Black Box Recursive Translations for Molecular Optimization

Farhan Damani, Vishnu Sresht, Stephen Ra

TL;DR: We introduce a black box algorithm for repeated optimization of compounds using a translation framework.

Abstract: Machine learning algorithms for generating molecular structures offer a promising new approach to drug discovery. We cast molecular optimization as a translation problem, where the goal is to map an input compound to a target compound with improved biochemical properties. Remarkably, we observe that when generated molecules are iteratively fed back into the translator, molecular compound attributes improve with each step. We show that this finding is invariant to the choice of translation model, making this a "black box" algorithm. We call this method Black Box Recursive Translation (BBRT), a new inference method for molecular property optimization. This simple, powerful technique operates strictly on the inputs and outputs of any translation model. We obtain new state-of-the-art results for molecular property optimization tasks using our simple drop-in replacement with well-known sequence and graph-based models. Our method provides a significant boost in performance relative to its non-recursive peers with just a simple "``for" loop. Further, BBRT is highly interpretable, allowing users to map the evolution of newly discovered compounds from known starting points.

Keywords: molecules, chemistry, drug design, generative models, application, translation

Community Implementations: [ 1 code implementation](https://www.catalyzex.com/paper/arxiv:1912.10156/code)