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BaderLab
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saber
Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.
https://baderlab.github.io/saber/
MIT License
102
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DISO model
#100
rishabh279
closed
5 years ago
5
⬆️ Bump spacy from 2.0.13 to 2.0.18
#99
dependabot-preview[bot]
closed
5 years ago
3
Add pre-trained DISO model
#98
JohnGiorgi
closed
5 years ago
0
Multi-task learning leads to NaNs
#97
JohnGiorgi
closed
5 years ago
1
Cannot use transfer learning and multi-task learning in conjunction
#96
JohnGiorgi
closed
5 years ago
0
Load all embeddings
#95
JohnGiorgi
closed
5 years ago
2
⬆️ Bump spacy from 2.0.13 to 2.0.17
#94
dependabot-preview[bot]
closed
5 years ago
3
Pretrained_model
#93
rishabh279
closed
5 years ago
5
Provide option to load all pre-trained embeddings.
#92
JohnGiorgi
closed
5 years ago
0
⬆️ Bump scikit-learn from 0.20.0 to 0.20.1
#91
dependabot-preview[bot]
closed
5 years ago
3
Grounding sometimes hangs
#90
JohnGiorgi
closed
5 years ago
2
LR Range Test Graphs
#89
JohnGiorgi
opened
5 years ago
0
Attending to character embeddings
#88
JohnGiorgi
closed
5 years ago
0
error with python enviornment setup process
#87
jswu18
closed
6 years ago
2
⬆️ Bump tensorflow from 1.11.0 to 1.12.0
#86
dependabot-preview[bot]
closed
5 years ago
2
Update readme
#85
JohnGiorgi
closed
6 years ago
2
Update Readme
#84
JohnGiorgi
closed
6 years ago
0
Add support for python3.5
#83
JohnGiorgi
closed
6 years ago
1
Add support for python 3.5
#82
JohnGiorgi
closed
6 years ago
0
The TravisCI builds fail with a cryptic error message
#81
JohnGiorgi
closed
6 years ago
0
Fix broken TravisCI config
#80
JohnGiorgi
closed
6 years ago
0
Fix transfer learning again
#79
JohnGiorgi
closed
6 years ago
0
Replace multi_task_lstm_crf load method with call to super
#78
JohnGiorgi
closed
5 years ago
0
Successive loading of Saber model
#77
JohnGiorgi
closed
5 years ago
0
Some command line arguments are useless
#76
JohnGiorgi
opened
6 years ago
0
User can now specify config filepath at command line
#75
JohnGiorgi
closed
6 years ago
0
Now only one set of weights saved when save_all_weights is false
#74
JohnGiorgi
closed
6 years ago
0
Fix issue that caused cross-validation to break on the 2nd fold
#73
JohnGiorgi
closed
6 years ago
0
Saving only the best model weights does not work as expected
#72
JohnGiorgi
closed
6 years ago
0
Cross-validation breaks on the nth fold
#71
JohnGiorgi
closed
6 years ago
0
Fix epoch issue
#70
JohnGiorgi
closed
6 years ago
0
Keras displays the wrong epoch number
#69
JohnGiorgi
closed
6 years ago
0
Try weighting the importance of target classes
#68
JohnGiorgi
opened
6 years ago
0
User no longer has to provide name of pre-trained models architecture
#67
JohnGiorgi
closed
6 years ago
0
Fix transfer learning
#66
JohnGiorgi
closed
6 years ago
0
debug argument should partially load a dataset
#65
JohnGiorgi
opened
6 years ago
0
Polishing (of grounding utils)
#64
IgorRodchenkov
closed
6 years ago
1
Should not have to provide the model name when loading a pre-trained model
#63
JohnGiorgi
closed
6 years ago
0
Find way to incorporate Igor's grounding function into the annotation process
#62
JohnGiorgi
closed
5 years ago
0
Add grounding capabilities to Saber
#61
IgorRodchenkov
closed
6 years ago
1
⬆️ Bump gensim from 3.4.0 to 3.6.0
#60
dependabot-preview[bot]
closed
6 years ago
1
⬆️ Bump spacy from 2.0.13 to 2.0.16
#59
dependabot-preview[bot]
closed
6 years ago
3
Do residual connection help?
#58
JohnGiorgi
closed
5 years ago
0
Clean up saber
#57
JohnGiorgi
closed
6 years ago
0
Cyclic learning rates
#56
JohnGiorgi
opened
6 years ago
0
Try Elmo Embeddings
#55
JohnGiorgi
closed
5 years ago
0
Cannot supply PMID when using Saber.annotate()
#54
JohnGiorgi
opened
6 years ago
0
Unit tests are breaking on Travis CI
#53
JohnGiorgi
closed
6 years ago
0
Fix multi-gpu bug
#52
JohnGiorgi
closed
6 years ago
0
Multi-GPU model doesn't work
#51
JohnGiorgi
closed
6 years ago
0
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