diff options
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 57 |
1 files changed, 31 insertions, 26 deletions
@@ -1,5 +1,5 @@ # Manuscript -# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to tour installation +# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to your installation ARTICLE_FILE = mutagenicity.md PANDOC_SCHOLAR_PATH = pandoc-scholar @@ -13,7 +13,13 @@ include $(PANDOC_SCHOLAR_PATH)/Makefile # Lazar -LAZAR_DIR = "../lazar" +LAZAR_DIR = ../lazar +LAZAR_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity +LAZAR_PADEL_MODEL_DIR = $(LAZAR_DIR)/models/mutagenicity-padel +LAZAR_SUMMARY_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/summaries +LAZAR_PADEL_SUMMARY_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/summaries +LAZAR_CONFUSION_MATRIX_DIR = $(LAZAR_MODEL_DIR)/crossvalidation/confusion_matrices +LAZAR_PADEL_CONFUSION_MATRIX_DIR = $(LAZAR_PADEL_MODEL_DIR)/crossvalidation/confusion_matrices # Experiments @@ -21,16 +27,17 @@ SUMMARIES_DIR = 10-fold-crossvalidations/summaries CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices R_CV_DIR = 10-fold-crossvalidations/R TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow -LAZAR_CV_DIR = 10-fold-crossvalidations/lazar #tables = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv -SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv -# TODO lazar model/cv with PaDEL descriptors +SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv $(SUMMARIES_DIR)/lazar-padel-all.csv $(SUMMARIES_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 DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv all: $(SUMMARIES) $(DATA) #$(tables) +export: $(DATA) # summaries @@ -57,35 +64,33 @@ $(CONFUSION_MATRICES_DIR)/R-DL.csv: $(R_CV_DIR)/Sgl-Observations-DL.csv scripts/cv-r-confusion-matrix.rb $< > $@ ## lazar -$(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id - scripts/cv-lazar-confusion-matrix.rb all $< > $@ +$(CONFUSION_MATRICES_DIR)/lazar-all.csv: $(LAZAR_CONFUSION_MATRIX_DIR) + cp $</all $@ + +$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CONFUSION_MATRIX_DIR) + cp $</high_confidence $@ -$(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id - scripts/cv-lazar-confusion-matrix.rb high-confidence $< > $@ +$(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR) + cp $</all $@ -# TODO lazar model/cv with PaDEL descriptors +$(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv: $(LAZAR_PADEL_CONFUSION_MATRIX_DIR) + cp $</high_confidence $@ # exports -data/mutagenicity-fingerprints.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id - scripts/export-fingerprints.rb $< > $@ +data/mutagenicity-fingerprints.csv: $(LAZAR_DIR)/models/mutagenicity + $(LAZAR_DIR)/bin/export-fingerprints.rb $< > $@ -data/mutagenicity.csv: $(LAZAR_CV_DIR)/lazar-crossvalidation.id - scripts/export.rb $< training_csv > $@ +data/mutagenicity.csv: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv + cp $< > $@ -data/mutagenicity.sdf: $(LAZAR_CV_DIR)/lazar-crossvalidation.id - scripts/export.rb $< sdf > $@ +data/mutagenicity.sdf: $(LAZAR_DIR)/models/mutagenicity/Mutagenicity-Salmonella_typhimurium.csv + $(LAZAR_DIR)/bin/export-sdf.rb $< > $@ # lazar models and crossvalidations +$(LAZAR_SUMMARY_DIR): + make -C $(LAZAR_MODEL_DIR) -$(LAZAR_CV_DIR)/lazar-crossvalidation.id: ../lazar/data/Mutagenicity-Salmonella_typhimurium.csv # adjust to match the location of your lazar libraries - scripts/lazar-crossvalidation.rb $< > $@ - -# import -# TODO lazar model/cv with PaDEL descriptors - -# cleanup - -drop-database: - scripts/drop-database.rb +$(LAZAR_PADEL_SUMMARY_DIR): + make -C $(LAZAR_PADEL_MODEL_DIR) |