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Piir, G.; Sild, S.; Maran, U. Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model. SAR QSAR Environ. Res. 2014, 25, 967-981.

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Piir, G.; Sild, S.; Maran, U. Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model. SAR QSAR Environ. Res. 2014, 25, 967-981.

QDB archive DOI: 10.15152/QDB.116   DOWNLOAD

QsarDB content

Property BCF_class: Experimental BCF class (nB - non-bio-accumulative, B - bioaccumulative)

Tab1.Model1: Imbalanced model towards nB-compounds

Random forest (classification)

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Name Type n Accuracy
Training set training 673 1.000
Out of bag set i internal validation 673 0.854
Validation set external validation 334 0.874
Tab1.Model2: Balanced model

Random forest (classification)

Open in:QDB Explorer QDB Predictor

Name Type n Accuracy
Training set training 673 0.878
Out of bag set i internal validation 673 0.842
Validation set external validation 334 0.844
Tab1.Model3: Imbalanced model towards B-compounds

Random forest (classification)

Open in:QDB Explorer QDB Predictor

Name Type n Accuracy
Training set training 673 0.767
Out of bag set i internal validation 673 0.761
Validation set external validation 334 0.737

Property logBCF: Experimental logarithmic BCF

Citing

When using this QDB archive, please cite (see details) it together with the original article:

  • Piir, G.; Sild, S.; Maran, U. Data for: Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model. QsarDB repository, QDB.116. 2014. http://dx.doi.org/10.15152/QDB.116

  • Piir, G.; Sild, S.; Maran, U. Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model. SAR QSAR Environ. Res. 2014, 25, 967-981. http://dx.doi.org/10.1080/1062936X.2014.969310

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dc.date.accessioned 2014-07-30T06:02:22Z
dc.date.available 2014-07-30T06:02:22Z
dc.date.issued 2014-07-30
dc.identifier.uri http://hdl.handle.net/10967/116
dc.identifier.uri http://dx.doi.org/10.15152/QDB.116
dc.description.abstract In environmental risk assessment, the bio-concentration factor (BCF) is a widely used parameter in the estimation of the bio-accumulation potential of chemicals. BCF data often have an uneven distribution of classes (bio-accumulative vs. non-bio-accumulative), which could severely bias the classification results towards the prevailing class. The present study focuses on the influence of uneven distribution of the classes in training phase of Random Forest (RF) classification models. Three different training set designs were used and descriptors selected to the models based on the occurrence frequency in RF trees and considering the mechanistic aspects they reflect. Models were compared and their classification performance was analysed, indicating good predictive characteristics (sensitivity = 0.90 and specificity = 0.83) for the balanced set; also imbalanced sets have their strengths in certain application scenarios. The confidence of classifications was assessed with a new schema for the applicability domain that makes use of the RF proximity matrix by analysing the similarity between the predicted compound and the training set of the model. All developed models were made available in the transparent, accessible and reproducible way in QsarDB repository (http://dx.doi.org/10.15152/QDB.116).
dc.publisher Geven Piir
dc.publisher Sulev Sild
dc.publisher Uko Maran
dc.rights Attribution 4.0 International
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Piir, G.; Sild, S.; Maran, U. Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model. SAR QSAR Environ. Res. 2014, 25, 967-981.
qdb.property.endpoint 2. Environmental fate parameters 2.4. Bioconcentration en_US
qdb.descriptor.application XLOGP3 3.2.2 en_US
qdb.descriptor.application PaDEL-Descriptor 2.18 en_US
bibtex.entry article en_US
bibtex.entry.author Piir, G.
bibtex.entry.author Sild, S.
bibtex.entry.author Maran, U.
bibtex.entry.doi 10.1080/1062936X.2014.969310
bibtex.entry.journal SAR QSAR Environ. Res.
bibtex.entry.number 12
bibtex.entry.pages 967-981
bibtex.entry.title Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model en_US
bibtex.entry.volume 25
bibtex.entry.year 2014
qdb.model.type Random forest (classification) en_US


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