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makefile
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ORIGINAL_ZIP=original/Benchmark_Data.zip
ORIGINAL_DIR=data/00-original
ORIGINAL_STATUS=$(ORIGINAL_DIR)/status
# ORIGINAL_DATA_A=$(ORIGINAL_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
# ORIGINAL_DATA_B=$(ORIGINAL_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
# ORIGINAL_DATA_C=$(ORIGINAL_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
# ORIGINAL_DATA_D=$(ORIGINAL_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
# ORIGINAL_DATA_E=$(ORIGINAL_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
FLAT_DIR=data/01-flat
FLAT_STATUS=$(FLAT_DIR)/status
FLAT_GENERATOR=00-original2flat.py
FLAT_DATA_A=$(FLAT_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
FLAT_DATA_B=$(FLAT_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
FLAT_DATA_C=$(FLAT_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
FLAT_DATA_D=$(FLAT_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
FLAT_DATA_E=$(FLAT_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
CT_DIR=data/02-ct
CT_STATUS=$(CT_DIR)/status
CT_GENERATOR=01-flat2ct.py
# CT_DATA_A=$(CT_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
# CT_DATA_B=$(CT_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
# CT_DATA_C=$(CT_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
# CT_DATA_D=$(CT_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
# CT_DATA_E=$(CT_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
CT_BIN_DIR=data/02-ct-bin
CT_BIN_STATUS=$(CT_BIN_DIR)/status
CT_BIN_GENERATOR=01-flat2ct-bin.py
# CT_BIN_DATA_A=$(CT_BIN_DIR)/hppids-train-ppis.bin
# CT_BIN_DATA_B=$(CT_BIN_DIR)/hppids-train-labels.bin
# CT_BIN_DATA_C=$(CT_BIN_DIR)/hppids-test-ppis.bin
# CT_BIN_DATA_D=$(CT_BIN_DIR)/hppids-test-labels.bin
AC_DIR=data/03-ac
AC_STATUS=$(AC_DIR)/status
AC_GENERATOR=02-flat2ac.py
# AC_DATA_A=$(AC_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
# AC_DATA_B=$(AC_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
# AC_DATA_C=$(AC_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
# AC_DATA_D=$(AC_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
# AC_DATA_E=$(AC_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
AC_BIN_DIR=data/03-ac-bin
AC_BIN_STATUS=$(AC_BIN_DIR)/status
AC_BIN_GENERATOR=02-flat2ac-bin.py
# AC_BIN_DATA_A=$(AC_BIN_DIR)/hppids-train-ppis.bin
# AC_BIN_DATA_B=$(AC_BIN_DIR)/hppids-train-labels.bin
# AC_BIN_DATA_C=$(AC_BIN_DIR)/hppids-test-ppis.bin
# AC_BIN_DATA_D=$(AC_BIN_DIR)/hppids-test-labels.bin
LD_DIR=data/04-ld
LD_STATUS=$(LD_DIR)/status
LD_GENERATOR=03-flat2ld.py
# LD_DATA_A=$(LD_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
# LD_DATA_B=$(LD_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
# LD_DATA_C=$(LD_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
# LD_DATA_D=$(LD_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
# LD_DATA_E=$(LD_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
LD_BIN_DIR=data/04-ld-bin
LD_BIN_STATUS=$(LD_BIN_DIR)/status
LD_BIN_GENERATOR=03-flat2ld-bin.py
# LD_BIN_DATA_A=$(LD_BIN_DIR)/hppids-train-ppis.bin
# LD_BIN_DATA_B=$(LD_BIN_DIR)/hppids-train-labels.bin
# LD_BIN_DATA_C=$(LD_BIN_DIR)/hppids-test-ppis.bin
# LD_BIN_DATA_D=$(LD_BIN_DIR)/hppids-test-labels.bin
MOS_DIR=data/05-mos
MOS_STATUS=$(MOS_DIR)/status
MOS_GENERATOR=04-flat2mos.py
# MOS_DATA_A=$(MOS_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
# MOS_DATA_B=$(MOS_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
# MOS_DATA_C=$(MOS_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
# MOS_DATA_D=$(MOS_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
# MOS_DATA_E=$(MOS_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
MOS_BIN_DIR=data/05-mos-bin
MOS_BIN_STATUS=$(MOS_BIN_DIR)/status
MOS_BIN_GENERATOR=04-flat2mos-bin.py
# MOS_BIN_DATA_A=$(MOS_BIN_DIR)/hppids-train-ppis.bin
# MOS_BIN_DATA_B=$(MOS_BIN_DIR)/hppids-train-labels.bin
# MOS_BIN_DATA_C=$(MOS_BIN_DIR)/hppids-test-ppis.bin
# MOS_BIN_DATA_D=$(MOS_BIN_DIR)/hppids-test-labels.bin
MOS0_DIR=data/06-mos0
MOS0_STATUS=$(MOS0_DIR)/status
MOS0_GENERATOR=05-flat2mos0.py
# MOS0_DATA_A=$(MOS0_DIR)/Supp-A-36630-HPRD-positive-interaction.txt
# MOS0_DATA_B=$(MOS0_DIR)/Supp-B-36480-HPRD-negative-interaction.txt
# MOS0_DATA_C=$(MOS0_DIR)/Supp-C-3899-HPRD-positive-interaction-below-0.25.txt
# MOS0_DATA_D=$(MOS0_DIR)/Supp-D-4262-HPRD-negative-interaction-below-0.25.txt
# MOS0_DATA_E=$(MOS0_DIR)/Supp-E-1882-interacting-0.5-non-interacting-0.5.txt
MOS0_BIN_DIR=data/06-mos0-bin
MOS0_BIN_STATUS=$(MOS0_BIN_DIR)/status
MOS0_BIN_GENERATOR=05-flat2mos0-bin.py
# MOS0_BIN_DATA_A=$(MOS0_BIN_DIR)/hppids-train-ppis.bin
# MOS0_BIN_DATA_B=$(MOS0_BIN_DIR)/hppids-train-labels.bin
# MOS0_BIN_DATA_C=$(MOS0_BIN_DIR)/hppids-test-ppis.bin
# MOS0_BIN_DATA_D=$(MOS0_BIN_DIR)/hppids-test-labels.bin
CTAC_BIN_DIR=data/09-hppids
CTAC_BIN_STATUS=$(CTAC_BIN_DIR)/status
CTAC_BIN_GENERATOR=09-to-final.py
# CTAC_BIN_DATA_A=$(CTAC_BIN_DIR)/hppids-train-ppis.bin
# CTAC_BIN_DATA_B=$(CTAC_BIN_DIR)/hppids-train-labels.bin
# CTAC_BIN_DATA_C=$(CTAC_BIN_DIR)/hppids-test-ppis.bin
# CTAC_BIN_DATA_D=$(CTAC_BIN_DIR)/hppids-test-labels.bin
CD_CT_ZIP=data/Benchmark_CD_CT.zip
CD_AC_ZIP=data/Benchmark_CD_AC.zip
CD_LD_ZIP=data/Benchmark_CD_LD.zip
CD_MOS_ZIP=data/Benchmark_CD_MOS.zip
CD_DATAS_STATUS=data/cd_datas_status
PREDICT_PPI_ZIP=original/predict_PPI.zip
PREDICT_PPI_DIR=data/predict_PPI
PREDICT_PPI_STATUS=$(PREDICT_PPI_DIR)/status
PREDICT_PPI_GENERATOR=20-predict_ppi-bin.py
CT_MODEL_RESULTS= \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_128_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_1024_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256x256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256x256x256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.1.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.3.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.4.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.5.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.6.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.9.csv \
\
model/result_of_tf_estimator_ct(686x2)_64_relu_Adagrad_0.01_dropout_0.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_RMSProp_0.01_dropout_0.csv \
\
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.01_dropout_0_batch_032.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.01_dropout_0_batch_064.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.01_dropout_0_batch_128.csv \
model/result_of_tf_estimator_ct(686x2)_64_relu_Adam_0.01_dropout_0_batch_256.csv \
AC_MODEL_RESULTS= \
model/result_of_tf_estimator_ac(420x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_128_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_1024_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.1.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.3.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.5.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.8.csv \
model/result_of_tf_estimator_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.9.csv \
LD_MODEL_RESULTS= \
model/result_of_tf_estimator_ld(1260x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_128_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_256_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_512_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_1024_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_128x128_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_128x128x128_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_128x128x128x128_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_128x64x32_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64x32_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_512x256x128x64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64x32_relu_Adam_0.0001_dropout_0.001.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64x32_relu_Adam_0.0001_dropout_0.01.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64x32_relu_Adam_0.0001_dropout_0.1.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64x32_relu_Adam_0.0001_dropout_0.3.csv \
model/result_of_tf_estimator_ld(1260x2)_256x128x64x32_relu_Adam_0.0001_dropout_0.5.csv \
MOS_MODEL_RESULTS= \
model/result_of_tf_estimator_mos(58x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_128_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_256_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_1024_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x512_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512x512_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512x512x512_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512_relu_Adam_0.01_dropout_0.1.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512_relu_Adam_0.01_dropout_0.3.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512_relu_Adam_0.01_dropout_0.5.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512_relu_Adam_0.01_dropout_0.7.csv \
model/result_of_tf_estimator_mos(58x2)_512x512x512_relu_Adam_0.01_dropout_0.9.csv \
model/result_of_tf_estimator_mos(58x2)_128_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_1024_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_64x32x16_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_128x64x32_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_256x128x64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x256x128_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_mos(58x2)_512x512_relu_Adam_0.001_dropout_0.csv \
CD_RESULTS= \
model/result_of_tf_estimator_cd_mos(58x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_128_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_1024_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512x512_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512_relu_Adam_0.001_dropout_0.1.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512_relu_Adam_0.001_dropout_0.3.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512_relu_Adam_0.001_dropout_0.5.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_cd_mos(58x2)_512x512x512x512_relu_Adam_0.001_dropout_0.9.csv \
\
model/result_of_tf_estimator_cd_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_cd_ld(1260x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
PREDICT_PPI_RESULTS= \
model/result_of_tf_estimator_c_elegan_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_c_elegan_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_c_elegan_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_drosophila_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_drosophila_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_drosophila_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_e_coli_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_e_coli_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_e_coli_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_human_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_human_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_human_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_yeast_ct(686x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_yeast_ac(420x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_yeast_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_rice_ct(686x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_rice_ct(686x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_rice_ct(686x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_rice_ct(686x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_rice_ac(420x2)_64_relu_Adam_0.01_dropout_0.csv \
model/result_of_tf_estimator_rice_ac(420x2)_64_relu_Adam_0.001_dropout_0.csv \
model/result_of_tf_estimator_rice_ac(420x2)_64_relu_Adam_0.0001_dropout_0.csv \
model/result_of_tf_estimator_rice_ac(420x2)_64_relu_Adam_1e-05_dropout_0.csv \
model/result_of_tf_estimator_rice2_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_c_elegan_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_drosophila_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_e_coli_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_human_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
model/result_of_tf_estimator_yeast_ct+ac(1106x2)_256x256x256_relu_Adam_0.001_dropout_0.7.csv \
MODEL_RESULTS=$(CT_MODEL_RESULTS) $(AC_MODEL_RESULTS) $(LD_MODEL_RESULTS) $(MOS_MODEL_RESULTS) $(CD_RESULTS) $(PREDICT_PPI_RESULTS)
FINAL_RESULTS=$(subst model/,results/, $(MODEL_RESULTS))
.PHONY: default
default: main
$(ORIGINAL_STATUS):$(ORIGINAL_ZIP)
mkdir -p $(ORIGINAL_DIR)
unzip -o $(ORIGINAL_ZIP) -d $(ORIGINAL_DIR)
@touch -m $(ORIGINAL_STATUS)
@echo "$(ORIGINAL_DIR) is ok"
$(FLAT_STATUS):$(FLAT_GENERATOR) $(ORIGINAL_STATUS)
python $(FLAT_GENERATOR)
@touch -m $(FLAT_STATUS)
@echo "$(FLAT_DIR) is ok"
.PHONY:statistics
statistics: statistics.py $(FLAT_STATUS)
python statistics.py --input $(FLAT_DATA_A) --output $(FLAT_DATA_A).csv
python statistics.py --input $(FLAT_DATA_B) --output $(FLAT_DATA_B).csv
python statistics.py --input $(FLAT_DATA_C) --output $(FLAT_DATA_C).csv
python statistics.py --input $(FLAT_DATA_D) --output $(FLAT_DATA_D).csv
python statistics.py --input $(FLAT_DATA_E) --output $(FLAT_DATA_E).csv
$(CT_STATUS):$(CT_GENERATOR) $(FLAT_STATUS)
python $(CT_GENERATOR)
@touch -m $(CT_STATUS)
@echo "$(CT_DIR) is ok"
$(CT_BIN_STATUS):$(CT_BIN_GENERATOR) $(CT_STATUS)
python $(CT_BIN_GENERATOR)
@touch -m $(CT_BIN_STATUS)
@echo "$(CT_BIN_DIR) is ok"
$(AC_STATUS):$(AC_GENERATOR) $(FLAT_STATUS)
python $(AC_GENERATOR)
@touch -m $(AC_STATUS)
@echo "$(AC_DIR) is ok"
$(AC_BIN_STATUS):$(AC_BIN_GENERATOR) $(AC_STATUS)
python $(AC_BIN_GENERATOR)
@touch -m $(AC_BIN_STATUS)
@echo "$(AC_BIN_DIR) is ok"
$(LD_STATUS):$(LD_GENERATOR) $(FLAT_STATUS)
python $(LD_GENERATOR)
@touch -m $(LD_STATUS)
@echo "$(LD_DIR) is ok"
$(LD_BIN_STATUS):$(LD_BIN_GENERATOR) $(LD_STATUS)
python $(LD_BIN_GENERATOR)
@touch -m $(LD_BIN_STATUS)
@echo "$(LD_BIN_DIR) is ok"
$(MOS_STATUS):$(MOS_GENERATOR) $(FLAT_STATUS)
python $(MOS_GENERATOR)
@touch -m $(MOS_STATUS)
@echo "$(MOS_DIR) is ok"
$(MOS_BIN_STATUS):$(MOS_BIN_GENERATOR) $(MOS_STATUS)
python $(MOS_BIN_GENERATOR)
@touch -m $(MOS_BIN_STATUS)
@echo "$(MOS_BIN_DIR) is ok"
$(MOS0_STATUS):$(MOS0_GENERATOR) $(FLAT_STATUS)
python $(MOS0_GENERATOR)
@touch -m $(MOS0_STATUS)
@echo "$(MOS0_DIR) is ok"
$(MOS0_BIN_STATUS):$(MOS0_BIN_GENERATOR) $(MOS0_STATUS)
python $(MOS0_BIN_GENERATOR)
@touch -m $(MOS0_BIN_STATUS)
@echo "$(MOS0_BIN_DIR) is ok"
$(CTAC_BIN_STATUS):$(CTAC_BIN_GENERATOR) $(CT_STATUS) $(AC_STATUS)
python $(CTAC_BIN_GENERATOR)
@touch -m $(CTAC_BIN_STATUS)
@echo "$(CTAC_BIN_DIR) is ok"
$(CD_CT_ZIP):$(FLAT_DATA_C) $(FLAT_DATA_D)
python util_create_ppi_dataset.py -p "$(FLAT_DATA_C)" -n "$(FLAT_DATA_D)" -o "$(patsubst %.zip,%, $(CD_CT_ZIP))" -m ct -s 0.6
$(CD_AC_ZIP):$(FLAT_DATA_C) $(FLAT_DATA_D)
python util_create_ppi_dataset.py -p "$(FLAT_DATA_C)" -n "$(FLAT_DATA_D)" -o "$(patsubst %.zip,%, $(CD_AC_ZIP))" -m ac -s 0.6
$(CD_LD_ZIP):$(FLAT_DATA_C) $(FLAT_DATA_D)
python util_create_ppi_dataset.py -p "$(FLAT_DATA_C)" -n "$(FLAT_DATA_D)" -o "$(patsubst %.zip,%, $(CD_LD_ZIP))" -m ld -s 0.6
$(CD_MOS_ZIP):$(FLAT_DATA_C) $(FLAT_DATA_D)
python util_create_ppi_dataset.py -p "$(FLAT_DATA_C)" -n "$(FLAT_DATA_D)" -o "$(patsubst %.zip,%, $(CD_MOS_ZIP))" -m mos -s 0.6
$(CD_DATAS_STATUS):$(CD_CT_ZIP) $(CD_AC_ZIP) $(CD_LD_ZIP) $(CD_MOS_ZIP)
unzip -o $(CD_CT_ZIP) -d $(patsubst %.zip,%, $(CD_CT_ZIP))
unzip -o $(CD_AC_ZIP) -d $(patsubst %.zip,%, $(CD_AC_ZIP))
unzip -o $(CD_LD_ZIP) -d $(patsubst %.zip,%, $(CD_LD_ZIP))
unzip -o $(CD_MOS_ZIP) -d $(patsubst %.zip,%, $(CD_MOS_ZIP))
@touch -m $(CD_DATAS_STATUS)
$(PREDICT_PPI_STATUS):$(PREDICT_PPI_GENERATOR) $(PREDICT_PPI_ZIP)
unzip -o $(PREDICT_PPI_ZIP) -d $(PREDICT_PPI_DIR)
mkdir -p $(PREDICT_PPI_DIR)/Rice
cp -up rppi/Rice/{Positive,Negative}_protein_{A,B}.txt $(PREDICT_PPI_DIR)/Rice
mkdir -p $(PREDICT_PPI_DIR)/Rice2
cp -up rppi/Rice2/{Positive,Negative}_protein_{A,B}.txt $(PREDICT_PPI_DIR)/Rice2
python $(PREDICT_PPI_GENERATOR)
@touch -m $(PREDICT_PPI_STATUS)
@echo "$(PREDICT_PPI_DIR) is ok"
.PHONY:data
data: $(CT_BIN_STATUS) $(AC_BIN_STATUS) $(LD_BIN_STATUS) $(MOS_BIN_STATUS) $(MOS0_BIN_STATUS) $(CTAC_BIN_STATUS) \
$(CD_DATAS_STATUS) \
$(PREDICT_PPI_STATUS)
model/%.txt:
python train_with_tf_estimator_hppi.py `echo "$(patsubst %.txt,%, $@)"|cut -c30-`
$(FINAL_RESULTS):results/%.csv:model/%.txt
mkdir -p results
python util_txt_2_csv.py "$<" "$@"
.PHONY:model
model: $(FINAL_RESULTS)
.PHONY:sklearn
sklearn:
python train_with_sklearn.py svm
python train_with_sklearn.py random_forest
python train_with_sklearn.py ada_boost
python train_with_sklearn.py decision_tree
python train_with_sklearn.py kneighbors
.PHONY:main
main: data model sklearn