Ecosyste.ms: Issues

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GitHub / alan-turing-institute/grace issues and pull requests

#338 - README & setup reversals

Pull Request - State: closed - Opened by KristinaUlicna 10 months ago
Labels: documentation

#337 - [DEVELOPMENT] Consider using a KNN to construct the intial graph

Issue - State: open - Opened by quantumjot 11 months ago
Labels: methodology

#336 - [FEATURE REQUEST] Add citation.cff to repo

Issue - State: open - Opened by mooniean 11 months ago
Labels: enhancement

#334 - [DEVELOPMENT] Compare IoU of inference datasets across multiple runs

Issue - State: open - Opened by KristinaUlicna 12 months ago
Labels: methodology

#333 - MILESTONE: Merging `development` into `main` 🎉

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: methodology

#332 - Refactor node features ✍️

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: documentation

#331 - Separate inference into assessment module 🧹

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: enhancement, methodology

#330 - [DEVELOPMENT] Concatenate Laplacian-multiplied node features

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: methodology

#329 - Graph Laplacian 🌐

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago
Labels: methodology

#328 - Catch auroc error 🚫

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago
Labels: bug, methodology

#327 - [DEVELOPMENT] AUROC metric throws an error

Issue - State: closed - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: bug, methodology

#326 - Revitalise tests 🧪

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago
Labels: tests

#325 - [DEVELOPMENT] Inject uncorrelated Gaussian noise into images

Issue - State: open - Opened by KristinaUlicna 12 months ago
Labels: methodology

#324 - [FEATURE REQUEST] Contribute a README.md describing augmentations

Issue - State: open - Opened by KristinaUlicna 12 months ago
Labels: documentation

#323 - Write a CONTRIBUTING.md doc 📝

Issue - State: open - Opened by KristinaUlicna 12 months ago
Labels: documentation, good first issue

#322 - [DEVELOPMENT] Consider config validation to be a property of config

Issue - State: open - Opened by KristinaUlicna 12 months ago
Labels: methodology

#318 - [FEATURE REQUEST] Separate inference into a stand-alone module

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: enhancement

#317 - Tidy up `run.py` by separating inference into assessment module 🧹

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: enhancement

#316 - Catching `roc_auc_score` error 🚫

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 2 comments
Labels: bug, tests

#313 - Revert "Issue closer 📕 "

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago
Labels: documentation

#312 - Issue closer 📕

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago
Labels: documentation

#311 - Minor comment to check for issue closing

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: documentation

#310 - Clarify which properties are used in the training

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: documentation

#309 - Testing project board workflow.

Issue - State: closed - Opened by crangelsmith 12 months ago
Labels: methodology

#308 - Simplify `run.py` 🏃‍♀️

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 3 comments
Labels: methodology

#307 - Edge properties documentation 📜

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 2 comments
Labels: documentation

#306 - Model Architecture Summary 🏗️

Pull Request - State: closed - Opened by KristinaUlicna 12 months ago - 2 comments
Labels: bug, documentation

#305 - [DEVELOPMENT] Consider implementing an `RGCN`

Issue - State: open - Opened by KristinaUlicna 12 months ago
Labels: methodology

#304 - [DEVELOPMENT] Define an `EdgePropertyCruncher`

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: methodology

#303 - [DEVELOPMENT] Compute edge properties

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: methodology

#301 - Write up an extended abstract for introducing GRACE

Issue - State: open - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: documentation, help wanted

#300 - [FEATURE REQUEST] Create a discussion on metrics evaluation

Issue - State: closed - Opened by KristinaUlicna 12 months ago - 1 comment
Labels: help wanted, question

#299 - [DEVELOPMENT] Write proper documentation for `EdgePropertyCruncher`

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: documentation

#297 - [DEVELOPMENT] Allow feature / property extraction to be computed at run-time

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: methodology

#296 - [BUG] Model architecture summary doesn't save up GNN layers by name

Issue - State: closed - Opened by KristinaUlicna 12 months ago
Labels: bug

#295 - Minor typo edits + typing specs

Pull Request - State: closed - Opened by KristinaUlicna almost 1 year ago
Labels: documentation

#294 - [FEATURE REQUEST] Consider visualising the edge properties in the dataset

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, visualisation

#293 - Updating tests of an evolving pipeline ✍️

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: tests

#292 - Pytest: Automated tests refactoring ✍️

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 1 comment
Labels: tests

#291 - Add more sophisticated classifier model options

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology

#290 - Automated tests refactoring ✍️

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 2 comments
Labels: tests

#289 - Implement commented `features` code as an optional display in napari annotator

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: visualisation

#288 - Click.option with flexibility to show features in napari annotator 🎨

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, enhancement

#287 - Decide whether overwriting `.parquet` files is the best design approach

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: question

#286 - Store graph `NODE_FEATURES` in the graph once for development 🌐

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, methodology

#285 - Edge properties for reasonable edge classification 📊

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 6 comments
Labels: methodology, visualisation

#284 - [DEVELOPMENT] Store edge properties in `Data` object for training

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#283 - Separate hidden layers for graph convolutions + dense Linear layers

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 4 comments
Labels: documentation, tests, methodology

#282 - [FEATURE REQUEST] Output the summary of the model architecture for completeness

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement

#281 - [DEVELOPMENT] Allow specifying variable number of graph conv & dense linear layers

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#280 - [DEVELOPMENT] Implement BatchNorm before/after GCN layers

Issue - State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology

#278 - [DEVELOPMENT] Use distance / weighting as feature for edge embedding learning

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#277 - Storing the `NODE_FEATURES` in the annotation graph once for speed-up

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 1 comment
Labels: enhancement, methodology

#276 - [FEATURE REQUEST] Append node features to the graph once and for all

Issue - State: closed - Opened by KristinaUlicna about 1 year ago - 1 comment
Labels: enhancement

#275 - Image annotation in napari: launch from command line 💻

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 2 comments
Labels: enhancement

#273 - Config hyperparameters for enhanced training

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, enhancement

#272 - [BUG] Introduce timeout on poor models which struggle to project TSNE manifold

Issue - State: open - Opened by KristinaUlicna about 1 year ago
Labels: bug, enhancement

#271 - Customise the logger to print epochs into new lines

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation

#270 - Separate training from inference in `run.py`

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

#269 - [DEVELOPMENT] Include F1-score into training metrics monitoring in TensorBoard

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#268 - [DEVELOPMENT] Return TSNE plot as figure to save / show downstream

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#267 - [DEVELOPMENT] Extend `GraphLabelPredictor` to perform inference on entire batch

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#266 - [DEVELOPMENT] Allow classifier training from `config.yaml` file

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#264 - [BUG] Add cvxopt to napari env yaml

Issue - State: open - Opened by mooniean about 1 year ago
Labels: bug, setup

#263 - [FEATURE REQUEST] Pool all colour selections into `styling.py` script

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, visualisation

#261 - [FEATURE REQUEST] Implement optimiser weight decay

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology

#260 - [FEATURE REQUEST] Implement loss weighing by class

Issue - State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement

#258 - [FEATURE REQUEST] Define a configurable dictonary of colormaps throughout the pipeline

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, visualisation

#257 - [FEATURE REQUEST] Log F1-score metric to Tensorboard log

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology, visualisation

#256 - [FEATURE REQUEST] Validate required config hyperparameters

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement

#255 - [DEVELOPMENT] Transfer the `PREDICTION` probabilities into a dictionary

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#254 - [FEATURE REQUEST] Consider using `.yaml` files for hyperparameter config

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, enhancement, methodology

#253 - [DEVELOPMENT] Update config.json + training subfolder README documentation

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation

#252 - [DEVELOPMENT] Optimise graphs & save out connected components fig

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#251 - [DEVELOPMENT] Animate the output of validation graphs

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology

#250 - Inference & optimisation (+ visualisation) all in automated pipeline 🚀

Pull Request - State: closed - Opened by KristinaUlicna about 1 year ago - 4 comments
Labels: documentation, enhancement, methodology

#249 - [DEVELOPMENT] Store numerical performance metrics in `infer` subfolder

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#248 - [DEVELOPMENT] Add infer dataset performance to Tensorboard log

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology

#247 - [DEVELOPMENT] How to set a global config with different font attributes in matplotlib?

Issue - State: closed - Opened by KristinaUlicna about 1 year ago - 1 comment
Labels: help wanted, question, visualisation

#246 - [DEVELOPMENT] Serialise inference for more than just single graph

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#245 - [DEVELOPMENT] Create a helper function to create datasets in `run.py`

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#244 - [DEVELOPMENT] Generalise `GCN` for `GNNClassifier` object for training

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#243 - [DEVELOPMENT] Calculate GNN perfomance metrics after the last epoch on valid image

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#242 - [DEVELOPMENT] Run inference on an unseen graph in `run.py`

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#241 - [DEVELOPMENT] Define validation whole graph plotter param with certain frequency

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#239 - [DEVELOPMENT] Separate train & valid image datasets for GCN training

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology

#238 - [DEVELOPMENT] Remove redundant `run_dir` argument from config

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, methodology

#236 - [FEATURE REQUEST] Plot the subgraphs with highlighted nodes & edges per label

Issue - State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement