diff --git a/README.md b/README.md index c8c7b2c..7725b95 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,7 @@ # A federated graph learning method to multi-party collaboration for molecular discovery +

+ +

This is an implementation for Federated Learning Lanczos Graph (FedLG). @@ -14,6 +17,7 @@ This is an implementation for Federated Learning Lanczos Graph (FedLG). - [DrugBank](#drugbank) - [BIOSNAP](#biosnap) - [CoCrystal](#cocrystal) + - [Preprocess](#preprocess) - [Usage](#usage) - [Acknowledgements](#acknowledgements) @@ -65,46 +69,47 @@ CUDA_VISIBLE_DEVICES=${your_gpu_id} python main.py --save_dir 'result' --alg fed All parameters of main: ``` usage: main.py [--alg] [--root] [--dataset] [--node_size] [--bond_size] [--hidden_size] [--extend_dim] [--output_size] [--model] [--split] [dropout] [--message_steps] [--num_clients] [--alpha] [--null_value] [--seed] - [--weight_decay] [--eps] [constant] [--delta] [--dp] [--batch_size] [--device] [--save_dir] [--beta1] [--beta2] [--local_round] [--proj_dims] [--lanczos_iter] [--global_round] [--lr] [--clip] + [--weight_decay] [--eps] [constant] [--delta] [--dp] [--batch_size] [--device] [--save_dir] [--beta1] [--beta2] [--local_round] [--proj_dims] [--lanczos_iter] [--global_round] [--comm_optimization] [--lr] [--clip] optional arguments: - --alg federated learning algorithm: - FedAvg, FedProx, FedSGD, FedLG, FedAdam, FedChem - --root root directory for differernt molecular discovery databases: - MoleculeNet, DrugBank, BIOSNAP, LITPCBA, CoCrystal - --dataset In different root directory, choose dataset of different databases - --node_size molecular node size - --bond_size molecular bond size - --hidden_size hidden size - --extend_dim extend dim for neural network - --output_size output size - --model graph neural network: - MPNN, GCN, GAT - --split split type for different root and dataset: - smi, smi1, smi2 - --drooput dropout rate - --message steps message step for graph neural network - --num_clients clients number, here we set the max clients number is up to 4 - --alpha alpha for molecule dirichlet distribution - --null_value null value - --seed fixed data initialization and training seed - --weight_decay weight decay for optimizer - --eps epsilons distribution - --constant constant for local differently privacy - --delta differential privacy parameter - --dp if True, use differential privacy - --batch_size batch size of the model training: - 32, 64 or 128 - --device cuda or cpu - --save_dir results save directory, the model test results is saved to ./results/ - --beta1 beta1 for Adam optimizer - --beta2 beta2 for Adam optimizer - --local_round local model training round - --proj_dims project dim of lanczos algorithm - --lanczos_iter the iterations of lanczos - --global_round global model training round - --lr the learning rate of graph model - --clip clip value for local differently privacy + --alg federated learning algorithm: + fedavg, fedprox, fedsgd, fedlg, fedadam, fedchem + --root root directory for differernt molecular discovery databases: + MoleculeNet, DrugBank, BIOSNAP, LITPCBA, CoCrystal + --dataset In different root directory, choose dataset of different databases + --node_size molecular node size + --bond_size molecular bond size + --hidden_size hidden size + --extend_dim extend dim for neural network + --output_size output size + --model graph neural network: + MPNN, GCN, GAT + --split split type for different root and dataset: + smi, smi1, smi2 + --drooput dropout rate + --message steps message step for graph neural network + --num_clients clients number, here we set the max clients number is up to 4 + --alpha alpha for molecule dirichlet distribution + --null_value null value + --seed fixed data initialization and training seed + --weight_decay weight decay for optimizer + --eps epsilons distribution + --constant constant for local differently privacy + --delta differential privacy parameter + --dp if True, use differential privacy + --batch_size batch size of the model training: + 32, 64 or 128 + --device cuda or cpu + --save_dir results save directory, the model test results is saved to ./results/ + --beta1 beta1 for Adam optimizer + --beta2 beta2 for Adam optimizer + --local_round local model training round + --proj_dims project dim of lanczos algorithm + --lanczos_iter the iterations of lanczos + --global_round global model training round + --comm_optimization using Bayesian Optimization or not + --lr the learning rate of graph model + --clip clip value for local differently privacy ``` ## Acknowledgements