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
#235 - [DEVELOPMENT] Separate the `evaluation` and `visualisation` subfolders
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#234 - Subgraph visualisation 🌐 + plotting code re-organisation 📁
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: enhancement, methodology
#233 - Write a complete set of tests for inference, manifold & optimisation part of the pipeline
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: tests
#232 - Transform notebooks into proper pipeline in `run.py`
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology
#231 - Modifying the optimiser input to more elaborate `PREDICTION` vector dtype
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: tests, methodology
#230 - [DEVELOPMENT] Repurpose `logging` to `LOGGER` to recycle its config
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#229 - Graph visualisation & embedding dimensionality reduction
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 3 comments
Labels: enhancement, methodology
#228 - [DEVELOPMENT] Edit optimiser hypothesis rho value input type
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#227 - [DEVELOPMENT] Split the `read_grace.ipynb` viz function
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#226 - [DEVELOPMENT] Flip the edge probability multiplication from 0.1 to 0.9
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: methodology
#225 - [DEVELOPMENT] Repurpose 2x2 confusion matrix for use outside of object metrics
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#224 - [DEVELOPMENT] Rename `normalise` to `normalize` for tests to pass
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#223 - Inference of GCN model on unseen test data
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 4 comments
Labels: enhancement, methodology
#222 - [DEVELOPMENT] Visualise the whole graph inference after each epoch
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology, visualisation
#221 - [DEVELOPMENT] Split the unknown masking for nodes & edges
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#220 - [DEVELOPMENT] Utilise `edge_attr` in graph convolutions
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: help wanted, question, methodology
#219 - PR template update
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: documentation
#218 - Training of GC Network -> debugging
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: bug, documentation
#217 - updating image_reader_fn variable is changed in image_graph_dataset
Pull Request -
State: closed - Opened by marjanfamili about 1 year ago
- 4 comments
#216 - Split & properly orient graph & image visualisation functions
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#215 - Consider using pydantic for configuration
Issue -
State: open - Opened by quantumjot about 1 year ago
#214 - Make `Annotation.UNKNOWN` relabelling an optional configurable hyperparameter
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
#213 - Repurpose `GraphAttrs.Prediction` attributes to complete set
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#212 - Create tests for GCN with Linear layer(s) only
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: tests
#211 - Create template for contributing a PR
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, enhancement
#210 - [WIP] 🚧 TheTuringWay PR template 👷♀️
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#209 - Use `torch.nn.ModuleList` to include GC layers in model summary
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#208 - Allow empty `hidden_channels` list config hyperparam to create model with no GC layers
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug, tests, methodology
#207 - Implement new hyperparameters for training run config
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: documentation, enhancement
#206 - Add normalise hyperparameter to the config
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug, enhancement
#205 - Add train-to-valid split hyperparameter to the config
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#204 - Use `logging` rather than `print` for user feedback
Issue -
State: closed - Opened by quantumjot about 1 year ago
Labels: documentation, enhancement
#203 - Why are we padding the corner images if they don't contribute to training?
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: help wanted, question
#202 - Shuffle the dataset before train-to-valid split
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug, methodology
#201 - Print out image / graph node & edge statistics if desired
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, enhancement
#200 - Optional relabelling of nodes & edges with `Annotation.UNKNOWN` label
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 4 comments
Labels: enhancement, methodology
#199 - Tensorboard launch command instructions
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#198 - Avoid the matrix shape crash in tests - dynamically change embedding num_dims
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: bug, tests
#197 - Handle montage display with only 2 annotation classes
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug, enhancement
#196 - Added instructions to export conda environment
Pull Request -
State: closed - Opened by mooniean about 1 year ago
Labels: documentation
#195 - Real images: handle nodes that belong to more than one object
Issue -
State: open - Opened by mooniean about 1 year ago
Labels: methodology
#194 - Measure area under [receiver-operator, precision-recall] curve metrics
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology
#193 - Rename `test` to `valid` function in `train.py`
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#192 - Return node & edge embeddings from semi-last GCN layer
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: enhancement, methodology
#191 - Modify optimiser to read more elaborate `GraphAttrs.PREDICTION` data structures
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement, methodology
#190 - [BUG] Fix how the subgraph dataset is created at inference time
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug
#189 - Transform inference procedure from notebook to script
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#188 - Run model inference on random graph + real annotated data
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#187 - Include a `self.predict()` method into the GCN classifier
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: methodology
#186 - Pre-process predictions so that only `.long()` dtype vectors are passed into metrics
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: bug
#185 - Include optional argument to relabel `Annotation.UNKNOWN` label
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#184 - Add instructions on how to launch `tensorboard` from the terminal
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#183 - [Deprecated] Training & evaluation of GCN classifier 🏷️
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 7 comments
Labels: bug, documentation, enhancement
#182 - Apply loss weighting into `loss_criterion`
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#181 - What's the reasoning behind the dropout positioning?
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: help wanted, question
#180 - Export nodes and edges as separate `.parquet` files from automated annotation
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#179 - Starting `run.py` triggers this warning
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: bug
#178 - added run test
Pull Request -
State: closed - Opened by chris-soelistyo about 1 year ago
- 2 comments
Labels: tests
#177 - Tensorboard events logs into single file
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#176 - Revert "merged logs into one event file"
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug
#175 - Test for full run to train the classifier
Issue -
State: closed - Opened by chris-soelistyo about 1 year ago
Labels: tests
#174 - Attempt to classify edges using node feature dot product
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#173 - Condition `simulated_graph` so that shapes don't overarch the graph boundary
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: bug, enhancement
#172 - Visualise GCN predictions of node/edge probabilities on graph
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#170 - Create a metrics object wrapper
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#169 - Ensure all objects are evaluated for IoU even those with no overlap
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug
#168 - Pool `random_graph` & `random_graph_mixed_motifs`
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#165 - Account for object identity in ground truth from `random_graph`
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug, enhancement
#164 - Incorporate a strict IoU threshold into evaluation pipeline
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#163 - Evaluation of GRACE performance 📊
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: enhancement
#162 - Draw an automated annotation mask from simulated GT graph
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#161 - [FEATURE REQUEST] Allow user to perform dimensionality reduction on extracted patch features
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: enhancement
#160 - Reorganise all classifier training code into `training` subfolder
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: documentation
#159 - New conda environments don't train from `run.py`
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: bug, setup
#158 - Keep edge attributes by removing edges
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: bug, enhancement
#157 - Move all loose training code into a `training` subfolder
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#156 - Update README with synth data + env options
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#155 - Motivate the user to check out the synthetic dataset creation option
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation, enhancement
#154 - Fix the `.yml` vs `.yaml` typo in the new napari environment
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#153 - Specify difference between two conda environments
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: documentation
#152 - Generate the grace annotations automatically from the simulated image
Issue -
State: open - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#151 - Conda environment failing -> `conda env export --no-builds`
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
#150 - Start GRACE from napari plugin window
Issue -
State: open - Opened by marjanfamili about 1 year ago
Labels: enhancement, question, setup
#149 - Visualisation of the image & graph annotations
Pull Request -
State: closed - Opened by KristinaUlicna about 1 year ago
- 4 comments
Labels: bug, documentation, enhancement
#148 - Images converted into integers - why?
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: help wanted, question
#147 - [BUG]: Unable to train the model successfully
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 2 comments
Labels: bug
#146 - [FEATURE REQUEST] Implement enhanced training hparams
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#145 - Understand if / how the images are normalised prior to feeding into ResNet / GCN
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
#144 - [BUG]: Tensorboard struggles to save all the logging data per run
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
Labels: bug
#137 - Illustrate a hand written example of the optimisation matrix
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
- 1 comment
#136 - Adding visualisation of graph to grace as an optional plot out
Issue -
State: closed - Opened by marjanfamili about 1 year ago
Labels: enhancement
#135 - Create an environment.yaml which contains napari
Issue -
State: closed - Opened by KristinaUlicna about 1 year ago
Labels: enhancement
#133 - Graph pre-process
Issue -
State: closed - Opened by marjanfamili about 1 year ago
Labels: enhancement, methodology
#131 - Added show_starfile.py
Pull Request -
State: closed - Opened by mooniean about 1 year ago
- 4 comments
Labels: enhancement
#130 - merged logs into one event file
Pull Request -
State: closed - Opened by chris-soelistyo about 1 year ago
#127 - [FEATURE REQUEST] create show_starfile.py
Issue -
State: closed - Opened by mooniean about 1 year ago
Labels: enhancement
#123 - move to toml based setup
Pull Request -
State: closed - Opened by quantumjot about 1 year ago
- 1 comment
#122 - Move to toml only setup
Issue -
State: open - Opened by quantumjot about 1 year ago
Labels: setup
#106 - [Deprecated] GCN inference + optimisation on simulated objects
Pull Request -
State: closed - Opened by KristinaUlicna over 1 year ago
- 1 comment
Labels: bug, documentation, enhancement
#101 - [FEATURE REQUEST] Implement inference function
Issue -
State: closed - Opened by mooniean over 1 year ago
Labels: enhancement