corneto.methods.PHONEMeS#

class corneto.methods.PHONEMeS(default_edge_cost=1e-05, max_flow=None, epsilon=1, backend=None)#

Bases: FlowMethod

Infer acyclic signaling networks from phosphoproteomic scores.

PHONEMeS uses one directed flow per condition. Perturbations inject flow, measured phosphosites can extract it, and explicit binary vertex variables attach signed phosphosite scores to every selected biological node.

Parameters:

default_edge_cost (float) – Cost assigned to unspecified PKN edges.
max_flow (Optional[float]) – Upper bound for every flow. Defaults to the number of PKN edges.
epsilon (float) – Smallest positive flow associated with a selected edge.
backend (Optional[Backend]) – Optimization backend.

__init__(default_edge_cost=1e-05, max_flow=None, epsilon=1, backend=None)#

Parameters:

default_edge_cost (float)
max_flow (float | None)
epsilon (float)
backend (Backend | None)

Methods

`__init__`([default_edge_cost, max_flow, ...])
`build`(pkn, *, perturbations, phosphosite_scores)	Build a single-condition PHONEMeS problem.
`build_from_data`(graph[, data])	Build the complete optimization problem.
`build_many`(pkn, *, perturbations, ...[, ...])	Build a PHONEMeS problem for multiple named conditions.
`create_flow_based_problem`(flow_problem, ...)	Add vectorized PHONEMeS selection, role, and objective terms.
`create_problem`(graph, data)	Create selected biological flows without auxiliary-edge binaries.
`description`()	Return a short method description.
`get_flow_bounds`(graph, data)	Return condition-specific bounds for internal and boundary flows.
`name`()	Return the method name.
`preprocess`(graph, data)	Validate inputs, prune unreachable PKN regions, and add boundaries.
`references`()	Return PHONEMeS publication citation keys.
`show_bibtex`()	Display raw BibTeX entries in a formatted block for easy copying.
`show_references`()	Display formatted citations in a Jupyter notebook.

Attributes

backend

Return the optimization backend being used.

build(pkn, *, perturbations, phosphosite_scores, edge_costs=None)#

Build a single-condition PHONEMeS problem.

phosphosite_scores accepts a site mapping or a pandas Series when pandas is available.

Parameters:: pkn (BaseGraph)

build_many(pkn, *, perturbations, phosphosite_scores, edge_costs=None)#

Build a PHONEMeS problem for multiple named conditions.

phosphosite_scores accepts a named condition mapping or a pandas DataFrame with phosphosites as rows and conditions as columns.

Parameters:: pkn (BaseGraph)

preprocess(graph, data)#

Validate inputs, prune unreachable PKN regions, and add boundaries.

Parameters:

graph (BaseGraph)
data (Data)

get_flow_bounds(graph, data)#

Return condition-specific bounds for internal and boundary flows.

Parameters:

graph (BaseGraph)
data (Data)

create_problem(graph, data)#

Create selected biological flows without auxiliary-edge binaries.

Parameters:

graph (BaseGraph)
data (Data)

create_flow_based_problem(flow_problem, graph, data)#

Add vectorized PHONEMeS selection, role, and objective terms.

Parameters:

flow_problem (ProblemDef)
graph (BaseGraph)
data (Data)

static name()#

Return the method name.

Return type:: str

static description()#

Return a short method description.

Return type:: str

static references()#: Return PHONEMeS publication citation keys.