--- a +++ b/simdeep/simdeep_distributed.py @@ -0,0 +1,94 @@ +import ray +from simdeep.simdeep_analysis import SimDeep + +from simdeep.config import NB_CLUSTERS +from simdeep.config import CLUSTER_ARRAY +from simdeep.config import PVALUE_THRESHOLD +from simdeep.config import CINDEX_THRESHOLD +from simdeep.config import CLASSIFIER_TYPE + +from simdeep.config import MIXTURE_PARAMS +from simdeep.config import PATH_RESULTS +from simdeep.config import PROJECT_NAME +from simdeep.config import CLASSIFICATION_METHOD + +from simdeep.config import CLUSTER_EVAL_METHOD +from simdeep.config import CLUSTER_METHOD +from simdeep.config import NB_THREADS_COXPH +from simdeep.config import NB_SELECTED_FEATURES +from simdeep.config import LOAD_EXISTING_MODELS +from simdeep.config import NODES_SELECTION +from simdeep.config import PATH_TO_SAVE_MODEL + +from simdeep.config import USE_AUTOENCODERS +from simdeep.config import FEATURE_SURV_ANALYSIS +from simdeep.config import CLUSTERING_OMICS +from simdeep.config import USE_R_PACKAGES_FOR_SURVIVAL + + +@ray.remote +class SimDeepDistributed(SimDeep): + def __init__( + self, + nb_clusters=NB_CLUSTERS, + pvalue_thres=PVALUE_THRESHOLD, + cindex_thres=CINDEX_THRESHOLD, + use_autoencoders=USE_AUTOENCODERS, + feature_surv_analysis=FEATURE_SURV_ANALYSIS, + cluster_method=CLUSTER_METHOD, + cluster_eval_method=CLUSTER_EVAL_METHOD, + classifier_type=CLASSIFIER_TYPE, + project_name=PROJECT_NAME, + path_results=PATH_RESULTS, + cluster_array=CLUSTER_ARRAY, + nb_selected_features=NB_SELECTED_FEATURES, + mixture_params=MIXTURE_PARAMS, + node_selection=NODES_SELECTION, + nb_threads_coxph=NB_THREADS_COXPH, + classification_method=CLASSIFICATION_METHOD, + load_existing_models=LOAD_EXISTING_MODELS, + clustering_omics=CLUSTERING_OMICS, + path_to_save_model=PATH_TO_SAVE_MODEL, + metadata_usage=None, + feature_selection_usage='individual', + use_r_packages=USE_R_PACKAGES_FOR_SURVIVAL, + alternative_embedding=None, + kwargs_alternative_embedding={}, + do_KM_plot=True, + verbose=True, + _isboosting=False, + dataset=None, + deep_model_additional_args={}): + """ + """ + SimDeep.__init__( + self, + nb_clusters=nb_clusters, + pvalue_thres=pvalue_thres, + cindex_thres=cindex_thres, + cluster_method=cluster_method, + cluster_eval_method=cluster_eval_method, + classifier_type=classifier_type, + project_name=project_name, + clustering_omics=clustering_omics, + path_results=path_results, + use_autoencoders=use_autoencoders, + feature_surv_analysis=feature_surv_analysis, + cluster_array=cluster_array, + nb_selected_features=nb_selected_features, + mixture_params=mixture_params, + node_selection=node_selection, + nb_threads_coxph=nb_threads_coxph, + feature_selection_usage=feature_selection_usage, + metadata_usage=metadata_usage, + classification_method=classification_method, + load_existing_models=load_existing_models, + path_to_save_model=path_to_save_model, + do_KM_plot=do_KM_plot, + alternative_embedding=alternative_embedding, + kwargs_alternative_embedding=kwargs_alternative_embedding, + verbose=verbose, + use_r_packages=use_r_packages, + _isboosting=_isboosting, + dataset=dataset, + deep_model_additional_args=deep_model_additional_args)