Pytorch Geometric Tutorials

Last update: Jan 08, 2023

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Overview

PytorchGeometricTutorial

Hi! We are Antonio Longa and Giovanni Pellegrini, PhD students, and PhD Gabriele Santin, researcher, working between Fondazione Bruno Kessler and the University of Trento, Italy.

This project aims to present through a series of tutorials various techniques in the field of Geometric Deep Learning, focusing on how they work and how to implement them using the Pytorch geometric library, an extension to Pytorch to deal with graphs and structured data, developed by @rusty1s.

You can find our video tutorials on Youtube and at our official website here.

Feel free to join our weekly online tutorial! For more details, have a look at the official website.

Tutorials:

Tutorial1: What is Geometric Deep Learning? -
Tutorial2: PyTorch basics. -
Tutorial3: Graph Attention Network GAT. -
Tutorial4: Convolutional Layers - Spectral methods. -
Tutorial5: Aggregation Functions in GNNs. -
Tutorial6: Graph Autoencoders and Variational Graph Autoencoders. -
Tutorial7: Adversarially regularized GAE and VGAE. -
Tutorial8: Graph Generation.
Tutorial9: Recurrent Graph Neural Networks. -
Tutorial10: DeepWalk and Node2Vec (Theory).
Tutorial11: DeepWalk and Node2Vec (Practice). -
Tutorial12: Edge analysis. -
Tutorial13: Metapath2vec. -
Tutorial14: Data handling in Pyg (part 1) -
Tutorial15: Data handling in Pyg (part 2) -
Tutorial16: Special guest talk - Matthias Fey
Tutorial17: Special guest talk - Sergei Ivanov
Tutorial18: Graph pooling: DIFFPOOL. -

Installation of PyG:

In order to have running notebooks in Colab, we use the following installation commands:

!pip install torch-scatter -f https://data.pyg.org/whl/torch-1.9.0+cu111.html
!pip install torch-sparse -f https://data.pyg.org/whl/torch-1.9.0+cu111.html
!pip install torch-geometric

These version are tested and running in Colab. If instead you run the notebooks on your machine, have a look at the PyG's installation instructions to find suitable versions.

Comments

DiffPool tutorial does not work

Thank you for making the videos and notebooks available! They are very nice and helpful. I saw that the DiffPool model still does not work for the version that is uploaded here. I was wondering if you already have the working model available?

Thank you in advance!

opened by lisiq 4
Some tutorials no longer work with Google Colab

Tutorial 14 and 15 both no longer work with colab and give this error after the second cell

OSError Traceback (most recent call last) in () 2 import os 3 import pandas as pd ----> 4 from torch_geometric.data import InMemoryDataset, Data, download_url, extract_zip 5 from torch_geometric.utils.convert import to_networkx 6 import networkx as nx

6 frames /usr/lib/python3.7/ctypes/init.py in init(self, name, mode, handle, use_errno, use_last_error) 362 363 if handle is None: --> 364 self._handle = _dlopen(self._name, mode) 365 else: 366 self._handle = handle

OSError: /usr/local/lib/python3.7/dist-packages/torch_sparse/_convert_cpu.so: undefined symbol: _ZNK2at6Tensor5zero_Ev

opened by itamblyn 2
Modify the example1

https://github.com/AntonioLonga/PytorchGeometricTutorial/blob/main/Tutorial1/Tutorial1.ipynb

I think this example could be modified for the better. In fact, the nums_layer = 1 parameter should be defined in Net, and a layer of GNNStack should be defined according to this parameter in the forward method. This would solve the problem raised by YouTube video 43:29.

opened by abcdabcd989 2
Tutorial 3 code

Hi,

Thanks for this great tutorials and videos. Really nice work.

I was wondering about the GATLayer class in the code of tutorial 3. Once the class is made, it is no longer used after the 'Use it' heading in the notebook. Instead, the GATConv from torch geometric is used directly. Then why was the GATLayer class made?

Thanks, VR

opened by vandana-rajan 1
Error for running "from torch_geometric.nn import Node2Vec"

while running from torch_geometric.nn import Node2Vec in google colab an error occur OSError: /usr/local/lib/python3.7/dist-packages/torch_sparse/_convert_cpu.so: undefined symbol: _ZNK2at6Tensor5zero_Ev

what should I do?

opened by ayreen2 1
Adding Colab support for the tutorials

Thanks for your effort and great work!

I think, In order to make the tutorials more convenient for a wide audience it would be helpful to add a colab version of the notebooks with the special button, that redirects to the http://colab.research.google.com/.

All tutorials can be run in colab via adding the notebook from GitHub and adding the cell with the installation of the pytorch-geometric and all dependencies. But the version with native support would make it more convenient.

opened by Godofnothing 1
Question about Tutorial16.ipynb

Hello, Thank you for the nice tutorial, it helps a lot to get started! I have a few questions concerning Tutorial16.ipynb: 1/ what is the effect of the parameter lin=True? 2/ what's the effect of changing the number of hidden and output channels? 3/ what is the purpose of l1, e1, l2, e2? Best, Claire

opened by claireguepin 0
Some questions I found in this tutorial
Hi, this is a nice tutorial. However, I find that there are some minor problems with the materials.

I fond that they are same links so I think you can delete one.

In the node2vec practice colab notebook, the current installation requirement will lead the colab environment to break down. I tried this combination and it works: Could you please figure out why? Thanks a lot!
opened by HelloWorldLTY 0