Check whether a model satisfies a property (indra.explanation.model_checker)

Shared Model Checking Functionality (indra.explanation.model_checker.model_checker)

class indra.explanation.model_checker.model_checker.ModelChecker(model, statements=None, do_sampling=False, seed=None)

The parent class of all ModelCheckers.

Parameters:

• model (pysb.Model or indra.assemblers.indranet.IndraNet or PyBEL.Model) – Depending on the ModelChecker class, can be different type.
• statements (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to check the model against.
• do_sampling (bool) – Whether to use breadth-first search or weighted sampling to generate paths. Default is False (breadth-first search).
• seed (int) – Random seed for sampling (optional, default is None).

graph

A DiGraph with signed nodes to find paths in.

Type:nx.Digraph

add_statements(stmts)

Add to the list of statements to check against the model.

Parameters:stmts (list[indra.statements.Statement]) – The list of Statements to be added for checking.

check_model(max_paths=1, max_path_length=5)

Check all the statements added to the ModelChecker.

Parameters:

• max_paths (Optional[int]) – The maximum number of specific paths to return for each Statement to be explained. Default: 1
• max_path_length (Optional[int]) – The maximum length of specific paths to return. Default: 5

Returns:

Each tuple contains the Statement checked against the model and a PathResult object describing the results of model checking.

Return type:

list of (Statement, PathResult)

check_statement(stmt, max_paths=1, max_path_length=5)

Check a single Statement against the model.

Parameters:

• stmt (indra.statements.Statement) – The Statement to check.
• max_paths (Optional[int]) – The maximum number of specific paths to return for each Statement to be explained. Default: 1
• max_path_length (Optional[int]) – The maximum length of specific paths to return. Default: 5

Returns:

result – A PathResult object containing the result of a test.

Return type:

indra.explanation.modelchecker.PathResult

find_paths(input_set, target, max_paths=1, max_path_length=5, loop=False)

Check for a source/target path in the model.

Parameters:

• input_set (list or None) – A list of potenital sources or None if the test statement subject is None.
• target (tuple) – Tuple representing the target node (usually common target node).
• max_paths (int) – The maximum number of specific paths to return.
• max_path_length (int) – The maximum length of specific paths to return.
• loop (bool) – Whether we are looking for a loop path.

Returns:

PathResult object indicating the results of the attempt to find a path.

Return type:

PathResult

get_graph(**kwargs)

Return a graph with signed nodes to find the path.

process_statement(stmt)

This method processes the test statement to get the data about subject and object, according to the specific model requirements for model checking, e.g. PysbModelChecker gets subject monomer patterns and observables, while graph based ModelCheckers will return signed nodes corresponding to subject and object. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Parameters:stmt (indra.statements.Statement) – A statement to process. Returns:

• subj_data (list or None) – Data about statement subject to be used as source nodes.
• obj_data (list or None) – Data about statement object to be used as target nodes.
• result_code (str or None) – Result code to construct PathResult.

process_subject(subj_data)

Processes the subject of the test statement and returns the necessary information to check the statement. In case of PysbModelChecker, method returns input_rule_set. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

class indra.explanation.model_checker.model_checker.PathMetric(source_node, target_node, length)

Describes results of simple path search (path existence).

source_node

The source node of the path

Type:str

target_node

The target node of the path

Type:str

length

The length of the path

Type:int

class indra.explanation.model_checker.model_checker.PathResult(path_found, result_code, max_paths, max_path_length)

Describes results of running the ModelChecker on a single Statement.

path_found

True if a path was found, False otherwise.

Type:bool

result_code

• STATEMENT_TYPE_NOT_HANDLED - The provided statement type is not handled
• SUBJECT_MONOMERS_NOT_FOUND or SUBJECT_NOT_FOUND - Statement subject not found in model
• OBSERVABLES_NOT_FOUND or OBJECT_NOT_FOUND - Statement has no associated observable
• NO_PATHS_FOUND - Statement has no path for any observable
• MAX_PATH_LENGTH_EXCEEDED - Statement has no path len <= MAX_PATH_LENGTH
• PATHS_FOUND - Statement has path len <= MAX_PATH_LENGTH
• INPUT_RULES_NOT_FOUND - No rules with Statement subject found
• MAX_PATHS_ZERO - Path found but MAX_PATHS is set to zero

Type:string

max_paths

The maximum number of specific paths to return for each Statement to be explained.

Type:int

max_path_length

The maximum length of specific paths to return.

Type:int

path_metrics

A list of PathMetric objects, each describing the results of a simple path search (path existence).

Type:list[indra.explanation.model_checker.PathMetric]

paths

A list of paths obtained from path finding. Each path is a list of tuples (which are edges in the path), with the first element of the tuple the name of a rule, and the second element its polarity in the path.

Type:list[list[tuple[str, int]]]

indra.explanation.model_checker.model_checker.prune_signed_nodes(graph)

Prune nodes with sign (1) if they do not have predecessors.

indra.explanation.model_checker.model_checker.signed_edges_to_signed_nodes(graph, prune_nodes=True, edge_signs={'neg': 1, 'pos': 0}, copy_edge_data=False)

Convert a graph with signed edges to a graph with signed nodes.

Each pair of nodes linked by an edge in an input graph are represented as four nodes and two edges in the new graph. For example, an edge (a, b, 0), where a and b are nodes and 0 is a sign of an edge (positive), will be represented as edges ((a, 0), (b, 0)) and ((a, 1), (b, 1)), where (a, 0), (a, 1), (b, 0), (b, 1) are signed nodes. An edge (a, b, 1) with sign 1 (negative) will be represented as edges ((a, 0), (b, 1)) and ((a, 1), (b, 0)).

Parameters:

• graph (networkx.MultiDiGraph) – Graph with signed edges to convert. Can have multiple edges between a pair of nodes.
• prune_nodes (Optional[bool]) – If True, iteratively prunes negative (with sign 1) nodes without predecessors.
• edge_signs (dict) – A dictionary representing the signing policy of incoming graph. The dictionary should have strings ‘pos’ and ‘neg’ as keys and integers as values.
• copy_edge_data (bool|set(keys)) – Option for copying edge data as well from graph. If False (default), no edge data is copied (except sign). If True, all edge data is copied. If a set of keys is provided, only the keys appearing in the set will be copied, assuming the key is part of a nested dictionary.

Returns:

signed_nodes_graph

Return type:

networkx.DiGraph

Checking PySB model (indra.explanation.model_checker.pysb)

class indra.explanation.model_checker.pysb.PysbModelChecker(model, statements=None, agent_obs=None, do_sampling=False, seed=None, model_stmts=None)

Check a PySB model against a set of INDRA statements.

Parameters:

• model (pysb.Model) – A PySB model to check.
• statements (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to check the model against.
• agent_obs (Optional[list[indra.statements.Agent]]) – A list of INDRA Agents in a given state to be observed.
• do_sampling (bool) – Whether to use breadth-first search or weighted sampling to generate paths. Default is False (breadth-first search).
• seed (int) – Random seed for sampling (optional, default is None).
• model_stmts (list[indra.statements.Statement]) – A list of INDRA statements used to assemble PySB model.

draw_im(fname)

Draw and save the influence map in a file.

Parameters:fname (str) – The name of the file to save the influence map in. The extension of the file will determine the file format, typically png or pdf.

generate_im(model)

Return a graph representing the influence map generated by Kappa

Parameters:model (pysb.Model) – The PySB model whose influence map is to be generated Returns:graph – A MultiDiGraph representing the influence map Return type:networkx.MultiDiGraph

get_graph(prune_im=True, prune_im_degrade=True, prune_im_subj_obj=False)

Get influence map and convert it to a graph with signed nodes.

get_im(force_update=False)

Get the influence map for the model, generating it if necessary.

Parameters:force_update (bool) – Whether to generate the influence map when the function is called. If False, returns the previously generated influence map if available. Defaults to True. Returns:The influence map can be rendered as a pdf using the dot layout program as follows:

im_agraph = nx.nx_agraph.to_agraph(influence_map)
im_agraph.draw('influence_map.pdf', prog='dot')

Return type:networkx MultiDiGraph object containing the influence map.

process_statement(stmt)

This method processes the test statement to get the data about subject and object, according to the specific model requirements for model checking, e.g. PysbModelChecker gets subject monomer patterns and observables, while graph based ModelCheckers will return signed nodes corresponding to subject and object. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Parameters:stmt (indra.statements.Statement) – A statement to process. Returns:

• subj_data (list or None) – Data about statement subject to be used as source nodes.
• obj_data (list or None) – Data about statement object to be used as target nodes.
• result_code (str or None) – Result code to construct PathResult.

process_subject(subj_mp)

Processes the subject of the test statement and returns the necessary information to check the statement. In case of PysbModelChecker, method returns input_rule_set. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

prune_influence_map()

Remove edges between rules causing problematic non-transitivity.

First, all self-loops are removed. After this initial step, edges are removed between rules when they share all child nodes except for each other; that is, they have a mutual relationship with each other and share all of the same children.

Note that edges must be removed in batch at the end to prevent edge removal from affecting the lists of rule children during the comparison process.

prune_influence_map_degrade_bind_positive(model_stmts)

Prune positive edges between X degrading and X forming a complex with Y.

prune_influence_map_subj_obj()

Prune influence map to include only edges where the object of the upstream rule matches the subject of the downstream rule.

score_paths(paths, agents_values, loss_of_function=False, sigma=0.15, include_final_node=False)

Return scores associated with a given set of paths.

Parameters:

• paths (list[list[tuple[str, int]]]) – A list of paths obtained from path finding. Each path is a list of tuples (which are edges in the path), with the first element of the tuple the name of a rule, and the second element its polarity in the path.
• agents_values (dict[indra.statements.Agent, float]) – A dictionary of INDRA Agents and their corresponding measured value in a given experimental condition.
• loss_of_function (Optional[boolean]) – If True, flip the polarity of the path. For instance, if the effect of an inhibitory drug is explained, set this to True. Default: False
• sigma (Optional[float]) – The estimated standard deviation for the normally distributed measurement error in the observation model used to score paths with respect to data. Default: 0.15
• include_final_node (Optional[boolean]) – Determines whether the final node of the path is included in the score. Default: False

indra.explanation.model_checker.pysb.remove_im_params(model, im)

Remove parameter nodes from the influence map.

Parameters:

• model (pysb.core.Model) – PySB model.
• im (networkx.MultiDiGraph) – Influence map.

Returns:

Influence map with the parameter nodes removed.

Return type:

networkx.MultiDiGraph

Checking Signed Graph (indra.explanation.model_checker.signed_graph)

class indra.explanation.model_checker.signed_graph.SignedGraphModelChecker(model, statements=None, do_sampling=False, seed=None)

Check an signed MultiDiGraph against a set of INDRA statements.

Parameters:

• model (networkx.MultiDiGraph) – Signed MultiDiGraph to check.
• statements (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to check the model against.
• do_sampling (bool) – Whether to use breadth-first search or weighted sampling to generate paths. Default is False (breadth-first search).
• seed (int) – Random seed for sampling (optional, default is None).

get_graph()

Return a graph with signed nodes to find the path.

process_statement(stmt)

This method processes the test statement to get the data about subject and object, according to the specific model requirements for model checking, e.g. PysbModelChecker gets subject monomer patterns and observables, while graph based ModelCheckers will return signed nodes corresponding to subject and object. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Parameters:stmt (indra.statements.Statement) – A statement to process. Returns:

• subj_data (list or None) – Data about statement subject to be used as source nodes.
• obj_data (list or None) – Data about statement object to be used as target nodes.
• result_code (str or None) – Result code to construct PathResult.

process_subject(subj)

Processes the subject of the test statement and returns the necessary information to check the statement. In case of PysbModelChecker, method returns input_rule_set. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Checking Unsigned Graph (indra.explanation.model_checker.unsigned_graph)

class indra.explanation.model_checker.unsigned_graph.UnsignedGraphModelChecker(model, statements=None, do_sampling=False, seed=None)

Check an unsigned DiGraph against a set of INDRA statements.

Parameters:

• model (networkx.DiGraph) – Unsigned DiGraph to check.
• statements (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to check the model against.
• do_sampling (bool) – Whether to use breadth-first search or weighted sampling to generate paths. Default is False (breadth-first search).
• seed (int) – Random seed for sampling (optional, default is None).

get_graph()

Return a graph with signed nodes to find the path.

process_statement(stmt)

This method processes the test statement to get the data about subject and object, according to the specific model requirements for model checking, e.g. PysbModelChecker gets subject monomer patterns and observables, while graph based ModelCheckers will return signed nodes corresponding to subject and object. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Parameters:stmt (indra.statements.Statement) – A statement to process. Returns:

• subj_data (list or None) – Data about statement subject to be used as source nodes.
• obj_data (list or None) – Data about statement object to be used as target nodes.
• result_code (str or None) – Result code to construct PathResult.

process_subject(subj)

Processes the subject of the test statement and returns the necessary information to check the statement. In case of PysbModelChecker, method returns input_rule_set. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Checking PyBEL Graph (indra.explanation.model_checker.pybel)

class indra.explanation.model_checker.pybel.PybelModelChecker(model, statements=None, do_sampling=False, seed=None)

Check a PyBEL model against a set of INDRA statements.

Parameters:

• model (pybel.BELGraph) – A Pybel model to check.
• statements (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to check the model against.
• do_sampling (bool) – Whether to use breadth-first search or weighted sampling to generate paths. Default is False (breadth-first search).
• seed (int) – Random seed for sampling (optional, default is None).

get_graph(include_variants=False, symmetric_variant_links=False, include_components=True, symmetric_component_links=True)

Convert a PyBELGraph to a graph with signed nodes.

process_statement(stmt)

This method processes the test statement to get the data about subject and object, according to the specific model requirements for model checking, e.g. PysbModelChecker gets subject monomer patterns and observables, while graph based ModelCheckers will return signed nodes corresponding to subject and object. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.

Parameters:stmt (indra.statements.Statement) – A statement to process. Returns:

• subj_data (list or None) – Data about statement subject to be used as source nodes.
• obj_data (list or None) – Data about statement object to be used as target nodes.
• result_code (str or None) – Result code to construct PathResult.

process_subject(subj)

Processes the subject of the test statement and returns the necessary information to check the statement. In case of PysbModelChecker, method returns input_rule_set. If any of the requirements are not satisfied, result code is also returned to construct PathResult object.