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Register a new userMolecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits
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The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional constraints, which requires proposing alternative chemical reactions. With this in mind, we present Molecule Edit Graph Attention Network (MEGAN), an end-to-end encoder-decoder neural model. MEGAN is inspired by models that express a chemical reaction as a sequence of graph edits, akin to the arrow pushing formalism. We extend this model to retrosynthesis prediction (predicting substrates given the product of a chemical reaction) and scale it up to large datasets. We argue that representing the reaction as a sequence of edits enables MEGAN to efficiently explore the space of plausible chemical reactions, maintaining the flexibility of modeling the reaction in an end-to-end fashion, and achieving state-of-the-art accuracy in standard benchmarks. Code and trained models are made available online at https://github.com/molecule-one/megan.
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Graph neural network (GNN) has shown superior performance in dealing with graphs, which has attracted considerable research attention recently. However, most of the existing GNN models are primarily designed for graphs in Euclidean spaces. Recent research has proven that the graph data exhibits non-Euclidean latent anatomy. Unfortunately, there was rarely study of GNN in non-Euclidean settings so far. To bridge this gap, in this paper, we study the GNN with attention mechanism in hyperbolic spaces at the first attempt. The research of hyperbolic GNN has some unique challenges: since the hyperbolic spaces are not vector spaces, the vector operations (e.g., vector addition, subtraction, and scalar multiplication) cannot be carried. To tackle this problem, we employ the gyrovector spaces, which provide an elegant algebraic formalism for hyperbolic geometry, to transform the features in a graph; and then we propose the hyperbolic proximity based attention mechanism to aggregate the features. Moreover, as mathematical operations in hyperbolic spaces could be more complicated than those in Euclidean spaces, we further devise a novel acceleration strategy using logarithmic and exponential mappings to improve the efficiency of our proposed model. The comprehensive experimental results on four real-world datasets demonstrate the performance of our proposed hyperbolic graph attention network model, by comparisons with other state-of-the-art baseline methods.
Graph Neural Networks (GNNs) have recently demonstrated superior capability of tackling graph analytical problems in various applications. Nevertheless, with the wide-spreading practice of GNNs in high-stake decision-making processes, there is an increasing societal concern that GNNs could make discriminatory decisions that may be illegal towards certain demographic groups. Although some explorations have been made towards developing fair GNNs, existing approaches are tailored for a specific GNN model. However, in practical scenarios, myriads of GNN variants have been proposed for different tasks, and it is costly to train and fine-tune existing debiasing models for different GNNs. Also, bias in a trained model could originate from training data, while how to mitigate bias in the graph data is usually overlooked. In this work, different from existing work, we first propose novel definitions and metrics to measure the bias in an attributed network, which leads to the optimization objective to mitigate bias. Based on the optimization objective, we develop a framework named EDITS to mitigate the bias in attributed networks while preserving useful information. EDITS works in a model-agnostic manner, which means that it is independent of the specific GNNs applied for downstream tasks. Extensive experiments on both synthetic and real-world datasets demonstrate the validity of the proposed bias metrics and the superiority of EDITS on both bias mitigation and utility maintenance. Open-source implementation: https://github.com/yushundong/EDITS.
Graph convolutional networks (GCN) have recently demonstrated their potential in analyzing non-grid structure data that can be represented as graphs. The core idea is to encode the local topology of a graph, via convolutions, into the feature of a center node. In this paper, we propose a novel GCN model, which we term as Shortest Path Graph Attention Network (SPAGAN). Unlike conventional GCN models that carry out node-based attentions within each layer, the proposed SPAGAN conducts path-based attention that explicitly accounts for the influence of a sequence of nodes yielding the minimum cost, or shortest path, between the center node and its higher-order neighbors. SPAGAN therefore allows for a more informative and intact exploration of the graph structure and further {a} more effective aggregation of information from distant neighbors into the center node, as compared to node-based GCN methods. We test SPAGAN on the downstream classification task on several standard datasets, and achieve performances superior to the state of the art. Code is publicly available at https://github.com/ihollywhy/SPAGAN.
Designing a network to learn a molecule structure given its physical/chemical properties is a hard problem, but is useful for drug discovery tasks. In this paper, we incorporate higher-order relational learning of Factor Graphs with strong approximation power of Neural Networks to create a molecule-structure learning network that has strong generalization power and can enforce higher-order relationship and valence constraints. We further propose methods to tackle problems such as the efficient design of factor nodes, conditional parameter sharing among factors, and symmetry problems in molecule structure prediction. Our experiment evaluation shows that the factor learning is effective and outperforms related methods.
Scene Graph, as a vital tool to bridge the gap between language domain and image domain, has been widely adopted in the cross-modality task like VQA. In this paper, we propose a new method to edit the scene graph according to the user instructions, which has never been explored. To be specific, in order to learn editing scene graphs as the semantics given by texts, we propose a Graph Edit Distance Reward, which is based on the Policy Gradient and Graph Matching algorithm, to optimize neural symbolic model. In the context of text-editing image retrieval, we validate the effectiveness of our method in CSS and CRIR dataset. Besides, CRIR is a new synthetic dataset generated by us, which we will publish it soon for future use.
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