Ecosyste.ms: Issues

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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

#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

#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

#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