Lazy Learning for Predictive Toxicology based on a Chemical Ontology

2006 ◽  
pp. 1-18 ◽  
Author(s):  
Eva Armengol ◽  
Enric Plaza
Keyword(s):  
Lazy Learning ◽  
Predictive Toxicology ◽  
Chemical Ontology

Evaluation of QSAR for Use in Predictive Toxicology Modeling

1993 ◽  
Author(s):  
W. T. Brashear ◽  
P. P. Lu
Keyword(s):  
Predictive Toxicology

scholarly journals Trade-off Predictivity and Explainability for Machine-Learning Powered Predictive Toxicology: An in-Depth Investigation with Tox21 Data Sets

2021 ◽  
Vol 34 (2) ◽  
pp. 541-549 ◽  
Author(s):  
Leihong Wu ◽  
Ruili Huang ◽  
Igor V. Tetko ◽  
Zhonghua Xia ◽  
Joshua Xu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Data Sets ◽  
Predictive Toxicology ◽  
Trade Off

scholarly journals Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Janna Hastings ◽  
Martin Glauer ◽  
Adel Memariani ◽  
Fabian Neuhaus ◽  
Till Mossakowski
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Short Term Memory ◽  
Chemical Space ◽  
Chemical Data ◽  
Learning Approaches ◽  
Class Prediction ◽  
Chemical Structures ◽  
Chemical Ontology ◽  
Chemical Ontologies

AbstractChemical data is increasingly openly available in databases such as PubChem, which contains approximately 110 million compound entries as of February 2021. With the availability of data at such scale, the burden has shifted to organisation, analysis and interpretation. Chemical ontologies provide structured classifications of chemical entities that can be used for navigation and filtering of the large chemical space. ChEBI is a prominent example of a chemical ontology, widely used in life science contexts. However, ChEBI is manually maintained and as such cannot easily scale to the full scope of public chemical data. There is a need for tools that are able to automatically classify chemical data into chemical ontologies, which can be framed as a hierarchical multi-class classification problem. In this paper we evaluate machine learning approaches for this task, comparing different learning frameworks including logistic regression, decision trees and long short-term memory artificial neural networks, and different encoding approaches for the chemical structures, including cheminformatics fingerprints and character-based encoding from chemical line notation representations. We find that classical learning approaches such as logistic regression perform well with sets of relatively specific, disjoint chemical classes, while the neural network is able to handle larger sets of overlapping classes but needs more examples per class to learn from, and is not able to make a class prediction for every molecule. Future work will explore hybrid and ensemble approaches, as well as alternative network architectures including neuro-symbolic approaches.

Progress in predictive toxicology

1991 ◽  
Vol 29 (11) ◽  
pp. 788
Author(s):  
John Evans
Keyword(s):  
Predictive Toxicology
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