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cumc-dbmi
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cehrbert
CEHR-BERT: Incorporating temporal information from structured EHR data to improve prediction tasks
MIT License
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fixed the streaming bug
#75
ChaoPang
closed
1 week ago
0
Fixed Fine-tune example code in ReadME
#74
joshuasami
closed
1 week ago
2
Problems running the sample script
#73
joshuasami
closed
1 week ago
3
Extended the runner arg parser and fixed a typo in DataTrainingArguments
#72
ChaoPang
closed
3 weeks ago
0
Meds conversion time token fix
#71
ChaoPang
closed
3 weeks ago
0
fixed the MEDS ED visit type
#70
ChaoPang
closed
1 month ago
0
Revert "Fix omop meds order"
#69
ChaoPang
closed
1 month ago
0
Fix omop meds order
#68
ChaoPang
closed
1 month ago
0
fixed potential issues in finetuning
#67
ChaoPang
closed
1 month ago
0
Check whether patient_id exists in the meds_reader database
#66
ChaoPang
closed
1 month ago
0
upgraded cehrbert_data from v0.0.3 to v0.0.4
#65
ChaoPang
closed
1 month ago
0
created a helper function to convert the existing huggingface dataset to an iterable dataset
#64
ChaoPang
closed
1 month ago
0
used the existing subject_split in meds_reader to split the cohort automatically instead of doing it manually
#63
ChaoPang
closed
1 month ago
0
The zero division bug for calculating the unit probabilities for numeric concepts
#62
ChaoPang
closed
1 month ago
0
Fixed the relative paths in the finetuning runner
#61
ChaoPang
closed
1 month ago
0
Added units to meds to cehrbert data transformation and added unit in normalizing numeric values
#60
ChaoPang
closed
1 month ago
0
Convert OMOP MEDS data to CEHR-BERT data by linking events by visit_id
#59
ChaoPang
closed
1 month ago
0
Fix the data and model relative paths
#58
ChaoPang
closed
1 month ago
0
Implemented TruncatedOnlineStatistics to collect truncated stats in a distributed way
#57
ChaoPang
closed
2 months ago
0
Update test prediction columns
#56
ChaoPang
closed
2 months ago
0
Implement a custom do_predict because the HF trainer predict has memory leakage for large test sets
#55
ChaoPang
closed
2 months ago
0
Stopped using the transformers (4.39.3) trainer compute_metrics to calculate custom metrics as large validation sets will crash
#54
ChaoPang
closed
2 months ago
0
added python-build.yml
#53
ChaoPang
closed
2 months ago
0
Deleted all spark related code and included the new cehrbert_data dependency
#52
ChaoPang
closed
2 months ago
0
Updated meds_reader to 0.1.9
#51
ChaoPang
closed
2 months ago
0
removed the abosolute model and tokenizer paths from pretraining and finetuning
#50
ChaoPang
closed
2 months ago
0
removed fastparquet from the dependency list
#49
ChaoPang
closed
2 months ago
0
updated the image references in README to reference the ones on github
#48
ChaoPang
closed
2 months ago
0
Apply pre-commit code formatters
#47
ChaoPang
closed
2 months ago
0
Create pylint.yml
#46
ChaoPang
closed
2 months ago
0
Error when pretraining data
#45
ChungsooKim
closed
1 year ago
5
Syntax error when creating training data
#44
schuemie
closed
1 year ago
2
Unit tests for Tensorflow layers used in CEHR-BERT
#43
ChaoPang
closed
1 year ago
0
Removed temporal tensorflow layers that are not used
#42
ChaoPang
closed
1 year ago
0
Removed temporal tensorflow layers that are not used
#41
ChaoPang
closed
1 year ago
0
added the missing parenthesis
#40
ChaoPang
closed
1 year ago
0
Create unit-tests for tensorflow layers
#39
ChaoPang
closed
1 year ago
0
Create python-app.yml
#38
ChaoPang
closed
1 year ago
0
Integration tests
#37
ChaoPang
closed
1 year ago
0
Switch from our own implementation of MultiHeadAttention to the one created by tensorflow
#36
ChaoPang
closed
2 months ago
0
Removed temporal Bert fine-tuning models
#35
ChaoPang
closed
1 year ago
0
Restored the normalization in PositionalEncoderLayer for backward compatbility, Added a unit-test for PositionalEncoderLayer
#34
ChaoPang
closed
1 year ago
0
Normalize visit_concept_orders before padding
#33
schuemie
closed
1 year ago
0
Remove the experimental code on temporal bert model/layer/trainer
#32
ChaoPang
closed
1 year ago
0
Remove the experimental code on temporal bert model/layer/trainer
#31
ChaoPang
closed
1 year ago
0
The model trainer doesn't work when the use_dask option is enabled
#30
ChaoPang
closed
1 year ago
0
specified pyarrow as the engine when using dask dataframe
#29
ChaoPang
closed
1 year ago
0
set oov_token to -1 in case the OMOP intance contains concept_id=0
#28
ChaoPang
closed
1 year ago
0
Tokenizer doesn't work properly if the OMOP instance contains "concept_id=0"
#27
ChaoPang
closed
1 year ago
0
Link events to same day visits (option 2) and add parameter to creating visits (option 3)
#26
egillax
closed
1 year ago
0
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