Gplasdi timing documentation

src/lasdi/enums.py

@@ -1,13 +1,13 @@
 from enum import Enum
 
 class NextStep(Enum):
-    Train = 1
-    PickSample = 2
-    RunSample = 3
-    CollectSample = 4
+    Train           = 1
+    PickSample      = 2
+    RunSample       = 3
+    CollectSample   = 4
 
 class Result(Enum):
-    Unexecuted = 1
-    Success = 2
-    Fail = 3
-    Complete = 4
+    Unexecuted      = 1
+    Success         = 2
+    Fail            = 3
+    Complete        = 4

src/lasdi/gp.py

@@ -1,80 +1,194 @@
-import numpy as np
-from sklearn.gaussian_process.kernels import ConstantKernel, Matern, RBF
-from sklearn.gaussian_process import GaussianProcessRegressor
+import  numpy                               as      np
+from    sklearn.gaussian_process.kernels    import  ConstantKernel, Matern, RBF
+from    sklearn.gaussian_process            import  GaussianProcessRegressor
 
-def fit_gps(X, Y):
 
-    '''
-    Trains each GP given the interpolation dataset.
-    X: (n_train, n_param) numpy 2d array
-    Y: (n_train, n_coef) numpy 2d array
+
+
+# -------------------------------------------------------------------------------------------------
+# Gaussian Process functions! 
+# -------------------------------------------------------------------------------------------------
+
+def fit_gps(X : np.ndarray, Y : np.ndarray) -> list[GaussianProcessRegressor]:
+    """
+    Trains a GP for each column of Y. If Y has shape N x k, then we train k GP regressors. In this 
+    case, we assume that X has shape N x M. Thus, the Input to the GP is in \mathbb{R}^M. For each
+    k, we train a GP where the i'th row of X is the input and the i,k component of Y is the
+    corresponding target. Thus, we return a list of k GP Regressor objects, the k'th one of which 
+    makes predictions for the k'th coefficient in the latent dynamics. 
+
     We assume each target coefficient is independent with each other.
-    gp_dictionnary is a dataset containing the trained GPs (as sklearn objects)
 
-    '''
 
-    n_coef = 1 if (Y.ndim == 1) else Y.shape[1]
+    -----------------------------------------------------------------------------------------------
+    Arguments
+    -----------------------------------------------------------------------------------------------
+
+    X: A 2d numpy array of shape (n_train, input_dim), where n_train is the number of training 
+    examples and input_dim is the number of components in each input (e.g., the number of 
+    parameters)
+
+    Y: A 2d numpy array of shape (n_train, n_coef), where n_train is the number of training 
+    examples and n_coef is the number of coefficients in the latent dynamics. 
+
+
+    -----------------------------------------------------------------------------------------------
+    Returns
+    -----------------------------------------------------------------------------------------------
+
+    A list of trained GP regressor objects. If Y has k columns, then the returned list has k 
+    elements. It's i'th element holds a trained GP regressor object whose training inputs are the 
+    columns of X and whose corresponding target values are the elements of the i'th column of Y.
+    """
+
+    # Determine the number of components (columns) of Y. Since this is a regression task, we will
+    # perform a GP regression fit on each component (column) of Y.
+    n_coef : int = 1 if (Y.ndim == 1) else Y.shape[1]
+
+    # Transpose Y so that each row corresponds to a particular coefficient. This allows us to 
+    # iterate over the coefficients by iterating through the rows of Y.
     if (n_coef > 1):
         Y = Y.T
 
+    # Sklearn requires X to be a 2D array... so make sure this holds.
     if X.ndim == 1:
         X = X.reshape(-1, 1)
 
-    gp_dictionnary = []
+    # Initialize a list to hold the trained GP objects.
+    gp_list : list[GaussianProcessRegressor] = []
 
+    # Cycle through the rows of Y (which we transposed... so this just cycles through the 
+    # coefficients)
     for yk in Y:
+        # Make the kernel.
         # kernel = ConstantKernel() * Matern(length_scale_bounds = (0.01, 1e5), nu = 1.5)
-        kernel = ConstantKernel() * RBF(length_scale_bounds = (0.1, 1e5))
+        kernel  = ConstantKernel() * RBF(length_scale_bounds = (0.1, 1e5))
 
-        gp = GaussianProcessRegressor(kernel = kernel, n_restarts_optimizer = 10, random_state = 1)
-        gp.fit(X, yk)
+        # Initialize the GP object.
+        gp      = GaussianProcessRegressor(kernel = kernel, n_restarts_optimizer = 10, random_state = 1)
 
-        gp_dictionnary += [gp]
+        # Fit it to the data (train), then add it to the list of trained GPs
+        gp.fit(X, yk)
+        gp_list += [gp]
 
-    return gp_dictionnary
+    # All done!
+    return gp_list
 
-def eval_gp(gp_dictionnary, param_grid):
 
-    '''
 
+def eval_gp(gp_list : list[GaussianProcessRegressor], param_grid : np.ndarray) -> tuple[np.ndarray, np.ndarray]:
+    """
     Computes the GPs predictive mean and standard deviation for points of the parameter space grid
 
-    '''
 
-    n_coef = len(gp_dictionnary)
+    -----------------------------------------------------------------------------------------------
+    Arguments
+    -----------------------------------------------------------------------------------------------
+
+    gp_list: a list of trained GP regressor objects. The number of elements in this list should 
+    match the number of columns in param_grid. The i'th element of this list is a GP regressor 
+    object that predicts the i'th coefficient. 
+
+    param_grid: A 2d numpy.ndarray object of shape (number of parameter combination, number of 
+    parameters). The i,j element of this array specifies the value of the j'th parameter in the 
+    i'th combination of parameters. We use this as the testing set for the GP evaluation.
+
+
+    -----------------------------------------------------------------------------------------------
+    Returns
+    -----------------------------------------------------------------------------------------------  
+
+    A two element tuple. Both are 2d numpy arrays of shape (number of parameter combinations, 
+    number of coefficients). The two arrays hold the predicted means and std's for each parameter
+    at each training example, respectively. 
+
+    Thus, the i,j element of the first return variable holds the predicted mean of the j'th 
+    coefficient in the latent dynamics at the i'th training example. Likewise, the i,j element of 
+    the second return variable holds the standard deviation in the predicted distribution for the 
+    j'th coefficient in the latent dynamics at the i'th combination of parameter values.
+    """
+
+    # Fetch the numbers coefficients. Since there is one GP Regressor per SINDy coefficient, this 
+    # just the length of the gp_list.
+    n_coef : int = len(gp_list)
+
+    # Fetch the number of parameters, make sure the grid is 2D. 
     if (param_grid.ndim == 1):
         param_grid = param_grid.reshape(1, -1)
     n_points = param_grid.shape[0]
 
+    # Initialize arrays to hold the mean, STD.
     pred_mean, pred_std = np.zeros([n_points, n_coef]), np.zeros([n_points, n_coef])
-    for k, gp in enumerate(gp_dictionnary):
+
+    # Cycle through the GPs (one for each coefficient in the SINDy coefficients!).
+    for k, gp in enumerate(gp_list):
+        # Make predictions using the parameters in the param_grid.
         pred_mean[:, k], pred_std[:, k] = gp.predict(param_grid, return_std = True)
 
+    # All done!
     return pred_mean, pred_std
 
-def sample_coefs(gp_dictionnary, param, n_samples):
 
-    '''
 
-    Generates sample sets of ODEs for one given parameter.
-    coef_samples is a list of length n_samples, where each terms is a matrix of SINDy coefficients sampled from the GP predictive
-    distributions
+def sample_coefs(   gp_list     : list[GaussianProcessRegressor], 
+                    param       : np.ndarray, 
+                    n_samples   : int):
+    """
+    Generates sets of ODE (SINDy) coefficients sampled from the predictive distribution for those 
+    coefficients at the specified parameter value (parma). Specifically, for the k'th SINDy 
+    coefficient, we draw n_samples samples of the predictive distribution for the k'th coefficient
+    when param is the parameter. 
+
+
+    -----------------------------------------------------------------------------------------------
+    Arguments
+    -----------------------------------------------------------------------------------------------
+
+    gp_list: a list of trained GP regressor objects. The number of elements in this list should 
+    match the number of columns in param_grid. The i'th element of this list is a GP regressor 
+    object that predicts the i'th coefficient. 
+
+    param: A combination of parameter values. i.e., a single test example. We evaluate each GP in 
+    the gp_list at this parameter value (getting a prediction for each coefficient).
+
+    n_samples: Number of samples of the predicted latent dynamics used to build ensemble of fom 
+    predictions. N_s in the paper. 
+
+
+    -----------------------------------------------------------------------------------------------
+    Returns
+    -----------------------------------------------------------------------------------------------
+
+    A 2d numpy ndarray object called coef_samples. It has shape (n_samples, n_coef), where n_coef 
+    is the number of coefficients (length of gp_list). The i,j element of this list is the i'th 
+    sample of the j'th SINDy coefficient.
+    """
 
-    '''
+    # Fetch the number of coefficients (since there is one GP Regressor per coefficient, this is
+    # just the length of the gp_list).
+    n_coef          : int           = len(gp_list)
 
-    n_coef = len(gp_dictionnary)
-    coef_samples = np.zeros([n_samples, n_coef])
+    # Initialize an array to hold the coefficient samples.
+    coef_samples    : np.ndarray    = np.zeros([n_samples, n_coef])
 
+    # Make sure param is a 2d array with one row, we need this when evaluating the GP Regressor
+    # object.
     if param.ndim == 1:
         param = param.reshape(1, -1)
-    n_points = param.shape[0]
+
+    # Make sure we only have a single sample.
+    n_points : int = param.shape[0]
     assert(n_points == 1)
 
-    pred_mean, pred_std = eval_gp(gp_dictionnary, param)
+    # Evaluate the predicted mean and std at the parameter value.
+    pred_mean, pred_std = eval_gp(gp_list, param)
     pred_mean, pred_std = pred_mean[0], pred_std[0]
 
+    # Cycle through the samples and coefficients. For each sample of the k'th coefficient, we draw
+    # a sample from the normal distribution with mean pred_mean[k] and std pred_std[k].
     for s in range(n_samples):
         for k in range(n_coef):
             coef_samples[s, k] = np.random.normal(pred_mean[k], pred_std[k])
 
+    # All done!
     return coef_samples