Adaptive Invariance for Molecule Property Prediction

05/05/2020
by   Wengong Jin, et al.
0

Effective property prediction methods can help accelerate the search for COVID-19 antivirals either through accurate in-silico screens or by effectively guiding on-going at-scale experimental efforts. However, existing prediction tools have limited ability to accommodate scarce or fragmented training data currently available. In this paper, we introduce a novel approach to learn predictors that can generalize or extrapolate beyond the heterogeneous data. Our method builds on and extends recently proposed invariant risk minimization, adaptively forcing the predictor to avoid nuisance variation. We achieve this by continually exercising and manipulating latent representations of molecules to highlight undesirable variation to the predictor. To test the method we use a combination of three data sources: SARS-CoV-2 antiviral screening data, molecular fragments that bind to SARS-CoV-2 main protease and large screening data for SARS-CoV-1. Our predictor outperforms state-of-the-art transfer learning methods by significant margin. We also report the top 20 predictions of our model on Broad drug repurposing hub.

READ FULL TEXT

page 1

page 2

page 3

page 4

research
12/15/2020

Molecular machine learning with conformer ensembles

Virtual screening can accelerate drug discovery by identifying top candi...
research
06/06/2020

Domain Extrapolation via Regret Minimization

Many real prediction tasks such as molecular property prediction require...
research
07/16/2021

Property-aware Adaptive Relation Networks for Molecular Property Prediction

Molecular property prediction plays a fundamental role in drug discovery...
research
03/27/2023

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comp...
research
11/30/2018

Corresponding Projections for Orphan Screening

We propose a novel transfer learning approach for orphan screening calle...
research
06/12/2018

ToxicBlend: Virtual Screening of Toxic Compounds with Ensemble Predictors

Timely assessment of compound toxicity is one of the biggest challenges ...
research
01/28/2022

Biases in In Silico Evaluation of Molecular Optimization Methods and Bias-Reduced Evaluation Methodology

We are interested in in silico evaluation methodology for molecular opti...

Please sign up or login with your details

Forgot password? Click here to reset