Source code for micom.problems

"""Implements tradeoff optimization between community and egoistic growth."""

from cobra.util import interface_to_str
from micom.util import (
from micom.logger import logger
from micom.solution import (
from optlang.symbolics import Zero
from optlang.interface import OPTIMAL
from import Sized
from functools import partial
import pandas as pd
import numpy as np
from rich.progress import track

[docs] def regularize_l2_norm(community, min_growth): """Add an objective to find the most "egoistic" solution. This adds an optimization objective finding a solution that maintains a (sub-)optimal community growth rate but is the closest solution to the community members individual maximal growth rates. So it basically finds the best possible tradeoff between maximizing community growth and individual (egoistic) growth. Here the objective is given as the sum of squared differences between the individuals current and maximal growth rate. In the linear case squares are substituted by absolute values (Manhattan distance). Arguments --------- community : micom.Community The community to modify. min_growth : positive float The minimal community growth rate that has to be mantained. linear : boolean Whether to use a non-linear (sum of squares) or linear version of the cooperativity cost. If set to False requires a QP-capable solver. max_gcs : None or dict The precomputed maximum individual growth rates. """"adding L2 norm to %s" % l2 = Zero = min_growth context = get_context(community) if context is not None: context(partial(reset_min_community_growth, community)) for sp in community.taxa: taxa_obj = community.constraints["objective_" + sp] ex = sum(v for v in taxa_obj.variables if (v.ub - > 1e-6) if not isinstance(ex, int): l2 += (community.scale * (ex**2)).expand() community.objective = -l2 community.modification = "l2 regularization""finished adding tradeoff objective to %s" %
[docs] def cooperative_tradeoff(community, min_growth, fraction, fluxes, pfba, atol, rtol): """Find the best tradeoff between community and individual growth.""" with community as com: solver = interface_to_str(community.problem) check_modification(community) min_growth = _format_min_growth(min_growth, community.taxa) _apply_min_growth(community, min_growth) com.objective = com.scale * com.variables.community_objective min_growth = ( optimize_with_retry(com, message="could not get community growth rate.") / com.scale ) if not isinstance(fraction, Sized): fraction = [fraction] else: fraction = np.sort(fraction)[::-1] # Add needed variables etc. regularize_l2_norm(com, 0.0) results = [] for fr in fraction: = fr * min_growth com.variables.community_objective.ub = min_growth sol = solve(community, fluxes=fluxes, pfba=pfba, atol=atol, rtol=rtol) if not pfba and sol.status != OPTIMAL: sol = crossover(com, sol, fluxes=fluxes) results.append((fr, sol)) if len(results) == 1: return results[0][1] return pd.DataFrame.from_records(results, columns=["tradeoff", "solution"])
[docs] def knockout_taxa(community, taxa, fraction, method, progress, diag=True): """Knockout a taxon from the community.""" with community as com: check_modification(com) min_growth = _format_min_growth(0.0, com.taxa) _apply_min_growth(com, min_growth) com.objective = com.scale * com.variables.community_objective community_min_growth = ( optimize_with_retry(com, "could not get community growth rate.") / com.scale ) regularize_l2_norm(com, fraction * community_min_growth) old = com.optimize().members["growth_rate"] results = [] iter = track(taxa, description="Knockouts") if progress else taxa for sp in iter: with com:"getting growth rates for %s knockout." % sp) [ r.knock_out() for r in com.reactions.query(lambda ri: ri.community_id == sp) ] sol = optimize_with_fraction(com, fraction) new = sol.members["growth_rate"] if "change" in method: new = new - old if "relative" in method: new /= old results.append(new) ko = pd.DataFrame(results, index=taxa).drop("medium", axis=1) ko = ko.loc[ko.index.sort_values(), ko.columns.sort_values()] if not diag: np.fill_diagonal(ko.values, np.NaN) return ko