Source code for dynamo.simulation.evaluation

import numpy as np
from sklearn.metrics import mean_squared_error

from import einsum_correlation

[docs]def evaluate(reference: np.ndarray, prediction: np.ndarray, metric: str = "cosine") -> float: """Function to evaluate the vector field related reference quantities vs. that from vector field prediction. Args: reference: The reference quantity of the vector field (for example, simulated velocity vectors at each point or trajectory, or estimated RNA velocity vector) prediction: The predicted quantity of the vector field (for example, velocity vectors calculated based on reconstructed vector field function at each point or trajectory, or reconstructed RNA velocity vector) metric: The metric for benchmarking the vector field quantities after reconstruction. Returns: res: The score between the reference vs. reconstructed quantities based on the metric. """ if metric == "cosine": true_normalized = reference / (np.linalg.norm(reference, axis=1).reshape(-1, 1) + 1e-20) predict_normalized = prediction / (np.linalg.norm(prediction, axis=1).reshape(-1, 1) + 1e-20) res = np.mean(true_normalized * predict_normalized) * prediction.shape[1] elif metric == "rmse": res = mean_squared_error(y_true=reference, y_pred=prediction) return res