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input_yeast_comb.yaml
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# ----------------Loading graph parameters-----------------------------
dir_nm: "yeast" # Options: toy_network, toy_network_old, humap, humap2
sep: " " # Options: " ", "\t"
netf_nm: "/CombinedYeast.txt"
comf_nm: "/res_train_complexes_wo2s.txt"
comf_test_nm: "/res_test_complexes_wo2s.txt" # Make sure no extra rows are present
comf_nm_all: "/all_complexes_yeast.txt"
out_comp_nm: "/results/res"
use_full: 1
classifier_file: "tpot_classifiers_comb_full.txt"
scale_factor: 1.1 # Number of times negatives should be higher than positives
split_flag: 0
mode: gen # gen means only feature extraction, non_gen is all
# -------------------Training parameters--------------------------------
feats: 6
model_type: "tpot" # Options: tpot, NN
train_feat_mat: "TPOT/res_train_dat_comb_full.csv"
test_feat_mat: "TPOT/res_test_dat_comb_full.csv"
model_name: "tpot_select" #Options: FF_1hidden, log_reg, SVM, rand_forest, extra_trees, estimator_SVM
# humap with separted train and test sets - tpot result - extra_trees
# best_classifier: "GradientBoostingClassifier" # Only for tpot_select - ExtraTreesClassifier
model_dir: ""
# --------------------Search parameters ------------------------------
seed_mode: "all_nodes_known_comp" # Options:all_nodes_known_comp, all_nodes, n_nodes
num_comp: 10 # Options: 10, 7778, 1500 - only for n_nodes mode
run_mode: "serial" # Options: serial, parallel
max_size_thres: 50
search_method: "search_max_neig" # isa, metropolis, search_top_neigs, search_max_neig
# All methods except max_neig
thres_neig: 30 # Maximum number of neighbors sampled for checking
min_thres_neig_sorted: 100 # Threshold above which only a percentage of neigs are considered as per sorted weights
perc: 0.9 # Percentage of neighbors to check for adding new node
explore_prob: 0.01 # use 0.1 for top_neigs
# Metropolis algorithm params
prob_metropolis: 0.01
# ISA params
T0: 0.88
alpha: 1.8
over_t: 0.99 # Overlap threshold = 0.7/0.9
# Evaluation parameters
eval_p: 0.5 # threshold in metric for evaluation of complexes