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Tristan Aumentado-Armstrong

Publications and source records attributed to Tristan Aumentado-Armstrong.

21 records · Page 2Linked to original sources

Geometric Disentanglement for Generative Latent Shape Models

Representing 3D shape is a fundamental problem in artificial intelligence, which has numerous applications within computer vision and graphics. One avenue that has recently begun to be explored is the use of latent representations of generative models. However, it remains an open problem to learn a generative model of shape that is interpretable and easily manipulated, particularly in the absence of supervised labels. In this paper, we propose an unsupervised approach to partitioning the latent space of a variational autoencoder for 3D point clouds in a natural way, using only geometric information. Our method makes use of tools from spectral differential geometry to separate intrinsic and extrinsic shape information, and then considers several hierarchical disentanglement penalties for dividing the latent space in this manner, including a novel one that penalizes the Jacobian of the latent representation of the decoded output with respect to the latent encoding. We show that the resulting representation exhibits intuitive and interpretable behavior, enabling tasks such as pose transfer and pose-aware shape retrieval that cannot easily be performed by models with an entangled representation.

cs.CV↗

Latent Molecular Optimization for Targeted Therapeutic Design

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory pharmacological properties. This problem is made difficult by the enormity and discreteness of the space of potential therapeutics, as well as the graph-structured nature of biomolecular surface sites. Using a dataset of protein-ligand complexes, we surmount these issues by extracting a signature of the target site with a graph convolutional network and by encoding the discrete chemical into a continuous latent vector space. The latter embedding permits gradient-based optimization in molecular space, which we perform using learned differentiable models of binding affinity and other pharmacological properties. We show that our approach is able to efficiently optimize these multiple objectives and discover new molecules with potentially useful binding properties, validated via docking methods.

cs.AI↗

Boutiques: a flexible framework for automated application integration in computing platforms

We present Boutiques, a system to automatically publish, integrate and execute applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitate the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

cs.SE↗