From 0987ef1a39e33f5f467371cb2c9e62aac8e0a1c4 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 21 Oct 2020 00:24:56 +0200 Subject: typos fixed, pdf build --- mutagenicity.md | 20 ++++++++++++++------ mutagenicity.pdf | Bin 1847966 -> 1853596 bytes 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/mutagenicity.md b/mutagenicity.md index dd1aa77..896e088 100644 --- a/mutagenicity.md +++ b/mutagenicity.md @@ -654,10 +654,18 @@ with simple set operations. Pyrrolizidine alkaloid mutagenicity predictions ----------------------------------------------- -`lazar` models with MolPrint2D descriptors predicted {{lazar.mp2d.all.n_perc}}% of the pyrrolizidine alkaloids (PAs) ({{lazar.mp2d.high_confidence.n_perc}}% with high confidence), the remaining compounds are not within its applicability domain. All other models predicted 100% of the 602 compounds, indicating that all compounds are within their applicability domain. - -Mutagenicity predictions from different models show little agreement in general (table 4). 42 from 602 PAs have non-conflicting predictions (all of them non-mutagenic). -Most models predict predominantly a non-mutagenic outcome for PAs, with exception of the R deep learning (DL) and the Tensorflow Scikit logistic regression models ({{pa.dl.mut_perc}} and {{pa.tf.lr_scikit.mut_perc}}% positive predictions). +`lazar` models with MolPrint2D descriptors predicted {{pa.lazar.mp2d.all.n_perc}}% +of the pyrrolizidine alkaloids (PAs) ({{pa.lazar.mp2d.high_confidence.n_perc}}% +with high confidence), the remaining compounds are not within its applicability +domain. All other models predicted 100% of the 602 compounds, indicating that +all compounds are within their applicability domain. + +Mutagenicity predictions from different models show little agreement in general +(table 4). 42 from 602 PAs have non-conflicting predictions (all of them +non-mutagenic). Most models predict predominantly a non-mutagenic outcome for +PAs, with exception of the R deep learning (DL) and the Tensorflow Scikit +logistic regression models ({{pa.tf.dl.mut_perc}} and +{{pa.tf.lr_scikit.mut_perc}}% positive predictions). -R RF and SVM models favor very strongly non-mutagenic predictions (only {{pa.r.rf.mut_perc}} and {{pa.r.svm.mut_perc}} % mutagenic PAs), while Tensorflow models classify approximately half of the PAs as mutagenic (RF {{pa.tf.rf.mut_perc}}%, LR-sgd {{pa.tf.lr_sgd}}%, LR-scikit:{{pa.tf.lr_scikit.mut_perc}}, LR-NN:{{pa.tf.nn.mut_perc}}%). `lazar` models predict predominately non-mutagenicity, but to a lesser extend than R models (MP2D:{{pa.lazar.all.mut_perc}}, PaDEL:{{pa.lazar.padel.mut_perc}}). +R RF and SVM models favor very strongly non-mutagenic predictions (only {{pa.r.rf.mut_perc}} and {{pa.r.svm.mut_perc}} % mutagenic PAs), while Tensorflow models classify approximately half of the PAs as mutagenic (RF {{pa.tf.rf.mut_perc}}%, LR-sgd {{pa.tf.lr_sgd}}%, LR-scikit:{{pa.tf.lr_scikit.mut_perc}}, LR-NN:{{pa.tf.nn.mut_perc}}%). `lazar` models predict predominately non-mutagenicity, but to a lesser extend than R models (MP2D:{{pa.lazar.mp2d.all.mut_perc}}, PaDEL:{{pa.lazar.padel.all.mut_perc}}). -It is interesting to note, that different implementations of the same algorithm show little accordance in their prediction (see e.g R-RF vs. Tensorflow-RF and LR-sgd vs. LR-scikit in Table4 and @tab:pa-summary). +It is interesting to note, that different implementations of the same algorithm show little accordance in their prediction (see e.g R-RF vs. Tensorflow-RF and LR-sgd vs. LR-scikit in Table 4 and @tbl:pa-summary). **TODO** **Verena, Philipp** habt ihr eine Erklaerung dafuer? diff --git a/mutagenicity.pdf b/mutagenicity.pdf index af2434a..a873f27 100644 Binary files a/mutagenicity.pdf and b/mutagenicity.pdf differ -- cgit v1.2.3