BaderLab/saber issues and pull requests

#200 - Installing the package

Issue - State: open - Opened by omermesser about 1 year ago

#199 - Tensorflow error while the container running

Issue - State: closed - Opened by laleye about 4 years ago - 1 comment

#198 - Error with sb.load('PRGE')

Issue - State: closed - Opened by sammiyo about 4 years ago - 1 comment

#197 - reproduce a score

Issue - State: closed - Opened by chiyuan1126 about 4 years ago - 2 comments

#196 - SABER not working with recent keras/tensorflow versions

Issue - State: closed - Opened by DmitryMalishev over 4 years ago - 1 comment

#195 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.3.3

Pull Request - State: open - Opened by dependabot-preview[bot] over 4 years ago - 2 comments
Labels: dependencies

#194 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.3.2

Pull Request - State: closed - Opened by dependabot-preview[bot] over 4 years ago - 3 comments
Labels: dependencies

#193 - ⬆️ Bump keras from 2.2.4 to 2.4.3

Pull Request - State: open - Opened by dependabot-preview[bot] over 4 years ago - 2 comments
Labels: dependencies

#192 - ⬆️ Bump keras from 2.2.4 to 2.4.2

Pull Request - State: closed - Opened by dependabot-preview[bot] over 4 years ago - 3 comments
Labels: dependencies

#191 - ⬆️ Bump keras from 2.2.4 to 2.4.0

Pull Request - State: closed - Opened by dependabot-preview[bot] over 4 years ago - 2 comments
Labels: dependencies

#190 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.3.1

Pull Request - State: closed - Opened by dependabot-preview[bot] over 4 years ago - 3 comments
Labels: dependencies

#189 - Expose pretrained model performance and evaluation datasets

Issue - State: closed - Opened by swartchris8 over 4 years ago - 1 comment

#188 - ⬆️ Bump msgpack from 0.5.6 to 1.0.0

Pull Request - State: open - Opened by dependabot-preview[bot] almost 5 years ago - 2 comments
Labels: dependencies

#187 - Cannot evaluate model with a suggested workaround

Issue - State: closed - Opened by AlbinaGalimzyanova almost 5 years ago - 5 comments

#186 - ⬆️ Bump keras from 2.2.4 to 2.3.1

Pull Request - State: closed - Opened by dependabot-preview[bot] about 5 years ago - 3 comments
Labels: dependencies

#185 - Cannot install saber (broken library dependencies)

Issue - State: closed - Opened by AlbinaGalimzyanova about 5 years ago - 2 comments

#184 - Migrate from pytorch_transformers to transformers

Pull Request - State: closed - Opened by JohnGiorgi about 5 years ago - 1 comment

#183 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.2.2

Pull Request - State: closed - Opened by dependabot-preview[bot] about 5 years ago - 5 comments
Labels: dependencies

#182 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.2.1

Pull Request - State: closed - Opened by dependabot-preview[bot] about 5 years ago - 3 comments
Labels: dependencies

#181 - Update to Transformers 2.0 API

Issue - State: closed - Opened by JohnGiorgi about 5 years ago
Labels: dependencies

#180 - Stratified cross val

Pull Request - State: closed - Opened by JohnGiorgi about 5 years ago
Labels: enhancement, feature

#179 - Stratified cross val

Pull Request - State: closed - Opened by JohnGiorgi about 5 years ago - 2 comments
Labels: enhancement, feature

#178 - Implements entity pre-training

Pull Request - State: closed - Opened by JohnGiorgi about 5 years ago - 2 comments
Labels: feature

#177 - :recycle: Re-purpose decay argument for weight decay

Pull Request - State: closed - Opened by JohnGiorgi about 5 years ago - 1 comment

#176 - Faster att mask gen

Pull Request - State: closed - Opened by JohnGiorgi about 5 years ago - 2 comments
Labels: enhancement, optimization

#175 - Bump pytorch dependencies

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: dependencies

#174 - Switch to AutoModel API

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature, design

#173 - 2D Dropout in RE module

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: enhancement

#172 - Remove embeddings

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: chore, design

#171 - Drop Embeddings class

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: chore, design

#170 - Fix random seeds

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: enhancement, feature

#169 - Fix TravisCI build

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: bug, production

#168 - Implement transformer

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: enhancement, feature

#167 - AMP only works on CUDA devices

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: bug, invalid

#166 - Truncating should effect only the train set

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: invalid

#165 - Better use of validation split

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature

#164 - Removing Keras / Tensorflow dependencies

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: dependencies

#163 - Add support for mixed precision

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, optimization, feature

#162 - Migrate to pytorch-transformers

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, dependencies

#161 - Add link to Slack channel

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment

#160 - Implement mixed precision training

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, optimization, feature

#159 - Update BERT based models to use new PyTorch Transformer API

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement

#158 - Pad sequences with something other than keras.preprocessing.text

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: chore

#157 - Remove BiLSTM-CRF

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: optimization, in progress, design

#156 - Swap out time comments with decorators

Issue - State: open - Opened by JohnGiorgi over 5 years ago

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

Issue - State: open - Opened by JohnGiorgi over 5 years ago

#154 - Providing both k_folds and validation_split argument should work

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature

#153 - Splitting of training data should be model agnostic.

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, invalid

#152 - Switch token alignment to SpaCy

Issue - State: open - Opened by JohnGiorgi over 5 years ago

#151 - Add rc performance to metrics

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature

#150 - Better control over type of training strategy

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement

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

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, invalid, chore

#148 - Joint, BERT-based model for NER and RC

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: feature

#147 - Try out new grounding service

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature

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

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature

#145 - Change default save directory

Issue - State: open - Opened by JohnGiorgi over 5 years ago

#144 - Switch to absolute imports

Issue - State: closed - Opened by JohnGiorgi over 5 years ago

#143 - Put tensors returned under predict on CPU

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago

#142 - Remove large files from commit history

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: invalid, production

#141 - Multi-task BERT for NER

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: enhancement, feature

#140 - Need nicely formatted string representation of a PyTorch model

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, design, production

#139 - Multi-task BERT

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature, in progress

#138 - BioBERT

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: enhancement, feature

#137 - Optimizers not being reset during cross-validation

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: bug, invalid, in progress

#136 - Switch to SciSpacy

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, optimization, production

#135 - Load BioBERT weights

Issue - State: closed - Opened by JohnGiorgi over 5 years ago - 9 comments
Labels: enhancement, feature

#134 - Add pre-trained model to Google Drive

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: production

#133 - Fix Bert Preprocessing

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: bug, invalid

#132 - Evaluation is slow

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, optimization, feature, production

#131 - Better Handling of Rare Words

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, optimization, feature

#130 - Better Batching

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, optimization

#129 - Simplify BiLSTM-CRF Architecture

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement

#128 - Update NeuralCoref

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 4 comments
Labels: dependencies

#127 - NeuralCoref is now on pip

Issue - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, production

#126 - Multiple models

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago - 1 comment
Labels: enhancement, feature

#125 - Easy way to evaluate a model

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, invalid

#124 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.1.2

Pull Request - State: closed - Opened by dependabot-preview[bot] over 5 years ago - 6 comments
Labels: dependencies

#123 - ⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.1.1

Pull Request - State: closed - Opened by dependabot-preview[bot] over 5 years ago - 4 comments
Labels: dependencies

#122 - Dependabot can't evaluate your Python dependency files

Issue - State: closed - Opened by dependabot-preview[bot] over 5 years ago

#121 - Save load annotate with bert

Pull Request - State: closed - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, feature

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

Issue - State: open - Opened by JohnGiorgi over 5 years ago
Labels: enhancement, invalid

#119 - Add grounding for major entity types using EXTRACT 2.0 API

Pull Request - State: closed - Opened by JohnGiorgi almost 6 years ago - 2 comments
Labels: enhancement, feature

#118 - Min functioning pytorch model

Pull Request - State: closed - Opened by JohnGiorgi almost 6 years ago - 3 comments

#117 - Add CHED base model

Pull Request - State: closed - Opened by JohnGiorgi almost 6 years ago - 1 comment
Labels: enhancement, feature, production

#113 - Update long description in setup.py

Issue - State: closed - Opened by JohnGiorgi almost 6 years ago
Labels: production

#109 - ⬆️ Bump waitress from 1.1.0 to 1.2.0

Pull Request - State: closed - Opened by dependabot-preview[bot] almost 6 years ago - 3 comments
Labels: dependencies

#106 - Try Yogi Optimizer

Issue - State: closed - Opened by JohnGiorgi almost 6 years ago
Labels: optimization

#101 - Somewhat refs #90: fixed a syntax error; also used asyncio

Pull Request - State: closed - Opened by IgorRodchenkov almost 6 years ago - 2 comments

#96 - Cannot use transfer learning and multi-task learning in conjunction

Issue - State: closed - Opened by JohnGiorgi almost 6 years ago
Labels: bug, invalid

#90 - Grounding sometimes hangs

Issue - State: closed - Opened by JohnGiorgi about 6 years ago - 2 comments
Labels: bug, invalid

#88 - Attending to character embeddings

Issue - State: closed - Opened by JohnGiorgi about 6 years ago
Labels: enhancement, discussion, feature

#78 - Replace multi_task_lstm_crf load method with call to super

Issue - State: closed - Opened by JohnGiorgi about 6 years ago
Labels: in progress, design

#77 - Successive loading of Saber model

Issue - State: closed - Opened by JohnGiorgi about 6 years ago
Labels: enhancement, feature

#65 - debug argument should partially load a dataset

Issue - State: open - Opened by JohnGiorgi about 6 years ago
Labels: enhancement, invalid

#58 - Do residual connection help?

Issue - State: closed - Opened by JohnGiorgi about 6 years ago
Labels: enhancement, feature

#56 - Cyclic learning rates

Issue - State: open - Opened by JohnGiorgi about 6 years ago
Labels: enhancement, feature

#55 - Try Elmo Embeddings

Issue - State: closed - Opened by JohnGiorgi about 6 years ago
Labels: enhancement, feature

#35 - Publish this tool on PyPI

Issue - State: open - Opened by JohnGiorgi over 6 years ago - 15 comments
Labels: enhancement, production

#23 - Implement Named Entity Normalization (NEN)

Issue - State: closed - Opened by JohnGiorgi over 6 years ago
Labels: feature

#14 - Beef up unit tests

Issue - State: open - Opened by JohnGiorgi over 6 years ago
Labels: invalid, optimization, production

GitHub / BaderLab/saber issues and pull requests