Literature DB >> 24797111

Introducing conformal prediction in predictive modeling. A transparent and flexible alternative to applicability domain determination.

Ulf Norinder1, Lars Carlsson, Scott Boyer, Martin Eklund.   

Abstract

Conformal prediction is introduced as an alternative approach to domain applicability estimation. The advantages of using conformal prediction are as follows: First, the approach is based on a consistent and well-defined mathematical framework. Second, the understanding of the confidence level concept in conformal predictions is straightforward, e.g. a confidence level of 0.8 means that the conformal predictor will commit, at most, 20% errors (i.e., true values outside the assigned prediction range). Third, the confidence level can be varied depending on the situation where the model is to be applied and the consequences of such changes are readily understandable, i.e. prediction ranges are increased or decreased, and the changes can immediately be inspected. We demonstrate the usefulness of conformal prediction by applying it to 10 publicly available data sets.

Mesh:

Year:  2014        PMID: 24797111     DOI: 10.1021/ci5001168

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  25 in total

1.  Modelling compound cytotoxicity using conformal prediction and PubChem HTS data.

Authors:  Fredrik Svensson; Ulf Norinder; Andreas Bender
Journal:  Toxicol Res (Camb)       Date:  2016-10-31       Impact factor: 3.524

Review 2.  In silico toxicology: From structure-activity relationships towards deep learning and adverse outcome pathways.

Authors:  Jennifer Hemmerich; Gerhard F Ecker
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2020-03-31

3.  Bayesian Additive Regression Trees using Bayesian Model Averaging.

Authors:  Belinda Hernández; Adrian E Raftery; Stephen R Pennington; Andrew C Parnell
Journal:  Stat Comput       Date:  2017-07-27       Impact factor: 2.559

4.  Assigning confidence to molecular property prediction.

Authors:  AkshatKumar Nigam; Robert Pollice; Matthew F D Hurley; Riley J Hickman; Matteo Aldeghi; Naruki Yoshikawa; Seyone Chithrananda; Vincent A Voelz; Alán Aspuru-Guzik
Journal:  Expert Opin Drug Discov       Date:  2021-06-15       Impact factor: 7.050

5.  Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

Authors:  Isidro Cortés-Ciriano; Gerard J P van Westen; Guillaume Bouvier; Michael Nilges; John P Overington; Andreas Bender; Thérèse E Malliavin
Journal:  Bioinformatics       Date:  2015-09-08       Impact factor: 6.937

6.  Efficiency of different measures for defining the applicability domain of classification models.

Authors:  Waldemar Klingspohn; Miriam Mathea; Antonius Ter Laak; Nikolaus Heinrich; Knut Baumann
Journal:  J Cheminform       Date:  2017-08-03       Impact factor: 5.514

7.  A molecular portrait of microsatellite instability across multiple cancers.

Authors:  Isidro Cortes-Ciriano; Sejoon Lee; Woong-Yang Park; Tae-Min Kim; Peter J Park
Journal:  Nat Commun       Date:  2017-06-06       Impact factor: 14.919

8.  Maximizing gain in high-throughput screening using conformal prediction.

Authors:  Fredrik Svensson; Avid M Afzal; Ulf Norinder; Andreas Bender
Journal:  J Cheminform       Date:  2018-02-21       Impact factor: 5.514

9.  ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities.

Authors:  Marina Garcia de Lomana; Andrea Morger; Ulf Norinder; Roland Buesen; Robert Landsiedel; Andrea Volkamer; Johannes Kirchmair; Miriam Mathea
Journal:  J Chem Inf Model       Date:  2021-06-21       Impact factor: 4.956

10.  How accurately can we predict the melting points of drug-like compounds?

Authors:  Igor V Tetko; Yurii Sushko; Sergii Novotarskyi; Luc Patiny; Ivan Kondratov; Alexander E Petrenko; Larisa Charochkina; Abdullah M Asiri
Journal:  J Chem Inf Model       Date:  2014-12-09       Impact factor: 4.956

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