diff options
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 24 |
1 files changed, 22 insertions, 2 deletions
@@ -12,6 +12,7 @@ TEMPLATE_FILE_LATEX = pandoc-scholar.latex # Experiments +# crossvalidations LAZAR_CONFUSION_MATRIX_DIR = 10-fold-crossvalidations/lazar/crossvalidation/confusion_matrices LAZAR_PADEL_CONFUSION_MATRIX_DIR = 10-fold-crossvalidations/lazar-padel/crossvalidation/confusion_matrices R_CV_DIR = 10-fold-crossvalidations/R @@ -21,10 +22,16 @@ CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.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 CV_SUMMARY = 10-fold-crossvalidations/summary.yaml -TABLES = tables/lazar-summary.csv tables/r-summary.csv tables/tensorflow-summary.csv -FIGURES = figures/roc.png figures/tsne-mp2d.png figures/tsne-padel.png #figures/pa-predictions.png + +# PA predictions +PA_DIR = pyrrolizidine-alkaloids +PA_LAZAR_DIR = $(PA_DIR)/lazar +#PA_LAZAR_MP2D_DIR = $(PA_LAZAR_DIR)/mp2d +#PA_LAZAR_PADEL_DIR = $(PA_LAZAR_DIR)/padel # manuscript +TABLES = tables/lazar-summary.csv tables/r-summary.csv tables/tensorflow-summary.csv tables/pa-tab.tex +FIGURES = figures/roc.png figures/tsne-mp2d.png figures/tsne-padel.png #figures/pa-predictions.png all: $(TABLES) $(FIGURES) mutagenicity.pdf include $(PANDOC_SCHOLAR_PATH)/Makefile @@ -53,6 +60,8 @@ figures/roc.csv: $(CV_SUMMARY) scripts/results2csv.rb $< > $@ # tables +tables/pa-tab.tex: scripts/pa-table.rb + scripts/pa-table.rb > $@ tables/lazar-summary.csv: $(CV_SUMMARY) scripts/summaries2table.rb lazar > $@ @@ -68,6 +77,17 @@ tables/tensorflow-summary.csv: $(CV_SUMMARY) $(CV_SUMMARY): $(CONFUSION_MATRICES) scripts/confusion-matrix-summary.rb $^ > $@ +# PA predictions + +$(PA_LAZAR_DIR)/pa-padel-predictions.csv: 10-fold-crossvalidations/lazar-pa-padel/pa_independent_variables + ../lazar/bin/batch_padel_classification.rb 10-fold-crossvalidations/lazar-pa-padel $< > $@ + +$(PA_LAZAR_DIR)/pa-mp2d-predictions.csv: $(PA_LAZAR_DIR)/pa-smiles.csv + ../lazar/bin/batch_fingerprint_classification.rb ../lazar/models/mutagenicity $< > $@ + +$(PA_LAZAR_DIR)/pa-smiles.csv: pyrrolizidine-alkaloids/180920_PA_complete_SMILES.csv + cut -f1,4 -d ';' $< | sed 's/;/,/' > $@ + # confusion matrices ## lazar |