PALMER: improving pathway annotation based on the biomedical literature mining with a constrained latent block model.

ABSTRACT:

Background

In systems biology, it is of great interest to identify previously unreported associations between genes. Recently, biomedical literature has been considered as a valuable resource for this purpose. While classical clustering algorithms have popularly been used to investigate associations among genes, they are not tuned for the literature mining data and are also based on strong assumptions, which are often violated in this type of data. For example, these approaches often assume homogeneity and independence among observations. However, these assumptions are often violated due to both redundancies in functional descriptions and biological functions shared among genes. Latent block models can be alternatives in this case but they also often show suboptimal performances, e

SUBMITTER: Nam JH 

PROVIDER: S-EPMC7532116 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature