Fig 1. The denoising process using DEWÄKSS.

The procedure is as follows: (i) The PCA of the expression matrix X is computed. (ii) A cell-to-cell similarity structure is inferred from a k-Nearest Neighbor Graph (kNN-G). (iii) An invariant and independent mapping function is constructed. (iv) The objective function, with a defined optimum for denoising, minimizes the mean squared error (MSE) between the predicted weighted average of the neighbor cells’ state and the observed cell state. DEWÄKSS tunes its objective function with two main input parameters, the number of PCs and the number k of neighbors.