiases -i MM -f biases.lst -o MM.new
SEE ALSO
mpreptxt(1)
mtrain(1)
mtag(1)
mcreate(1)
mtagfreq(1)
mprint(1)
mdiff(1)
mdiffb(1)
mcontext(1)
mhandtag(1)
AUTHOR
Gilbert ROBERT
(Gilbert.Robert@issco.unige.ch)
ISSCO, 54 route des Acacias
1227 Geneva, Switzerland
Comments, suggestions, and bug reports are always welcome.