Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Unveiling new disease, pathway, and gene associations via multi-scale
  neural networks   Diseases involve complex processes and modifications to the cellular
machinery. The gene expression profile of the affected cells contains
characteristic patterns linked to a disease. Hence, biological knowledge
pertaining to a disease can be derived from a patient cell's profile, improving
our diagnosis ability, as well as our grasp of disease risks. This knowledge
can be used for drug re-purposing, or by physicians to evaluate a patient's
condition and co-morbidity risk. Here, we look at differential gene expression
obtained from microarray technology for patients diagnosed with various
diseases. Based on this data and cellular multi-scale organization, we aim to
uncover disease--disease links, as well as disease-gene and disease--pathways
associations. We propose neural networks with structures inspired by the
multi-scale organization of a cell. We show that these models are able to
correctly predict the diagnosis for the majority of the patients. Through the
analysis of the trained models, we predict and validate disease-disease,
disease-pathway, and disease-gene associations with comparisons to known
interactions and literature search, proposing putative explanations for the
novel predictions that come from our study.

35
The categories of this paper are: mtrl-th
16
The categories of this paper are: stat
13
The categories of this paper are: quant-ph
19
The categories of this paper are: eess
21
The categories of this paper are: adap-org
31
The categories of this paper are: ao-sci
5
The categories of this paper are: gr-qc
36
The categories of this paper are: cmp-lg
12
The categories of this paper are: nucl-th
7
The categories of this paper are: hep-th
26
The categories of this paper are: bayes-an
22
The categories of this paper are: chao-dyn
11
The categories of this paper are: hep-lat
6
The categories of this paper are: astro-ph
32
The categories of this paper are: atom-ph
9
The categories of this paper are: nlin