Related papers: Learning Graph Models for Retrosynthesis Predictio…

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are…

Synthesizability in generative molecular design remains a pressing challenge. Existing methods to assess synthesizability span heuristics-based methods, retrosynthesis models, and synthesizability-constrained molecular generation. The…

Recent advances in graph convolutional networks have significantly improved the performance of chemical predictions, raising a new research question: "how do we explain the predictions of graph convolutional networks?" A possible approach…

We argue that Transformers are essentially graph-to-graph models, with sequences just being a special case. Attention weights are functionally equivalent to graph edges. Our Graph-to-Graph Transformer architecture makes this ability…

Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…

Graph Neural Networks (GNNs) are a predominant method for graph representation learning. However, beyond subgraph frequency estimation, their application to network motif significance-profile (SP) prediction remains under-explored, with no…

Predicting the chemical properties of compounds is crucial in discovering novel materials and drugs with specific desired characteristics. Recent significant advances in machine learning technologies have enabled automatic predictive…

Graph learning models have demonstrated great prowess in learning expressive representations from large-scale graph data in a wide variety of real-world scenarios. As a prevalent strategy for training powerful graph learning models, the…

Reaction prediction is a fundamental problem in computational chemistry. Existing approaches typically generate a chemical reaction by sampling tokens or graph edits sequentially, conditioning on previously generated outputs. These…

Retrosynthesis prediction aims to infer the reactant molecule based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing models rely on static pattern-matching paradigm, which limits their…

Program synthesis is the task to automatically generate programs based on user specification. In this paper, we present a framework that synthesizes programs from flow charts that serve as accurate and intuitive specifications. In order…

Transformer-based pre-trained models have gained much advance in recent years, becoming one of the most important backbones in natural language processing. Recent work shows that the attention mechanism inside Transformer may not be…

Molecular property calculations are the bedrock of chemical physics. High-fidelity \textit{ab initio} modeling techniques for computing the molecular properties can be prohibitively expensive, and motivate the development of…

Recent advances in AI-powered image editing tools have significantly lowered the barrier to image modification, raising pressing security concerns those related to spreading misinformation and disinformation on social platforms. Image…

Graph neural networks use relational information as an inductive bias to enhance prediction performance. Not rarely, task-relevant relations are unknown and graph structure learning approaches have been proposed to learn them from data.…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

We examine two fundamental tasks associated with graph representation learning: link prediction and semi-supervised node classification. We present a novel autoencoder architecture capable of learning a joint representation of both local…

In recent years, graph prompting has emerged as a promising research direction, enabling the learning of additional tokens or subgraphs appended to the original graphs without requiring retraining of pre-trained graph models across various…

Graphs have a superior ability to represent relational data, like chemical compounds, proteins, and social networks. Hence, graph-level learning, which takes a set of graphs as input, has been applied to many tasks including comparison,…

We define a novel type of ensemble Graph Convolutional Network (GCN) model. Using optimized linear projection operators to map between spatial scales of graph, this ensemble model learns to aggregate information from each scale for its…