Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships
Abstract
Neural networks were widely used for quantitative structure-activity relationships (QSAR) in the 1990s. Because of various practical issues (e.g., slow on large problems, difficult to train, prone to overfitting, etc.), they were superseded by more robust methods like support vector machine (SVM) and random forest (RF), which arose in the early 2000s. The last 10 years has witnessed a revival of neural networks in the machine learning community thanks to new methods for preventing overfitting, more efficient training algorithms, and advancements in computer hardware. In particular, deep neural nets (DNNs), i.e. neural nets with more than one hidden layer, have found great successes in many applications, such as computer vision and natural language processing. Here we show that DNNs can routinely make better prospective predictions than RF on a set of large diverse QSAR data sets that are taken from Merck's drug discovery effort. The number of adjustable parameters needed for DNNs is fairly large, but our results show that it is not necessary to optimize them for individual data sets, and a single set of recommended parameters can achieve better performance than RF for most of the data sets we studied. The usefulness of the parameters is demonstrated on additional data sets not used in the calibration. Although training DNNs is still computationally intensive, using graphical processing units (GPUs) can make this issue manageable.
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Advances in artificial intelligence (AI) are driving a revolution across science, enabling exciting new results across chemistry, biology, and medicine.
“Advances in artificial intelligence (AI) are driving a revolution across science, enabling exciting new results across chemistry,80–82 biology,83,84 and medicine.85–88”
From Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review (2021) · cites this paper as [82]
DNNs began to be applied to QSAR after the Merck Molecular Activity Challenge in 2012.
“DNNs began to be applied to QSAR51 after the Merck Molecular Activity Challenge in 2012.52”
From QSAR without borders (2020) · cites this paper as [51]
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- Authors
- Ma, J., Sheridan, R. P., Liaw, A., Dahl, G. E., & Svetnik, V.
- Affiliations
- Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
- University of Toronto (CA)
- Corresponding author
- Ma, Junshui
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-02-17
- Volume
- 55
- Issue
- 2
- Pages
- 263-274
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W1999798000
- Cited by
- 1,159
- References
- 4
- Citations by year
- 2026: 47 · 2025: 88 · 2024: 126 · 2023: 107 · 2022: 147 · 2021: 142 · 2020: 152 · 2019: 139 · 2018: 101 · 2017: 53 · 2016: 45 · 2015: 12
- FWCI
- 72.37
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
- Physical Sciences › Computer Science › Artificial Intelligence › Neural Networks and Applications
- Keywords
- deep neural network, QSAR, random forest comparison, drug discovery, prospective prediction, overfitting, hyperparameter optimization, GPU training
- MeSH terms
- Machine Learning, Algorithms, Prospective Studies, Neural Networks, Computer, Quantitative Structure-Activity Relationship, Drug Discovery, Workflow, Support Vector Machine
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