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| """Functions for finding and manipulating cliques. | |
| Finding the largest clique in a graph is NP-complete problem, so most of | |
| these algorithms have an exponential running time; for more information, | |
| see the Wikipedia article on the clique problem [1]_. | |
| .. [1] clique problem:: https://en.wikipedia.org/wiki/Clique_problem | |
| """ | |
| from collections import Counter, defaultdict, deque | |
| from itertools import chain, combinations, islice | |
| import networkx as nx | |
| from networkx.utils import not_implemented_for | |
| __all__ = [ | |
| "find_cliques", | |
| "find_cliques_recursive", | |
| "make_max_clique_graph", | |
| "make_clique_bipartite", | |
| "node_clique_number", | |
| "number_of_cliques", | |
| "enumerate_all_cliques", | |
| "max_weight_clique", | |
| ] | |
| def enumerate_all_cliques(G): | |
| """Returns all cliques in an undirected graph. | |
| This function returns an iterator over cliques, each of which is a | |
| list of nodes. The iteration is ordered by cardinality of the | |
| cliques: first all cliques of size one, then all cliques of size | |
| two, etc. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| An undirected graph. | |
| Returns | |
| ------- | |
| iterator | |
| An iterator over cliques, each of which is a list of nodes in | |
| `G`. The cliques are ordered according to size. | |
| Notes | |
| ----- | |
| To obtain a list of all cliques, use | |
| `list(enumerate_all_cliques(G))`. However, be aware that in the | |
| worst-case, the length of this list can be exponential in the number | |
| of nodes in the graph (for example, when the graph is the complete | |
| graph). This function avoids storing all cliques in memory by only | |
| keeping current candidate node lists in memory during its search. | |
| The implementation is adapted from the algorithm by Zhang, et | |
| al. (2005) [1]_ to output all cliques discovered. | |
| This algorithm ignores self-loops and parallel edges, since cliques | |
| are not conventionally defined with such edges. | |
| References | |
| ---------- | |
| .. [1] Yun Zhang, Abu-Khzam, F.N., Baldwin, N.E., Chesler, E.J., | |
| Langston, M.A., Samatova, N.F., | |
| "Genome-Scale Computational Approaches to Memory-Intensive | |
| Applications in Systems Biology". | |
| *Supercomputing*, 2005. Proceedings of the ACM/IEEE SC 2005 | |
| Conference, pp. 12, 12--18 Nov. 2005. | |
| <https://doi.org/10.1109/SC.2005.29>. | |
| """ | |
| index = {} | |
| nbrs = {} | |
| for u in G: | |
| index[u] = len(index) | |
| # Neighbors of u that appear after u in the iteration order of G. | |
| nbrs[u] = {v for v in G[u] if v not in index} | |
| queue = deque(([u], sorted(nbrs[u], key=index.__getitem__)) for u in G) | |
| # Loop invariants: | |
| # 1. len(base) is nondecreasing. | |
| # 2. (base + cnbrs) is sorted with respect to the iteration order of G. | |
| # 3. cnbrs is a set of common neighbors of nodes in base. | |
| while queue: | |
| base, cnbrs = map(list, queue.popleft()) | |
| yield base | |
| for i, u in enumerate(cnbrs): | |
| # Use generators to reduce memory consumption. | |
| queue.append( | |
| ( | |
| chain(base, [u]), | |
| filter(nbrs[u].__contains__, islice(cnbrs, i + 1, None)), | |
| ) | |
| ) | |
| def find_cliques(G, nodes=None): | |
| """Returns all maximal cliques in an undirected graph. | |
| For each node *n*, a *maximal clique for n* is a largest complete | |
| subgraph containing *n*. The largest maximal clique is sometimes | |
| called the *maximum clique*. | |
| This function returns an iterator over cliques, each of which is a | |
| list of nodes. It is an iterative implementation, so should not | |
| suffer from recursion depth issues. | |
| This function accepts a list of `nodes` and only the maximal cliques | |
| containing all of these `nodes` are returned. It can considerably speed up | |
| the running time if some specific cliques are desired. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| An undirected graph. | |
| nodes : list, optional (default=None) | |
| If provided, only yield *maximal cliques* containing all nodes in `nodes`. | |
| If `nodes` isn't a clique itself, a ValueError is raised. | |
| Returns | |
| ------- | |
| iterator | |
| An iterator over maximal cliques, each of which is a list of | |
| nodes in `G`. If `nodes` is provided, only the maximal cliques | |
| containing all the nodes in `nodes` are returned. The order of | |
| cliques is arbitrary. | |
| Raises | |
| ------ | |
| ValueError | |
| If `nodes` is not a clique. | |
| Examples | |
| -------- | |
| >>> from pprint import pprint # For nice dict formatting | |
| >>> G = nx.karate_club_graph() | |
| >>> sum(1 for c in nx.find_cliques(G)) # The number of maximal cliques in G | |
| 36 | |
| >>> max(nx.find_cliques(G), key=len) # The largest maximal clique in G | |
| [0, 1, 2, 3, 13] | |
| The size of the largest maximal clique is known as the *clique number* of | |
| the graph, which can be found directly with: | |
| >>> max(len(c) for c in nx.find_cliques(G)) | |
| 5 | |
| One can also compute the number of maximal cliques in `G` that contain a given | |
| node. The following produces a dictionary keyed by node whose | |
| values are the number of maximal cliques in `G` that contain the node: | |
| >>> from collections import Counter | |
| >>> from itertools import chain | |
| >>> counts = Counter(chain.from_iterable(nx.find_cliques(G))) | |
| >>> pprint(dict(counts)) | |
| {0: 13, | |
| 1: 6, | |
| 2: 7, | |
| 3: 3, | |
| 4: 2, | |
| 5: 3, | |
| 6: 3, | |
| 7: 1, | |
| 8: 3, | |
| 9: 2, | |
| 10: 2, | |
| 11: 1, | |
| 12: 1, | |
| 13: 2, | |
| 14: 1, | |
| 15: 1, | |
| 16: 1, | |
| 17: 1, | |
| 18: 1, | |
| 19: 2, | |
| 20: 1, | |
| 21: 1, | |
| 22: 1, | |
| 23: 3, | |
| 24: 2, | |
| 25: 2, | |
| 26: 1, | |
| 27: 3, | |
| 28: 2, | |
| 29: 2, | |
| 30: 2, | |
| 31: 4, | |
| 32: 9, | |
| 33: 14} | |
| Or, similarly, the maximal cliques in `G` that contain a given node. | |
| For example, the 4 maximal cliques that contain node 31: | |
| >>> [c for c in nx.find_cliques(G) if 31 in c] | |
| [[0, 31], [33, 32, 31], [33, 28, 31], [24, 25, 31]] | |
| See Also | |
| -------- | |
| find_cliques_recursive | |
| A recursive version of the same algorithm. | |
| Notes | |
| ----- | |
| To obtain a list of all maximal cliques, use | |
| `list(find_cliques(G))`. However, be aware that in the worst-case, | |
| the length of this list can be exponential in the number of nodes in | |
| the graph. This function avoids storing all cliques in memory by | |
| only keeping current candidate node lists in memory during its search. | |
| This implementation is based on the algorithm published by Bron and | |
| Kerbosch (1973) [1]_, as adapted by Tomita, Tanaka and Takahashi | |
| (2006) [2]_ and discussed in Cazals and Karande (2008) [3]_. It | |
| essentially unrolls the recursion used in the references to avoid | |
| issues of recursion stack depth (for a recursive implementation, see | |
| :func:`find_cliques_recursive`). | |
| This algorithm ignores self-loops and parallel edges, since cliques | |
| are not conventionally defined with such edges. | |
| References | |
| ---------- | |
| .. [1] Bron, C. and Kerbosch, J. | |
| "Algorithm 457: finding all cliques of an undirected graph". | |
| *Communications of the ACM* 16, 9 (Sep. 1973), 575--577. | |
| <http://portal.acm.org/citation.cfm?doid=362342.362367> | |
| .. [2] Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi, | |
| "The worst-case time complexity for generating all maximal | |
| cliques and computational experiments", | |
| *Theoretical Computer Science*, Volume 363, Issue 1, | |
| Computing and Combinatorics, | |
| 10th Annual International Conference on | |
| Computing and Combinatorics (COCOON 2004), 25 October 2006, Pages 28--42 | |
| <https://doi.org/10.1016/j.tcs.2006.06.015> | |
| .. [3] F. Cazals, C. Karande, | |
| "A note on the problem of reporting maximal cliques", | |
| *Theoretical Computer Science*, | |
| Volume 407, Issues 1--3, 6 November 2008, Pages 564--568, | |
| <https://doi.org/10.1016/j.tcs.2008.05.010> | |
| """ | |
| if len(G) == 0: | |
| return | |
| adj = {u: {v for v in G[u] if v != u} for u in G} | |
| # Initialize Q with the given nodes and subg, cand with their nbrs | |
| Q = nodes[:] if nodes is not None else [] | |
| cand = set(G) | |
| for node in Q: | |
| if node not in cand: | |
| raise ValueError(f"The given `nodes` {nodes} do not form a clique") | |
| cand &= adj[node] | |
| if not cand: | |
| yield Q[:] | |
| return | |
| subg = cand.copy() | |
| stack = [] | |
| Q.append(None) | |
| u = max(subg, key=lambda u: len(cand & adj[u])) | |
| ext_u = cand - adj[u] | |
| try: | |
| while True: | |
| if ext_u: | |
| q = ext_u.pop() | |
| cand.remove(q) | |
| Q[-1] = q | |
| adj_q = adj[q] | |
| subg_q = subg & adj_q | |
| if not subg_q: | |
| yield Q[:] | |
| else: | |
| cand_q = cand & adj_q | |
| if cand_q: | |
| stack.append((subg, cand, ext_u)) | |
| Q.append(None) | |
| subg = subg_q | |
| cand = cand_q | |
| u = max(subg, key=lambda u: len(cand & adj[u])) | |
| ext_u = cand - adj[u] | |
| else: | |
| Q.pop() | |
| subg, cand, ext_u = stack.pop() | |
| except IndexError: | |
| pass | |
| def find_cliques_recursive(G, nodes=None): | |
| """Returns all maximal cliques in a graph. | |
| For each node *v*, a *maximal clique for v* is a largest complete | |
| subgraph containing *v*. The largest maximal clique is sometimes | |
| called the *maximum clique*. | |
| This function returns an iterator over cliques, each of which is a | |
| list of nodes. It is a recursive implementation, so may suffer from | |
| recursion depth issues, but is included for pedagogical reasons. | |
| For a non-recursive implementation, see :func:`find_cliques`. | |
| This function accepts a list of `nodes` and only the maximal cliques | |
| containing all of these `nodes` are returned. It can considerably speed up | |
| the running time if some specific cliques are desired. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| An undirected graph. | |
| nodes : list, optional (default=None) | |
| If provided, only yield *maximal cliques* containing all nodes in `nodes`. | |
| If `nodes` isn't a clique itself, a ValueError is raised. | |
| Returns | |
| ------- | |
| iterator | |
| An iterator over maximal cliques, each of which is a list of | |
| nodes in `G`. If `nodes` is provided, only the maximal cliques | |
| containing all the nodes in `nodes` are yielded. The order of | |
| cliques is arbitrary. | |
| Raises | |
| ------ | |
| NetworkXNotImplemented | |
| If `G` is directed. | |
| ValueError | |
| If `nodes` is not a clique. | |
| See Also | |
| -------- | |
| find_cliques | |
| An iterative version of the same algorithm. See docstring for examples. | |
| Notes | |
| ----- | |
| To obtain a list of all maximal cliques, use | |
| `list(find_cliques_recursive(G))`. However, be aware that in the | |
| worst-case, the length of this list can be exponential in the number | |
| of nodes in the graph. This function avoids storing all cliques in memory | |
| by only keeping current candidate node lists in memory during its search. | |
| This implementation is based on the algorithm published by Bron and | |
| Kerbosch (1973) [1]_, as adapted by Tomita, Tanaka and Takahashi | |
| (2006) [2]_ and discussed in Cazals and Karande (2008) [3]_. For a | |
| non-recursive implementation, see :func:`find_cliques`. | |
| This algorithm ignores self-loops and parallel edges, since cliques | |
| are not conventionally defined with such edges. | |
| References | |
| ---------- | |
| .. [1] Bron, C. and Kerbosch, J. | |
| "Algorithm 457: finding all cliques of an undirected graph". | |
| *Communications of the ACM* 16, 9 (Sep. 1973), 575--577. | |
| <http://portal.acm.org/citation.cfm?doid=362342.362367> | |
| .. [2] Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi, | |
| "The worst-case time complexity for generating all maximal | |
| cliques and computational experiments", | |
| *Theoretical Computer Science*, Volume 363, Issue 1, | |
| Computing and Combinatorics, | |
| 10th Annual International Conference on | |
| Computing and Combinatorics (COCOON 2004), 25 October 2006, Pages 28--42 | |
| <https://doi.org/10.1016/j.tcs.2006.06.015> | |
| .. [3] F. Cazals, C. Karande, | |
| "A note on the problem of reporting maximal cliques", | |
| *Theoretical Computer Science*, | |
| Volume 407, Issues 1--3, 6 November 2008, Pages 564--568, | |
| <https://doi.org/10.1016/j.tcs.2008.05.010> | |
| """ | |
| if len(G) == 0: | |
| return iter([]) | |
| adj = {u: {v for v in G[u] if v != u} for u in G} | |
| # Initialize Q with the given nodes and subg, cand with their nbrs | |
| Q = nodes[:] if nodes is not None else [] | |
| cand_init = set(G) | |
| for node in Q: | |
| if node not in cand_init: | |
| raise ValueError(f"The given `nodes` {nodes} do not form a clique") | |
| cand_init &= adj[node] | |
| if not cand_init: | |
| return iter([Q]) | |
| subg_init = cand_init.copy() | |
| def expand(subg, cand): | |
| u = max(subg, key=lambda u: len(cand & adj[u])) | |
| for q in cand - adj[u]: | |
| cand.remove(q) | |
| Q.append(q) | |
| adj_q = adj[q] | |
| subg_q = subg & adj_q | |
| if not subg_q: | |
| yield Q[:] | |
| else: | |
| cand_q = cand & adj_q | |
| if cand_q: | |
| yield from expand(subg_q, cand_q) | |
| Q.pop() | |
| return expand(subg_init, cand_init) | |
| def make_max_clique_graph(G, create_using=None): | |
| """Returns the maximal clique graph of the given graph. | |
| The nodes of the maximal clique graph of `G` are the cliques of | |
| `G` and an edge joins two cliques if the cliques are not disjoint. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| create_using : NetworkX graph constructor, optional (default=nx.Graph) | |
| Graph type to create. If graph instance, then cleared before populated. | |
| Returns | |
| ------- | |
| NetworkX graph | |
| A graph whose nodes are the cliques of `G` and whose edges | |
| join two cliques if they are not disjoint. | |
| Notes | |
| ----- | |
| This function behaves like the following code:: | |
| import networkx as nx | |
| G = nx.make_clique_bipartite(G) | |
| cliques = [v for v in G.nodes() if G.nodes[v]["bipartite"] == 0] | |
| G = nx.bipartite.projected_graph(G, cliques) | |
| G = nx.relabel_nodes(G, {-v: v - 1 for v in G}) | |
| It should be faster, though, since it skips all the intermediate | |
| steps. | |
| """ | |
| if create_using is None: | |
| B = G.__class__() | |
| else: | |
| B = nx.empty_graph(0, create_using) | |
| cliques = list(enumerate(set(c) for c in find_cliques(G))) | |
| # Add a numbered node for each clique. | |
| B.add_nodes_from(i for i, c in cliques) | |
| # Join cliques by an edge if they share a node. | |
| clique_pairs = combinations(cliques, 2) | |
| B.add_edges_from((i, j) for (i, c1), (j, c2) in clique_pairs if c1 & c2) | |
| return B | |
| def make_clique_bipartite(G, fpos=None, create_using=None, name=None): | |
| """Returns the bipartite clique graph corresponding to `G`. | |
| In the returned bipartite graph, the "bottom" nodes are the nodes of | |
| `G` and the "top" nodes represent the maximal cliques of `G`. | |
| There is an edge from node *v* to clique *C* in the returned graph | |
| if and only if *v* is an element of *C*. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| An undirected graph. | |
| fpos : bool | |
| If True or not None, the returned graph will have an | |
| additional attribute, `pos`, a dictionary mapping node to | |
| position in the Euclidean plane. | |
| create_using : NetworkX graph constructor, optional (default=nx.Graph) | |
| Graph type to create. If graph instance, then cleared before populated. | |
| Returns | |
| ------- | |
| NetworkX graph | |
| A bipartite graph whose "bottom" set is the nodes of the graph | |
| `G`, whose "top" set is the cliques of `G`, and whose edges | |
| join nodes of `G` to the cliques that contain them. | |
| The nodes of the graph `G` have the node attribute | |
| 'bipartite' set to 1 and the nodes representing cliques | |
| have the node attribute 'bipartite' set to 0, as is the | |
| convention for bipartite graphs in NetworkX. | |
| """ | |
| B = nx.empty_graph(0, create_using) | |
| B.clear() | |
| # The "bottom" nodes in the bipartite graph are the nodes of the | |
| # original graph, G. | |
| B.add_nodes_from(G, bipartite=1) | |
| for i, cl in enumerate(find_cliques(G)): | |
| # The "top" nodes in the bipartite graph are the cliques. These | |
| # nodes get negative numbers as labels. | |
| name = -i - 1 | |
| B.add_node(name, bipartite=0) | |
| B.add_edges_from((v, name) for v in cl) | |
| return B | |
| def node_clique_number(G, nodes=None, cliques=None, separate_nodes=False): | |
| """Returns the size of the largest maximal clique containing each given node. | |
| Returns a single or list depending on input nodes. | |
| An optional list of cliques can be input if already computed. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| An undirected graph. | |
| cliques : list, optional (default=None) | |
| A list of cliques, each of which is itself a list of nodes. | |
| If not specified, the list of all cliques will be computed | |
| using :func:`find_cliques`. | |
| Returns | |
| ------- | |
| int or dict | |
| If `nodes` is a single node, returns the size of the | |
| largest maximal clique in `G` containing that node. | |
| Otherwise return a dict keyed by node to the size | |
| of the largest maximal clique containing that node. | |
| See Also | |
| -------- | |
| find_cliques | |
| find_cliques yields the maximal cliques of G. | |
| It accepts a `nodes` argument which restricts consideration to | |
| maximal cliques containing all the given `nodes`. | |
| The search for the cliques is optimized for `nodes`. | |
| number_of_cliques | |
| """ | |
| if cliques is None: | |
| if nodes is not None: | |
| # Use ego_graph to decrease size of graph | |
| # check for single node | |
| if nodes in G: | |
| return max(len(c) for c in find_cliques(nx.ego_graph(G, nodes))) | |
| # handle multiple nodes | |
| return { | |
| n: max(len(c) for c in find_cliques(nx.ego_graph(G, n))) for n in nodes | |
| } | |
| # nodes is None--find all cliques | |
| cliques = list(find_cliques(G)) | |
| # single node requested | |
| if nodes in G: | |
| return max(len(c) for c in cliques if nodes in c) | |
| # multiple nodes requested | |
| # preprocess all nodes (faster than one at a time for even 2 nodes) | |
| size_for_n = defaultdict(int) | |
| for c in cliques: | |
| size_of_c = len(c) | |
| for n in c: | |
| if size_for_n[n] < size_of_c: | |
| size_for_n[n] = size_of_c | |
| if nodes is None: | |
| return size_for_n | |
| return {n: size_for_n[n] for n in nodes} | |
| def number_of_cliques(G, nodes=None, cliques=None): | |
| """Return the number of maximal cliques each node is part of. | |
| Output is a single value or dict depending on `nodes`. | |
| Optional list of cliques can be input if already computed. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| An undirected graph. | |
| nodes : list or None, optional (default=None) | |
| A list of nodes to return the number of maximal cliques for. | |
| If `None`, return the number of maximal cliques for all nodes. | |
| cliques : list or None, optional (default=None) | |
| A precomputed list of maximal cliques to use for the calculation. | |
| Returns | |
| ------- | |
| int or dict | |
| If `nodes` is a single node, return the number of maximal cliques it is | |
| part of. If `nodes` is a list, return a dictionary keyed by node to the | |
| number of maximal cliques it is part of. | |
| Raises | |
| ------ | |
| NetworkXNotImplemented | |
| If `G` is directed. | |
| See Also | |
| -------- | |
| find_cliques | |
| node_clique_number | |
| Examples | |
| -------- | |
| Compute the number of maximal cliques a node is part of: | |
| >>> G = nx.complete_graph(3) | |
| >>> nx.add_cycle(G, [0, 3, 4]) | |
| >>> nx.number_of_cliques(G, nodes=0) | |
| 2 | |
| >>> nx.number_of_cliques(G, nodes=1) | |
| 1 | |
| Or, for a list of nodes: | |
| >>> nx.number_of_cliques(G, nodes=[0, 1]) | |
| {0: 2, 1: 1} | |
| If no explicit `nodes` are provided, all nodes are considered: | |
| >>> nx.number_of_cliques(G) | |
| {0: 2, 1: 1, 2: 1, 3: 1, 4: 1} | |
| The list of maximal cliques can also be precomputed: | |
| >>> cl = list(nx.find_cliques(G)) | |
| >>> nx.number_of_cliques(G, cliques=cl) | |
| {0: 2, 1: 1, 2: 1, 3: 1, 4: 1} | |
| """ | |
| if cliques is None: | |
| cliques = find_cliques(G) | |
| if nodes is None: | |
| nodes = list(G.nodes()) # none, get entire graph | |
| if not isinstance(nodes, list): # check for a list | |
| v = nodes | |
| # assume it is a single value | |
| numcliq = sum(1 for c in cliques if v in c) | |
| else: | |
| numcliq = Counter(chain.from_iterable(cliques)) | |
| numcliq = {v: numcliq[v] for v in nodes} # return a dict | |
| return numcliq | |
| class MaxWeightClique: | |
| """A class for the maximum weight clique algorithm. | |
| This class is a helper for the `max_weight_clique` function. The class | |
| should not normally be used directly. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| The undirected graph for which a maximum weight clique is sought | |
| weight : string or None, optional (default='weight') | |
| The node attribute that holds the integer value used as a weight. | |
| If None, then each node has weight 1. | |
| Attributes | |
| ---------- | |
| G : NetworkX graph | |
| The undirected graph for which a maximum weight clique is sought | |
| node_weights: dict | |
| The weight of each node | |
| incumbent_nodes : list | |
| The nodes of the incumbent clique (the best clique found so far) | |
| incumbent_weight: int | |
| The weight of the incumbent clique | |
| """ | |
| def __init__(self, G, weight): | |
| self.G = G | |
| self.incumbent_nodes = [] | |
| self.incumbent_weight = 0 | |
| if weight is None: | |
| self.node_weights = {v: 1 for v in G.nodes()} | |
| else: | |
| for v in G.nodes(): | |
| if weight not in G.nodes[v]: | |
| errmsg = f"Node {v!r} does not have the requested weight field." | |
| raise KeyError(errmsg) | |
| if not isinstance(G.nodes[v][weight], int): | |
| errmsg = f"The {weight!r} field of node {v!r} is not an integer." | |
| raise ValueError(errmsg) | |
| self.node_weights = {v: G.nodes[v][weight] for v in G.nodes()} | |
| def update_incumbent_if_improved(self, C, C_weight): | |
| """Update the incumbent if the node set C has greater weight. | |
| C is assumed to be a clique. | |
| """ | |
| if C_weight > self.incumbent_weight: | |
| self.incumbent_nodes = C[:] | |
| self.incumbent_weight = C_weight | |
| def greedily_find_independent_set(self, P): | |
| """Greedily find an independent set of nodes from a set of | |
| nodes P.""" | |
| independent_set = [] | |
| P = P[:] | |
| while P: | |
| v = P[0] | |
| independent_set.append(v) | |
| P = [w for w in P if v != w and not self.G.has_edge(v, w)] | |
| return independent_set | |
| def find_branching_nodes(self, P, target): | |
| """Find a set of nodes to branch on.""" | |
| residual_wt = {v: self.node_weights[v] for v in P} | |
| total_wt = 0 | |
| P = P[:] | |
| while P: | |
| independent_set = self.greedily_find_independent_set(P) | |
| min_wt_in_class = min(residual_wt[v] for v in independent_set) | |
| total_wt += min_wt_in_class | |
| if total_wt > target: | |
| break | |
| for v in independent_set: | |
| residual_wt[v] -= min_wt_in_class | |
| P = [v for v in P if residual_wt[v] != 0] | |
| return P | |
| def expand(self, C, C_weight, P): | |
| """Look for the best clique that contains all the nodes in C and zero or | |
| more of the nodes in P, backtracking if it can be shown that no such | |
| clique has greater weight than the incumbent. | |
| """ | |
| self.update_incumbent_if_improved(C, C_weight) | |
| branching_nodes = self.find_branching_nodes(P, self.incumbent_weight - C_weight) | |
| while branching_nodes: | |
| v = branching_nodes.pop() | |
| P.remove(v) | |
| new_C = C + [v] | |
| new_C_weight = C_weight + self.node_weights[v] | |
| new_P = [w for w in P if self.G.has_edge(v, w)] | |
| self.expand(new_C, new_C_weight, new_P) | |
| def find_max_weight_clique(self): | |
| """Find a maximum weight clique.""" | |
| # Sort nodes in reverse order of degree for speed | |
| nodes = sorted(self.G.nodes(), key=lambda v: self.G.degree(v), reverse=True) | |
| nodes = [v for v in nodes if self.node_weights[v] > 0] | |
| self.expand([], 0, nodes) | |
| def max_weight_clique(G, weight="weight"): | |
| """Find a maximum weight clique in G. | |
| A *clique* in a graph is a set of nodes such that every two distinct nodes | |
| are adjacent. The *weight* of a clique is the sum of the weights of its | |
| nodes. A *maximum weight clique* of graph G is a clique C in G such that | |
| no clique in G has weight greater than the weight of C. | |
| Parameters | |
| ---------- | |
| G : NetworkX graph | |
| Undirected graph | |
| weight : string or None, optional (default='weight') | |
| The node attribute that holds the integer value used as a weight. | |
| If None, then each node has weight 1. | |
| Returns | |
| ------- | |
| clique : list | |
| the nodes of a maximum weight clique | |
| weight : int | |
| the weight of a maximum weight clique | |
| Notes | |
| ----- | |
| The implementation is recursive, and therefore it may run into recursion | |
| depth issues if G contains a clique whose number of nodes is close to the | |
| recursion depth limit. | |
| At each search node, the algorithm greedily constructs a weighted | |
| independent set cover of part of the graph in order to find a small set of | |
| nodes on which to branch. The algorithm is very similar to the algorithm | |
| of Tavares et al. [1]_, other than the fact that the NetworkX version does | |
| not use bitsets. This style of algorithm for maximum weight clique (and | |
| maximum weight independent set, which is the same problem but on the | |
| complement graph) has a decades-long history. See Algorithm B of Warren | |
| and Hicks [2]_ and the references in that paper. | |
| References | |
| ---------- | |
| .. [1] Tavares, W.A., Neto, M.B.C., Rodrigues, C.D., Michelon, P.: Um | |
| algoritmo de branch and bound para o problema da clique máxima | |
| ponderada. Proceedings of XLVII SBPO 1 (2015). | |
| .. [2] Warren, Jeffrey S, Hicks, Illya V.: Combinatorial Branch-and-Bound | |
| for the Maximum Weight Independent Set Problem. Technical Report, | |
| Texas A&M University (2016). | |
| """ | |
| mwc = MaxWeightClique(G, weight) | |
| mwc.find_max_weight_clique() | |
| return mwc.incumbent_nodes, mwc.incumbent_weight | |