BioAutoMATED
Automated machine learning for analyzing, interpreting, and designing biological sequences
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- 01_BioAutoMATED_Small_System_Test_START_HERE-checkpoint.ipynb
- Classification_Main_Figures_Final_Loop-checkpoint.ipynb
- Exemplars-Regression-checkpoint.ipynb
- Interpretation_Module_Example-checkpoint.ipynb
- ESM_test-checkpoint.ipynb
- large_synthetic_classification.csv
- medium_rbs_hollerer_classification.csv
- peptides_no_j_classification.csv
- small_synthetic_classification.csv
- toehold_classification.csv
- bioautoml_test.md
- bad_peptides_decision_tree_binary_automl.tsv
- bad_peptides_mlp_binary_automl.tsv
- bad_peptides_rf_binary_automl.tsv
- large_synthetic_decision_tree_binary_automl.tsv
- large_synthetic_mlp_binary_automl.tsv
- large_synthetic_rf_binary_automl.tsv
- large_synthetic_xgboost_binary_automl.tsv
- peptides_classification_decision_tree_binary_automl.tsv
- peptides_classification_mlp_binary_automl.tsv
- peptides_classification_rf_binary_automl.tsv
- peptides_classification_xgboost_binary_automl.tsv
- rbs_medium_train_decision_tree_binary_automl.tsv
- rbs_medium_train_mlp_binary_automl.tsv
- rbs_medium_train_rf_binary_automl.tsv
- rbs_medium_train_xgboost_binary_automl.tsv
- small_synthetic_decision_tree_binary_automl.tsv
- small_synthetic_mlp_binary_automl.tsv
- small_synthetic_rf_binary_automl.tsv
- small_synthetic_xgboost_binary_automl.tsv
- toeholds_decision_tree_binary_automl.tsv
- toeholds_mlp_binary_automl.tsv
- toeholds_rf_binary_automl.tsv
- toeholds_xgboost_binary_automl.tsv
- ilearnplus_test.md
- DNABERT_test.ipynb
- ESM_test.ipynb
- 01_clean_datasets-checkpoint.ipynb
- 02_generate_synthetic_dataset-checkpoint.ipynb
- 03_multiclass_classification-checkpoint.ipynb
- 04_test_longer_range_proteins-checkpoint.ipynb
- 05A_prep_data_for_automl_benchmarks_ilearnplus-checkpoint.ipynb
- 05B_prep_data_for_automl_benchmarks_bioautoml-checkpoint.ipynb
- 2021_03_18_generate_scrambled_versions-checkpoint.ipynb
- 2021_07_20_new_rbs_dataset-checkpoint.ipynb
- classification_hollerer_rbs_mediumtrain.csv
- classification_hollerer_rbs_mediumtrain.fasta
- classification_hollerer_rbs_mediumtrain_negseqs.fasta
- classification_hollerer_rbs_mediumtrain_posseqs.fasta
- classification_hollerer_rbs_train.csv
- classification_hollerer_rbs_train.fasta
- classification_hollerer_rbs_train_negseqs.fasta
- classification_hollerer_rbs_train_posseqs.fasta
- classification_large_synthetic.csv
- classification_large_synthetic.fasta
- classification_large_synthetic_negseqs.fasta
- classification_large_synthetic_posseqs.fasta
- classification_small_synthetic.csv
- classification_small_synthetic.fasta
- classification_small_synthetic_negseqs.fasta
- classification_small_synthetic_posseqs.fasta
- classification_small_toeholds.csv
- classification_small_toeholds.fasta
- classification_small_toeholds_negseqs.fasta
- classification_small_toeholds_posseqs.fasta
- classification_toeholds.csv
- classification_toeholds.fasta
- classification_toeholds_negseqs.fasta
- classification_toeholds_posseqs.fasta
- classification_train_NO_J_peptides.csv
- classification_train_NO_J_peptides.fasta
- classification_train_NO_J_peptides_negseqs.fasta
- classification_train_NO_J_peptides_posseqs.fasta
- classification_train_peptides.csv
- classification_train_peptides.fasta
- classification_train_peptides_negseqs.fasta
- classification_train_peptides_posseqs.fasta
- classification_train_smallpeptides_negseqs.fasta
- classification_train_smallpeptides_posseqs.fasta
- classification_hollerer_rbs_mediumtrain_fasta.txt
- classification_hollerer_rbs_test_fasta.txt
- classification_hollerer_rbs_train_fasta.txt
- classification_large_synthetic_fasta.txt
- classification_peptides_fasta.txt
- classification_small_synthetic_fasta.txt
- classification_test_peptides_fasta.txt
- classification_toeholds_fasta.txt
- hollerer_rbs_mediumtrain_fasta.txt
- hollerer_rbs_test_fasta.txt
- hollerer_rbs_train_fasta.txt
- large_synthetic_fasta.txt
- regression_peptides_fasta.txt
- small_synthetic_fasta.txt
- toeholds_fasta.txt
- .DS_Store
- avgfp.csv
- classification_test_peptides.csv
- classification_train_peptides.csv
- clean_pardee_sequences_toehold_test_set.csv
- flip_protein_test.csv
- flip_protein_train.csv
- green_sequences_toehold_test_set.csv
- hollerer_rbs_mediumtrain.csv
- hollerer_rbs_smalltrain.csv
- hollerer_rbs_test.csv
- hollerer_rbs_train.csv
- immunogenic_glycans.csv
- large_synthetic.csv
- large_synthetic_10perc_dataset.csv
- large_synthetic_90perc_dataset.csv
- medium_synthetic.csv
- pardee_sequences_toehold_test_set.csv
- peptides.csv
- regression_all_peptides.csv
- small_synthetic.csv
- toehold_10perc_dataset.csv
- toehold_90perc_dataset.csv
- toeholds.csv
- toeholds_small.csv
- .DS_Store
- domain_glycans.csv
- large_synthetic_multiclass.csv
- peptides_multiclass.csv
- rbs_full_multiclass.csv
- rbs_medium_multiclass.csv
- small_synthetic_multiclass.csv
- toeholds_multiclass.csv
- amino_acid_genotypes_to_brightness.tsv
- avGFP_reference_sequence.fa
- barcodes_to_brightness.tsv
- Data_flow.png
- genotypes.tsv
- nucleotide_genotypes_to_brightness.tsv
- avgfp.tsv
- .DS_Store
- classification_test_x.tsv
- classification_test_y.txt
- classification_train_x.tsv
- classification_train_y.txt
- regression_all_data_x.tsv
- regression_all_data_y.txt
- 4g_nuspeak_experimental_data.xlsx
- 4h_storm_experimental_data.xlsx
- Green2014_clean.csv
- Pardee2016_clean.xlsx
- .DS_Store
- combined_database_long.csv
- mmc2.xlsx
- mmc3.xlsx
- rbs_sequences_test.npy
- rbs_sequences_train_validation.npy
- rbs_targets_test.npy
- rbs_targets_train_validation.npy
- .DS_Store
- 01_clean_datasets.ipynb
- 02_generate_synthetic_dataset.ipynb
- 03_multiclass_classification.ipynb
- 04_test_longer_range_proteins.ipynb
- 05A_prep_data_for_automl_benchmarks_ilearnplus.ipynb
- 05B_prep_data_for_automl_benchmarks_bioautoml.ipynb
- toehold_constraints.xlsx
- comprbs_MCC.svg
- comptoeholds_MCC.svg
- glycans_immunogenic_auROC.svg
- glycans_immunogenic_breakdown_time.svg
- glycans_immunogenic_MCC.svg
- glycans_immunogenic_time.svg
- large_synthetic_nucleic_acids_auROC.svg
- large_synthetic_nucleic_acids_breakdown_time.svg
- large_synthetic_nucleic_acids_MCC.svg
- large_synthetic_nucleic_acids_robustness_MCC.svg
- large_synthetic_nucleic_acids_time.svg
- lengthglycans_domain_MCC.svg
- lengthglycans_immunogenic_MCC.svg
- multiclass_glycan_domain_average_MCC.svg
- multiclass_large_synthetic_nucleic_acids_MCC.svg
- multiclass_peptides_MCC.svg
- multiclass_rbs_MCC.svg
- multiclass_toeholds_MCC.svg
- peptides_auROC.svg
- peptides_breakdown_time.svg
- peptides_MCC.svg
- peptides_robustness_MCC.svg
- peptides_time.svg
- rbs_auROC.svg
- rbs_breakdown_time.svg
- rbs_MCC.svg
- rbs_robustness_MCC.svg
- rbs_time.svg
- regression_large_synthetic_nucleic_acids.svg
- regression_peptides.svg
- regression_rbs.svg
- regression_toeholds.svg
- small_synthetic_nucleic_acids_auROC.svg
- small_synthetic_nucleic_acids_MCC.svg
- toeholds_auROC.svg
- toeholds_breakdown_time.svg
- toeholds_mcc.svg
- toeholds_robustness_auROC.svg
- toeholds_robustness_MCC.svg
- toeholds_time.svg
- 0.graph
- best_model.txt
- classifier
- module
- optimized_autokeras_pipeline_classification.h5
- run_29_01_2023_14_04.log
- temp_model
- deepswarm_base_model.h5
- deepswarm_topology.h5
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- autokeras_classification_ROC_1.png
- autokeras_classification_ROC_2.png
- autokeras_classification_ROC_3.png
- autokeras_classification_ROC_compiled.png
- autokeras_classification_zoomedROC_1.png
- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
- compiled_results_autokeras_classification.csv
- final_autokeras_classification_graph
- final_autokeras_classification_graph.pdf
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
- deepswarm_classification_ROC_1.png
- deepswarm_classification_ROC_2.png
- deepswarm_classification_ROC_3.png
- deepswarm_classification_ROC_compiled.png
- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- compiled_results_tpot_classification.csv
- final_model_tpot_classification.pkl
- runtime_statistics.txt
- tpot_classification_ROC_1.png
- tpot_classification_ROC_2.png
- tpot_classification_ROC_3.png
- tpot_classification_ROC_compiled.png
- tpot_classification_zoomedROC_1.png
- tpot_classification_zoomedROC_2.png
- tpot_classification_zoomedROC_3.png
- tpot_classification_zoomedROC_compiled.png
- 0.graph
- 1.graph
- best_model.txt
- classifier
- module
- optimized_autokeras_pipeline_classification.h5
- run_29_01_2023_23_06.log
- temp_model
- deepswarm_base_model.h5
- deepswarm_topology.h5
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- autokeras_classification_ROC_1.png
- autokeras_classification_ROC_2.png
- autokeras_classification_ROC_3.png
- autokeras_classification_ROC_compiled.png
- autokeras_classification_zoomedROC_1.png
- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
- compiled_results_autokeras_classification.csv
- final_autokeras_classification_graph
- final_autokeras_classification_graph.pdf
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
- deepswarm_classification_ROC_1.png
- deepswarm_classification_ROC_2.png
- deepswarm_classification_ROC_3.png
- deepswarm_classification_ROC_compiled.png
- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- compiled_results_tpot_classification.csv
- final_model_tpot_classification.pkl
- runtime_statistics.txt
- tpot_classification_ROC_1.png
- tpot_classification_ROC_2.png
- tpot_classification_ROC_3.png
- tpot_classification_ROC_compiled.png
- tpot_classification_zoomedROC_1.png
- tpot_classification_zoomedROC_2.png
- tpot_classification_zoomedROC_3.png
- tpot_classification_zoomedROC_compiled.png
- 0.graph
- 1.graph
- 2.graph
- best_model.txt
- classifier
- module
- optimized_autokeras_pipeline_classification.h5
- run_23_01_2023_21_49.log
- temp_model
- deepswarm_base_model.h5
- deepswarm_topology.h5
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- pipeline_gen_10_idx_1_2023.01.24_04-27-12.py
- pipeline_gen_10_idx_2_2023.01.24_04-27-12.py
- pipeline_gen_1_idx_0_2023.01.24_03-16-38.py
- pipeline_gen_3_idx_1_2023.01.24_03-21-40.py
- pipeline_gen_4_idx_1_2023.01.24_03-23-21.py
- pipeline_gen_5_idx_1_2023.01.24_03-24-35.py
- pipeline_gen_6_idx_0_2023.01.24_03-26-26.py
- pipeline_gen_6_idx_1_2023.01.24_03-26-26.py
- pipeline_gen_7_idx_0_2023.01.24_03-28-12.py
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- autokeras_classification_ROC_1.png
- autokeras_classification_ROC_2.png
- autokeras_classification_ROC_3.png
- autokeras_classification_ROC_compiled.png
- autokeras_classification_zoomedROC_1.png
- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
- compiled_results_autokeras_classification.csv
- final_autokeras_classification_graph
- final_autokeras_classification_graph.pdf
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
- deepswarm_classification_ROC_1.png
- deepswarm_classification_ROC_2.png
- deepswarm_classification_ROC_3.png
- deepswarm_classification_ROC_compiled.png
- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- compiled_results_tpot_classification.csv
- final_model_tpot_classification.pkl
- runtime_statistics.txt
- tpot_classification_ROC_1.png
- tpot_classification_ROC_2.png
- tpot_classification_ROC_3.png
- tpot_classification_ROC_compiled.png
- tpot_classification_zoomedROC_1.png
- tpot_classification_zoomedROC_2.png
- tpot_classification_zoomedROC_3.png
- tpot_classification_zoomedROC_compiled.png
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- best_model.txt
- classifier
- module
- optimized_autokeras_pipeline_classification.h5
- run_23_01_2023_13_08.log
- temp_model
- deepswarm_base_model.h5
- deepswarm_topology.h5
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- pipeline_gen_10_idx_0_2023.01.23_14-32-02.py
- pipeline_gen_12_idx_1_2023.01.23_14-34-29.py
- pipeline_gen_14_idx_2_2023.01.23_14-42-06.py
- pipeline_gen_16_idx_0_2023.01.23_14-53-00.py
- pipeline_gen_16_idx_2_2023.01.23_14-53-00.py
- pipeline_gen_17_idx_1_2023.01.23_14-53-52.py
- pipeline_gen_1_idx_0_2023.01.23_14-23-51.py
- pipeline_gen_20_idx_0_2023.01.23_15-05-18.py
- pipeline_gen_22_idx_1_2023.01.23_15-16-52.py
- pipeline_gen_2_idx_0_2023.01.23_14-24-54.py
- pipeline_gen_7_idx_1_2023.01.23_14-29-26.py
- pipeline_gen_9_idx_1_2023.01.23_14-31-07.py
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
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- all_results.txt
- autokeras_classification_ROC_1.png
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- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
- compiled_results_autokeras_classification.csv
- final_autokeras_classification_graph
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- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
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- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
- deepswarm_classification_ROC_1.png
- deepswarm_classification_ROC_2.png
- deepswarm_classification_ROC_3.png
- deepswarm_classification_ROC_compiled.png
- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- compiled_results_tpot_classification.csv
- final_model_tpot_classification.pkl
- runtime_statistics.txt
- tpot_classification_ROC_1.png
- tpot_classification_ROC_2.png
- tpot_classification_ROC_3.png
- tpot_classification_ROC_compiled.png
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- pipeline_gen_12_idx_0_2023.01.23_08-30-04.py
- pipeline_gen_12_idx_1_2023.01.23_08-30-04.py
- pipeline_gen_12_idx_2_2023.01.23_08-30-04.py
- pipeline_gen_13_idx_2_2023.01.23_08-30-41.py
- pipeline_gen_15_idx_1_2023.01.23_08-32-07.py
- pipeline_gen_18_idx_0_2023.01.23_08-35-34.py
- pipeline_gen_1_idx_0_2023.01.23_08-23-51.py
- pipeline_gen_1_idx_1_2023.01.23_08-23-51.py
- pipeline_gen_3_idx_0_2023.01.23_08-24-49.py
- pipeline_gen_3_idx_2_2023.01.23_08-24-49.py
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- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- autokeras_classification_ROC_1.png
- autokeras_classification_ROC_2.png
- autokeras_classification_ROC_3.png
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- autokeras_classification_zoomedROC_3.png
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- compiled_results_autokeras_classification.csv
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- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
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- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
- deepswarm_classification_ROC_1.png
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- deepswarm_deploy_model.h5
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- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- compiled_results_tpot_classification.csv
- final_model_tpot_classification.pkl
- runtime_statistics.txt
- tpot_classification_ROC_1.png
- tpot_classification_ROC_2.png
- tpot_classification_ROC_3.png
- tpot_classification_ROC_compiled.png
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- run_26_01_2022_20_57.log
- temp_model
- deepswarm_base_model.h5
- deepswarm_topology.h5
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- pipeline_gen_10_idx_0_2022.01.27_02-15-20.py
- pipeline_gen_16_idx_0_2022.01.27_02-18-15.py
- pipeline_gen_18_idx_0_2022.01.27_02-18-54.py
- pipeline_gen_2_idx_0_2022.01.27_02-12-46.py
- pipeline_gen_4_idx_0_2022.01.27_02-13-27.py
- pipeline_gen_6_idx_0_2022.01.27_02-14-08.py
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
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- autokeras_classification_ROC_2.png
- autokeras_classification_ROC_3.png
- autokeras_classification_ROC_compiled.png
- autokeras_classification_zoomedROC_1.png
- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
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- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
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- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
- deepswarm_classification_ROC_1.png
- deepswarm_classification_ROC_2.png
- deepswarm_classification_ROC_3.png
- deepswarm_classification_ROC_compiled.png
- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
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- classification_zoomedROC_compiled.png
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- pipeline_gen_10_idx_2_2022.01.25_20-05-14.py
- pipeline_gen_12_idx_1_2022.01.25_20-05-57.py
- pipeline_gen_12_idx_2_2022.01.25_20-05-57.py
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- pipeline_gen_30_idx_0_2022.01.25_20-13-02.py
- pipeline_gen_30_idx_1_2022.01.25_20-13-02.py
- pipeline_gen_35_idx_0_2022.01.25_20-14-15.py
- pipeline_gen_41_idx_2_2022.01.25_20-15-28.py
- pipeline_gen_6_idx_1_2022.01.25_20-02-29.py
- pipeline_gen_8_idx_0_2022.01.25_20-03-20.py
- pipeline_gen_8_idx_1_2022.01.25_20-03-20.py
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- all_results.txt
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- autokeras_classification_ROC_3.png
- autokeras_classification_ROC_compiled.png
- autokeras_classification_zoomedROC_1.png
- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
- compiled_results_autokeras_classification.csv
- final_autokeras_classification_graph
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- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- best_classification_topology.txt
- compiled_results_deepswarm_classification.csv
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- deepswarm_classification_ROC_2.png
- deepswarm_classification_ROC_3.png
- deepswarm_classification_ROC_compiled.png
- deepswarm_classification_zoomedROC_1.png
- deepswarm_classification_zoomedROC_2.png
- deepswarm_classification_zoomedROC_3.png
- deepswarm_classification_zoomedROC_compiled.png
- deepswarm_deploy_model.h5
- runtime_statistics.txt
- all_scrambled_control_results.txt
- classification_ROC_compiled.png
- classification_zoomedROC_compiled.png
- all_results.txt
- compiled_results_tpot_classification.csv
- final_model_tpot_classification.pkl
- runtime_statistics.txt
- tpot_classification_ROC_1.png
- tpot_classification_ROC_2.png
- tpot_classification_ROC_3.png
- tpot_classification_ROC_compiled.png
- tpot_classification_zoomedROC_1.png
- tpot_classification_zoomedROC_2.png
- tpot_classification_zoomedROC_3.png
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- classifier
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- run_22_01_2023_01_50.log
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- deepswarm_base_model.h5
- deepswarm_topology.h5
- deepswarm_base_model.h5
- deepswarm_topology.h5
- deepswarm_base_model.h5
- deepswarm_topology.h5
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- pipeline_gen_1_idx_0_2022.12.17_18-31-14.py
- optimized_tpot_pipeline_classification.py
- optimized_tpot_pipeline_classification_updated.py
- pipeline_gen_1_idx_0_2022.12.21_00-41-52.py
- pipeline_gen_1_idx_1_2022.12.21_00-41-52.py
- optimized_tpot_pipeline_regression.py
- optimized_tpot_pipeline_regression_updated.py
- pipeline_gen_1_idx_0_2023.01.22_05-03-20.py
- Class0.0_violinplot_design.png
- Class0.0_violinplot_design.png.svg
- Class1.0_violinplot_design.png
- Class1.0_violinplot_design.png.svg
- plot_denovo_cosine_dist.png
- plot_denovo_cosine_dist.png.svg
- plot_original_seqs_control_cosine_dist.png
- plot_original_seqs_control_cosine_dist.png.svg
- seq_logo_class_0.0_original.png
- seq_logo_class_0.0_original.svg
- seq_logo_class_1.0_original.png
- seq_logo_Mutated-Class0.0.png
- seq_logo_Mutated-Class0.0.svg
- seq_logo_Mutated-Class1.0.png
- seq_logo_Mutated-Class1.0.svg
- all_results.txt
- autokeras_classification_ROC_1.png
- autokeras_classification_ROC_2.png
- autokeras_classification_ROC_3.png
- autokeras_classification_ROC_compiled.png
- autokeras_classification_zoomedROC_1.png
- autokeras_classification_zoomedROC_2.png
- autokeras_classification_zoomedROC_3.png
- autokeras_classification_zoomedROC_compiled.png
- compiled_results_autokeras_classification.csv
- .DS_Store
- .gitignore
- 01_BioAutoMATED_Small_System_Test_START_HERE.ipynb
- 02_External_Validation_Tests.ipynb
- 03_Interpretation_Module_Example.ipynb
- 04_Design_Module_Example.ipynb
- 05_Fine_Tuning_Model_Examples.ipynb
- BioAutoMATED_Installation_Guide.md
- Dockerfile
- environment.yml
- LICENSE.md
- README.md
// repository documentation
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