From 73f236606451b52a483a073dc43f786bc9f63d9a Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Mon, 19 Oct 2020 22:01:36 +0200 Subject: lazar-padel pa predictions fixed --- Makefile | 5 +- mutagenicity.md | 4 +- .../lazar/pa-padel-predictions.csv | 1204 +++++++++---------- scripts/pa-table.rb | 88 +- scripts/pa-tex-table.rb | 52 + tables/pa-tab.tex | 1207 ++++++++++---------- tables/pa-table.csv | 603 ++++++++++ 7 files changed, 1892 insertions(+), 1271 deletions(-) create mode 100755 scripts/pa-tex-table.rb create mode 100644 tables/pa-table.csv diff --git a/Makefile b/Makefile index 4dc6134..5ceb4aa 100644 --- a/Makefile +++ b/Makefile @@ -62,7 +62,10 @@ figures/roc.csv: $(CV_SUMMARY) scripts/summary2roc.rb $< > $@ # tables -tables/pa-tab.tex: scripts/pa-table.rb $(PA_PREDICTIONS) +tables/pa-tab.tex: tables/pa-table.csv + scripts/pa-tex-table.rb $< > $@ + +tables/pa-table.csv: $(PA_PREDICTIONS) scripts/pa-table.rb > $@ tables/lazar-summary.csv: $(CV_SUMMARY) diff --git a/mutagenicity.md b/mutagenicity.md index 3cba82b..9f7e349 100644 --- a/mutagenicity.md +++ b/mutagenicity.md @@ -554,7 +554,7 @@ similar to the experimental variability (@Helma2018). The lowest number of predictions ({{lazar-padel-high-confidence.n}}) has been obtained from `lazar`-PaDEL high confidence predictions, the largest number of -predictions comes from Tensorflow models ({{tensorflow-rf.n}}). Standard +predictions comes from Tensorflow models ({{tensorflow-rf.v3.n}}). Standard `lazar` give a slightly lower number of predictions ({{lazar-all.n}}) than R and Tensorflow models. This is not necessarily a disadvantage, because `lazar` abstains from predictions, if the query compound is very dissimilar from the @@ -631,8 +631,6 @@ with simple set operations. Pyrrolizidine alkaloid mutagenicity predictions ----------------------------------------------- -**TODO**: **Philipp** Ich wuerde fuer meinen Teil (generelle Uebersicht, applicability domain) noch die Tensorflow Ergebnisse brauchen. - **TODO**: **Verena** Ich wuerde den Grossteil der Diskussion hier dir ueberlassen. Wenn Du lazar Ergebnisse konkret diskutieren willst, kann ich Dir ausfuehrliche Vorhersagen (mit aehnlichen Verbindungen und deren Aktivitaet) fuer einzelne Beispiele zusammenstellen