Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models
Artikel i vetenskaplig tidskrift, 2023

Accurate methods to predict solubility from molecular structure are highly sought after in the chemical sciences. To assess the state of the art, the American Chemical Society organized a "Second Solubility Challenge"in 2019, in which competitors were invited to submit blinded predictions of the solubilities of 132 drug-like molecules. In the first part of this article, we describe the development of two models that were submitted to the Blind Challenge in 2019 but which have not previously been reported. These models were based on computationally inexpensive molecular descriptors and traditional machine learning algorithms and were trained on a relatively small data set of 300 molecules. In the second part of the article, to test the hypothesis that predictions would improve with more advanced algorithms and higher volumes of training data, we compare these original predictions with those made after the deadline using deep learning models trained on larger solubility data sets consisting of 2999 and 5697 molecules. The results show that there are several algorithms that are able to obtain near state-of-the-art performance on the solubility challenge data sets, with the best model, a graph convolutional neural network, resulting in an RMSE of 0.86 log units. Critical analysis of the models reveals systematic differences between the performance of models using certain feature sets and training data sets. The results suggest that careful selection of high quality training data from relevant regions of chemical space is critical for prediction accuracy but that other methodological issues remain problematic for machine learning solubility models, such as the difficulty in modeling complex chemical spaces from sparse training data sets.

Learning algorithms

Convolutional neural networks

Deep learning

Solubility prediction



Jonathan G.M. Conn

University of Strathclyde

James W. Carter

University of Strathclyde

Justin J.A. Conn

University of Strathclyde

Vigneshwari Subramanian

AstraZeneca AB

Andrew Baxter


Ola Engkvist

Chalmers, Data- och informationsteknik

AstraZeneca AB

Antonio Llinas

AstraZeneca AB

Ekaterina L. Ratkova

AstraZeneca AB

Stephen D. Pickett


James L. Mcdonagh

IBM Research Europe

David S. Palmer

University of Strathclyde

Journal of Chemical Information and Modeling

1549-9596 (ISSN) 1549960x (eISSN)

Vol. 63 4 1099-1113


Annan data- och informationsvetenskap

Bioinformatik (beräkningsbiologi)

Bioinformatik och systembiologi





Relaterade dataset

Blinded Predictions and Post-hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models [dataset]

DOI: 10.5281/zenodo.7130064

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