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cbf76bd
minor edits to README
Aug 1, 2014
6470c73
Minor edits in install.sh
Aug 1, 2014
38d8b1d
Minor edits in install.sh
Aug 1, 2014
d13df47
Added pip install for nose
Aug 1, 2014
d232763
Added pip install for nose
Aug 1, 2014
d55c6f2
Forgot to mention install.sh must be run with 'source', not 'bash'
Aug 1, 2014
d92b861
Forgot to mention install.sh must be run with 'source', not 'bash'
Aug 1, 2014
1959614
typo in README
Aug 1, 2014
344a25c
typo in README
Aug 1, 2014
4da7ae2
adjust model.py to use crfsuite's SWIG wrapper
Aug 5, 2014
7ffb0ae
adjust model.py to use crfsuite's SWIG wrapper
Aug 5, 2014
5f309bd
Merge branch 'master' into machine-learning
Aug 5, 2014
6e6f3b9
Merge branch 'master' into machine-learning
Aug 5, 2014
5f2f2f5
get rid of self.type
Aug 5, 2014
38554b3
get rid of self.type
Aug 5, 2014
1b6a054
Fold CRF back using python-crfsuite (with model file workaround)
Aug 10, 2014
e7b56e3
Fold CRF back using python-crfsuite (with model file workaround)
Aug 10, 2014
5332de1
Add CRF installation to install.sh
Aug 10, 2014
c55a836
Add CRF installation to install.sh
Aug 10, 2014
09cadc0
modify install.sh to use machine-learning branch (until merged back t…
Aug 10, 2014
80529dd
modify install.sh to use machine-learning branch (until merged back t…
Aug 10, 2014
0c3cca4
Update README.rst
arumshisky Aug 12, 2014
e5d7f72
Update README.rst
arumshisky Aug 12, 2014
cd193ad
Set crf to use default parameters
Aug 12, 2014
77cd924
Set crf to use default parameters
Aug 12, 2014
9b2b18f
Added sanity checks for first pass predictions
Aug 13, 2014
cc089bb
Added sanity checks for first pass predictions
Aug 13, 2014
c530798
Modified install script so it doesn't git clone the project
Aug 13, 2014
e73efbe
Modified install script so it doesn't git clone the project
Aug 13, 2014
d944a80
Merge branch 'command-line-interface' of https://github.com/mitmedg/C…
kwaco Aug 16, 2014
9541714
Merge branch 'command-line-interface' of https://github.com/mitmedg/C…
kwaco Aug 16, 2014
5c3b88b
merging scripting and cli
kwaco Aug 16, 2014
db4e828
merging scripting and cli
kwaco Aug 16, 2014
025d927
Reorganized features_dir module
Aug 16, 2014
2ca49f8
Reorganized features_dir module
Aug 16, 2014
4a04e4c
Changed features/ to features_dir/
Aug 16, 2014
f3bb55c
Changed features/ to features_dir/
Aug 16, 2014
af894da
Extend returned values (for easier testing of first pass results)
Aug 16, 2014
e0de65b
Extend returned values (for easier testing of first pass results)
Aug 16, 2014
97e7bd2
Extend for first pass development
Aug 16, 2014
6445540
Extend for first pass development
Aug 16, 2014
7468b43
Added crf back into first pass
Aug 16, 2014
5402da6
Added crf back into first pass
Aug 16, 2014
e76c4fa
Merging machine-learning branch
Aug 16, 2014
97670e3
Merging machine-learning branch
Aug 16, 2014
e41a0d3
Merge branch 'master' of https://github.com/mitmedg/CliCon
Aug 16, 2014
c08f7a3
Merge branch 'master' of https://github.com/mitmedg/CliCon
Aug 16, 2014
0cb448a
Added a few examples to readme
Aug 21, 2014
b4dc9ef
Added a few examples to readme
Aug 21, 2014
a2c674f
updating readme with examples
Aug 21, 2014
847b8e8
updating readme with examples
Aug 21, 2014
dde9857
Add usage examples to readme & extend support for xml format
Aug 21, 2014
c372f76
Add usage examples to readme & extend support for xml format
Aug 21, 2014
41daf0c
Update README.rst
wboag Aug 21, 2014
7878c9d
Update README.rst
wboag Aug 21, 2014
4e7a12d
Update README.rst
arumshisky Aug 21, 2014
6803d67
Update README.rst
arumshisky Aug 21, 2014
efd973f
Update README.rst
arumshisky Aug 21, 2014
f30e7c8
Update README.rst
arumshisky Aug 21, 2014
cdc61a6
Update README.rst
arumshisky Aug 21, 2014
7e20318
Update README.rst
arumshisky Aug 21, 2014
31b66e0
Update README.rst
arumshisky Aug 21, 2014
f601fc6
Update README.rst
arumshisky Aug 21, 2014
ddf412b
Update README.rst
arumshisky Aug 21, 2014
15ea336
Update README.rst
arumshisky Aug 21, 2014
7348653
Update README.rst
arumshisky Aug 21, 2014
c83b0ae
Update README.rst
arumshisky Aug 21, 2014
515e8ae
Update README.rst
arumshisky Aug 21, 2014
ed775f9
Update README.rst
arumshisky Aug 21, 2014
544348e
Update README.rst
arumshisky Aug 21, 2014
bac75d1
Update README.rst
arumshisky Aug 21, 2014
0b592c9
Update README.rst
arumshisky Aug 21, 2014
1c8ecec
Update README.rst
arumshisky Aug 21, 2014
ab9d50d
Update README.rst
arumshisky Aug 21, 2014
9eac288
Update README.rst
arumshisky Aug 21, 2014
6c4292c
Update README.rst
arumshisky Aug 21, 2014
91aefbf
Update README.rst
arumshisky Aug 21, 2014
7b8865d
Update README.rst
arumshisky Aug 21, 2014
9fc858c
Update README.rst
arumshisky Aug 21, 2014
08b8827
Update README.rst
arumshisky Aug 21, 2014
98b29d7
Update README.rst
arumshisky Aug 21, 2014
db7c2d5
Update README.rst
arumshisky Aug 21, 2014
56b87c5
Update README.rst
arumshisky Aug 21, 2014
c3ee6be
Update README.rst
arumshisky Aug 21, 2014
df1d1b4
Update README.rst
arumshisky Aug 21, 2014
e2ad2ee
Update README.rst
arumshisky Aug 21, 2014
286a3f6
Update README.rst
arumshisky Aug 21, 2014
7258616
Update README.rst
arumshisky Aug 21, 2014
f35f1f7
Update README.rst
arumshisky Aug 21, 2014
9cf64e3
Update README.rst
arumshisky Aug 21, 2014
dba51aa
Update README.rst
arumshisky Aug 21, 2014
20a1ad2
Update README.rst
arumshisky Aug 21, 2014
87ef90d
Update README.rst
arumshisky Aug 21, 2014
9177334
Update README.rst
arumshisky Aug 21, 2014
73e745e
Update README.rst
arumshisky Aug 21, 2014
30438d7
Update README.rst
arumshisky Aug 21, 2014
f7ce6e9
Update README.rst
arumshisky Aug 21, 2014
1565c6a
Added CLICON_DIR stuff and package check into install.sh
Aug 22, 2014
98748ea
Added CLICON_DIR stuff and package check into install.sh
Aug 22, 2014
8eaffb0
Update README.rst
wboag Aug 22, 2014
215f231
Update README.rst
wboag Aug 22, 2014
afb7138
Update README.rst
wboag Aug 22, 2014
346328b
Update README.rst
wboag Aug 22, 2014
49bbb78
Add cli flag to enabled/disable CRF (default is enable)
Aug 26, 2014
800c6bf
Add cli flag to enabled/disable CRF (default is enable)
Aug 26, 2014
2f82823
Merge branch 'master' of https://github.com/mitmedg/CliCon
Aug 26, 2014
b06a8b9
Merge branch 'master' of https://github.com/mitmedg/CliCon
Aug 26, 2014
9427842
Update README.rst
arumshisky Aug 26, 2014
17c94ac
Update README.rst
arumshisky Aug 26, 2014
4566fee
Update README.rst
arumshisky Aug 26, 2014
1f1ad80
Update README.rst
arumshisky Aug 26, 2014
ba4be9f
Modified install.sh to skip compilation of existing libraries
Aug 27, 2014
2a601f6
Modified install.sh to skip compilation of existing libraries
Aug 27, 2014
8c2ab2d
Update README.rst
Aug 27, 2014
6f43a82
Update README.rst
Aug 27, 2014
f39c731
merge readme
Aug 27, 2014
083aabf
merge readme
Aug 27, 2014
887f589
Add demo script of usage example for running system
Aug 27, 2014
2093b66
Add demo script of usage example for running system
Aug 27, 2014
3d0453d
replace depricated ImmutableSet with frozenset
Aug 27, 2014
99adaed
replace depricated ImmutableSet with frozenset
Aug 27, 2014
d0e97dd
Replace depricated ImmutableSet with frozenset
Aug 27, 2014
7d2490a
Replace depricated ImmutableSet with frozenset
Aug 27, 2014
b6e3d42
Update README.rst
wboag Aug 27, 2014
94a5cc1
Update README.rst
wboag Aug 27, 2014
36b57a2
Update README.rst
wboag Aug 27, 2014
856bb63
Update README.rst
wboag Aug 27, 2014
d42b283
Removing broken badge images from README.rst.
tnaumann Aug 29, 2014
8eafa16
Removing broken badge images from README.rst.
tnaumann Aug 29, 2014
ed13f0d
Adding Apache license.
tnaumann Aug 29, 2014
5f74c75
Adding Apache license.
tnaumann Aug 29, 2014
89d838f
Updating development team.
tnaumann Aug 29, 2014
e978067
Updating development team.
tnaumann Aug 29, 2014
5077f47
Removing features section from README.rst
tnaumann Aug 29, 2014
35bf236
Removing features section from README.rst
tnaumann Aug 29, 2014
d9201af
Create COPYRIGHT file
tnaumann Aug 30, 2014
7d2eeb0
Create COPYRIGHT file
tnaumann Aug 30, 2014
7ad1b54
Updating OSX dependencies.
tnaumann Aug 30, 2014
b289a48
Updating OSX dependencies.
tnaumann Aug 30, 2014
167a266
Removing cookiecutter installation/usage.
tnaumann Aug 30, 2014
863bced
Removing cookiecutter installation/usage.
tnaumann Aug 30, 2014
0d1aa8e
Update README.rst
arumshisky Aug 30, 2014
02ff782
Update README.rst
arumshisky Aug 30, 2014
c5b4c66
Update README to have include proper license.
tnaumann Aug 30, 2014
21a7cb5
Update README to have include proper license.
tnaumann Aug 30, 2014
57096f4
Update README.rst
wboag Aug 31, 2014
de528a3
Update README.rst
wboag Aug 31, 2014
3417c6f
i2b2 eval update
kwaco Sep 1, 2014
734f9b3
i2b2 eval update
kwaco Sep 1, 2014
e687392
user friendly installation messages and log
Sep 1, 2014
5d623f5
user friendly installation messages and log
Sep 1, 2014
7cd135c
Safe guard against duplicate entries in concept file
Sep 1, 2014
e3bcc6e
Safe guard against duplicate entries in concept file
Sep 1, 2014
6164152
cache genia features
Sep 1, 2014
84e5d58
cache genia features
Sep 1, 2014
6a4159e
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 1, 2014
bbd4c42
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 1, 2014
87226c0
update install.sh
Sep 1, 2014
d1144c5
update install.sh
Sep 1, 2014
a7fa32f
update install.sh
Sep 2, 2014
17ed6e4
update install.sh
Sep 2, 2014
90a22c5
update install.sh
Sep 2, 2014
b476f93
update install.sh
Sep 2, 2014
3f677f6
update install.sh
Sep 2, 2014
b972b97
update install.sh
Sep 2, 2014
6808955
Update install.sh
wboag Sep 2, 2014
3410857
Update install.sh
wboag Sep 2, 2014
267a055
update install.sh
Sep 2, 2014
7f094b7
update install.sh
Sep 2, 2014
6477589
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 2, 2014
c82fb6b
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 2, 2014
d4b27e3
Update install.sh
wboag Sep 2, 2014
ddff571
Update install.sh
wboag Sep 2, 2014
d2ee78f
Update install.sh
wboag Sep 2, 2014
89127cc
Update install.sh
wboag Sep 2, 2014
dd53b54
add genia cache
Sep 2, 2014
e3dd34d
add genia cache
Sep 2, 2014
68c1191
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 2, 2014
52474f2
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 2, 2014
84f0eeb
go back to new eval script
Sep 2, 2014
55cdc30
go back to new eval script
Sep 2, 2014
389aa50
Escape command inside string
wboag Sep 2, 2014
afc539e
Escape command inside string
wboag Sep 2, 2014
7ad0310
Strip non-printable characters from text
Sep 3, 2014
4cd469b
Strip non-printable characters from text
Sep 3, 2014
66b5c87
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 3, 2014
cfa0523
Merge branch 'master' of https://github.com/mitmedg/CliCon
Sep 3, 2014
2775973
Update SQLookup.py
Sep 24, 2014
0f59a11
Update SQLookup.py
Sep 24, 2014
013f27d
Update demos & calls using clicon script
Oct 6, 2014
697064c
Update demos & calls using clicon script
Oct 6, 2014
11877eb
move all data format logic into Note and add author descriptions
Oct 6, 2014
2cc04d4
move all data format logic into Note and add author descriptions
Oct 6, 2014
f495d7f
Add trie for UMLS lookups (not fully done yet)
Oct 6, 2014
ca42c34
Add trie for UMLS lookups (not fully done yet)
Oct 6, 2014
b8e6644
Bugfixes in features directory
Oct 6, 2014
c2f7512
Bugfixes in features directory
Oct 6, 2014
d335feb
Merge branch 'master' of https://github.com/mitmedg/CliCon
Oct 6, 2014
008cb58
Merge branch 'master' of https://github.com/mitmedg/CliCon
Oct 6, 2014
7fc1602
Add support for semeval reader
Oct 6, 2014
38697e5
Add support for semeval reader
Oct 6, 2014
2792e56
Update note.py
Oct 8, 2014
b42a52e
Update note.py
Oct 8, 2014
1a22650
semeval reader
kwaco Oct 22, 2014
6574252
semeval reader
kwaco Oct 22, 2014
29033b1
A little work for UMLS trie stuff
wboag Oct 28, 2014
f8cc1c8
A little work for UMLS trie stuff
wboag Oct 28, 2014
c72bf3d
Merge branch 'master' into character_offsets
wboag Nov 4, 2014
e053923
Merge branch 'master' into character_offsets
wboag Nov 4, 2014
d6e79b4
Update README.rst
arumshisky Nov 5, 2014
812c7c1
Update README.rst
arumshisky Nov 5, 2014
f88100f
Update README.rst
arumshisky Nov 5, 2014
2de1fc0
Update README.rst
arumshisky Nov 5, 2014
474e868
Update README.rst
arumshisky Nov 5, 2014
36b9813
Update README.rst
arumshisky Nov 5, 2014
0fee8e8
Update README.rst
arumshisky Nov 5, 2014
880384c
Update README.rst
arumshisky Nov 5, 2014
9318efd
fixed off-by-one error in writer
wboag Nov 5, 2014
5bc6925
fixed off-by-one error in writer
wboag Nov 5, 2014
56fee0a
Merge branch 'master' of https://github.com/mitmedg/CliCon
wboag Nov 5, 2014
0a49725
Merge branch 'master' of https://github.com/mitmedg/CliCon
wboag Nov 5, 2014
60d7aba
reorganized structure to localize all machine learning code
wboag Nov 6, 2014
befbf6c
reorganized structure to localize all machine learning code
wboag Nov 6, 2014
d3c6aac
removing statistics.py
wboag Nov 6, 2014
6ec4a92
removing statistics.py
wboag Nov 6, 2014
e2f7f9c
removing runall.py
wboag Nov 6, 2014
5cd2b50
removing runall.py
wboag Nov 6, 2014
3164000
removing libml.py
wboag Nov 6, 2014
286bd3d
removing libml.py
wboag Nov 6, 2014
f44d355
Restructured notes representation for extendability
wboag Nov 10, 2014
7761840
Restructured notes representation for extendability
wboag Nov 10, 2014
d5e2c68
rearranging features_dir organization for consistency
wboag Nov 11, 2014
3a40a04
rearranging features_dir organization for consistency
wboag Nov 11, 2014
dd57828
fixed index error in note_i2b2
wboag Nov 11, 2014
80c4467
fixed index error in note_i2b2
wboag Nov 11, 2014
7bb573d
renamed SQLookup to interface_umls
wboag Nov 11, 2014
48e6cc9
renamed SQLookup to interface_umls
wboag Nov 11, 2014
ca082ab
renamed umls to interpret_umls
wboag Nov 11, 2014
103f09d
renamed umls to interpret_umls
wboag Nov 11, 2014
b1e68b4
Fixed should-never-get-here bug to work even if reached
wboag Nov 11, 2014
3e4ba2e
Fixed should-never-get-here bug to work even if reached
wboag Nov 11, 2014
212e4a5
Added getText selector to notes
wboag Nov 11, 2014
80380f1
Added getText selector to notes
wboag Nov 11, 2014
287c304
Repair write methods for notes
wboag Nov 13, 2014
aa53fdd
Repair write methods for notes
wboag Nov 13, 2014
aec3850
took out some files
wboag Nov 13, 2014
c81bf63
Merge branch 'master' of https://github.com/mitmedg/CliCon
wboag Nov 18, 2014
549c74c
fixed issue with note in master
kwaco Jan 28, 2015
f6dc484
Replacing project with relocation notice.
tnaumann Feb 28, 2015
d3bf0be
Replacing project with relocation notice.
tnaumann Feb 28, 2015
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22 changes: 0 additions & 22 deletions .gitattributes

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50 changes: 0 additions & 50 deletions .gitignore

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1 change: 1 addition & 0 deletions README
Original file line number Diff line number Diff line change
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This project has relocated to https://github.com/text-machine-lab/CliNER.
2 changes: 0 additions & 2 deletions README.md

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138 changes: 0 additions & 138 deletions code/evaluate.py

This file was deleted.

21 changes: 0 additions & 21 deletions code/helper.py

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