Graph Neural Network

The ARMA GNN layer implements a rational graph filter with a recursive approximation.

DiffPool is a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Description and image from: Hierarchical Graph Representation Learning with Differentiable Pooling

DistDGL is a system for training GNNs in a mini-batch fashion on a cluster of machines. It is is based on the Deep Graph Library (DGL), a popular GNN development framework. DistDGL distributes the graph and its associated data (initial features and embeddings) across the machines and uses this distribution to derive a computational decomposition by following an owner-compute rule. DistDGL follows a synchronous training approach and allows ego-networks forming the mini-batches to include non-local nodes. To minimize the overheads associated with distributed computations, DistDGL uses a high-quality and light-weight mincut graph partitioning algorithm along with multiple balancing constraints. This allows it to reduce communication overheads and statically balance the computations. It further reduces the communication by replicating halo nodes and by using sparse embedding updates. The combination of these design choices allows DistDGL to train high-quality models while achieving high parallel efficiency and memory scalability

A GNN for dags, which injects their topological order as an inductive bias via asynchronous message passing.

Graph Contrastive Coding is a self-supervised graph neural network pre-training framework to capture the universal network topological properties across multiple networks. GCC's pre-training task is designed as subgraph instance discrimination in and across networks and leverages contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations.

MinCutPool is a trainable pooling operator for graphs that learns to map nodes into clusters. The method is trained to approximate the minimum K-cut of the graph to ensure that the clusters are balanced, while also jointly optimizing the objective of the task at hand.

\emph{Canonical partition} $\mathcal{P}$ crops the index-restricted d-hop neighborhood around the center node from the target graph. $\mathcal{D}(G_t,v_i,v_c)$ means the shortest distance between $v_i$ and $v_c$ on $G_t$. \begin{equation} \mathcal{P}(G_t, v_c, d) = G_c, \operatorname{ s.t. } G_c \subseteq G_t, V_c = { v_i \in V_t|\mathcal{D}(G_t,v_i,v_c) \leq d , v_i \leq v_c} \end{equation} The graph $G_c$ obtained by canonical partition is called the \emph{canonical neighborhood}. Canonical neighborhoods can correctly substitute the target graph in canonical count. The subgraph count of query in target equals the summation of the canonical count of query in canonical neighborhoods for all target nodes. Canonical neighborhoods are acquired with canonical partition $\mathcal{P}$, given any $d$ greater than the diameter of the query. \begin{equation} \mathcal{C}(G_q,G_t) = \sum_{v_c \in V_t} \mathcal{C}c(G_q, \mathcal{P}(G_t, v_c, d),v_c), d \geq \max{v_i, v_j \in V_q} \mathcal{D}(G_q, v_i, v_j) \end{equation}

GAGNN, or Group-aware Graph Neural Network, is a hierarchical model for nationwide city air quality forecasting. The model constructs a city graph and a city group graph to model the spatial and latent dependencies between cities, respectively. GAGNN introduces differentiable grouping network to discover the latent dependencies among cities and generate city groups. Based on the generated city groups, a group correlation encoding module is introduced to learn the correlations between them, which can effectively capture the dependencies between city groups. After the graph construction, GAGNN implements message passing mechanism to model the dependencies between cities and city groups.

As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular graphs in which atoms are modeled as nodes. They characterize each atom's chemical environment by modeling its pairwise interactions with other atoms in the molecule. Although these methods achieve a great success, limited amount of works explicitly take many-body interactions, i.e., interactions between three and more atoms, into consideration. In this paper, we introduce a novel graph representation of molecules, heterogeneous molecular graph (HMG) in which nodes and edges are of various types, to model many-body interactions. HMGs have the potential to carry complex geometric information. To leverage the rich information stored in HMGs for chemical prediction problems, we build heterogeneous molecular graph neural networks (HMGNN) on the basis of a neural message passing scheme. HMGNN incorporates global molecule representations and an attention mechanism into the prediction process. The predictions of HMGNN are invariant to translation and rotation of atom coordinates, and permutation of atom indices. Our model achieves state-of-the-art performance in 9 out of 12 tasks on the QM9 dataset.

The Multiplex Molecular Graph Neural Network (MXMNet) is an approach for the representation learning of molecules. The molecular interactions are divided into two categories: local and global. Then a two-layer multiplex graph $G = \\{ G_{l}, G_{g} \\}$ is constructed for a molecule. In $G$, the local layer $G_{l}$ only contains the local connections that mainly capture covalent interactions, and the global layer $G_{g}$ contains the global connections that cover non-covalent interactions. MXMNet uses the Multiplex Molecular (MXM) module that contains a novel angle-aware message passing operated on $G_{l}$ and an efficient message passing operated on $G_{g}$.

Point-GNN is a graph neural network for detecting objects from a LiDAR point cloud. It predicts the category and shape of the object that each vertex in the graph belongs to. In Point-GNN, there is an auto-registration mechanism to reduce translation variance, as well as a box merging and scoring operation to combine detections from multiple vertices accurately.

TaxoExpan is a self-supervised taxonomy expansion framework. It automatically generates a set of <query concept, anchor concept> pairs from the existing taxonomy as training data. Using such self-supervision data, TaxoExpan learns a model to predict whether a query concept is the direct hyponym of an anchor concept. TaxoExpan features: (1) a position-enhanced graph neural network that encodes the local structure of an anchor concept in the existing taxonomy, and (2) a noise-robust training objective that enables the learned model to be insensitive to the label noise in the self-supervision data.