Existing deep models for code tend to be trained on syntactic program representations. We present an alternative, called Neural Attribute Grammars, that exposes the semantics of the target language to the training procedure using an attribute grammar. During training, our model learns to replicate the relationship between the syntactic rules used to construct a program, and the semantic attributes (for example, symbol tables) constructed from the context in which the rules are fired. We implement the approach as a system for conditional generation of Java programs modulo eleven natural requirements. Our experiments show that the system generates constraint-abiding programs with significantly higher frequency than a baseline model trained on syntactic program representations, and also in terms of generation accuracy.

Archetypal analysis is a type of factor analysis where data is fit by a convex polytope whose corners are "archetypes" of the data, with the data represented as a convex combination of these archetypal points. While archetypal analysis has been used on biological data, it has not achieved widespread adoption because most data are not well fit by a convex polytope in either the ambient space or after standard data transformations. We propose a new approach to archetypal analysis. Instead of fitting a convex polytope directly on data or after a specific data transformation, we train a neural network (AAnet) to learn a transformation under which the data can best fit into a polytope. We validate this approach on synthetic data where we add nonlinearity. Here, AAnet is the only method that correctly identifies the archetypes. We also demonstrate AAnet on two biological datasets. In a T cell dataset measured with single cell RNA-sequencing, AAnet identifies several archetypal states corresponding to naive, memory, and cytotoxic T cells. In a dataset of gut microbiome profiles, AAnet recovers both previously described microbiome states and identifies novel extrema in the data. Finally, we show that AAnet has generative properties allowing us to uniformly sample from the data geometry even when the input data is not uniformly distributed.

Unsupervised domain mapping has attracted substantial attention in recent years due to the success of models based on the cycle-consistency assumption. These models map between two domains by fooling a probabilistic discriminator, thereby matching the probability distributions of the real and generated data. Instead of this probabilistic approach, we cast the problem in terms of aligning the geometry of the manifolds of the two domains. We introduce the Manifold Geometry Matching Generative Adversarial Network (MGM GAN), which adds two novel mechanisms to facilitate GANs sampling from the geometry of the manifold rather than the density and then aligning two manifold geometries: (1) an importance sampling technique that reweights points based on their density on the manifold, making the discriminator only able to discern geometry and (2) a penalty adapted from traditional manifold alignment literature that explicitly enforces the geometry to be preserved. The MGM GAN leverages the manifolds arising from a pre-trained autoencoder to bridge the gap between formal manifold alignment literature and existing GAN work, and demonstrate the advantages of modeling the manifold geometry over its density.

Deep neural networks can learn meaningful representations of data. However, these representations are hard to interpret. For example, visualizing a latent layer is generally only possible for at most three dimensions. Neural networks are able to learn and benefit from much higher dimensional representationsm but these are not visually interpretable because neurons have arbitrary ordering within a layer. Here, we utilize the ability of a human observer to identify patterns in structured representations to visualize higher dimensions. To do so, we propose a class of regularizations we call Graph Spectral Regularizations that impose graph structure on latent layers. This is achieved by treating activations as signals on a predefined graph and constraining those activations using graph filters, such as low pass and wavelet-like filters. This framework allows for any kind of graphs and filters to achieve a wide range of structured regularizations depending on the inference needs of the data. First, we show a synthetic example where a graph-structured layer reveals topological features of the data. Next, we show that a smoothing regularization imposes semantically consistent ordering of nodes when applied to capsule nets. Further, we show that the graph-structured layer, using wavelet-like spatially localized filters, can form local receptive fields for improved image and biomedical data interpretation. In other words, the mapping between latent layer, neurons and the output space becomes clear due to the localization of the activations. Finally, we show that when structured as a grid, the representations create coherent images that allow for image processing techniques such as convolutions.