Fast and exact ILP-based solvers for the Minimum Flow Decomposition (MFD) problem, and variants of it.

Related tags

Deep LearningMFD-ILP
Overview

MFD-ILP

Fast and exact ILP-based solvers for the Minimum Flow Decomposition (MFD) problem, and variants of it.

The solvers are implemented using Python with the API for two different linear programming solvers: CPLEX and Gurobi.

Requirements

Python:

  • itertools
  • more_itertools
  • math
  • os
  • networkx

CPLEX Python API or Gurobi Python API (both version of the codes are available) Jupyter Notebook

Inputs

For each solvers, an example of the inputs are available in "Example" folder.

Different Formulations

There are three different solvers available: the "Standard" files corresponds to the original and standard formulation; the "Inexact" files corresponds to the original formulations adjusted to incorporate inexact flow constraints and the "Subpath" files corresponds to the original formulations with the addition to the subpath constraints.

Running the solvers

In each solvers, in order to run each formulation, open the respective notebook and change the variable $path$ in the last cell to the folder where all the input files are. For the subpath constraints formulation, also change the $number_paths$ to the appropriated amount. The default value is 4.

As reminder, all the input files are in Catfish format. See folder "Example" for sample of inputs.

Outputs

Each solvers outputs 2 files: the first file called "results_[CPLEX or Gurobi].txt" contains the optimal number of $k$ flow paths and the runtime required to solve such instance, each instance is displayed in a single line; the second file called "results_[CPLEX or Gurobi]-details.txt" contains in each line the corresponding value of $w_k$ and the $k$ flow path associated with that solution, different instances are separated by "------------".

Owner
Algorithmic Bioinformatics Group @ University of Helsinki
Algorithmic Bioinformatics Group @ University of Helsinki
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