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Relation extraction #173

Merged
merged 119 commits into from
May 1, 2024
Merged

Relation extraction #173

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b20e7c8
Added files.
vladd-bit Aug 24, 2021
eec6c59
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Aug 31, 2021
56220aa
More additions to rel extraction.
vladd-bit Sep 1, 2021
7ad88f5
Rel base.
vladd-bit Sep 3, 2021
233ce36
Update.
vladd-bit Sep 6, 2021
85a7015
Updates.
vladd-bit Sep 10, 2021
5003548
Dependency parsing.
vladd-bit Oct 1, 2021
541b47d
Updates.
vladd-bit Oct 13, 2021
c042b0d
Added pre-training steps.
vladd-bit Oct 15, 2021
87d0c0c
Added training & model utils.
vladd-bit Oct 18, 2021
4f42696
Cleanup & fixes.
vladd-bit Oct 19, 2021
018d811
Update.
vladd-bit Oct 21, 2021
f3d3f44
Evaluation updates for pretraining.
vladd-bit Oct 27, 2021
e5f354e
Removed duplicate relation storage.
vladd-bit Nov 9, 2021
c69de67
Merged master.
vladd-bit Nov 9, 2021
031d256
Moved RE model file location.
vladd-bit Nov 12, 2021
2259a6b
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Nov 16, 2021
1c469e9
Structure revisions.
vladd-bit Nov 22, 2021
423b4e1
Added custom config for RE.
vladd-bit Dec 13, 2021
8ae9abb
Implemented custom dataset loader for RE.
vladd-bit Dec 13, 2021
186416c
More changes.
vladd-bit Dec 13, 2021
451e33f
Small fix.
vladd-bit Dec 13, 2021
8b36413
Latest additions to RelCAT (pipe + predictions)
vladd-bit Jan 19, 2022
2fb8fc9
Setup.py fix.
vladd-bit Jan 19, 2022
930dd11
RE utils update.
vladd-bit Jan 19, 2022
24b2841
rel model update.
vladd-bit Jan 19, 2022
193ecb1
rel dataset + tokenizer improvements.
vladd-bit Jan 19, 2022
03111a7
RelCAT updates.
vladd-bit Jan 19, 2022
7ab60f4
RelCAT saving/loading improvements.
vladd-bit Jan 21, 2022
40875f3
RelCAT saving/loading improvements.
vladd-bit Jan 21, 2022
810d1dc
RelCAT model fixes.
vladd-bit Jan 21, 2022
11dcb32
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Jan 21, 2022
72187f6
Attempted gpu learning fix. Dataset label generation fixes.
vladd-bit Jan 24, 2022
5f67a4c
Minor train dataset gen fix.
vladd-bit Jan 24, 2022
cfc0e91
Minor train dataset gen fix No.2.
vladd-bit Jan 24, 2022
9f4b220
Config updates.
vladd-bit Jan 25, 2022
19afa81
Gpu support fixes. Added label stats.
vladd-bit Jan 25, 2022
8eb1665
Evaluation stat fixes.
vladd-bit Jan 26, 2022
6e86fa2
Cleaned stat output mode during training.
vladd-bit Jan 26, 2022
5cee8cf
Build fix.
vladd-bit Jan 26, 2022
223ac9a
removed unused dependencies and fixed code formatting
vladd-bit Jan 26, 2022
ea7d68c
Mypy compliance.
vladd-bit Jan 26, 2022
1ea9738
Fixed linting.
vladd-bit Jan 27, 2022
9f6609e
More Gpu mode train fixes.
vladd-bit Jan 28, 2022
1782c0b
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Jan 28, 2022
fb86869
Fixed model saving/loading issues when using other baes models.
vladd-bit Jan 31, 2022
df21543
More fixes to stat evaluation. Added proper CAT integration of RelCAT.
vladd-bit Feb 3, 2022
92a5e08
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Feb 3, 2022
87d1a9c
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Mar 11, 2022
ced1627
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Mar 14, 2022
7b69710
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Mar 28, 2022
37fd212
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Apr 4, 2022
f0eda2b
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Apr 8, 2022
10269b9
Setup.py typo fix.
vladd-bit Apr 8, 2022
b8a45b2
Merge branch 'relation_extraction' of https://github.com/CogStack/Med…
vladd-bit Apr 8, 2022
20203ac
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit May 10, 2022
f057139
RelCAT loading fix.
vladd-bit May 10, 2022
197a27a
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Jul 21, 2022
86fd509
RelCAT Config changes.
vladd-bit Aug 1, 2022
79dc069
Type fix. Minor additions to RelCAT model.
vladd-bit Aug 1, 2022
323c895
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Aug 1, 2022
f1c56bf
Type fixes.
vladd-bit Aug 1, 2022
a78ff86
Type corrections.
vladd-bit Aug 2, 2022
f09ceb2
RelCAT update.
vladd-bit Mar 21, 2023
32574f2
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Mar 21, 2023
c081c3e
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit May 22, 2023
e2e48b5
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Dec 11, 2023
4ce5ba3
Type fixes.
vladd-bit Dec 12, 2023
21c09ff
Merge branch 'relation_extraction' of https://github.com/CogStack/Med…
vladd-bit Dec 13, 2023
8123689
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Dec 13, 2023
57ab0c5
Fixed type issue.
vladd-bit Dec 13, 2023
9da5aa6
RelCATConfig: added seed param.
vladd-bit Dec 13, 2023
009e832
Adaptations to the new codebase + type fixes..
vladd-bit Dec 15, 2023
1a7d130
Doc/type fixes.
vladd-bit Dec 19, 2023
53dba6a
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Dec 20, 2023
92613ed
Fixed input size issue for model.
vladd-bit Jan 8, 2024
a49a44a
Fixed issue(s) with model size and config.
vladd-bit Jan 16, 2024
6456e6e
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Jan 16, 2024
5aac9ab
RelCAT: updated configs to new style.
vladd-bit Jan 19, 2024
9c50b30
RelCAT: removed old refs to logging.
vladd-bit Jan 19, 2024
b071607
Merge branches 'relation_extraction' and 'master' of https://github.c…
vladd-bit Jan 29, 2024
89d9128
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Feb 7, 2024
e6e99cb
Fixed GPU training + added extra stat print for train set.
vladd-bit Feb 7, 2024
307d194
Type fixes.
vladd-bit Feb 7, 2024
fb7efe3
Updated dev requirements.
vladd-bit Feb 7, 2024
c235daf
Linting.
vladd-bit Feb 7, 2024
fcdf2e3
Merge branches 'relation_extraction' and 'master' of https://github.c…
vladd-bit Feb 9, 2024
aad0a73
Fixed pin_memory issue when training on CPU.
vladd-bit Feb 9, 2024
8a9026b
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Mar 8, 2024
f94e349
Updated RelCAT dataset get + default config.
vladd-bit Mar 21, 2024
0770356
Updated RelDS generator + default config
vladd-bit Mar 25, 2024
bdf20f5
Linting.
vladd-bit Mar 25, 2024
f7b5aaf
Updated RelDatset + config.
vladd-bit Apr 3, 2024
3e827cf
Merge branch 'relation_extraction' of https://github.com/CogStack/Med…
vladd-bit Apr 3, 2024
aaf6533
Pushing updates to model
shubham-s-agarwal Apr 8, 2024
18f9bb8
Fixing formatting
shubham-s-agarwal Apr 8, 2024
503513c
Update rel_dataset.py
shubham-s-agarwal Apr 8, 2024
040821b
Update rel_dataset.py
shubham-s-agarwal Apr 8, 2024
ed7c8d5
Update rel_dataset.py
shubham-s-agarwal Apr 8, 2024
8d0bfe4
RelCAT: added test resource files.
vladd-bit Apr 9, 2024
3f3a780
RelCAT: Fixed model load/checkpointing.
vladd-bit Apr 10, 2024
3f56824
RelCAT: updated to pipe spacy doc call.
vladd-bit Apr 12, 2024
b7a4987
RelCAT: added tests.
vladd-bit Apr 12, 2024
77d27b0
Merge branch 'relation_extraction' of https://github.com/CogStack/Med…
vladd-bit Apr 12, 2024
a9258a2
Fixed lint/type issues & added rel tag to test DS.
vladd-bit Apr 15, 2024
0ed70fb
Fixed ann id to token issue.
vladd-bit Apr 15, 2024
8db2e76
RelCAT: updated test dataset + tests.
vladd-bit Apr 18, 2024
6eea6b7
RelCAT: updates to requested changes + dataset improvements.
vladd-bit Apr 18, 2024
6972310
RelCAT: updated docs/logs according to commends.
vladd-bit Apr 18, 2024
d03316c
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Apr 18, 2024
8cb12a4
RelCAT: type fix.
vladd-bit Apr 18, 2024
d10318a
RelCAT: mct export dataset updates.
vladd-bit Apr 19, 2024
12acaeb
RelCAT: test updates + requested changes p2.
vladd-bit Apr 19, 2024
4c14a3a
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Apr 19, 2024
382cefc
RelCAT: log for MCT export train.
vladd-bit Apr 19, 2024
35b0913
Updated docs + split train_test & dataset for benchmarks.
vladd-bit Apr 26, 2024
d48bc41
type fixes.
vladd-bit Apr 26, 2024
3068516
Merge branch 'master' of https://github.com/CogStack/MedCAT into rela…
vladd-bit Apr 26, 2024
72643fc
Merge branch 'master' into relation_extraction
mart-r Apr 29, 2024
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10 changes: 9 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,9 @@ venv
db.sqlite3
.ipynb_checkpoints

# vscode
.vscode

#tmp and similar files
.nfs*
*.log
Expand All @@ -42,4 +45,9 @@ tmp.py

# models files
*.dat
!examples/*.dat
# others
/medcat/config/*
/medcat/models/*
/tutorial/version_control/docker_ssh_config

!examples/*.dat
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