RT Journal Article
SR Electronic
T1 PALLAS: Penalized mAximum LikeLihood and pArticle Swarms for Inference of Gene Regulatory Networks from Time Series Data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.13.093674
DO 10.1101/2020.05.13.093674
A1 Yukun Tan
A1 Fernando B. Lima Neto
A1 Ulisses Braga Neto
YR 2020
UL http://biorxiv.org/content/early/2020/05/15/2020.05.13.093674.abstract
AB We present PALLAS, a practical method for gene regulatory network (GRN) inference from time series data, which employs penalized maximum likelihood and particle swarms for optimization. PALLAS is based on the Partially-Observable Boolean Dynamical System (POBDS) model and thus does not require ad-hoc binarization of the data. The penalty in the likelihood is a LASSO regularization term, which encourages the resulting network to be sparse. PALLAS is able to scale to large networks under no prior knowledge, by virtue of a novel continuous-discrete Fish School Search particle swarm algorithm for efficient simultaneous maximization of the penalized likelihood over the discrete space of networks and the continuous space of observational parameters. The performance of PALLAS is demonstrated by a comprehensive set of experiments using synthetic data generated from real and artificial networks, as well as real time series microarray and RNA-seq data, where it is competed to several other well-known methods for gene regulatory network inference. The results show that PALLAS can infer GRNs efficiently and accurately. PALLAS is a fully-fledged program with a commandline user interface, written in python, and available on GitHub (https://github.com/yukuntan92/PALLAS).Competing Interest StatementThe authors have declared no competing interest.