We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

Amortized variational inference (AVI) replaces instance-specific local inference with a global inference network. While AVI has enabled efficient training of deep generative models such as variational autoencoders (VAE), recent empirical work suggests that inference networks can produce suboptimal variational parameters. We propose a hybrid approach, to use AVI to initialize the variational parameters and run stochastic variational inference (SVI) to refine them. Crucially, the local SVI procedure is itself differentiable, so the inference network and generative model can be trained end-to-end with gradient-based optimization. This semi-amortized approach enables the use of rich generative models without experiencing the posterior-collapse phenomenon common in training VAEs for problems like text generation. Experiments show this approach outperforms strong autoregressive and variational baselines on standard text and image datasets.

Inference models are a key component in scaling variational inference to deep latent variable models, most notably as encoder networks in variational auto-encoders (VAEs). By replacing conventional optimization-based inference with a learned model, inference is amortized over data examples and therefore more computationally efficient. However, standard inference models are restricted to direct mappings from data to approximate posterior estimates. The failure of these models to reach fully optimized approximate posterior estimates results in an amortization gap. We aim toward closing this gap by proposing iterative inference models, which learn to perform inference optimization through repeatedly encoding gradients. Our approach generalizes standard inference models in VAEs and provides insight into several empirical findings, including top-down inference techniques. We demonstrate the inference optimization capabilities of iterative inference models and show that they outperform standard inference models on several benchmark data sets of images and text.

Training of discrete latent variable models remains challenging because passing gradient information through discrete units is difficult. We propose a new class of smoothing transformations based on a mixture of two overlapping distributions, and show that the proposed transformation can be used for training binary latent models with either directed or undirected priors. We derive a new variational bound to efficiently train with Boltzmann machine priors. Using this bound, we develop DVAE++, a generative model with a global discrete prior and a hierarchy of convolutional continuous variables. Experiments on several benchmarks show that overlapping transformations outperform other recent continuous relaxations of discrete latent variables including Gumbel-Softmax (Maddison et al., 2016; Jang et al., 2016), and discrete variational autoencoders (Rolfe 2016).