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Publish this tool on PyPI
#35 · JohnGiorgi opened on Aug 17, 2018
15
Train models for each major entity class
#6 · JohnGiorgi opened on Aug 2, 2018
3

Installing the package
BaderLab/saber#200 · opened on Nov 15, 2023
Switch to AutoModel API
BaderLab/saber#174 · opened on Aug 20, 2019
Truncating should effect only the train set
BaderLab/saber#166 · opened on Aug 6, 2019
Pad sequences with something other than keras.preprocessing.text
BaderLab/saber#158 · opened on Jul 29, 2019
Swap out time comments with decorators
BaderLab/saber#156 · opened on Jul 25, 2019
Loading models that don't exist should throw an error.
BaderLab/saber#155 · opened on Jul 24, 2019
Splitting of training data should be model agnostic.
BaderLab/saber#153 · opened on Jul 24, 2019
Switch token alignment to SpaCy
BaderLab/saber#152 · opened on Jul 17, 2019
Metrics class should behave more like Keras's default History Callback
BaderLab/saber#149 · opened on Jul 8, 2019
Try out new grounding service
BaderLab/saber#147 · opened on Jul 3, 2019
saber.load_dataset() should be able to pull from pubannotation.
BaderLab/saber#146 · opened on Jun 15, 2019
Change default save directory
BaderLab/saber#145 · opened on Jun 7, 2019
Need nicely formatted string representation of a PyTorch model
BaderLab/saber#140 · opened on Jun 3, 2019
Switch to SciSpacy
BaderLab/saber#136 · opened on May 20, 2019
Evaluation is slow
BaderLab/saber#132 · opened on May 16, 2019
Better Handling of Rare Words
BaderLab/saber#131 · opened on May 16, 2019
Easy way to evaluate a model
BaderLab/saber#125 · opened on Mar 21, 2019
Config file needs to be re-written to better handle multiple models
BaderLab/saber#120 · opened on Feb 28, 2019
Argument fine_tune_word_embeddings has no effect when transfer learning
BaderLab/saber#105 · opened on Dec 14, 2018
LR Range Test Graphs
BaderLab/saber#89 · opened on Nov 13, 2018
Some command line arguments are useless
BaderLab/saber#76 · opened on Oct 26, 2018
Try weighting the importance of target classes
BaderLab/saber#68 · opened on Oct 20, 2018
debug argument should partially load a dataset
BaderLab/saber#65 · opened on Oct 20, 2018
Cyclic learning rates
BaderLab/saber#56 · opened on Oct 15, 2018
Cannot supply PMID when using Saber.annotate()
BaderLab/saber#54 · opened on Oct 5, 2018

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Issues

Issues

Installing the package

Switch to AutoModel API

Truncating should effect only the train set

Pad sequences with something other than keras.preprocessing.text

Swap out time comments with decorators

Loading models that don't exist should throw an error.

Splitting of training data should be model agnostic.

Switch token alignment to SpaCy

Metrics class should behave more like Keras's default History Callback

Try out new grounding service

saber.load_dataset() should be able to pull from pubannotation.

Change default save directory

Need nicely formatted string representation of a PyTorch model

Switch to SciSpacy

Evaluation is slow

Better Handling of Rare Words

Easy way to evaluate a model

Config file needs to be re-written to better handle multiple models

Argument `fine_tune_word_embeddings` has no effect when transfer learning

LR Range Test Graphs

Some command line arguments are useless

Try weighting the importance of target classes

debug argument should partially load a dataset

Cyclic learning rates

Cannot supply PMID when using Saber.annotate()