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Register a new userFactor Graph Molecule Network for Structure Elucidation
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Added by
Hieu Le Trung
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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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.
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Most of the successful deep neural network architectures are structured, often consisting of elements like convolutional neural networks and gated recurrent neural networks. Recently, graph neural networks have been successfully applied to graph structured data such as point cloud and molecular data. These networks often only consider pairwise dependencies, as they operate on a graph structure. We generalize the graph neural network into a factor graph neural network (FGNN) in order to capture higher order dependencies. We show that FGNN is able to represent Max-Product Belief Propagation, an approximate inference algorithm on probabilistic graphical models; hence it is able to do well when Max-Product does well. Promising results on both synthetic and real datasets demonstrate the effectiveness of the proposed model.
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.
In graph neural networks (GNNs), message passing iteratively aggregates nodes information from their direct neighbors while neglecting the sequential nature of multi-hop node connections. Such sequential node connections e.g., metapaths, capture critical insights for downstream tasks. Concretely, in recommender systems (RSs), disregarding these insights leads to inadequate distillation of collaborative signals. In this paper, we employ collaborative subgraphs (CSGs) and metapaths to form metapath-aware subgraphs, which explicitly capture sequential semantics in graph structures. We propose metatextbf{P}ath and textbf{E}ntity-textbf{A}ware textbf{G}raph textbf{N}eural textbf{N}etwork (PEAGNN), which trains multilayer GNNs to perform metapath-aware information aggregation on such subgraphs. This aggregated information from different metapaths is then fused using attention mechanism. Finally, PEAGNN gives us the representations for node and subgraph, which can be used to train MLP for predicting score for target user-item pairs. To leverage the local structure of CSGs, we present entity-awareness that acts as a contrastive regularizer on node embedding. Moreover, PEAGNN can be combined with prominent layers such as GAT, GCN and GraphSage. Our empirical evaluation shows that our proposed technique outperforms competitive baselines on several datasets for recommendation tasks. Further analysis demonstrates that PEAGNN also learns meaningful metapath combinations from a given set of metapaths.
Recently, Graph Neural Network (GNN) has achieved remarkable success in various real-world problems on graph data. However in most industries, data exists in the form of isolated islands and the data privacy and security is also an important issue. In this paper, we propose FedVGCN, a federated GCN learning paradigm for privacy-preserving node classification task under data vertically partitioned setting, which can be generalized to existing GCN models. Specifically, we split the computation graph data into two parts. For each iteration of the training process, the two parties transfer intermediate results to each other under homomorphic encryption. We conduct experiments on benchmark data and the results demonstrate the effectiveness of FedVGCN in the case of GraphSage.
Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative models and reinforcement learning approaches made initial success, but still face difficulties in simultaneously optimizing multiple drug properties. To address such challenges, we propose the MultI-constraint MOlecule SAmpling (MIMOSA) approach, a sampling framework to use input molecule as an initial guess and sample molecules from the target distribution. MIMOSA first pretrains two property agnostic graph neural networks (GNNs) for molecule topology and substructure-type prediction, where a substructure can be either atom or single ring. For each iteration, MIMOSA uses the GNNs prediction and employs three basic substructure operations (add, replace, delete) to generate new molecules and associated weights. The weights can encode multiple constraints including similarity and drug property constraints, upon which we select promising molecules for next iteration. MIMOSA enables flexible encoding of multiple property- and similarity-constraints and can efficiently generate new molecules that satisfy various property constraints and achieved up to 49.6% relative improvement over the best baseline in terms of success rate.
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