Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Iterative Random Forests to detect predictive and stable high-order
  interactions   Genomics has revolutionized biology, enabling the interrogation of whole
transcriptomes, genome-wide binding sites for proteins, and many other
molecular processes. However, individual genomic assays measure elements that
interact in vivo as components of larger molecular machines. Understanding how
these high-order interactions drive gene expression presents a substantial
statistical challenge. Building on Random Forests (RF), Random Intersection
Trees (RITs), and through extensive, biologically inspired simulations, we
developed the iterative Random Forest algorithm (iRF). iRF trains a
feature-weighted ensemble of decision trees to detect stable, high-order
interactions with same order of computational cost as RF. We demonstrate the
utility of iRF for high-order interaction discovery in two prediction problems:
enhancer activity in the early Drosophila embryo and alternative splicing of
primary transcripts in human derived cell lines. In Drosophila, among the 20
pairwise transcription factor interactions iRF identifies as stable (returned
in more than half of bootstrap replicates), 80% have been previously reported
as physical interactions. Moreover, novel third-order interactions, e.g.
between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order
relationships that are candidates for follow-up experiments. In human-derived
cells, iRF re-discovered a central role of H3K36me3 in chromatin-mediated
splicing regulation, and identified novel 5th and 6th order interactions,
indicative of multi-valent nucleosomes with specific roles in splicing
regulation. By decoupling the order of interactions from the computational cost
of identification, iRF opens new avenues of inquiry into the molecular
mechanisms underlying genome biology.

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The categories of this paper are: nucl-ex
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The categories of this paper are: astro-ph
21
The categories of this paper are: adap-org
5
The categories of this paper are: gr-qc
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The categories of this paper are: acc-phys
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The categories of this paper are: eess
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The categories of this paper are: patt-sol
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The categories of this paper are: q-alg
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The categories of this paper are: dg-ga
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The categories of this paper are: chem-ph
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The categories of this paper are: bayes-an
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The categories of this paper are: hep-th
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The categories of this paper are: econ
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The categories of this paper are: hep-lat
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The categories of this paper are: mtrl-th
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The categories of this paper are: plasm-ph