def get_model_spec_time_varying_with_covariates(covariate_delay): """Return model specification with hyperparameters and covariates.""" result = model_spec_lib.ModelSpec( hparams={ "initial_learning_rate": 0.003061242915556316, "momentum": 0.2, "decay_steps": 1000, "fine_tuning_steps": 100, "fine_tuning_decay": 1.0, "decay_rate": 1.0, "location_dependent_init": False, "infected_threshold": 3, "restart_threshold": 1000, "time_scale_weight": 0.00006243159539906051, "train_loss_coefs": [0, 0.001, 0.2, 0.1, 0.01, 0.01, 0.2, 0.1, 0.01], "valid_loss_coefs": [0, 0.001, 0.2, 0.1, 0.01, 0.01, 0.2, 0.1, 0.01], "sync_coef": 1.0, "reduced_sync_undoc": 1.0, "smooth_coef": 0.5, "first_dose_vaccine_ratio_per_day_init": 0.0, "second_dose_vaccine_ratio_per_day_init": 0.0, "average_contact_id_rate_init": -1.9131825459930378, "average_contact_iud_rate_init": -1.071866945725303, "reinfectable_rate_init": -5.548940468292865, "alpha_rate_init": -2.272765554778715, "diagnosis_rate_init": -2.095597433974376, "recovery_id_rate_init": -1.495660223962899, "recovery_iud_rate_init": -1.475605314236803, "recovery_h_rate_init": -1.9032896753850963, "hospitalization_rate_init": -1.4331763640928012, "death_id_rate_init": -1.8060447968974489, "death_h_rate_init": -1.4886876719378206, "bias_penalty_coef": 0.2835406167308398, "r_eff_penalty_coef": 2.0, "acceleration_death_coef": 0.1, "acceleration_confirm_coef": 0.1, "acceleration_hospital_coef": 0.1, "quantile_encoding_window": 7, "quantile_smooth_coef": 0.9, "quantile_training_iteration_ratio": 0.5, "width_coef_train": 10.0, "width_coef_valid": 5.0, "quantile_cum_viol_coef": 500.0, "increment_loss_weight": 0.0, "lasso_penalty_coef": 1.0, "covariate_training_mixing_coef": 1.0, "train_window_range": 2.0, "partial_mean_interval": 4, "direction_loss_coef": 2000.0, "train_crps_weight": 0.25, "valid_crps_weight": 0.25 }, encoder_specs=[ model_spec_lib.EncoderSpec( encoder_name="first_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="first_dose", covariate_feature_specs=[ first_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="second_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="second_dose", covariate_feature_specs=[ second_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="average_contact_id_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, income_per_capita, aqi_mean_2018, household, ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, mobility_index, mobility_samples, confirmed_per_csrp_tests ] + extra_covariates + npi_features, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="average_contact_iud_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, income_per_capita, aqi_mean_2018, household, ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, mobility_index, mobility_samples, confirmed_per_csrp_tests ] + extra_covariates + npi_features, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="reinfectable_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population ] + extra_static_features, covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec(encoder_name="alpha_rate", encoder_type="gam", static_feature_specs=[], covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec( encoder_name="diagnosis_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, confirmed_per_csrp_tests, total_tests_per_capita, dow_feature, ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_id_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_iud_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_h_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population, icu_beds ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="hospitalization_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, confirmed_per_csrp_tests, total_tests_per_capita, ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_id_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population, icu_beds ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_h_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, rating_average, aqi_mean_2018, kaiser_60plus_population, icu_beds ] + extra_static_features, covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ] + extra_covariates, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), ]) return result
"bias_penalty_coef": 0.27315803186400106, "boundary_penalty_coef": 2.600265396382176, "lasso_penalty_coef": 1.0, "r_eff_penalty_coef": 1.0, "quantile_encoding_window": 7, "quantile_smooth_coef": 0.8, "increment_loss_weight": 0.0, "covariate_training_mixing_coef": 1.0, "direction_loss_coef": 2000.0 }, encoder_specs=[ model_spec_lib.EncoderSpec( encoder_name="first_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="first_dose", covariate_feature_specs=[ first_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="second_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="second_dose", covariate_feature_specs=[ second_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec(
def get_model_spec_time_varying_with_covariates(covariate_delay): """Return model specification with hyperparameters and covariates.""" result = model_spec_lib.ModelSpec( hparams={ "initial_learning_rate": 0.003778327764151733, "momentum": 0.1, "decay_steps": 1000, "fine_tuning_steps": 100, "fine_tuning_decay": 1.0, "decay_rate": 1.0, "location_dependent_init": False, "infected_threshold": 10, "restart_threshold": 1000, "time_scale_weight": 0.00006243159539906051, "train_loss_coefs": [0, 0.001, 1.0, 0.1, 0.05, 0.05, 0.01, 0.001], "valid_loss_coefs": [0, 0.001, 1.0, 0.1, 0.05, 0.05, 0.01, 0.001], "sync_coef": 1.0, "reduced_sync_undoc": 1.0, "smooth_coef": 0.5, "first_dose_vaccine_ratio_per_day_init": 0.0, "second_dose_vaccine_ratio_per_day_init": 0.0, "average_contact_id_rate_init": -1.9131825459930378, "average_contact_iud_rate_init": -1.071866945725303, "reinfectable_rate_init": -5.548940468292865, "alpha_rate_init": -2.272765554778715, "diagnosis_rate_init": -2.095597433974376, "recovery_id_rate_init": -1.495660223962899, "recovery_iud_rate_init": -1.475605314236803, "recovery_h_rate_init": -1.9032896753850963, "recovery_i_rate_init": -1.354652366086861, "recovery_v_rate_init": -1.2872596880548643, "hospitalization_rate_init": -1.4331763640928012, "icu_rate_init": -1.7697853537123167, "ventilator_rate_init": -1.747746088542831, "death_id_rate_init": -1.8060447968974489, "death_h_rate_init": -1.4886876719378206, "death_i_rate_init": -1.525990911868795, "death_v_rate_init": -1.0072190496934017, "bias_penalty_coef": 0.2835406167308398, "r_eff_penalty_coef": 2.0, "r_eff_penalty_cutoff": 5.5, "acceleration_death_coef": 0.1, "acceleration_confirm_coef": 0.1, "acceleration_hospital_coef": 0.1, "quantile_encoding_window": 7, "quantile_smooth_coef": 0.9, "quantile_training_iteration_ratio": 1.0, "width_coef_train": 1.0, "width_coef_valid": 1.0, "quantile_cum_viol_coef": 1000.0, "increment_loss_weight": 0.0, "lasso_penalty_coef": 1.0, "covariate_training_mixing_coef": 1.0, "direction_loss_coef": 15000.0, "train_window_range": 2.0, "partial_mean_interval": 4, "train_crps_weight": 0.5, "valid_crps_weight": 0.5 }, encoder_specs=[ model_spec_lib.EncoderSpec( encoder_name="first_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="first_dose", covariate_feature_specs=[ first_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="second_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="second_dose", covariate_feature_specs=[ second_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="average_contact_id_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, income_per_capita, aqi_mean_2018, household, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, mobility_index, mobility_samples, average_temperature, rainfall, snowfall, antigen_positive_ratio, antibody_negative_ratio, confirmed_per_total_tests ] + npi_features, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="average_contact_iud_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, income_per_capita, aqi_mean_2018, household, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, mobility_index, mobility_samples, average_temperature, rainfall, snowfall, antigen_positive_ratio, antibody_negative_ratio, confirmed_per_total_tests ] + npi_features, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="reinfectable_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, income_per_capita, household_food_stamp, household, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, population_60plus_ratio ], covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec( encoder_name="alpha_rate", encoder_type="gam", static_feature_specs=[], covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec( encoder_name="diagnosis_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, income_per_capita, household, rating_average, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, total_tests_per_capita, confirmed_per_total_tests, dow_feature, antigen_positive_ratio, antibody_negative_ratio, average_temperature, rainfall, snowfall, ] + symptoms_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_id_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, income_per_capita, household_food_stamp, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, antigen_positive_ratio, antibody_negative_ratio, average_temperature, rainfall, snowfall, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_iud_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, income_per_capita, household_food_stamp, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, antigen_positive_ratio, antibody_negative_ratio, average_temperature, rainfall, snowfall, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_h_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, income_per_capita, household_food_stamp, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_i_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, income_per_capita, household_food_stamp, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_v_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, income_per_capita, household_food_stamp, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="hospitalization_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, household, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio, ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, total_tests_per_capita, confirmed_per_total_tests, antigen_positive_ratio, antibody_negative_ratio, average_temperature, rainfall, snowfall ] + symptoms_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="icu_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, household, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="ventilator_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, household, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_id_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_h_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_i_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_v_rate", encoder_type="gam", static_feature_specs=[ population_density_per_sq_km, household, household_food_stamp, income_per_capita, patient_experience_above_the_national_average, patient_experience_below_the_national_average, patient_experience_same_as_the_national_average, hospital_type_critical_access_hospitals, hospital_type_acute_care_department_of_defense, service_type_emergency_services_supported, service_type_non_emergency_services, rating_average, aqi_mean_2018, icu_beds, population_60plus_ratio ], covariate_feature_specs=[ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), ]) return result
def get_model_spec_time_varying_with_covariates(covariate_delay): """Return model specification with hyperparameters and covariates.""" result = model_spec_lib.ModelSpec( hparams={ "initial_learning_rate": 0.003061242915556316, "momentum": 0.2, "decay_steps": 1000, "fine_tuning_steps": 100, "fine_tuning_decay": 1.0, "decay_rate": 1.0, "location_dependent_init": False, "infected_threshold": 3, "restart_threshold": 3000, "time_scale_weight": 0.00006243159539906051, "train_loss_coefs": [0.01, 0.01, 0.1, 0.3, 0.01, 0.01], "valid_loss_coefs": [0.01, 0.01, 0.1, 0.3, 0.01, 0.01], "sync_coef": 1.0, "reduced_sync_undoc": 1.0, "smooth_coef": 0.5, "first_dose_vaccine_ratio_per_day_init": 0.0, "second_dose_vaccine_ratio_per_day_init": 0.0, "average_contact_id_rate_init": -1.9131825459930378, "average_contact_iud_rate_init": -1.071866945725303, "reinfectable_rate_init": -5.548940468292865, "alpha_rate_init": -2.272765554778715, "diagnosis_rate_init": -2.095597433974376, "recovery_h_rate_init": -1.9032896753850963, "recovery_id_rate_init": -1.495660223962899, "recovery_iud_rate_init": -1.475605314236803, "hospitalization_rate_init": -1.4331763640928012, "death_h_rate_init": -1.4886876719378206, "death_id_rate_init": -1.8060447968974489, "bias_penalty_coef": 0.2835406167308398, "r_eff_penalty_coef": 2.0, "r_eff_penalty_cutoff": 5.0, "acceleration_death_coef": 0.1, "acceleration_confirm_coef": 0.1, "acceleration_hospital_coef": 0.1, "quantile_encoding_window": 7, "quantile_smooth_coef": 0.90, "quantile_training_iteration_ratio": 1.0, "width_coef_train": 1.0, "width_coef_valid": 1.0, "quantile_cum_viol_coef": 500.0, "increment_loss_weight": 0.0, "lasso_penalty_coef": 1.0, "covariate_training_mixing_coef": 1.0, "train_window_range": 2.0, "partial_mean_interval": 3, "direction_loss_coef": 2000.0, "train_crps_weight": 0.75, "valid_crps_weight": 0.75 }, encoder_specs=[ model_spec_lib.EncoderSpec( encoder_name="first_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="first_dose", covariate_feature_specs=[ first_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="second_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="second_dose", covariate_feature_specs=[ second_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="average_contact_id_rate", encoder_type="gam", static_feature_specs=demographics + wellness, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, state_of_emergency, reproductive_number ] + survey_all + mobility_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="average_contact_iud_rate", encoder_type="gam", static_feature_specs=demographics + wellness, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, state_of_emergency, reproductive_number ] + survey_all + mobility_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec(encoder_name="reinfectable_rate", encoder_type="gam", static_feature_specs=demographics + wellness, covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec(encoder_name="alpha_rate", encoder_type="gam", static_feature_specs=[], covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec( encoder_name="diagnosis_rate", encoder_type="gam", static_feature_specs=healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, total_tests, dow_feature, ] + survey_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_id_rate", encoder_type="gam", static_feature_specs=demographics + wellness + healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ] + survey_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_iud_rate", encoder_type="gam", static_feature_specs=demographics + wellness + healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, ] + survey_all, covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="recovery_h_rate", encoder_type="gam", static_feature_specs=demographics + wellness + healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, discharged, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="hospitalization_rate", encoder_type="gam", static_feature_specs=demographics + wellness + healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, discharged, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_id_rate", encoder_type="gam", static_feature_specs=demographics + wellness + healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), model_spec_lib.EncoderSpec( encoder_name="death_h_rate", encoder_type="gam", static_feature_specs=demographics + wellness + healthcare, covariate_feature_specs=[ confirmed_preprocessed, death_preprocessed, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, discharged, dow_feature, ], covariate_feature_time_offset=covariate_delay, covariate_feature_window=DEFAULT_WINDOW_SIZE, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": USE_FIXED_COVARIATE_MASK, }), ]) return result
def get_model_spec( self, model_type, covariate_delay=0, **kwargs, ): # Static feature candidates population_density_per_sq_km = model_spec_lib.FeatureSpec( name=constants.POPULATION_DENSITY_PER_SQKM, initializer=None) # Time-varying feature candidates preprocessed_confirmed = model_spec_lib.FeatureSpec( name=constants.CONFIRMED_PREPROCESSED, initializer=None, forecast_method=model_spec_lib.ForecastMethod.NONE) preprocessed_death = model_spec_lib.FeatureSpec( name=constants.DEATH_PREPROCESSED, initializer=None, forecast_method=model_spec_lib.ForecastMethod.NONE) preprocessed_confirmed_mean_to_sum = model_spec_lib.FeatureSpec( name=constants.CONFIRMED_PREPROCESSED_MEAN_TO_SUM_RATIO, initializer=None, forecast_method=model_spec_lib.ForecastMethod.NONE) preprocessed_death_mean_to_sum = model_spec_lib.FeatureSpec( name=constants.DEATH_PREPROCESSED_MEAN_TO_SUM_RATIO, initializer=None, forecast_method=model_spec_lib.ForecastMethod.NONE) first_dose_vaccine_ratio_per_day = model_spec_lib.FeatureSpec( name=constants.VACCINATED_RATIO_FIRST_DOSE_PER_DAY_PREPROCESSED, initializer=None) second_dose_vaccine_ratio_per_day = model_spec_lib.FeatureSpec( name=constants.VACCINATED_RATIO_SECOND_DOSE_PER_DAY_PREPROCESSED, initializer=None) first_dose_vaccine_effectiveness = model_spec_lib.FeatureSpec( name=constants.VACCINATED_EFFECTIVENESS_FIRST_DOSE, initializer=None) second_dose_vaccine_effectiveness = model_spec_lib.FeatureSpec( name=constants.VACCINATED_EFFECTIVENESS_SECOND_DOSE, initializer=None) mobility_index = model_spec_lib.FeatureSpec( name=constants.MOBILITY_INDEX, initializer=None) all_static_covariates = [population_density_per_sq_km] base_ts_covariates = [ preprocessed_confirmed, preprocessed_death, preprocessed_confirmed_mean_to_sum, preprocessed_death_mean_to_sum, ] default_window_size = 7 use_fixed_covariate_mask = True return model_spec_lib.ModelSpec( hparams={ "initial_learning_rate": 0.003061242915556316, "momentum": 0.2, "decay_steps": 1000, "fine_tuning_steps": 500, "fine_tuning_decay": 1.0, "decay_rate": 1.0, "location_dependent_init": False, "infected_threshold": 3, "restart_threshold": 300, "time_scale_weight": 0.00006243159539906051, "train_loss_coefs": [0, 0.001, 0.2, 0.1, 0.01, 0.01], "valid_loss_coefs": [0, 0.001, 0.2, 0.1, 0.01, 0.01], "sync_coef": 0.3, "reduced_sync_undoc": 2.0, "smooth_coef": 0.5, "first_dose_vaccine_ratio_per_day_init": 0.0, "second_dose_vaccine_ratio_per_day_init": 0.0, "average_contact_id_rate_init": -1.9131825459930378, "average_contact_iud_rate_init": -1.071866945725303, "reinfectable_rate_init": -5.548940468292865, "alpha_rate_init": -2.272765554778715, "diagnosis_rate_init": -2.095597433974376, "recovery_id_rate_init": -1.495660223962899, "recovery_iud_rate_init": -1.475605314236803, "recovery_h_rate_init": -1.9032896753850963, "hospitalization_rate_init": -1.4331763640928012, "death_id_rate_init": -1.8060447968974489, "death_h_rate_init": -1.4886876719378206, "bias_penalty_coef": 0.2835406167308398, "r_eff_penalty_coef": 2.0, "acceleration_death_coef": 0.1, "acceleration_confirm_coef": 0.1, "acceleration_hospital_coef": 0.1, "quantile_encoding_window": 7, "quantile_smooth_coef": 0.9, "quantile_training_iteration_ratio": 0.5, "width_coef_train": 10.0, "width_coef_valid": 5.0, "quantile_cum_viol_coef": 500.0, "increment_loss_weight": 0.0, "lasso_penalty_coef": 1.0, "covariate_training_mixing_coef": 1.0, "train_window_range": 2.0, "direction_loss_coef": 5000.0, "train_crps_weight": 0.25, "valid_crps_weight": 0.25 }, encoder_specs=[ model_spec_lib.EncoderSpec( encoder_name="first_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="first_dose", covariate_feature_specs=[ first_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="second_dose_vaccine_ratio_per_day", encoder_type="vaccine", vaccine_type="second_dose", covariate_feature_specs=[ second_dose_vaccine_ratio_per_day, first_dose_vaccine_effectiveness, second_dose_vaccine_effectiveness ], ), model_spec_lib.EncoderSpec( encoder_name="average_contact_id_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates + [mobility_index], covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="average_contact_iud_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates + [mobility_index], covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="reinfectable_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec(encoder_name="alpha_rate", encoder_type="gam", static_feature_specs=[], covariate_feature_specs=None, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, }), model_spec_lib.EncoderSpec( encoder_name="diagnosis_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="recovery_id_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="recovery_iud_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="recovery_h_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="hospitalization_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="death_id_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), model_spec_lib.EncoderSpec( encoder_name="death_h_rate", encoder_type="gam", static_feature_specs=all_static_covariates, covariate_feature_specs=base_ts_covariates, covariate_feature_window=default_window_size, encoder_kwargs={ "initial_bias": 0, "location_dependent_bias": True, "use_fixed_covariate_mask": use_fixed_covariate_mask, }), ])