## Mercurial > repos > shellac > sam_consensus_v3

### view env/lib/python3.9/site-packages/networkx/algorithms/chordal.py @ 0:4f3585e2f14b draft default tip

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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |

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""" Algorithms for chordal graphs. A graph is chordal if every cycle of length at least 4 has a chord (an edge joining two nodes not adjacent in the cycle). https://en.wikipedia.org/wiki/Chordal_graph """ import sys import warnings import networkx as nx from networkx.algorithms.components import connected_components from networkx.utils import arbitrary_element, not_implemented_for __all__ = [ "is_chordal", "find_induced_nodes", "chordal_graph_cliques", "chordal_graph_treewidth", "NetworkXTreewidthBoundExceeded", "complete_to_chordal_graph", ] class NetworkXTreewidthBoundExceeded(nx.NetworkXException): """Exception raised when a treewidth bound has been provided and it has been exceeded""" def is_chordal(G): """Checks whether G is a chordal graph. A graph is chordal if every cycle of length at least 4 has a chord (an edge joining two nodes not adjacent in the cycle). Parameters ---------- G : graph A NetworkX graph. Returns ------- chordal : bool True if G is a chordal graph and False otherwise. Raises ------ NetworkXError The algorithm does not support DiGraph, MultiGraph and MultiDiGraph. If the input graph is an instance of one of these classes, a :exc:`NetworkXError` is raised. Examples -------- >>> e = [ ... (1, 2), ... (1, 3), ... (2, 3), ... (2, 4), ... (3, 4), ... (3, 5), ... (3, 6), ... (4, 5), ... (4, 6), ... (5, 6), ... ] >>> G = nx.Graph(e) >>> nx.is_chordal(G) True Notes ----- The routine tries to go through every node following maximum cardinality search. It returns False when it finds that the separator for any node is not a clique. Based on the algorithms in [1]_. References ---------- .. [1] R. E. Tarjan and M. Yannakakis, Simple linear-time algorithms to test chordality of graphs, test acyclicity of hypergraphs, and selectively reduce acyclic hypergraphs, SIAM J. Comput., 13 (1984), pp. 566–579. """ if G.is_directed(): raise nx.NetworkXError("Directed graphs not supported") if G.is_multigraph(): raise nx.NetworkXError("Multiply connected graphs not supported.") if len(_find_chordality_breaker(G)) == 0: return True else: return False def find_induced_nodes(G, s, t, treewidth_bound=sys.maxsize): """Returns the set of induced nodes in the path from s to t. Parameters ---------- G : graph A chordal NetworkX graph s : node Source node to look for induced nodes t : node Destination node to look for induced nodes treewith_bound: float Maximum treewidth acceptable for the graph H. The search for induced nodes will end as soon as the treewidth_bound is exceeded. Returns ------- Induced_nodes : Set of nodes The set of induced nodes in the path from s to t in G Raises ------ NetworkXError The algorithm does not support DiGraph, MultiGraph and MultiDiGraph. If the input graph is an instance of one of these classes, a :exc:`NetworkXError` is raised. The algorithm can only be applied to chordal graphs. If the input graph is found to be non-chordal, a :exc:`NetworkXError` is raised. Examples -------- >>> G = nx.Graph() >>> G = nx.generators.classic.path_graph(10) >>> induced_nodes = nx.find_induced_nodes(G, 1, 9, 2) >>> sorted(induced_nodes) [1, 2, 3, 4, 5, 6, 7, 8, 9] Notes ----- G must be a chordal graph and (s,t) an edge that is not in G. If a treewidth_bound is provided, the search for induced nodes will end as soon as the treewidth_bound is exceeded. The algorithm is inspired by Algorithm 4 in [1]_. A formal definition of induced node can also be found on that reference. References ---------- .. [1] Learning Bounded Treewidth Bayesian Networks. Gal Elidan, Stephen Gould; JMLR, 9(Dec):2699--2731, 2008. http://jmlr.csail.mit.edu/papers/volume9/elidan08a/elidan08a.pdf """ if not is_chordal(G): raise nx.NetworkXError("Input graph is not chordal.") H = nx.Graph(G) H.add_edge(s, t) Induced_nodes = set() triplet = _find_chordality_breaker(H, s, treewidth_bound) while triplet: (u, v, w) = triplet Induced_nodes.update(triplet) for n in triplet: if n != s: H.add_edge(s, n) triplet = _find_chordality_breaker(H, s, treewidth_bound) if Induced_nodes: # Add t and the second node in the induced path from s to t. Induced_nodes.add(t) for u in G[s]: if len(Induced_nodes & set(G[u])) == 2: Induced_nodes.add(u) break return Induced_nodes def chordal_graph_cliques(G): """Returns the set of maximal cliques of a chordal graph. The algorithm breaks the graph in connected components and performs a maximum cardinality search in each component to get the cliques. Parameters ---------- G : graph A NetworkX graph Returns ------- cliques : A set containing the maximal cliques in G. Raises ------ NetworkXError The algorithm does not support DiGraph, MultiGraph and MultiDiGraph. If the input graph is an instance of one of these classes, a :exc:`NetworkXError` is raised. The algorithm can only be applied to chordal graphs. If the input graph is found to be non-chordal, a :exc:`NetworkXError` is raised. Examples -------- >>> e = [ ... (1, 2), ... (1, 3), ... (2, 3), ... (2, 4), ... (3, 4), ... (3, 5), ... (3, 6), ... (4, 5), ... (4, 6), ... (5, 6), ... (7, 8), ... ] >>> G = nx.Graph(e) >>> G.add_node(9) >>> setlist = nx.chordal_graph_cliques(G) """ msg = "This will return a generator in 3.0." warnings.warn(msg, DeprecationWarning) return {c for c in _chordal_graph_cliques(G)} def chordal_graph_treewidth(G): """Returns the treewidth of the chordal graph G. Parameters ---------- G : graph A NetworkX graph Returns ------- treewidth : int The size of the largest clique in the graph minus one. Raises ------ NetworkXError The algorithm does not support DiGraph, MultiGraph and MultiDiGraph. If the input graph is an instance of one of these classes, a :exc:`NetworkXError` is raised. The algorithm can only be applied to chordal graphs. If the input graph is found to be non-chordal, a :exc:`NetworkXError` is raised. Examples -------- >>> e = [ ... (1, 2), ... (1, 3), ... (2, 3), ... (2, 4), ... (3, 4), ... (3, 5), ... (3, 6), ... (4, 5), ... (4, 6), ... (5, 6), ... (7, 8), ... ] >>> G = nx.Graph(e) >>> G.add_node(9) >>> nx.chordal_graph_treewidth(G) 3 References ---------- .. [1] https://en.wikipedia.org/wiki/Tree_decomposition#Treewidth """ if not is_chordal(G): raise nx.NetworkXError("Input graph is not chordal.") max_clique = -1 for clique in nx.chordal_graph_cliques(G): max_clique = max(max_clique, len(clique)) return max_clique - 1 def _is_complete_graph(G): """Returns True if G is a complete graph.""" if nx.number_of_selfloops(G) > 0: raise nx.NetworkXError("Self loop found in _is_complete_graph()") n = G.number_of_nodes() if n < 2: return True e = G.number_of_edges() max_edges = (n * (n - 1)) / 2 return e == max_edges def _find_missing_edge(G): """ Given a non-complete graph G, returns a missing edge.""" nodes = set(G) for u in G: missing = nodes - set(list(G[u].keys()) + [u]) if missing: return (u, missing.pop()) def _max_cardinality_node(G, choices, wanna_connect): """Returns a the node in choices that has more connections in G to nodes in wanna_connect. """ max_number = -1 for x in choices: number = len([y for y in G[x] if y in wanna_connect]) if number > max_number: max_number = number max_cardinality_node = x return max_cardinality_node def _find_chordality_breaker(G, s=None, treewidth_bound=sys.maxsize): """ Given a graph G, starts a max cardinality search (starting from s if s is given and from an arbitrary node otherwise) trying to find a non-chordal cycle. If it does find one, it returns (u,v,w) where u,v,w are the three nodes that together with s are involved in the cycle. """ unnumbered = set(G) if s is None: s = arbitrary_element(G) unnumbered.remove(s) numbered = {s} current_treewidth = -1 while unnumbered: # and current_treewidth <= treewidth_bound: v = _max_cardinality_node(G, unnumbered, numbered) unnumbered.remove(v) numbered.add(v) clique_wanna_be = set(G[v]) & numbered sg = G.subgraph(clique_wanna_be) if _is_complete_graph(sg): # The graph seems to be chordal by now. We update the treewidth current_treewidth = max(current_treewidth, len(clique_wanna_be)) if current_treewidth > treewidth_bound: raise nx.NetworkXTreewidthBoundExceeded( f"treewidth_bound exceeded: {current_treewidth}" ) else: # sg is not a clique, # look for an edge that is not included in sg (u, w) = _find_missing_edge(sg) return (u, v, w) return () def _chordal_graph_cliques(G): """Returns all maximal cliques of a chordal graph. The algorithm breaks the graph in connected components and performs a maximum cardinality search in each component to get the cliques. Parameters ---------- G : graph A NetworkX graph Returns ------- iterator An iterator over maximal cliques, each of which is a frozenset of nodes in `G`. The order of cliques is arbitrary. Raises ------ NetworkXError The algorithm does not support DiGraph, MultiGraph and MultiDiGraph. If the input graph is an instance of one of these classes, a :exc:`NetworkXError` is raised. The algorithm can only be applied to chordal graphs. If the input graph is found to be non-chordal, a :exc:`NetworkXError` is raised. Examples -------- >>> e = [ ... (1, 2), ... (1, 3), ... (2, 3), ... (2, 4), ... (3, 4), ... (3, 5), ... (3, 6), ... (4, 5), ... (4, 6), ... (5, 6), ... (7, 8), ... ] >>> G = nx.Graph(e) >>> G.add_node(9) >>> cliques = [c for c in _chordal_graph_cliques(G)] >>> cliques[0] frozenset({1, 2, 3}) """ if not is_chordal(G): raise nx.NetworkXError("Input graph is not chordal.") for C in (G.subgraph(c).copy() for c in connected_components(G)): if C.number_of_nodes() == 1: yield frozenset(C.nodes()) else: unnumbered = set(C.nodes()) v = arbitrary_element(C) unnumbered.remove(v) numbered = {v} clique_wanna_be = {v} while unnumbered: v = _max_cardinality_node(C, unnumbered, numbered) unnumbered.remove(v) numbered.add(v) new_clique_wanna_be = set(C.neighbors(v)) & numbered sg = C.subgraph(clique_wanna_be) if _is_complete_graph(sg): new_clique_wanna_be.add(v) if not new_clique_wanna_be >= clique_wanna_be: yield frozenset(clique_wanna_be) clique_wanna_be = new_clique_wanna_be else: raise nx.NetworkXError("Input graph is not chordal.") yield frozenset(clique_wanna_be) @not_implemented_for("directed") def complete_to_chordal_graph(G): """Return a copy of G completed to a chordal graph Adds edges to a copy of G to create a chordal graph. A graph G=(V,E) is called chordal if for each cycle with length bigger than 3, there exist two non-adjacent nodes connected by an edge (called a chord). Parameters ---------- G : NetworkX graph Undirected graph Returns ------- H : NetworkX graph The chordal enhancement of G alpha : Dictionary The elimination ordering of nodes of G Notes ------ There are different approaches to calculate the chordal enhancement of a graph. The algorithm used here is called MCS-M and gives at least minimal (local) triangulation of graph. Note that this triangulation is not necessarily a global minimum. https://en.wikipedia.org/wiki/Chordal_graph References ---------- .. [1] Berry, Anne & Blair, Jean & Heggernes, Pinar & Peyton, Barry. (2004) Maximum Cardinality Search for Computing Minimal Triangulations of Graphs. Algorithmica. 39. 287-298. 10.1007/s00453-004-1084-3. Examples -------- >>> from networkx.algorithms.chordal import complete_to_chordal_graph >>> G = nx.wheel_graph(10) >>> H, alpha = complete_to_chordal_graph(G) """ H = G.copy() alpha = {node: 0 for node in H} if nx.is_chordal(H): return H, alpha chords = set() weight = {node: 0 for node in H.nodes()} unnumbered_nodes = list(H.nodes()) for i in range(len(H.nodes()), 0, -1): # get the node in unnumbered_nodes with the maximum weight z = max(unnumbered_nodes, key=lambda node: weight[node]) unnumbered_nodes.remove(z) alpha[z] = i update_nodes = [] for y in unnumbered_nodes: if G.has_edge(y, z): update_nodes.append(y) else: # y_weight will be bigger than node weights between y and z y_weight = weight[y] lower_nodes = [ node for node in unnumbered_nodes if weight[node] < y_weight ] if nx.has_path(H.subgraph(lower_nodes + [z, y]), y, z): update_nodes.append(y) chords.add((z, y)) # during calculation of paths the weights should not be updated for node in update_nodes: weight[node] += 1 H.add_edges_from(chords) return H, alpha