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Inferring a gene regulatory network (GRN) from gene expression data is a computationally expensive task, exacerbated by increasing data sizes due to advances in high-throughput gene profiling technology.

The Arboretum software library addresses this issue by providing a computational strategy that allows executing the class of GRN inference algorithms exemplified by GENIE3 [1] on hardware ranging from a single computer to a multi-node compute cluster. This class of GRN inference algorithms is defined by a series of steps, one for each target gene in the network, where the most important candidates from a set of regulators are determined from a regression model to predict a target gene’s expression profile.

Members of the above class of GRN inference algorithms are attractive from a computational point of view because they are parallelizable by nature. In arboretum, we specify the parallelizable computation as a dask graph [2], a data structure that represents the task schedule of a computation. A dask scheduler assigns the tasks in a dask graph to the available computational resources. Arboretum uses the dask distributed scheduler to spread out the computational tasks over multiple processes running on one or multiple machines.

Arboretum currently supports 2 GRN inference algorithms:

  1. GRNBoost2: a novel and fast GRN inference algorithm using Stochastic Gradient Boosting Machine [3] (SGBM) regression with early-stopping regularization.
  2. GENIE3: the classic GRN inference algorithm using Random Forest (RF) or ExtraTrees (ET) regression.

Usage Example

# import python modules
import pandas as pd
from arboretum.utils import load_tf_names
from arboretum.algo import grnboost2

# load the data
ex_matrix = pd.read_csv(<ex_path>, sep='\t')
tf_names = load_tf_names(<tf_path>)

# infer the gene regulatory network
network = grnboost2(expression_data=ex_matrix,

TF target importance
G109 G1406 151.648784
G16 G1440 136.741815
G188 G938 124.707570
G10 G1312 124.195566
G48 G1419 121.488200

Check out more examples.


BSD 3-Clause License


[1]Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P (2010) Inferring Regulatory Networks from Expression Data Using Tree-Based Methods. PLoS ONE
[2]Rocklin, M. (2015). Dask: parallel computation with blocked algorithms and task scheduling. In Proceedings of the 14th Python in Science Conference (pp. 130-136).
[3]Friedman, J. H. (2002). Stochastic gradient boosting. Computational Statistics & Data Analysis, 38(4), 367-378.
[4]Marbach, D., Costello, J. C., Kuffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., … & Dream5 Consortium. (2012). Wisdom of crowds for robust gene network inference. Nature methods, 9(8), 796-804.