Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain

TL;DR

This paper demonstrates that gradient boosting decision trees with learning-to-rank methods outperform traditional models in compound virtual screening, and introduces a new metric, NEDCG, for better evaluation of ranking quality.

Contribution

It compares GBDT-based learning-to-rank methods with RankSVM and regression models, and proposes NEDCG for improved assessment of compound screening performance.

Findings

GBDT with learning-to-rank outperforms RankSVM and regression models.

NEDCG effectively distinguishes worse-than-random predictions.

Proposed NEDCG provides a more accurate evaluation metric for compound ranking.

Abstract

Learning-to-rank, a machine learning technique widely used in information retrieval, has recently been applied to the problem of ligand-based virtual screening, to accelerate the early stages of new drug development. Ranking prediction models learn based on ordinal relationships, making them suitable for integrating assay data from various environments. Existing studies of rank prediction in compound screening have generally used a learning-to-rank method called RankSVM. However, they have not been compared with or validated against the gradient boosting decision tree (GBDT)-based learning-to-rank methods that have gained popularity recently. Furthermore, although the ranking metric called Normalized Discounted Cumulative Gain (NDCG) is widely used in information retrieval, it only determines whether the predictions are better than those of other models. In other words, NDCG is incapable of recognizing when a prediction model produces worse than random results. Nevertheless, NDCG is still used in the performance evaluation of compound screening using learning-to-rank. This study used the GBDT model with ranking loss functions, called lambdarank and lambdaloss, for ligand-based virtual screening; results were compared with existing RankSVM methods and GBDT models using regression. We also proposed a new ranking metric, Normalized Enrichment Discounted Cumulative Gain (NEDCG), which aims to properly evaluate the goodness of ranking predictions. Results showed that the GBDT model with learning-to-rank outperformed existing regression methods using GBDT and RankSVM on diverse datasets. Moreover, NEDCG showed that predictions by regression were comparable to random predictions in multi-assay, multi-family datasets, demonstrating its usefulness for a more direct assessment of compound screening performance.