eep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is pos-sible to side-step expensive search procedures in the discrete and vast space of chemical structures. We introduce MolGAN, an implicit, likelihood-free generative model for small molecular graphs that circumvents the need for expensive graph matching procedures or node ordering heuris-tics of previous likelihood-based methods. Our method adapts generative adversarial networks (GANs) to operate directly on graph-structured data. We combine our approach with a reinforce-ment learning objective to encourage the genera-tion of molecules with specific desired chemical properties. In experiments on the QM9 chemi-cal database, we demonstrate that our model is capable of generating close to 100 valid com-pounds. MolGAN compares favorably both to recent proposals that use string-based (SMILES) representations of molecules and to a likelihood-based method that directly generates graphs, al-beit being susceptible to mode collapse.
Several other works have explored training generative models on SMILES representations of molecules: CharacterVAE @cite_26 is the first such model that is based on a VAE with recurrent encoder and decoder networks. GrammarVAE @cite_14 and SDVAE @cite_17 constrain the decoding process to follow particular syntactic and semantic rules.
@cite_14 @cite_26 @cite_17
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Deep generative models have been enjoying success in modeling continuous data. However it remains challenging to capture the representations for discrete structures with formal grammars and semantics, e.g., computer programs and molecular structures. How to generate both syntactically and semantically correct data still remains largely an open problem. Inspired by the theory of compiler where the syntax and semantics check is done via syntax-directed translation (SDT), we propose a novel syntax-directed variational autoencoder (SD-VAE) by introducing stochastic lazy attributes. This approach converts the offline SDT check into on-the-fly generated guidance for constraining the decoder. Comparing to the state-of-the-art methods, our approach enforces constraints on the output space so that the output will be not only syntactically valid, but also semantically reasonable. We evaluate the proposed model with applications in programming language and molecules, including reconstruction and program molecule optimization. The results demonstrate the effectiveness in incorporating syntactic and semantic constraints in discrete generative models, which is significantly better than current state-of-the-art approaches. Recent work on generative modeling of text has found that variational auto-encoders (VAE) incorporating LSTM decoders perform worse than simpler LSTM language models (, 2015). This negative result is so far poorly understood, but has been attributed to the propensity of LSTM decoders to ignore conditioning information from the encoder. In this paper, we experiment with a new type of decoder for VAE: a dilated CNN. By changing the decoder's dilation architecture, we control the effective context from previously generated words. In experiments, we find that there is a trade off between the contextual capacity of the decoder and the amount of encoding information used. We show that with the right decoder, VAE can outperform LSTM language models. We demonstrate perplexity gains on two datasets, representing the first positive experimental result on the use VAE for generative modeling of text. Further, we conduct an in-depth investigation of the use of VAE (with our new decoding architecture) for semi-supervised and unsupervised labeling tasks, demonstrating gains over several strong baselines. Learning useful representations without supervision remains a key challenge in machine learning. In this paper, we propose a simple yet powerful generative model that learns such discrete representations. Our model, the Vector Quantised-Variational AutoEncoder (VQ-VAE), differs from VAEs in two key ways: the encoder network outputs discrete, rather than continuous, codes; and the prior is learnt rather than static. In order to learn a discrete latent representation, we incorporate ideas from vector quantisation (VQ). Using the VQ method allows the model to circumvent issues of posterior collapse'' -— where the latents are ignored when they are paired with a powerful autoregressive decoder -— typically observed in the VAE framework. Pairing these representations with an autoregressive prior, the model can generate high quality images, videos, and speech as well as doing high quality speaker conversion and unsupervised learning of phonemes, providing further evidence of the utility of the learnt representations. Learning useful representations without supervision remains a key challenge in machine learning. In this paper, we propose a simple yet powerful generative model that learns such discrete representations. Our model, the Vector Quantised-Variational AutoEncoder (VQ-VAE), differs from VAEs in two key ways: the encoder network outputs discrete, rather than continuous, codes; and the prior is learnt rather than static. In order to learn a discrete latent representation, we incorporate ideas from vector quantisation (VQ). Using the VQ method allows the model to circumvent issues of "posterior collapse" -- where the latents are ignored when they are paired with a powerful autoregressive decoder -- typically observed in the VAE framework. Pairing these representations with an autoregressive prior, the model can generate high quality images, videos, and speech as well as doing high quality speaker conversion and unsupervised learning of phonemes, providing further evidence of the utility of the learnt representations.