306 lines
11 KiB
Python
306 lines
11 KiB
Python
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"""Provides algorithms supporting the computation of graph polynomials.
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Graph polynomials are polynomial-valued graph invariants that encode a wide
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variety of structural information. Examples include the Tutte polynomial,
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chromatic polynomial, characteristic polynomial, and matching polynomial. An
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extensive treatment is provided in [1]_.
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For a simple example, the `~sympy.matrices.matrices.MatrixDeterminant.charpoly`
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method can be used to compute the characteristic polynomial from the adjacency
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matrix of a graph. Consider the complete graph ``K_4``:
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>>> import sympy
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>>> x = sympy.Symbol("x")
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>>> G = nx.complete_graph(4)
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>>> A = nx.adjacency_matrix(G)
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>>> M = sympy.SparseMatrix(A.todense())
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>>> M.charpoly(x).as_expr()
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x**4 - 6*x**2 - 8*x - 3
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.. [1] Y. Shi, M. Dehmer, X. Li, I. Gutman,
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"Graph Polynomials"
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"""
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from collections import deque
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import networkx as nx
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from networkx.utils import not_implemented_for
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__all__ = ["tutte_polynomial", "chromatic_polynomial"]
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@not_implemented_for("directed")
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@nx._dispatchable
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def tutte_polynomial(G):
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r"""Returns the Tutte polynomial of `G`
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This function computes the Tutte polynomial via an iterative version of
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the deletion-contraction algorithm.
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The Tutte polynomial `T_G(x, y)` is a fundamental graph polynomial invariant in
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two variables. It encodes a wide array of information related to the
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edge-connectivity of a graph; "Many problems about graphs can be reduced to
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problems of finding and evaluating the Tutte polynomial at certain values" [1]_.
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In fact, every deletion-contraction-expressible feature of a graph is a
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specialization of the Tutte polynomial [2]_ (see Notes for examples).
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There are several equivalent definitions; here are three:
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Def 1 (rank-nullity expansion): For `G` an undirected graph, `n(G)` the
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number of vertices of `G`, `E` the edge set of `G`, `V` the vertex set of
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`G`, and `c(A)` the number of connected components of the graph with vertex
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set `V` and edge set `A` [3]_:
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.. math::
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T_G(x, y) = \sum_{A \in E} (x-1)^{c(A) - c(E)} (y-1)^{c(A) + |A| - n(G)}
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Def 2 (spanning tree expansion): Let `G` be an undirected graph, `T` a spanning
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tree of `G`, and `E` the edge set of `G`. Let `E` have an arbitrary strict
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linear order `L`. Let `B_e` be the unique minimal nonempty edge cut of
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$E \setminus T \cup {e}$. An edge `e` is internally active with respect to
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`T` and `L` if `e` is the least edge in `B_e` according to the linear order
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`L`. The internal activity of `T` (denoted `i(T)`) is the number of edges
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in $E \setminus T$ that are internally active with respect to `T` and `L`.
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Let `P_e` be the unique path in $T \cup {e}$ whose source and target vertex
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are the same. An edge `e` is externally active with respect to `T` and `L`
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if `e` is the least edge in `P_e` according to the linear order `L`. The
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external activity of `T` (denoted `e(T)`) is the number of edges in
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$E \setminus T$ that are externally active with respect to `T` and `L`.
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Then [4]_ [5]_:
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.. math::
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T_G(x, y) = \sum_{T \text{ a spanning tree of } G} x^{i(T)} y^{e(T)}
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Def 3 (deletion-contraction recurrence): For `G` an undirected graph, `G-e`
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the graph obtained from `G` by deleting edge `e`, `G/e` the graph obtained
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from `G` by contracting edge `e`, `k(G)` the number of cut-edges of `G`,
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and `l(G)` the number of self-loops of `G`:
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.. math::
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T_G(x, y) = \begin{cases}
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x^{k(G)} y^{l(G)}, & \text{if all edges are cut-edges or self-loops} \\
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T_{G-e}(x, y) + T_{G/e}(x, y), & \text{otherwise, for an arbitrary edge $e$ not a cut-edge or loop}
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\end{cases}
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Parameters
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----------
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G : NetworkX graph
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Returns
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-------
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instance of `sympy.core.add.Add`
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A Sympy expression representing the Tutte polynomial for `G`.
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Examples
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--------
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>>> C = nx.cycle_graph(5)
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>>> nx.tutte_polynomial(C)
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x**4 + x**3 + x**2 + x + y
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>>> D = nx.diamond_graph()
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>>> nx.tutte_polynomial(D)
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x**3 + 2*x**2 + 2*x*y + x + y**2 + y
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Notes
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-----
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Some specializations of the Tutte polynomial:
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- `T_G(1, 1)` counts the number of spanning trees of `G`
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- `T_G(1, 2)` counts the number of connected spanning subgraphs of `G`
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- `T_G(2, 1)` counts the number of spanning forests in `G`
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- `T_G(0, 2)` counts the number of strong orientations of `G`
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- `T_G(2, 0)` counts the number of acyclic orientations of `G`
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Edge contraction is defined and deletion-contraction is introduced in [6]_.
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Combinatorial meaning of the coefficients is introduced in [7]_.
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Universality, properties, and applications are discussed in [8]_.
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Practically, up-front computation of the Tutte polynomial may be useful when
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users wish to repeatedly calculate edge-connectivity-related information
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about one or more graphs.
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References
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----------
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.. [1] M. Brandt,
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"The Tutte Polynomial."
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Talking About Combinatorial Objects Seminar, 2015
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https://math.berkeley.edu/~brandtm/talks/tutte.pdf
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.. [2] A. Björklund, T. Husfeldt, P. Kaski, M. Koivisto,
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"Computing the Tutte polynomial in vertex-exponential time"
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49th Annual IEEE Symposium on Foundations of Computer Science, 2008
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https://ieeexplore.ieee.org/abstract/document/4691000
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.. [3] Y. Shi, M. Dehmer, X. Li, I. Gutman,
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"Graph Polynomials," p. 14
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.. [4] Y. Shi, M. Dehmer, X. Li, I. Gutman,
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"Graph Polynomials," p. 46
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.. [5] A. Nešetril, J. Goodall,
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"Graph invariants, homomorphisms, and the Tutte polynomial"
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https://iuuk.mff.cuni.cz/~andrew/Tutte.pdf
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.. [6] D. B. West,
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"Introduction to Graph Theory," p. 84
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.. [7] G. Coutinho,
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"A brief introduction to the Tutte polynomial"
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Structural Analysis of Complex Networks, 2011
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https://homepages.dcc.ufmg.br/~gabriel/seminars/coutinho_tuttepolynomial_seminar.pdf
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.. [8] J. A. Ellis-Monaghan, C. Merino,
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"Graph polynomials and their applications I: The Tutte polynomial"
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Structural Analysis of Complex Networks, 2011
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https://arxiv.org/pdf/0803.3079.pdf
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"""
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import sympy
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x = sympy.Symbol("x")
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y = sympy.Symbol("y")
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stack = deque()
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stack.append(nx.MultiGraph(G))
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polynomial = 0
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while stack:
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G = stack.pop()
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bridges = set(nx.bridges(G))
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e = None
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for i in G.edges:
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if (i[0], i[1]) not in bridges and i[0] != i[1]:
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e = i
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break
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if not e:
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loops = list(nx.selfloop_edges(G, keys=True))
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polynomial += x ** len(bridges) * y ** len(loops)
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else:
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# deletion-contraction
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C = nx.contracted_edge(G, e, self_loops=True)
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C.remove_edge(e[0], e[0])
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G.remove_edge(*e)
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stack.append(G)
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stack.append(C)
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return sympy.simplify(polynomial)
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@not_implemented_for("directed")
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@nx._dispatchable
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def chromatic_polynomial(G):
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r"""Returns the chromatic polynomial of `G`
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This function computes the chromatic polynomial via an iterative version of
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the deletion-contraction algorithm.
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The chromatic polynomial `X_G(x)` is a fundamental graph polynomial
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invariant in one variable. Evaluating `X_G(k)` for an natural number `k`
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enumerates the proper k-colorings of `G`.
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There are several equivalent definitions; here are three:
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Def 1 (explicit formula):
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For `G` an undirected graph, `c(G)` the number of connected components of
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`G`, `E` the edge set of `G`, and `G(S)` the spanning subgraph of `G` with
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edge set `S` [1]_:
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.. math::
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X_G(x) = \sum_{S \subseteq E} (-1)^{|S|} x^{c(G(S))}
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Def 2 (interpolating polynomial):
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For `G` an undirected graph, `n(G)` the number of vertices of `G`, `k_0 = 0`,
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and `k_i` the number of distinct ways to color the vertices of `G` with `i`
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unique colors (for `i` a natural number at most `n(G)`), `X_G(x)` is the
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unique Lagrange interpolating polynomial of degree `n(G)` through the points
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`(0, k_0), (1, k_1), \dots, (n(G), k_{n(G)})` [2]_.
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Def 3 (chromatic recurrence):
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For `G` an undirected graph, `G-e` the graph obtained from `G` by deleting
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edge `e`, `G/e` the graph obtained from `G` by contracting edge `e`, `n(G)`
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the number of vertices of `G`, and `e(G)` the number of edges of `G` [3]_:
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.. math::
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X_G(x) = \begin{cases}
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x^{n(G)}, & \text{if $e(G)=0$} \\
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X_{G-e}(x) - X_{G/e}(x), & \text{otherwise, for an arbitrary edge $e$}
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\end{cases}
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This formulation is also known as the Fundamental Reduction Theorem [4]_.
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Parameters
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----------
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G : NetworkX graph
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Returns
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-------
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instance of `sympy.core.add.Add`
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A Sympy expression representing the chromatic polynomial for `G`.
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Examples
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--------
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>>> C = nx.cycle_graph(5)
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>>> nx.chromatic_polynomial(C)
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x**5 - 5*x**4 + 10*x**3 - 10*x**2 + 4*x
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>>> G = nx.complete_graph(4)
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>>> nx.chromatic_polynomial(G)
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x**4 - 6*x**3 + 11*x**2 - 6*x
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Notes
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-----
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Interpretation of the coefficients is discussed in [5]_. Several special
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cases are listed in [2]_.
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The chromatic polynomial is a specialization of the Tutte polynomial; in
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particular, ``X_G(x) = T_G(x, 0)`` [6]_.
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The chromatic polynomial may take negative arguments, though evaluations
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may not have chromatic interpretations. For instance, ``X_G(-1)`` enumerates
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the acyclic orientations of `G` [7]_.
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References
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----------
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.. [1] D. B. West,
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"Introduction to Graph Theory," p. 222
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.. [2] E. W. Weisstein
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"Chromatic Polynomial"
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MathWorld--A Wolfram Web Resource
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https://mathworld.wolfram.com/ChromaticPolynomial.html
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.. [3] D. B. West,
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"Introduction to Graph Theory," p. 221
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.. [4] J. Zhang, J. Goodall,
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"An Introduction to Chromatic Polynomials"
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https://math.mit.edu/~apost/courses/18.204_2018/Julie_Zhang_paper.pdf
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.. [5] R. C. Read,
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"An Introduction to Chromatic Polynomials"
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Journal of Combinatorial Theory, 1968
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https://math.berkeley.edu/~mrklug/ReadChromatic.pdf
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.. [6] W. T. Tutte,
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"Graph-polynomials"
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Advances in Applied Mathematics, 2004
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https://www.sciencedirect.com/science/article/pii/S0196885803000411
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.. [7] R. P. Stanley,
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"Acyclic orientations of graphs"
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Discrete Mathematics, 2006
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https://math.mit.edu/~rstan/pubs/pubfiles/18.pdf
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"""
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import sympy
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x = sympy.Symbol("x")
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stack = deque()
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stack.append(nx.MultiGraph(G, contraction_idx=0))
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polynomial = 0
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while stack:
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G = stack.pop()
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edges = list(G.edges)
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if not edges:
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polynomial += (-1) ** G.graph["contraction_idx"] * x ** len(G)
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else:
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e = edges[0]
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C = nx.contracted_edge(G, e, self_loops=True)
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C.graph["contraction_idx"] = G.graph["contraction_idx"] + 1
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C.remove_edge(e[0], e[0])
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G.remove_edge(*e)
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stack.append(G)
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stack.append(C)
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return polynomial
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