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GNN_MIP_CAMD

This repository is the official implementation of the paper "Optimizing over trained GNNs via symmetry breaking". The paper was published in NeurIPS 2023. Please cite as:

  • Shiqiang Zhang, Juan S. Campos, Christian Feldmann, David Walz, Frederik Sandfort, Miriam Mathea, Calvin Tsay, Ruth Misener. "Optimizing over trained GNNs via symmetry breaking." Advances in Neural Information Processing Systems 37 (2023).

The BibTeX reference is:

@article{zhang2023,
  title={Optimizing over trained GNNs via symmetry breaking},
  author={Shiqiang Zhang and Juan S. Campos and Christian Feldmann and David Walz and Frederik Sandfort and Miriam Mathea and Calvin Tsay and Ruth Misener},
  journal={Advances in Neural Information Processing Systems},
  volume={37},
  year={2023}
}

Requirements

To install requirements:

pip install -r requirements.txt

A license is needed to use Gurobi. Please follow the instructions to obtain a free academic license.

Data preparation

Two datasets (QM7 and QM9) used in this paper are avaiable in package chemprop (available under a MIT license in \data\LICENSE.txt). We already download and uncompress them here.

To preprocess the raw datasets, run this command (using QM7 as an example):

python QM7_dataset_generation.py

Training and transformation of GNNs

To train a GNN and then transform it into ONNX format, run this command:

python training_and_transformation.py $dataset $seed_gnn

where $dataset is the name of dataset (QM7 or QM9), $seed_gnn is the random seed for training GNN.

Count feasible solutions

To count the number of all feasible solutions given N, run this command:

python count_feasible.py $dataset $N $break_symmetry

where $dataset is the name of dataset (QM7 or QM9), $N is the number of atoms, $break_symmetry controls the level of breaking symmetry.

Optimization

To solve the optimization problem, run this command:

python optimality.py $dataset $N $formulation_type $break_symmetry $seed_gnn $seed_gurobi

where $dataset is the name of dataset (QM7 or QM9), $N is the number of atoms (chosen from {4,5,6,7,8}), $formulation_type denotes the type of formulation (0 for bi-linear, 1 for big-M), $break_symmetry is binary and indices adding symmetry-breaking constraints, $seed_gnn is the random seed for traing GNN, and $seed_gurobi is the random seed of Gurobi.

MIP formulations for CAMD

Constraints (C1) ~ (C25) in the paper correspond to line 88 ~ 245 in \optimality.py.

The bounds for both datasets are specified in line 35 ~ 52 in \optimality.py.

The symmetry-breaking constraints (C26) and (C27) are implemented in line 248 ~ 273 in \optimality.py.

MIP formulations for GNNs

The implementation of MIP formulation for GNNs is based on open-source package OMLT (available under a BSD license in \omlt\LICENSE.rst). We downloaded the source code of OMLT at 8/2/2023, which was still the newest version when we submitted the paper.

Two formulations full_space_gnn_layer_bilinear and full_space_gnn_layer_bigm are added in \omlt\neuralnet\layers\full_space.py (line 38 ~ 169).

To call one of these formulations, \omlt\neuralnet\nn_formulation.py is modified (line 185 ~ 190).

Contributors

Shiqiang Zhang. Funded by an Imperial College Hans Rausing PhD Scholarship.