Large-scale transformers on unsupervised text data have been wildly successful in recent years; arguably, the most successful single idea in the last ~3 years of machine learning. Given that, it's understandable that different domains within ML want to take their shot at seeing whether the same formula will work for them as well. This paper applies the principles of (1) transformers and (2) large-scale unlabeled data to the problem of learning informative embeddings of molecular graphs. 

Labeling is a problem in much of machine learning - it's costly, and narrowly defined in terms of a certain task - but that problem is even more exacerbated when it comes to labeling properties of molecules, since they typically require wetlab chemistry to empirically measure. Given that, and also given the fact that we often want to predict new properties - like effectiveness against a new targetable drug receptor - that we don't yet have data for, finding a way to learn and transfer from unsupervised data has the potential to be quite valuable in the molecular learning sphere. 

There are two main conceptual parts to this paper and its method - named GROVER, in true-to-ML-form tortured acronym style. The first is the actual architecture of their model itself, which combines both a message-passing Graph Neural Network to aggregate local information, and a Transformer to aggregate global information. The paper was a bit vague here, but the way I understand it is: 

https://i.imgur.com/JY4vRdd.png
- There are parallel GNN + Transformer stacks for both edges and nodes, each of which outputs both a node and edge embedding, for four embeddings total. I'll describe the one for nodes, and the parallel for edges operates the same way, except that hidden states live on edges rather than nodes, and attention is conducted over edges rather than nodes
- In the NodeTransformer version, a message passing NN (of I'm not sure how many layers) performs neighborhood aggregation (aggregating the hidden states of neighboring nodes and edges, then weight-transforming them, then aggregating again) until each node has a representation that has "absorbed" in information from a few hops out of its surrounding neighborhood. My understanding is that there is a separate MPNN for queries, keys, and values, and so each nodes end up with three different vectors for these three things.
- Multi-headed attention is then performed over these node representations, in the normal way, where all keys and queries are dot-product-ed together, and put into a softmax to calculate a weighted average over the values
- We now have node-level representations that combine both local and global information. These node representations are then aggregated into both node and edge representations, and each is put into a MLP layer and Layer Norm before finally outputting a node-based node and edge representation. This is then joined by an edge-based node and edge representation from the parallel stack. These are aggregated on a full-graph level to predict graph-level properties

https://i.imgur.com/NNl6v4Y.png

The other component of the GROVER model is the way this architecture is actually trained - without explicit supervised labels. The authors use two tasks - one local, and one global. The local task constructs labels based on local contextual properties of a given atom - for example, the atom here has one double-bonded Nitrogen and one single-bonded Oxygen in its local environment - and tries to predict those labels given the representations of that atom (or node). The global task uses RDKit (an analytically constructed molecular analysis kit) to identify 85 different modifs or functional groups in the molecule, and encodes those into an 85-long one-hot vector that is being predicted on a graph level. 

https://i.imgur.com/jzbYchA.png

With these two components, GROVER is pretrained on 10 million unlabeled molecules, and then evaluated in transfer settings where its representations are fine-tuned on small amounts of labeled data. The results are pretty impressive - it achieves new SOTA performance by relatively large amounts on all tasks, even relative to exist semi-supervised pretraining methods that similarly have access to more data. The authors perform ablations to show that it's important to do the graph-aggregation step before a transformer (the alternative being just doing a transformer on raw node and edge features), and also show that their architecture without pretraining (just used directly in downstream tasks) also performs worse. One thing I wish they'd directly ablated was the value-add of the local (also referred to as "contextual") and global semi-supervised tasks. Naively, I'd guess that most of the performance gain came from the global task, but it's hard to know without them having done the test directly.