diff options
| author | Christoph Helma <helma@in-silico.ch> | 2020-09-25 21:29:17 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2020-09-25 21:29:17 +0200 |
| commit | 70a221983448a818535239704fdd4771c151957d (patch) | |
| tree | 480fd3f16ea84943a348ed2342701f798c783b93 /Makefile | |
| parent | 5dbcec8d20b5f1fe3179877ea28cdb72d1e2ba38 (diff) | |
new tensorflow predictions, nix configuration, t-sne figure
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 28 |
1 files changed, 22 insertions, 6 deletions
@@ -29,27 +29,31 @@ R_CV_DIR = 10-fold-crossvalidations/R TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow #TABLES = tables/r-summary.csv tables/tf-summary.csv tables/lazar-summary.csv tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv tables/tensorflow-all.csv tables/tensorflow-selected.csv tables/lazar-all.csv tables/lazar-high-confidence.csv tables/lazar-padel-all.csv tables/lazar-padel-high-confidence.csv -TABLES = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv tables/tensorflow-all.csv tables/tensorflow-selected.csv tables/lazar-all.csv tables/lazar-high-confidence.csv tables/lazar-padel-all.csv tables/lazar-padel-high-confidence.csv +TABLES = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv tables/tensorflow-all.csv tables/tensorflow-selected.csv tables/lazar-all.csv tables/lazar-high-confidence.csv tables/lazar-padel-all.csv tables/lazar-padel-high-confidence.csv #tables/pred.rf.v3.csv tables/pred.lr.v3.csv tables/pred.lr2.v3.csv tables/pred.nn.v3.csv R_SUMMARIES = $(SUMMARIES_DIR)/R-SVM.json $(SUMMARIES_DIR)/R-RF.json $(SUMMARIES_DIR)/R-DL.json -TF_SUMMARIES = $(SUMMARIES_DIR)/tensorflow-all.json $(SUMMARIES_DIR)/tensorflow-selected.json +TF_SUMMARIES = $(SUMMARIES_DIR)/tensorflow-all.json $(SUMMARIES_DIR)/tensorflow-selected.json $(SUMMARIES_DIR)/pred.lr.v3.json $(SUMMARIES_DIR)/pred.lr2.v3.json $(SUMMARIES_DIR)/pred.nn.v3.json $(SUMMARIES_DIR)/pred.rf.v3.json LAZAR_SUMMARIES = $(SUMMARIES_DIR)/lazar-all.json $(SUMMARIES_DIR)/lazar-high-confidence.json $(SUMMARIES_DIR)/lazar-padel-all.json $(SUMMARIES_DIR)/lazar-padel-high-confidence.json #SUMMARIES = $(R_SUMMARIES) $(TF_SUMMARIES) $(LAZAR_SUMMARIES) -CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv - +CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv $(CONFUSION_MATRICES_DIR)/tensorflow-lr.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-lr2.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-nn.v3.csv $(CONFUSION_MATRICES_DIR)/tensorflow-rf.v3.csv DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv -FIGURES = figures/roc.png +FIGURES = figures/roc.png figures/tsne-mp2d.png all: $(DATA) $(TABLES) $(FIGURES) mutagenicity.pdf include $(PANDOC_SCHOLAR_PATH)/Makefile export: $(DATA) -mutagenicity.mustache.md: results.yaml mutagenicity.md +mutagenicity.mustache.md: results.yaml mutagenicity.md $(FIGURES) mustache $^ > $@ # figures +figures/tsne-mp2d.png: figures/tsne-mp2d.csv + scripts/mp2d-tsne.R + +figures/tsne-mp2d.csv: ../lazar/models/mutagenicity/independent_variables + scripts/mp2d-distances.rb > figures/tsne-mp2d.csv figures/roc.png: figures/results.csv scripts/roc.R @@ -91,6 +95,18 @@ $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv: $(TENSORFLOW_CV_DIR)/pred.sor $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv: $(TENSORFLOW_CV_DIR)/pred_ext.sorted.csv scripts/cv-tensorflow-confusion-matrix.rb $< > $@ +$(CONFUSION_MATRICES_DIR)/tensorflow-lr.v3.csv: $(TENSORFLOW_CV_DIR)/pred.lr.v3.sorted.csv + scripts/cv-tensorflow-confusion-matrix.rb $< > $@ + +$(CONFUSION_MATRICES_DIR)/tensorflow-lr2.v3.csv: $(TENSORFLOW_CV_DIR)/pred.lr2.v3.sorted.csv + scripts/cv-tensorflow-confusion-matrix.rb $< > $@ + +$(CONFUSION_MATRICES_DIR)/tensorflow-nn.v3.csv: $(TENSORFLOW_CV_DIR)/pred.nn.v3.sorted.csv + scripts/cv-tensorflow-confusion-matrix.rb $< > $@ + +$(CONFUSION_MATRICES_DIR)/tensorflow-rf.v3.csv: $(TENSORFLOW_CV_DIR)/pred.rf.v3.sorted.csv + scripts/cv-tensorflow-confusion-matrix.rb $< > $@ + ## R $(CONFUSION_MATRICES_DIR)/R-SVM.csv: $(R_CV_DIR)/Sgl-Observations-SVM.csv scripts/cv-r-confusion-matrix.rb $< > $@ |