Covid Epidemiology

This repository corresponds to the paper A prospective evaluation of AI-augmented epidemiology to forecast COVID-19 in the USA and Japan .

Contacts

For question, please reach out to [email protected] or [email protected].

Overview

• The tf_seir.py file contains the main functions to define, train and evaluate the proposed model, which integrates learnable encoders into compartmental (SEIR-extended) models. We have separate models for US country, state and country level models, as well as Japan prefecture-level model. Each of these have specific functions and config files, with names 'generic_seir_XXX_constructor.py' and 'generic_seir_specs_XXX.py'. The encoder-related functions are in the 'encoders' directory.

• To see how evaluation metrics were calculation, please see evaluation_metrics.ipynb.

Compartmental Modeling

The compartmental model's configuration, rates, and dynamics are defined via the ModelDefinition. A new custom model definition should inherit from models.definitions.base_model_definition.BaseModelDefinition and extra helper functions for common tasks like pre-processing features can be used by inheriting from the models.definitions.base_model_definition.BaseCovidModelDefinition instead. Further code pertaining to the compartmental dynamics can also be shared amoung multiple models by inheriting from the classes defined in models.definitions.compartmental_model_definitions.

Model Definition Components

There are four general (but interconnected) areas of the model definition which are:

1. Selecting or creating the model's features.
2. Defining the model's rates.
3. Constructing the model's states and dynamics.
4. Pairing model outputs with ground truth data.

While methods described in the sections below represent most of the main differences in the model there are additional helper methods which may need custom implementations as well and are documented more fully in the code.

1. Selecting or creating the model's features

All of the data used to create the model is stored in BigQuery data tables and the model definition is used to define which of these features are used as static or time-varying covariates, or the ground truth values for each of the compartments. To use features available in the BigQuery data tables the feature alias (name used to identify the feature in the code) and the feature_name (used to identify the feature in the BigQuery table) should be returned by get_static_features and get_ts_features for static and time series data respectively. The dictionaries returned by these functions should include all data needed from the BigQuery tables including the ground truth data and covariates.

Prior to being used by the model the BigQuery data is converted into the format used for the model using the extract_all_features method which allows for engineered features to be created for the model. This may be done either by modifying the input static and time series DataFrames directly or by constructing one feature from another (many models do this in the transform_{static|ts}_features method). If the features are added to the input DataFrames directly they must also be returned by the corresponding get_{static|ts}_features method.

The identification the ground truth data based on the incoming features is performed in the initialize_ground_truth_timeseries method. During this identification the method should also format the ground truth data into TensorFlow tensors so that it can be easily used for teacher forcing and computing the model's loss. The last function of this ground truth identification process is to determine when the infection should be considered active in each location.

2. Defining the model's rates

FeatureSpecs should be created for each of the features that will be used as a covariate in the model using the feature alias for the name. Which features are used by each encoder are defined using EncderSpecs. The ModelSpec is used to define which encoders are used and what the model's hyperparameters are.

There should be an encoder for each of the model's rates (variables). A list of the model's rates must be defined in the _ENCODER_RATE_LIST which must match the names of the encoders listed in the model's encoder_specs and there must also be a hyperparameter for each of the rates with the name {rate_name}_init to initialize the rate for the model.

To ensure that the model's rates are realistic, prior knowledge should be used to limit them between their expected bounds. This is done in the bound_variables method which maps the rates output by the encoders into the model's operating space using functions that constrain the output (e.g. sigmoid functions).

3. Constructing the model's states and dynamics

The model's current state is contained in a single tensor and the ordering of that tensor is defined in the initialize_seir_state method. The changes in the model's state at each timestep is calculated using the seir_dynamics method of the model constructor ( i.e. state[t + 1] = state[t] + seir_dynamics(state[t], variables[t])).

4. Pairing model outputs with ground truth data

The pairing of the ground truth data with the model's predicted states is important for both the model training and the evaluation. During training the sync_values method is used to implement teacher forcing where the model's predictions are combined with the ground truth values at each timestep using a weighted average to help the model's training and avoid error accumulation. The model's state estimates must also be paired with the ground truth data during model training in the model constructor method compute_losses, which calculates the model's loss function for the training and validation data sets. The method generate_compartment_predictions pairs states with their corresponding original ground truth values so that accuracy and error metrics can be calculated.