# Questions tagged [pytorch-geometric]

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### How to implement edge feature in message passing algorithm of Pytorch Geometric?

I am trying to implement a custom message passing function $x^k_i = x^{k-1}_i + m^k_i$ where $x_i$ is the node embedding of the i'th node and $m^k_i$ is the message getting delivered at the i'th node ...
25 views

### pytorch-geometric why size of num_node_features as input of GCN

Following a lecture about GCN and going through documentation: https://pytorch-geometric.readthedocs.io/en/latest/notes/introduction.html#learning-methods-on-graphs In ...
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1 vote
155 views

### Is it possible to combine models in pytorch and pytorch geometric?

I am working on a node classification problem with graphical data. I've used PyTorch to classify nodes by simply applying a network to the individual nodes (e.g., ignoring graphical structure), and I'...
• 113
199 views

### My model is not learning

I am using the ogb molhiv dataset for graph classification, I imported the data and created the DataLoader following the ogb documentation. The data is composed of 41127 graphs and there are 2 classes....
• 3
287 views

### How to extract node embeddings from PyTorch Geometric GAT model?

Dataset Structure: Temporal directed graph; Nodes have features; Edges don't have features; Nodes are labelled. Using the Elliptic Dataset Task: Classify nodes/ Predict node labels. Data Structure: 2 <...
1 vote
120 views

### Captum vs GNNExplainer for explainability in Graph Neural Networks

I'm new to Graph Neural Networks and interested in exploring frameworks that allow the identification of nodes/edges that underlie prediction. I came across : (1) a model architecture (GNNExplainer) ...
• 111
25 views

### Discrepancy between pytorch data and the corresponding networkx graph

I have generated an undirected graph using pytorch_geometric's data object. I used to_networkx functionality of pytorch_geometric to convert it to an undirected <...
• 1,067
1 vote
120 views

### Dying gradient issue in Graph Neural Networks

I am using Pytorch-Geometric library to implement a Graph Convolutional Layer(GCN) followed by few linear layers for a prediction task. But after training on graphs with np. of nodes being 10K and no. ...
• 11
594 views

### How to apply Geomertic mean in python

I am trying to built a function to calculate the Geometric mean for Growth column and Avg_growth. Year Company Name FH_PBIDT ...
• 1
31 views

### Weird train and validation curves

I would like to train a GCN for protien-ligand binding affinity regression. I use GCNConv from pytorch geometric, ReLU for all activations and Dropout (0.2) after 2 dense layers each. Using ReLU for ...
1k views

### What is the difference between FC and MLP in as used in PointNet?

I am trying to understand the PointNet network for dealing with point clouds and struggling with understanding the difference between FC and MLP: "FC is fully connected layer operating on each ...
• 77
174 views

### Graph Embedding Vs Graph Convolution Network

I'm new in Graph-Embedding and GCN(Graph/Geometric Convolution Network). I'm confused and not very much sure about "How training works in GCN"? As per my understanding, GCN training data will be ...
• 1,232
1 vote
3k views

### What does the collate function in pytorch (geometric)?

I am creating a message passing neural network and have some issues with the dataset creation. In pytorch (geometric) it is recommended to create a dataset with the following class. I wonder what is ...
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