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Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from both chemistry and computer science communities. Most existing approaches rely on template-based models that define subgraph matching rules, but whether or not a chemical reaction can proceed is not defined by hard decision rules. In this work, we propose a new approach to this task using the Conditional Graph Logic Network, a conditional graphical model built upon graph neural networks that learns when rules from reaction templates should be applied, implicitly considering whether the resulting reaction would be both chemically feasible and strategic. We also propose an efficient hierarchical sampling to alleviate the computation cost. While achieving a significant improvement of $8.1%$ over current state-of-the-art methods on the benchmark dataset, our model also offers interpretations for the prediction.
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Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is aligning model design with strategies adopted by chemists. Building on this viewpoint, this paper introduces a graph-based approach that capitalizes on the idea that the graph topology of precursor molecules is largely unaltered during a chemical reaction. The model first predicts the set of graph edits transforming the target into incomplete molecules called synthons. Next, the model learns to expand synthons into complete molecules by attaching relevant leaving groups. This decomposition simplifies the architecture, making its predictions more interpretable, and also amenable to manual correction. Our model achieves a top-1 accuracy of $53.7%$, outperforming previous template-free and semi-template-based methods.
A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template based approaches, but does not require domain knowledge and is much more scalable.
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can prioritize disease-causing mutations have, therefore, enormous applications. It is well-known that genes function through a complex regulatory network. However, existing variant effect prediction models only consider a variant in isolation. In contrast, we propose VEGN, which models variant effect prediction using a graph neural network (GNN) that operates on a heterogeneous graph with genes and variants. The graph is created by assigning variants to genes and connecting genes with an gene-gene interaction network. In this context, we explore an approach where a gene-gene graph is given and another where VEGN learns the gene-gene graph and therefore operates both on given and learnt edges. The graph neural network is trained to aggregate information between genes, and between genes and variants. Variants can exchange information via the genes they connect to. This approach improves the performance of existing state-of-the-art models.
Heterogeneous domain adaptation (HDA) tackles the learning of cross-domain samples with both different probability distributions and feature representations. Most of the existing HDA studies focus on the single-source scenario. In reality, however, it is not uncommon to obtain samples from multiple heterogeneous domains. In this article, we study the multisource HDA problem and propose a conditional weighting adversarial network (CWAN) to address it. The proposed CWAN adversarially learns a feature transformer, a label classifier, and a domain discriminator. To quantify the importance of different source domains, CWAN introduces a sophisticated conditional weighting scheme to calculate the weights of the source domains according to the conditional distribution divergence between the source and target domains. Different from existing weighting schemes, the proposed conditional weighting scheme not only weights the source domains but also implicitly aligns the conditional distributions during the optimization process. Experimental results clearly demonstrate that the proposed CWAN performs much better than several state-of-the-art methods on four real-world datasets.
Graph convolutional neural networks (GCNNs) have been attracting increasing research attention due to its great potential in inference over graph structures. However, insufficient effort has been devoted to the aggregation methods between different convolution graph layers. In this paper, we introduce a graph attribute aggregation network (GAAN) architecture. Different from the conventional pooling operations, a graph-transformation-based aggregation strategy, progressive margin folding, PMF, is proposed for integrating graph features. By distinguishing internal and margin elements, we provide an approach for implementing the folding iteratively. And a mechanism is also devised for preserving the local structures during progressively folding. In addition, a hypergraph-based representation is introduced for transferring the aggregated information between different layers. Our experiments applied to the public molecule datasets demonstrate that the proposed GAAN outperforms the existing GCNN models with significant effectiveness.
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