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Hoper_representation_generetor.yaml
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Hoper_representation_generetor.yaml
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parameters:
choice_of_module: [PPI] # Module selection PPI,Preprocessing,case_study
#*************************************MODULES********************************************************************
#********************PPI Module********************************
module_name: PPI
choice_of_representation_name: [HOPE]#,HOPE,Node2vec
interaction_data_path: [./data/hoper_PPI/PPI_example_data/example.edgelist]
protein_id_list: [./data/hoper_PPI/PPI_example_data/proteins_id.csv]
node2vec_module:
parameter_selection:
d: [10]
p: [0.25]
q: [0.25]
HOPE_module:
parameter_selection:
d: [5]
beta: [0.00390625]
#********************Text Representation Module********************************
module_name: text
choice_of_process: [generate,visualize]#,visualize,generate
generate_module:
choice_of_representation_type: [biosentvec]
uniprot_files_path: [./text_representations/representation_generation/data/uniprot/]
pubmed_files_path: [./text_representations/representation_generation/data/pubmed/]
model_download: y
visualize_module:
choice_of_visualization_type: [a]
result_files_path: [./text_representations/result_visualization/result_files/results/]
#********************Preprocessing Module********************************
module_name: Preprocessing
uniprot_dir: ./uniprot_sprot.xml.gz
#********************Fuse Representation*********************************
module_name: fuse_representations
representation_files: [./data/hoper_case_study_example_data/representation_files/node2vec_d_50_p_0.5_q_0.25_multi_col.csv,./data/hoper_case_study_example_data/representation_files/multi_modal_rep_ae_multi_col_256.csv]
min_fold_number: 2
representation_names: [modal_rep_ae,node2vec]
#*******************SimpleAe*********************************************
module_name: SimpleAe
representation_path: ./data/hoper_sequence_representations/modal_rep_ae_node2vec_binary_fused_representations_dataframe_multi_col.csv