2013. Implementing sequence specific bias correction in kallisto required working things out from scratch because of the way equivalence classes were being used with the EM algorithm, and not reads. I worked this out together with Páll Melsted during conversations that lasted about a month in the ...
Saul (Nonlinear dimensionality reduction by locally linear embedding [4]) introduced an unsupervised learning algorithm called locally linear embedding (LLE) that is better suited to identify patterns in the high-dimensional feature space and solves our problem of nonlinear dimensionality reduction for ...