MiNAA aligns two networks based their topologies and biologies.

This program requires C++20 or higher.

make

mkdir obj
make

In addition to C++20, Windows requires a special means to run the provided makefile. The MinGW Package Manager provides a lightweight make function. It is recommended to follow this guide, however any method for compiling C++ should suffice.

This utility takes two to five command-line arguments: ./minaa.exe <G> <H> [-B=bio] [-a=alpha] [-b=beta]

1. G: A network to align.
2. H: A network to align.

• Require:
  • The networks are represented by adjacency matrices in CSV format, with labels in both the first column and row.
  • The CSV delimiter must be one of {comma, semicolon, space, tab}, and will be detected automatically.
  • Any nonzero entry is considered an edge.
  • |G| should be lesser or equal to |H|.

• bio: The path to the biological cost matrix file.
  • Require: CSV adjacency matrix where the first column is the labels of G, and first row is the labels of H.
  • Default: the algorithm will run using only topological calculations.
• alpha: GDV-edge weight balancer
  • Require: a real number in range [0, 1].
  • Default: 1
• beta: topological-biological cost matrix balancer.
  • Require: a real number in range [0, 1].
  • Default: 1

• X-Y-T/: (where "X", "Y" are the input networks, "T" is the date and time of execution) The folder containing the output files specified below.
• log.txt: Record of the important details from the alignment.
• X_gdvs.csv: (where "X" is the input network) The Graphlet Degree Vectors for network "X".
• top_costs.csv: The topological cost matrix.
• bio_costs.csv: The biologocal cost matrix (as inputed). Not created unless biological input is given.
• overall_costs.csv: The combination of the topological and biological cost matrix. Not created unless biological input is given.
• alignment_list.csv: A complete list of all aligned nodes, with rows in the format g_node,h_node,similarity, descending acording to similarity. The first row in this list is the total cost of the alignment, or the sum of (1 - similarity) for all aligned pairs.
• alignment_matrix.csv: A matrix form of the same alignment, where the first column and row are the labels from the two input networks, respectively.

./minaa.exe network0.csv network1.csv -a=0.6

Here we align network0 with network1 using no biological data. -a=0.6 sets alpha equal to 0.6, meaning 60% of the topological cost function comes from similarity calculated by GDVs, and 40% from simpler node degree data.

./minaa.exe network0.csv network1.csv bio_costs.csv -b=0.85

Here we align network0 with network1 using topological information and the given biological cost matrix, bio_costs. Since alpha and gamma were unspecified, they default to 0.5 and 1 respectively. Since beta was set to 0.85, 85% of the cost weight is from the topological cost matrix, and 15% is from the given biological cost matrix.

All scripts and instructions to reproduce the analyses in the manuscript can be found in the simulations folder.

Users interested in expanding functionalities in MiNAA are welcome to do so. Issues reports are encouraged through Github's issue tracker. See details on how to contribute and report issues in CONTRIBUTING.md.

MiNAA is licensed under the MIT licence. © SolisLemus lab projects (2023)

If you use MiNAA in your work, we kindly ask that you cite the following paper:

@ARTICLE{Nelson2022,
  title         = "MiNAA: Microbiome Network Alignment Algorithm",
  author        = "Nelson, Reed and Aghdam, Rosa and
                   Solis-Lemus, Claudia",
  year          =  2022,
  archivePrefix = "arXiv",
  primaryClass  = "q-bio.PE",
  eprint        = "xxx"
}