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Questions tagged [graph-neural-network]

81 questions
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1 answer

PyTorch Geometric - How to sample huge graph to train GNN with mini-batching

I want to do node regression on a huge graph (around 1M nodes) using PyTorch Geometric, but I cannot create a Data object because the full graph does not fin in RAM, so I cannot use the DataLoader class for mini-batching and training. Some examples…
Gerard Ortega
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1 answer

PyTorch Geometric custom layer parameters not updating

I am developing a graph neural network using PyTorch Geometric. The idea is to start with multivariate time series, build a graph based on the correlation between those time series and then classify the graph. I have built a CorrelationLayer that…
Michele
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Tensorflow alternative/equivalent for torch_geometric.nn.radius_graph()

I am new to graph deep learning and I am trying to generate a graph from a matrix of node features by computing graph edges for all nodes within a given distance. I have found a concise way to do this with torch_geometric.nn.radius_graph() but I…
playerJX1
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1 answer

Finding all distinct graphs with n nodes(networkx)

For example, I want to find all the graphlets with 4 nodes. It will give me 11 distinct graphs.. Is there a function or easy way to generate all these graphs in networkx. I am new to networkx so I do not know all of its features. I am expecting to…
Some_Guy
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0 answers

Seq2Seq(GNN+RNN) - Odd predictions despite optimized loss

I’d like to ask for your advise/expertise on an issue that I am currently facing. Summary: I am training a Seq2Seq model that generates a natural language question based on a graph. Train and validation loss are decreasing throughout training but…
DustyAvocado
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1 answer

GNN adaptability to different number of node as input graph

I am looking at methods for GNN to process GNN based on entity graph generated on objects on the image. Node represent each object and edge is connected between two nodes if two objects' Euclidean distance is lower than a threshold. Let's say the…
user22346194
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Usage of activation function in node classification with GraphNets

I am currently trying to learn how Graph Neural Networks work with Deep Minds Graph-Nets-Library, but I am stuck for days with my understanding of this topic. Maybe someone of you can help me out. I am using Zacharys Karate Club as graph dataset,…
NickT2606
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How to predict links between present and a new node with PyG/GraphSage autoencoder?

I am a newbee in the field of GNN and want to use PyTorch Geometric (PyG) to train a Graph Neural Network (GNN) to predict links (edges) between nodes in a graph using an autoencoder (with a modified version of the PyG link prediction example with…
feinheitsbrei
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Convert NetworkX heterogeneous Multigraph into PyTorch Geometric data

I have a heterogeneous graph with different node types and attributes stored as NetworkX Multigraph. I want to train a GNN model on this graph, therefore I need to convert it into PyTorch Geometric datatype. I tried built-in function from…
tiurina
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torch_geometric.nn radius_graph example giving AttributeError

when trying to execute the example code for radius_graph from torch_geometric i get the following error: File "C:\Users\nico_\AppData\Local\Programs\Python\Python38\lib\site-packages\torch_geometric\nn\pool\__init__.py", line 210, in radius_graph …
Niccolò Tiezzi
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Tensorflow-GNN model.fit() error while training a skeleton-based GNN (index error)

I am using TFGNN library to build a skeleton based graph neural network for action recognition and while running a simple model I keep getting the following error. The model is simple and it is adapted from the official colab The input GraphSchema…
Marianna
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Issue with using pooling layers in Spektral package for graph neural networks

I am currently working on implementing graph neural networks using the Spektral package in Python. I am trying to include pooling layers (such as TopKPool) in my model, but I am running into dimension issues. I have created a sample code to…
Ali
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Pytorch Geometric gives me an 'edge_index' error

I am trying to use Pytorch Geometric on my own custom Dataset. However I keep getting this error "Please ensure that all indices in 'edge_index' point to valid indices in the interval [0, 13) in your node feature matrix and try again." I checked…
Aster Bot
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ImportError: cannot import name 'Sonnet' from 'graphs'

The code I am trying to run is import graph_nets as gn and the compiler returns ImportError: cannot import name 'Sonnet' from 'graphs' which traces back to a line in the sonnet package that says from graphs import Sonnet, D3Graph, MatplotGraph (I…
playerJX1
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How to plot Graph-neural-network model-graph when using tensorflow Model Subclass API with spektral layers?

I am unable to plot graph-neural-networking. I have seen few related questions(1, 2, 3) to this topic but their answers do not apply to graph-neural-networks. What makes it different is that the input vector include objects of different dimensions…
mindstorm84
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