Ecosyste.ms: Issues

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GitHub / Machine-Learning-for-Medical-Language/cnlp_transformers issues and pull requests

#224 - Add interactive `prepare_release.py`

Pull Request - State: closed - Opened by ianbulovic about 1 month ago

#223 - remove invalid references to app.state

Pull Request - State: closed - Opened by spencerthomas1722 about 2 months ago

#222 - add argument to cnn_rest.lifespan to fix a bug

Pull Request - State: closed - Opened by spencerthomas1722 about 2 months ago

#221 - Fix version

Pull Request - State: closed - Opened by tmills 2 months ago

#220 - retrain out of date models used in rest servers

Issue - State: open - Opened by tmills 2 months ago

#219 - Removing references to rest api models which are currently broken.

Pull Request - State: closed - Opened by tmills 2 months ago

#218 - Consolidate CLI into `cnlpt` command

Pull Request - State: closed - Opened by ianbulovic 2 months ago

#217 - Use setuptools-scm for versioning, update CONTRIBUTING.md

Pull Request - State: closed - Opened by ianbulovic 2 months ago

#216 - Remove punkt download. Fixes issue-213.

Pull Request - State: closed - Opened by tmills 3 months ago

#214 - Fixes to data processing for updates to hf libraries.

Pull Request - State: closed - Opened by tmills 3 months ago

#213 - Potentially unnecessary tokenizer download on package init

Issue - State: closed - Opened by ianbulovic 3 months ago - 2 comments

#212 - Fix CI error from merge and speed up test collection

Pull Request - State: closed - Opened by ianbulovic 3 months ago

#211 - Use uv for CI

Pull Request - State: closed - Opened by ianbulovic 3 months ago

#210 - Clean up api

Pull Request - State: closed - Opened by ianbulovic 3 months ago

#209 - Lint, format, update README.md and CONTRIBUTING.md

Pull Request - State: closed - Opened by ianbulovic 3 months ago - 2 comments

#208 - Dev tools

Pull Request - State: closed - Opened by ianbulovic 3 months ago

#207 - Add python 3.11, and update a bunch of other dependency versions.

Pull Request - State: closed - Opened by tmills 4 months ago

#206 - Error Analysis and Human Readable Predictions

Pull Request - State: closed - Opened by etgld 4 months ago

#205 - update hf transformers version for safetensors saving

Issue - State: closed - Opened by tmills 4 months ago - 1 comment

#203 - [FEAT] Add feature to export sentences. Modified output format

Pull Request - State: closed - Opened by wonjininfo 6 months ago

#202 - Dev v0.7.0

Pull Request - State: closed - Opened by tmills 6 months ago

#201 - Pytorch version requirements in setup.cfg

Issue - State: closed - Opened by wonjininfo 6 months ago - 1 comment

#200 - Experimental macOS/MPS support

Pull Request - State: closed - Opened by ianbulovic 7 months ago - 1 comment

#199 - first pass at MPS support

Pull Request - State: closed - Opened by ianbulovic 7 months ago - 1 comment

#197 - Deleted import line for ALL_PRETRAINED_CONFIG_ARCHIVE_MAP (deprecated)

Pull Request - State: closed - Opened by guo0O0o 8 months ago - 1 comment

#196 - Temporal extraction

Pull Request - State: open - Opened by spencerthomas1722 about 1 year ago

#195 - Deprecated logger.warn() to be removed in Python 3.13

Issue - State: open - Opened by angus-lherrou about 1 year ago

#194 - REST APIs Support Loading Models on Disk

Issue - State: open - Opened by etgld over 1 year ago - 1 comment

#193 - [FUNC] Add an option for truncation from left

Pull Request - State: closed - Opened by wonjininfo over 1 year ago - 2 comments

#192 - docker: tweak docker builds, mostly to get gpus working

Pull Request - State: closed - Opened by mikix over 1 year ago

#191 - Add docker build script & update the termexists model

Pull Request - State: closed - Opened by mikix over 1 year ago

#190 - Make sure eval_one_score metric is saved for Trainer

Pull Request - State: closed - Opened by mikix over 1 year ago - 3 comments

#189 - Examples for Probability Outputs and Error Analysis

Issue - State: closed - Opened by etgld over 1 year ago - 1 comment

#187 - Update drugs.com dataset URL

Pull Request - State: closed - Opened by mikix over 1 year ago - 1 comment

#186 - --do_eval with no --do_train crashes when checking for model selection labels

Issue - State: closed - Opened by etgld over 1 year ago - 2 comments

#185 - Label Names and Supports In cnlp_metrics

Issue - State: closed - Opened by etgld over 1 year ago - 1 comment

#184 - Add isort to pre-commit hooks

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago - 2 comments

#183 - Implement domain-adaptive pretraining

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago - 1 comment

#182 - dataset and metadata schema

Pull Request - State: open - Opened by angus-lherrou over 1 year ago

#181 - Cleanup of several functions, adding doc strings and type annotations.

Pull Request - State: closed - Opened by tmills over 1 year ago

#180 - add tests for functions

Issue - State: open - Opened by tmills over 1 year ago

#179 - move argument handling code into cnlp_args

Issue - State: closed - Opened by tmills over 1 year ago
Labels: enhancement

#178 - Add pre-commit

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago

#177 - Clean up data format table, add description of hier model.

Pull Request - State: closed - Opened by tmills over 1 year ago

#176 - Initial run of black formatter.

Pull Request - State: closed - Opened by tmills over 1 year ago

#175 - Output prediction probs

Pull Request - State: closed - Opened by wonjininfo over 1 year ago

#174 - Dev v0.6.1

Pull Request - State: closed - Opened by tmills over 1 year ago

#173 - added arguments for model selection metric

Pull Request - State: closed - Opened by spencerthomas1722 over 1 year ago - 1 comment

#172 - Dev error analysis

Pull Request - State: closed - Opened by etgld over 1 year ago - 2 comments

#171 - More human readable predictions and error analysis with no prediction re-runs

Issue - State: closed - Opened by etgld over 1 year ago - 3 comments

#170 - Keep existing classifiers (hier models)

Pull Request - State: closed - Opened by wonjininfo over 1 year ago

#167 - Dev v0.6.0

Pull Request - State: closed - Opened by tmills over 1 year ago

#166 - update CONTRIBUTING.md with docker build/test instructions

Issue - State: open - Opened by tmills over 1 year ago

#165 - add support for python 3.11

Issue - State: closed - Opened by tmills over 1 year ago - 1 comment

#163 - Added dev dockerfiles

Pull Request - State: closed - Opened by dogversioning over 1 year ago - 2 comments

#162 - Grab chunk attentions so that we can visualize hierarchical attention.

Pull Request - State: closed - Opened by tmills over 1 year ago - 1 comment

#161 - Drop support for Python 3.7

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago

#160 - Drop support for Python 3.7

Issue - State: closed - Opened by angus-lherrou over 1 year ago

#157 - Implement dev version of Dockerfiles

Issue - State: open - Opened by tmills over 1 year ago

#156 - writing predictions uses last model rather than best model

Issue - State: closed - Opened by tmills over 1 year ago

#154 - Adjust Sphinx docs

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago

#153 - Add requirements for transform_prot

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago - 5 comments

#152 - Add support for loading local encoders for fine-tuning

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago

#151 - Add reports for input truncation

Issue - State: open - Opened by angus-lherrou over 1 year ago

#150 - Realign baseline models with new task flow

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago

#148 - find a configuration of thyme tlinks only that finds signal

Issue - State: closed - Opened by tmills over 1 year ago

#147 - Character model support

Pull Request - State: closed - Opened by etgld over 1 year ago

#144 - merge docs and github actions changes into dev-v0.6.0

Pull Request - State: closed - Opened by angus-lherrou over 1 year ago

#143 - rename ClinicalNLPDataset

Issue - State: open - Opened by tmills over 1 year ago

#142 - Issue 138 datasets

Pull Request - State: closed - Opened by tmills over 1 year ago

#141 - re-implement sequential fine-tuning

Issue - State: open - Opened by tmills almost 2 years ago - 1 comment

#139 - Move versioning into cnlpt.__version__

Pull Request - State: closed - Opened by angus-lherrou almost 2 years ago

#138 - handle case with varying numbers of dataset arguments and task name arguments.

Issue - State: closed - Opened by tmills almost 2 years ago - 5 comments

#137 - trainer does not actually use multiple datasets

Issue - State: closed - Opened by tmills almost 2 years ago

#136 - Dockerize hierarchical model

Issue - State: closed - Opened by tmills almost 2 years ago - 2 comments

#135 - Update doctimerel rest to use current helper methods in cnlp_rest.

Pull Request - State: closed - Opened by tmills almost 2 years ago

#134 - Update tiny DTR model

Issue - State: closed - Opened by tmills almost 2 years ago

#133 - add warned-dataclasses

Pull Request - State: closed - Opened by angus-lherrou almost 2 years ago

#131 - Issue 130 - separate out hierarchical model to not inherit

Pull Request - State: closed - Opened by tmills almost 2 years ago - 1 comment

#130 - disentangle hierarchical and standard models

Issue - State: closed - Opened by tmills almost 2 years ago

#129 - V0.5.0 hoang specific to v0.5.0

Pull Request - State: closed - Opened by tmills almost 2 years ago

#128 - Memory error in pyplot hist

Issue - State: closed - Opened by yingyali almost 2 years ago - 4 comments

#127 - V0.5.0 hoang

Pull Request - State: closed - Opened by vanh17 almost 2 years ago

#126 - Preloading models for docker servers (#115)

Pull Request - State: closed - Opened by etgld almost 2 years ago

#125 - Move hierarchical encoder head config into CnlpConfig

Pull Request - State: closed - Opened by angus-lherrou almost 2 years ago