Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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` ๐
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
- 1 comment
Labels: methodology
#332 - Refactor node features โ๏ธ
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
- 1 comment
Labels: documentation
#331 - Separate inference into assessment module ๐งน
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 ๐
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
Labels: methodology
#328 - Catch auroc error ๐ซ
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 ๐งช
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 ๐
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
#321 - [DEVELOPMENT] Create a function which strips the graph attributes from the GRACE files
Issue -
State: open - Opened by KristinaUlicna 12 months ago
Labels: methodology
#320 - Re-implement graph / patch augmentation into the training loop
Issue -
State: open - Opened by KristinaUlicna 12 months ago
#319 - [FEATURE REQUEST] Allow user to specify control which / how many edge properties they want
Issue -
State: open - Opened by KristinaUlicna 12 months ago
Labels: enhancement
#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 ๐งน
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
- 1 comment
Labels: enhancement
#316 - Catching `roc_auc_score` error ๐ซ
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
- 2 comments
Labels: bug, tests
#315 - [BUG] Undefined `roc_auc_score` if only one class present in `y_true`
Issue -
State: closed - Opened by KristinaUlicna 12 months ago
Labels: bug
#313 - Revert "Issue closer ๐ "
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
Labels: documentation
#312 - Issue closer ๐
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` ๐โโ๏ธ
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
- 3 comments
Labels: methodology
#307 - Edge properties documentation ๐
Pull Request -
State: closed - Opened by KristinaUlicna 12 months ago
- 2 comments
Labels: documentation
#306 - Model Architecture Summary ๐๏ธ
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
#298 - [DEVELOPMENT] Click options to overwrite config file hyperparameter specification
Issue -
State: open - Opened by KristinaUlicna 12 months ago
Labels: methodology
#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 about 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 โ๏ธ
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: tests
#292 - Pytest: Automated tests refactoring โ๏ธ
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 โ๏ธ
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 ๐จ
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 ๐
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, methodology
#285 - Edge properties for reasonable edge classification ๐
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
#279 - [DEVELOPMENT] Consider splitting all classifier options into individual `torch.nn.Module` objects
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: 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 ๐ป
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: enhancement
#274 - [FEATURE REQUEST] Allow flexible click option to specify `IMAGE_PATH` for napari annotation
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
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
#265 - [FEATURE REQUEST] Consider removing `assume_annotations_from_dummy_predictions` function if not needed
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: documentation, duplicate
#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
#262 - [FEATURE REQUEST] Project the TSNE manifold & save out the visualisation from `run.py`
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#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
#259 - [FEATURE REQUEST] Consider replacing seaborn confusion matrices by `ConfusionMatrixDisplay`
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: visualisation
#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 ๐
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
#240 - [DEVELOPMENT] Change `transform` function to remove augmentations at valid / infer time
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
#237 - [FEATURE REQUEST] Add function to visualise subgraphs directly from whole graph information
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#236 - [FEATURE REQUEST] Plot the subgraphs with highlighted nodes & edges per label
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement