GNN Applications

An overview presentation by Xavier Bresson about applications of GNNs, which include chip design, protein folding, autonomous driving, energy physics, and more.

Connecting the Dots: Harness the Power of Graphs & ML

A new short book on graph ML that describes various algorithms on graphs and future challenges.

Fresh picks from ArXiv
This week on ArXiv: WL to solve planar graphs, efficient molecule generation, and compressing graphs 🤐

If I forgot to mention your paper, please shoot me a message and I will update the post.

Math
Logarithmic Weisfeiler-Leman Identifies All Planar Graphs

GNNs
Curvature Graph Neural Network
Relational VAE: A Continuous Latent Variable Model for Graph Structured Data
GraphPiece: Efficiently Generating High-Quality Molecular Graph with Substructures
Privacy-Preserving Representation Learning on Graphs: A Mutual Information Perspective KDD 2021
Partition and Code: learning how to compress graphs with Andreas Loukas and Michael M. Bronstein
Evolving-Graph Gaussian Processes ICML Workshop 2021

How to build E(n) Equivariant Normalizing Flows, for points with features?

A nice post that discusses how one can use normalizing flows and equivariant GNNs to generate realistic molecules.

Graph Machine Learning research groups: Andreas Krause

I do a series of posts on the groups in graph research, previous post is here. The 31st is Andreas Krause, a professor at ETH Zurich and an advisor for Stefanie Jegelka.

Andreas Krause (~1982)
- Affiliation: ETH Zurich
- Education: Ph.D. at CMU in 2008 (advisor: Carlos Guestrin)
- h-index 81
- Interests: social network analysis, community detection, graphical models.
- Awards: Rossler Prize, best papers (AISTATS, AAAI, KDD, ICML)

Fresh picks from ArXiv
This week on ArXiv: explanations of GNNs, generalization of GAE and generating natural proofs 👴

If I forgot to mention your paper, please shoot me a message and I will update the post.

GNN
* Automated Graph Learning via Population Based Self-Tuning GCN
* Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction
* Robust Counterfactual Explanations on Graph Neural Networks
* Probabilistic Graph Reasoning for Natural Proof Generation
* On Generalization of Graph Autoencoders with Adversarial Training
* Private Graph Data Release: A Survey

GNN User Group Meeting videos (June)

Video from the June meeting of GNN user group that includes talks about binary GNNs and dynamic graph models by Mahdi Saleh and
and about simplifying large-scale visual analysis of tricky data & models with GPUs, graphs, and ML by Leo Meyerovich.

Speeding Up the Webcola Graph Viz Library with Rust + WebAssembly

A captivating story about optimizing visualization of graphs in the browser. The code can be found here. Here is a performance comparison of different browser visualization libraries. And here is another efficient library for plotting graphs in a browser.

LOGML Videos

LOGML is an exciting summer school with projects and talks about graph ML happening this week. A collection of videos that includes presentations of the cutting edge research as well as industrial applications from leading companies are available now for everyone.

Effortless Distributed Training of Ultra-Wide GCNs

A great post about distributed training of GNNs on large graphs. The architecture splits the GNN into several submodules where each is trained independently on separate GPUs, providing the flexibility to increase significantly the hidden dimension of embeddings. As such this approach is GCN model agnostic, compatible with existing sampling methods, and performs the best in very large graphs.

Fresh picks from ArXiv
This week on ArXiv: QA in images, graph matching, and learning robot dynamics 🤖

If I forgot to mention your paper, please shoot me a message and I will update the post.

GNNs
* Train on Small, Play the Large: Scaling Up Board Games with AlphaZero and GNN
* Reasoning-Modulated Representations with Petar Veličković and Thomas Kipf
* SENSORIMOTOR GRAPH: Action-Conditioned Graph Neural Network for Learning Robotic Soft Hand Dynamics
* Scalable Optimal Transport in High Dimensions for Graph Distances, Embedding Alignment, and More with Stephan Günnemann
* Graphhopper: Multi-Hop Scene Graph Reasoning for Visual Question Answering with Stephan Günnemann
* Elastic Graph Neural Networks

Survey
* A Survey of Knowledge Graph Embedding and Their Applications

Graph Papers at ICML 2021

ICML 2021 is happening this week and here is a list of all relevant graph papers that you can encounter there. There are papers on improving expressiveness, explainability, robustness, normalization and theory.

Awesome Explainable Graph Reasoning

An awesome collection of research papers and software related to explainability in graph machine learning, provided by AstraZeneca. It covers papers on explainable predictions and reasoning, libraries, and survey papers.

labml.ai Annotated PyTorch Paper Implementations

A very cool collection of popular deep learning blocks, nicely formatted in the browser with extensive comments. Among others there is a GAT implementation.

Interpretable Deep Learning for New Physics Discovery

In this video, Miles Cranmer (Princeton) discusses a method for converting a neural network into an analytic equation using a particular set of inductive biases. The technique relies on a sparsification of latent spaces in a deep neural network, followed by symbolic regression. In their paper, they demonstrate that they can recover physical laws for various simple and complex systems. For example, they discover gravity along with planetary masses from data; they learn a technique for doing cosmology with cosmic voids and dark matter halos; and they show how to extract the Euler equation from a graph neural network trained on turbulence data.

Fresh picks from ArXiv
This week on ArXiv: SOTA for protein energy prediction, another solution to OGB-LSC challenge, and a new dataset based on Wikipedia 📚

If I forgot to mention your paper, please shoot me a message and I will update the post.

Applications
* X-GGM: Graph Generative Modeling for Out-of-Distribution Generalization in Visual Question Answering
* Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity KDD 2021

GNNs
* Local2Global: Scaling global representation learning on graphs via local training
* Ego-GNNs: Exploiting Ego Structures in Graph Neural Networks with William L. Hamilton
* Bridging the Gap between Spatial and Spectral Domains: A Theoretical Framework for Graph Neural Networks
* Large-scale graph representation learning with very deep GNNs and self-supervision with Petar Veličković
* Group Contrastive Self-Supervised Learning on Graphs with Shuiwang Ji

Datasets
* WikiGraphs: A Wikipedia Text - Knowledge Graph Paired Dataset with Oriol Vinyals

Graph Neural Networks User Group: July meeting

This month GNN user group talks about a new release of DGL and applications of GNNs. Please join this Thursday!

4:00 - 4:15 PM (PDT): DGL 0.7 release(Dr. Minjie Wang, Amazon)
4:15 - 4:30 PM (PDT): Storing Node Features in GPU memory to speedup billion-scale GNN training (Dr. Dominique LaSalle, NVIDIA)
4:30 - 5:00 PM (PDT): Locally Private Graph Neural Networks (Sina Sajadmanesh, Idiap Research Institute, Switzerland).
5:00 - 5:30 PM (PDT): Graph Embedding and Application in Meituan (Mengdi Zhang, Meituan).

Header-Only C++ Library for Graph Representation and Algorithms

In case you need the speed of C++ for the well-known graph algorithms there is a nice repo that collects many of them.

Graph Convolutional Neural Networks to Analyze Complex Carbohydrates

A blog post by Daniel Bojar about an application of GNN to analyzing glycan sequences and their proposed GNN architecture called SweetNet. There are other coverages of this work (here and here). The paper is here and the code is here.

Graph Machine Learning research groups: Shuiwang Ji

I do a series of posts on the groups in graph research, previous post is here. The 32nd is Shuiwang Ji, a professor at Texas A&M University. His teams were awarded at OGB-LSC and AI Cures challenges. He also recently advised graph libraries such as MoleculeX and DIG.

Shuiwang Ji (~1982)
- Affiliation: Texas A&M University
- Education: Ph.D. at Arizona State University in 2008 (advisor: Jieping Ye)
- h-index 44
- Interests: GNNs, self-supervised learning, surveys, libraries.
- Awards: best papers at KDD, WWW, ACM Distinguished Member

GNN User Group Videos

Videos from the last Thursday meeting of GNN user group are available now. This includes updates of DGL library, storing node feature for large graphs, and locally private GNNs.