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https://github.com/delta2323/GB-GNN
Optimization and Generalization Analysis of Transduction through Gradient Boosting and Application to Multi-scale Graph Neural Networks
https://github.com/delta2323/GB-GNN
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Optimization and Generalization Analysis of Transduction through Gradient Boosting and Application to Multi-scale Graph Neural Networks
- Host: GitHub
- URL: https://github.com/delta2323/GB-GNN
- Owner: delta2323
- License: other
- Created: 2020-06-15T06:10:31.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-06-16T01:02:54.000Z (over 4 years ago)
- Last Synced: 2024-08-02T03:02:30.356Z (4 months ago)
- Language: Jupyter Notebook
- Homepage: https://arxiv.org/abs/2006.08550
- Size: 444 KB
- Stars: 13
- Watchers: 3
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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- awesome-gradient-boosting-papers - [Code
README
This is the code for the paper titled
*Optimization and Generalization Analysis of Transduction through Gradient Boosting and Application to Multi-scale Graph Neural Networks* ([arXiv](https://arxiv.org/abs/2006.08550)).
# Dependency
- networkx==2.1
- numpy==1.15.1
- optuna==1.3.0
- pytorch-ignite==0.3.0
- scipy==1.1.0
- torch==1.5.0
- pytest==5.0.1 (for testing)
# Preparation
Place `https://github.com/tkipf/gcn/tree/master/gcn/data` as `lib/dataset/data/kipf/` (e.g., `gcn/data/ind.citeseer.allx` should be copied to `lib/dataset/data/kipf/ind.citeseer.allx`.)
# Testing
Unit test
```
PYTHONPATH=$PYTHONPATH:. pytest test/
```
Small experiment test (run on GPU device 0)
```
bash test.sh
```
# Usage
## Commands
### GB-GNN-Adj
```
bash run.sh --device --dataset --min-layer --max-layer --aggregation-model adj
```
### GB-GNN-Adj + Fine Tuning
```
bash run.sh --device --dataset --min-layer --max-layer --aggregation-model adj --fine-tune
```
### GB-GNN-KTA
```
bash run.sh --device --dataset --min-layer --max-layer --aggregation-model kta
```
### GB-GNN-KTA + Fine Tuning
```
bash run.sh --device --dataset --min-layer --max-layer [--n-weak-learners 40] --aggregation-model kta --fine-tune
```
We set the maximum number of weak learners to 40, as opposed to the default value 100 due to memory constraints in the main paper. To reproduce it, we should set `--n-weak-learners 40`.
### GB-GNN-II
```
bash run.sh --device --dataset --min-layer --max-layer --aggregation-model ii
```
### GB-GNN-II + Fine Tuning
```
bash run.sh --device --dataset --min-layer --max-layer --aggregation-model ii --fine-tune
```
## Option
- ``: GPU ID in use. If we use `-1`, the code runs on CPU
- ``: Dataset type. Either `cora`, `citeseer`, or `pubmed` values are allowed.
- ``, ``: The minimum and maximum number of hidden layer size of the hyperparameter optimization search space. If we want to fix the hidden layer size to `L`, use `L_min=L_max=L`.
## Output
It creates the output directory whose name is the execution time of the form `YYMMDD_HHMMSS`.
The directory has the following files (not a comprehensive list).
- `acc.json`: The accuracies on training, validation, and test datasets.
- `loss/`: The transition of loss values of the best hyperparameter set on training (`train.npy`), validation (`validation.npy`), and test (`test.npy`) datasets
- `cosine.npy`: The transition of cosine values between weak learners and negative gradient on the training dataset.
- `best_params.json`: Chosen hyperparameters.
Accuracies, loss values, and cosine values are for the model with the best hyperparameter set.
# Directory Structures
- `app`: Experiment execution scripts
- `lib`: Implementation of models and their training and evaluation procedures.
- `analysis`: Notebooks for post processing experiment results.
- `test`: Unit test code