Guide
Intro
This project is the previous project gcn_for_prediction_of_protein_interactions It can be applied to two data sets: a. with node feature; b. No node features.
a. Data sets with node characteristics, such as [data/cora]
b. Data sets without node characteristics, such as [data / year]
Model
Model
The model mainly uses graph neural network, such as gae, vgae, etc
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1.GCNModelVAE(src/vgae): volume product self coding and variational volume product self coding (self coding or variational self coding can be configured in config). gae/vgae is used as encoder and InnerProductDecoder is used as decoder. Variational Graph Auto-Encoders .
[the external chain picture transfer fails. The source station may have an anti-theft chain mechanism. It is recommended to save the picture and upload it directly (img-RKCl4fsY-1642238386462)(image/vgae.png)]
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2. GCN model Arga (SRC / Arga): anti regularization graph self coding, using gae/vgae as generator; A three-layer feedforward network is used as a discriminator. Adversarially Regularized Graph Autoencoder for Graph Embedding .
[the external chain picture transfer fails. The source station may have an anti-theft chain mechanism. It is recommended to save the picture and upload it directly (img-7TgksyBg-1642238386464)(image/arga.png)]
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3.GATModelVAE(src/graph_att_gae): graph product self coding and variational graph product self coding based on graph attention (self coding or variational self coding can be configured in config), using gae/vgae as encoder and InnerProductDecoder as decoder. I added a graph attention layer based on the above [1] method. For graph attention, see [GRAPH ATTENTION NETWORKS] in [Reference].
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4.GATModelGAN(src/graph_att_gan): anti regularization graph self coding based on graph attention, using gae/vgae as generator; A three-layer feedforward network is used as the discriminator. I added a graph attention layer based on the above [2] method. For graph attention, see [GRAPH ATTENTION NETWORKS] in [Reference].
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5.NHGATModelVAE(src/graph_nheads_att_gae): graph volume product self coding and variational graph volume product self coding based on graph multi head attention (self coding or variational self coding can be configured in config), gae/vgae is used as encoder and InnerProductDecoder is used as decoder. This method changes the graph attention layer to multi head attention layer on the basis of [3].
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6.NHGATModelGAN(src/graph_nheads_att_gan): anti regularization graph self coding based on graph multi head attention, using gae/vgae as generator; A three-layer feedforward network is used as the discriminator. Based on the method [4], this method changes the graph attention layer into multi head attention layer.
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Note: the program [src/util/cora_class_one_hot_process.py] sets Cora data into Cora The node labels in content are one-hot coded (the processed data set is: data/cora/cora.content_class) and used together with features as training features, which is equivalent to realizing conditional variational self coding [conditional variable auditor (CVAE)], and adding the restriction of node labels to the encoder and decoder.
Usage
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For the configuration of relevant parameters, see config. In each model folder Cfg file, which will be loaded during training and prediction.
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Training and prediction
1.model comparison
(1). Data set without node characteristics [data / year]
GCNModelVAE GCNModelARGA GATModelVAE GATModelGAN NHGATModelVAE NHGATModelVAE epochs 20 20 20 20 20 20 precision 0.8708 0.8700 0.8629 0.8715 0.8672 0.8680 roc_score 0.8814 0.8798 0.8758 0.8826 0.8770 0.8767 (2). Data set with node characteristics [data/cora]
GCNModelVAE GCNModelARGA GATModelVAE GATModelGAN NHGATModelVAE NHGATModelVAE epochs 200 200 200 200 200 200 precision 0.7451 0.8544 0.8509 0.8392 0.8078 0.8156 roc_score 0.7404 0.8437 0.8686 0.8312 0.8278 0.8240 2.usage
(1).train
Whether to bring node features can be configured through [config.cfg] in each model folder, as follows:
config has the following three parameters
node_cites_path = cora.cites # Reference data between nodes node_features_path = cora.content # Node characteristic data with_feats = True # Whether it has node characteristics. True, node_features_path is not None; False, node_features_path is None
# General format of train Code: from src.graph_nheads_att_gan.train import Train train = Train() train.train_model('config.cfg')
(2).predict
# General format of predict code: from src.graph_nheads_att_gan.predict import Predict predict = Predict() predict.load_model_adj('config_cfg') # The original graph adjacency matrix and the hidden embedding adjacency matrix after model coding and inner product decoding will be returned. The two matrices can be compared to obtain link prediction adj_orig, adj_rec = predict.predict()
Dataset
a. yeast dataset,[data/yeast]
Data from yeast protein interactions yeast .
The format of the data set is as follows. See data.
YLR418C YOL145C YOL145C YLR418C YLR418C YOR123C YOR123C YLR418C ...... ......
b. cora dataset,[data/cora]
The data is from the dataset of Machine Learning Paper cora .
The format of the data set is as follows. See data .
cora.cites:
35 1033 35 103482 35 103515 35 1050679 ...... ......
cora.content:
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Reference
- Variational Graph Auto-Encoders
- https://github.com/zfjsail/gae-pytorch/blob/master/gae/utils.py
- https://github.com/tkipf/gae/tree/master/gae
- http://snap.stanford.edu/deepnetbio-ismb/ipynb/Graph+Convolutional+Prediction+of+Protein+Interactions+in+Yeast.html
- Adversarially Regularized Graph Autoencoder for Graph Embedding
- https://www.biyezuopin.vip
- GRAPH ATTENTION NETWORKS