Rex Ying

• PhD Student at Stanford University

Searching for a path between two nodes in a graph is one of the most well-studied and fundamental problems in computer science. In numerous domains such as robotics, AI, or biology, practitioners develop search heuristics to accelerate their pathfinding algorithms. However, it is a laborious and complex process to hand-design heuristics based on th...

Despite the success of automated machine learning (AutoML), which aims to find the best design, including the architecture of deep networks and hyper-parameters, conventional AutoML methods are computationally expensive and hardly provide insights into the relations of different model design choices. To tackle the challenges, we propose FALCON, an...

Subsurface simulations use computational models to predict the flow of fluids (e.g., oil, water, gas) through porous media. These simulations are pivotal in industrial applications such as petroleum production, where fast and accurate models are needed for high-stake decision making, for example, for well placement optimization and field developmen...

Hierarchical relations are prevalent and indispensable for organizing human knowledge captured by a knowledge graph (KG). The key property of hierarchical relations is that they induce a partial ordering over the entities, which needs to be modeled in order to allow for hierarchical reasoning. However, current KG embeddings can model only a single...

The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that m...

Self-attention mechanism in graph neural networks (GNNs) led to state-of-the-art performance on many graph representation learning tasks. Currently, at every layer, attention is computed between connected pairs of nodes and depends solely on the representation of the two nodes. However, such attention mechanism does not account for nodes that are n...

Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot different...

Recent work on aspect-level sentiment classification has demonstrated the efficacy of incorporating syntactic structures such as dependency trees with graph neural networks(GNN), but these approaches are usually vulnerable to parsing errors. To better leverage syntactic information in the face of unavoidable errors, we propose a simple yet effectiv...

Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot different...

The rapid evolution of Graph Neural Networks (GNNs) has led to a growing number of new architectures as well as novel applications. However, current research focuses on proposing and evaluating specific architectural designs of GNNs, as opposed to studying the more general design space of GNNs that consists of a Cartesian product of different desig...

Introducing self-attention mechanism in graph neural networks (GNNs) achieved state-of-the-art performance for graph representation learning. However, at every layer, attention is only computed between two connected nodes and depends solely on the representation of both nodes. This attention computation cannot account for the multi-hop neighbors wh...

Here we present a general framework for learning simulation, and provide a single model implementation that yields state-of-the-art performance across a variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework---which we term "Graph Network-based Simulators" (GNS)-...

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs. GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models and explaining predictions made by GNNs rem...

Graph convolutional neural networks (GCNs) embed nodes in a graph into Euclidean space, which has been shown to incur a large distortion when embedding real-world graphs with scale-free or hierarchical structure. Hyperbolic geometry offers an exciting alternative, as it enables embeddings with much smaller distortion. However, extending GCNs to hyp...

Graph Attention Networks (GATs) are the state-of-the-art neural architecture for representation learning with graphs. GATs learn attention functions that assign weights to nodes so that different nodes have different influences in the feature aggregation steps. In practice, however, induced attention functions are prone to over-fitting due to the i...

Graph Neural Networks (GNNs) are a powerful representational tool for solving problems on graph-structured inputs. In almost all cases so far, however, they have been applied to directly recovering a final solution from raw inputs, without explicit guidance on how to structure their problem-solving. Here, instead, we focus on learning in the space...

Learning node embeddings that capture a node's position within the broader graph structure is crucial for many prediction tasks on graphs. However, existing Graph Neural Network (GNN) architectures have limited power in capturing the position/location of a given node with respect to all other nodes of the graph. Here we propose Position-aware Graph...

Graph Neural Networks (GNNs) are based on repeated aggregations of information across nodes' neighbors in a graph. However, because common neighbors are shared between different nodes, this leads to repeated and inefficient computations. We propose Hierarchically Aggregated computation Graphs (HAGs), a new GNN graph representation that explicitly a...

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs. GNNs combine node feature information with the graph structure by using neural networks to pass messages through edges in the graph. However, incorporating both graph structure and feature information leads to complex non-linear models and explaining predictions made b...

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---...

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph generation, whose goal is to discover novel molecules with desired properties such as drug-likeness and synthetic ac...

Recent advancements in deep neural networks for graph-structured data have led to state-of-the-art performance on recommender system benchmarks. However, making these methods practical and scalable to web-scale recommendation tasks with billions of items and hundreds of millions of users remains a challenge. Here we describe a large-scale deep reco...

Modeling and generating graphs is fundamental for studying networks in biology, engineering, and social sciences. However, modeling complex distributions over graphs and then efficiently sampling from these distributions is challenging due to the non-unique, high-dimensional nature of graphs and the complex, non-local dependencies that exist betwee...

Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph structure so that it can be easily exploited by machine learning models. Traditionally, machine learning appro...

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive an...

Dynamic time warping (DTW) is a widely used curve similarity measure. We present a simple and efficient (1 + ε)- approximation algorithm for DTW between a pair of point sequences, say, P and Q, each of which is sampled from a curve. We prove that the running time of the algorithm is O([EQUATION]n log σ) for a pair of k-packed curves with a total of...

Analyses of muscular activity during rhythmic behaviors provide critical data for biomechanical studies. Electrical potentials measured from muscles using electromyography (EMG) require discrimination of noise regions as the first step in analysis. An experienced analyst can accurately identify the onset and offset of EMG but this process takes hou...

We give the first subquadratic-time approximation schemes for dynamic time warping (DTW) and edit distance (ED) of several natural families of point sequences in $\mathbb{R}^d$, for any fixed $d \ge 1$. In particular, our algorithms compute $(1+\varepsilon)$-approximations of DTW and ED in time near-linear for point sequences drawn from k-packed or...