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Makefile_FINAL_TESTS
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Makefile_FINAL_TESTS
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# ---------------------------------------- #
# Arch 1 NN Model - Holdout & Test Targets #
# ---------------------------------------- #
arch_1_holdout:
python3 main.py \
--validation \
--sequence_type dna \
--path_source_data ./data/bins_translated \
--load_network ModelUnidirect \
--network_parameters models/ModelUnidirect.json \
--num_epochs 2 \
--batch_size 16 \
--lr 1e-4 \
--onehot_flag \
arch_1_test:
python3 main.py \
--test \
--load_network ModelUnidirect \
--sequence_type dna \
--onehot_flag \
--network_parameters models/ModelUnidirect.json \
--early_stopping_on_loss \
--pretrained_model pretrained_models/ModelUnidirect/my_model_weights.h5 \
# --pretrained_model pretrained_models/ModelUnidirect/model_checkpoint_weights.h5 \
# ---------------------------------------- #
# Arch 2 NN Model - Holdout & Test Targets #
# ---------------------------------------- #
arch_2_holdout:
python3 main.py \
--validation \
--path_source_data ./data/bins_translated \
--load_network ModelBidirectDNA \
--sequence_type dna \
--onehot_flag \
--num_epochs 2 \
--batch_size 20 \
--lr 5e-4 \
--network_parameters models/ModelBidirectDNA.json \
arch_2_test:
python3 main.py \
--test \
--load_network ModelBidirectDNA \
--sequence_type dna \
--onehot_flag \
--network_parameters models/ModelBidirectDNA.json \
--early_stopping_on_loss \
--pretrained_model pretrained_models/ModelBidirectDNA/my_model_weights.h5 \
# --pretrained_model pretrained_models/ModelBidirectDNA/model_checkpoint_weights.h5 \
# ---------------------------------------- #
# Arch 3 NN Model - Holdout & Test Targets #
# ---------------------------------------- #
arch_3_holdout:
python3 main.py \
--validation \
--path_source_data ./data/bins_translated \
--network_parameters models/ModelOneHotProtein.json \
--batch_size 32 \
--num_epochs 2 \
--lr 5e-4 \
--load_network ModelOneHotProtein \
--sequence_type protein \
--onehot_flag \
arch_3_test:
python3 main.py \
--test \
--load_network ModelOneHotProtein \
--network_parameters models/ModelOneHotProtein.json \
--sequence_type protein \
--onehot_flag \
--pretrained_model pretrained_models/ModelOneHotProtein/my_model_weights.h5 \
# --pretrained_model pretrained_models/ModelOneHotProtein/model_checkpoint_weights.h5 \
# --------------------------------- #
# Arch 4 (A & B) NN Model - Holdout #
# --------------------------------- #
arch_4_A_holdout:
python3 main.py \
--validation \
--path_source_data ./data/bins_translated \
--sequence_type protein \
--batch_size 32 \
--num_epochs 2 \
--lr 5e-4 \
--network_parameters models/ModelEmbeddingBidirect.json \
--load_network ModelEmbeddingBidirect
arch_4_B_holdout:
python3 main.py \
--validation \
--sequence_type protein \
--batch_size 20 \
--num_epochs 2 \
--lr 5e-4 \
--onehot_flag \
--network_parameters models/ModelConvBidirect.json \
--load_network ModelConvBidirect \
# ------------------------------- #
# Arch 4 (A & B) NN Model - Tests #
# ------------------------------- #
arch_4_A_test:
python3 main.py \
--test \
--path_source_data ./data/bins_translated \
--load_network ModelEmbeddingBidirect \
--network_parameters models/ModelEmbeddingBidirect.json \
--sequence_type protein \
--pretrained_model pretrained_models/ModelEmbeddingBidirect/my_model_weights.h5
# --pretrained_model pretrained_models/ModelEmbeddingBidirect/model_checkpoint_weights.h5
arch_4_B_test:
python3 main.py \
--test \
--path_source_data ./data/bins_translated \
--load_network ModelConvBidirect \
--network_parameters models/ModelConvBidirect.json \
--sequence_type protein \
--onehot_flag \
--pretrained_model pretrained_models/ModelConvBidirect/my_model_weights.h5 \
# --pretrained_model pretrained_models/ModelConvBidirect/model_checkpoint_weights.h5 \
# -------------------------------------------- #
# K-Mers based NN Model holdout & Test Targets #
# -------------------------------------------- #
arch_k_mers_holdout:
python3 main.py \
--validation \
--sequence_type kmers \
--batch_size 16 \
--num_epochs 2 \
--lr 1e-3 \
--network_parameters models/ModelKMers.json \
--load_network ModelKMers \
arch_k_mers_test:
python3 main.py \
--test \
--path_source_data ./data/bins_translated \
--load_network ModelKMers \
--network_parameters models/ModelKMers.json \
--sequence_type kmers \
--pretrained_model pretrained_models/ModelKMers/my_model_weights.h5 \