Conformal prediction of biological activity of chemical compounds

Conformal prediction of biological activity of chemical compounds The paper presents an application of Conformal Predictors to a chemoinformatics problem of predicting the biological activities of chemical compounds. The paper addresses some specific challenges in this domain: a large number of compounds (training examples), high-dimensionality of feature space, sparseness and a strong class imbalance. A variant of conformal predictors called Inductive Mondrian Conformal Predictor is applied to deal with these challenges. Results are presented for several non-conformity measures extracted from underlying algorithms and different kernels. A number of performance measures are used in order to demonstrate the flexibility of Inductive Mondrian Conformal Predictors in dealing with such a complex set of data. This approach allowed us to identify the most likely active compounds for a given biological target and present them in a ranking order. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Annals of Mathematics and Artificial Intelligence Springer Journals

Conformal prediction of biological activity of chemical compounds

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Publisher
Springer International Publishing
Copyright
Copyright © 2017 by The Author(s)
Subject
Computer Science; Artificial Intelligence (incl. Robotics); Mathematics, general; Computer Science, general; Complex Systems
ISSN
1012-2443
eISSN
1573-7470
D.O.I.
10.1007/s10472-017-9556-8
Publisher site
See Article on Publisher Site

Abstract

The paper presents an application of Conformal Predictors to a chemoinformatics problem of predicting the biological activities of chemical compounds. The paper addresses some specific challenges in this domain: a large number of compounds (training examples), high-dimensionality of feature space, sparseness and a strong class imbalance. A variant of conformal predictors called Inductive Mondrian Conformal Predictor is applied to deal with these challenges. Results are presented for several non-conformity measures extracted from underlying algorithms and different kernels. A number of performance measures are used in order to demonstrate the flexibility of Inductive Mondrian Conformal Predictors in dealing with such a complex set of data. This approach allowed us to identify the most likely active compounds for a given biological target and present them in a ranking order.

Journal

Annals of Mathematics and Artificial IntelligenceSpringer Journals

Published: Jun 16, 2017

References

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