corneto.methods.BidirectionalPHONEMeS#

class corneto.methods.BidirectionalPHONEMeS(default_edge_cost=1e-05, max_flow=None, epsilon=1, anchor_policy='either', backend=None)#

Bases: PHONEMeS

Infer one globally optimized network around regulated kinase anchors.

The method searches both upstream and downstream of each regulated kinase. Phosphosite scores and interaction costs are applied to the combined biological network rather than to two independently inferred networks.

Parameters:

default_edge_cost (float) – Cost assigned to unspecified PKN edges.
max_flow (Optional[float]) – Upper bound for every directional flow.
epsilon (float) – Smallest positive flow associated with a selected edge.
anchor_policy (Literal['either', 'both', 'downstream']) – Whether every anchor must participate on either side, both sides, or the downstream side.
backend (Optional[Backend]) – Optimization backend.

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

Parameters:

default_edge_cost (float)
max_flow (float | None)
epsilon (float)
anchor_policy (Literal['either', 'both', 'downstream'])
backend (Backend | None)

Methods

`__init__`([default_edge_cost, max_flow, ...])
`build`(pkn, *, regulated_kinases, ...[, ...])	Build one bidirectional PHONEMeS condition.
`build_from_data`(graph[, data])	Build the complete optimization problem.
`build_many`(pkn, *, regulated_kinases, ...[, ...])	Build named bidirectional PHONEMeS conditions.
`create_flow_based_problem`(flow_problem, ...)	Add vectorized PHONEMeS selection, role, and objective terms.
`create_problem`(graph, data)	Create the global vectorized bidirectional problem.
`description`()	Return a short method description.
`get_flow_bounds`(graph, data)	Return bounds for downstream and upstream flow columns.
`name`()	Return the method name.
`preprocess`(graph, data)	Validate, prune exact directional paths, and build the flow layout.
`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, *, regulated_kinases, phosphosite_scores, edge_costs=None)#

Build one bidirectional PHONEMeS condition.

Parameters:: pkn (BaseGraph)

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

Build named bidirectional PHONEMeS conditions.

Parameters:: pkn (BaseGraph)

preprocess(graph, data)#

Validate, prune exact directional paths, and build the flow layout.

Parameters:

graph (BaseGraph)
data (Data)

get_flow_bounds(graph, data)#

Return bounds for downstream and upstream flow columns.

Parameters:

graph (BaseGraph)
data (Data)

create_problem(graph, data)#

Create the global vectorized bidirectional problem.

Parameters:

graph (BaseGraph)
data (Data)

static name()#

Return the method name.

Return type:: str

static description()#

Return a short method description.

Return type:: str