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authorS. Solomon Darnell2025-03-28 21:52:21 -0500
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+"""
+Graph summarization finds smaller representations of graphs resulting in faster
+runtime of algorithms, reduced storage needs, and noise reduction.
+Summarization has applications in areas such as visualization, pattern mining,
+clustering and community detection, and more. Core graph summarization
+techniques are grouping/aggregation, bit-compression,
+simplification/sparsification, and influence based. Graph summarization
+algorithms often produce either summary graphs in the form of supergraphs or
+sparsified graphs, or a list of independent structures. Supergraphs are the
+most common product, which consist of supernodes and original nodes and are
+connected by edges and superedges, which represent aggregate edges between
+nodes and supernodes.
+
+Grouping/aggregation based techniques compress graphs by representing
+close/connected nodes and edges in a graph by a single node/edge in a
+supergraph. Nodes can be grouped together into supernodes based on their
+structural similarities or proximity within a graph to reduce the total number
+of nodes in a graph. Edge-grouping techniques group edges into lossy/lossless
+nodes called compressor or virtual nodes to reduce the total number of edges in
+a graph. Edge-grouping techniques can be lossless, meaning that they can be
+used to re-create the original graph, or techniques can be lossy, requiring
+less space to store the summary graph, but at the expense of lower
+reconstruction accuracy of the original graph.
+
+Bit-compression techniques minimize the amount of information needed to
+describe the original graph, while revealing structural patterns in the
+original graph. The two-part minimum description length (MDL) is often used to
+represent the model and the original graph in terms of the model. A key
+difference between graph compression and graph summarization is that graph
+summarization focuses on finding structural patterns within the original graph,
+whereas graph compression focuses on compressions the original graph to be as
+small as possible. **NOTE**: Some bit-compression methods exist solely to
+compress a graph without creating a summary graph or finding comprehensible
+structural patterns.
+
+Simplification/Sparsification techniques attempt to create a sparse
+representation of a graph by removing unimportant nodes and edges from the
+graph. Sparsified graphs differ from supergraphs created by
+grouping/aggregation by only containing a subset of the original nodes and
+edges of the original graph.
+
+Influence based techniques aim to find a high-level description of influence
+propagation in a large graph. These methods are scarce and have been mostly
+applied to social graphs.
+
+*dedensification* is a grouping/aggregation based technique to compress the
+neighborhoods around high-degree nodes in unweighted graphs by adding
+compressor nodes that summarize multiple edges of the same type to
+high-degree nodes (nodes with a degree greater than a given threshold).
+Dedensification was developed for the purpose of increasing performance of
+query processing around high-degree nodes in graph databases and enables direct
+operations on the compressed graph. The structural patterns surrounding
+high-degree nodes in the original is preserved while using fewer edges and
+adding a small number of compressor nodes. The degree of nodes present in the
+original graph is also preserved. The current implementation of dedensification
+supports graphs with one edge type.
+
+For more information on graph summarization, see `Graph Summarization Methods
+and Applications: A Survey <https://dl.acm.org/doi/abs/10.1145/3186727>`_
+"""
+
+from collections import Counter, defaultdict
+
+import networkx as nx
+
+__all__ = ["dedensify", "snap_aggregation"]
+
+
+@nx._dispatchable(mutates_input={"not copy": 3}, returns_graph=True)
+def dedensify(G, threshold, prefix=None, copy=True):
+ """Compresses neighborhoods around high-degree nodes
+
+ Reduces the number of edges to high-degree nodes by adding compressor nodes
+ that summarize multiple edges of the same type to high-degree nodes (nodes
+ with a degree greater than a given threshold). Dedensification also has
+ the added benefit of reducing the number of edges around high-degree nodes.
+ The implementation currently supports graphs with a single edge type.
+
+ Parameters
+ ----------
+ G: graph
+ A networkx graph
+ threshold: int
+ Minimum degree threshold of a node to be considered a high degree node.
+ The threshold must be greater than or equal to 2.
+ prefix: str or None, optional (default: None)
+ An optional prefix for denoting compressor nodes
+ copy: bool, optional (default: True)
+ Indicates if dedensification should be done inplace
+
+ Returns
+ -------
+ dedensified networkx graph : (graph, set)
+ 2-tuple of the dedensified graph and set of compressor nodes
+
+ Notes
+ -----
+ According to the algorithm in [1]_, removes edges in a graph by
+ compressing/decompressing the neighborhoods around high degree nodes by
+ adding compressor nodes that summarize multiple edges of the same type
+ to high-degree nodes. Dedensification will only add a compressor node when
+ doing so will reduce the total number of edges in the given graph. This
+ implementation currently supports graphs with a single edge type.
+
+ Examples
+ --------
+ Dedensification will only add compressor nodes when doing so would result
+ in fewer edges::
+
+ >>> original_graph = nx.DiGraph()
+ >>> original_graph.add_nodes_from(
+ ... ["1", "2", "3", "4", "5", "6", "A", "B", "C"]
+ ... )
+ >>> original_graph.add_edges_from(
+ ... [
+ ... ("1", "C"), ("1", "B"),
+ ... ("2", "C"), ("2", "B"), ("2", "A"),
+ ... ("3", "B"), ("3", "A"), ("3", "6"),
+ ... ("4", "C"), ("4", "B"), ("4", "A"),
+ ... ("5", "B"), ("5", "A"),
+ ... ("6", "5"),
+ ... ("A", "6")
+ ... ]
+ ... )
+ >>> c_graph, c_nodes = nx.dedensify(original_graph, threshold=2)
+ >>> original_graph.number_of_edges()
+ 15
+ >>> c_graph.number_of_edges()
+ 14
+
+ A dedensified, directed graph can be "densified" to reconstruct the
+ original graph::
+
+ >>> original_graph = nx.DiGraph()
+ >>> original_graph.add_nodes_from(
+ ... ["1", "2", "3", "4", "5", "6", "A", "B", "C"]
+ ... )
+ >>> original_graph.add_edges_from(
+ ... [
+ ... ("1", "C"), ("1", "B"),
+ ... ("2", "C"), ("2", "B"), ("2", "A"),
+ ... ("3", "B"), ("3", "A"), ("3", "6"),
+ ... ("4", "C"), ("4", "B"), ("4", "A"),
+ ... ("5", "B"), ("5", "A"),
+ ... ("6", "5"),
+ ... ("A", "6")
+ ... ]
+ ... )
+ >>> c_graph, c_nodes = nx.dedensify(original_graph, threshold=2)
+ >>> # re-densifies the compressed graph into the original graph
+ >>> for c_node in c_nodes:
+ ... all_neighbors = set(nx.all_neighbors(c_graph, c_node))
+ ... out_neighbors = set(c_graph.neighbors(c_node))
+ ... for out_neighbor in out_neighbors:
+ ... c_graph.remove_edge(c_node, out_neighbor)
+ ... in_neighbors = all_neighbors - out_neighbors
+ ... for in_neighbor in in_neighbors:
+ ... c_graph.remove_edge(in_neighbor, c_node)
+ ... for out_neighbor in out_neighbors:
+ ... c_graph.add_edge(in_neighbor, out_neighbor)
+ ... c_graph.remove_node(c_node)
+ ...
+ >>> nx.is_isomorphic(original_graph, c_graph)
+ True
+
+ References
+ ----------
+ .. [1] Maccioni, A., & Abadi, D. J. (2016, August).
+ Scalable pattern matching over compressed graphs via dedensification.
+ In Proceedings of the 22nd ACM SIGKDD International Conference on
+ Knowledge Discovery and Data Mining (pp. 1755-1764).
+ http://www.cs.umd.edu/~abadi/papers/graph-dedense.pdf
+ """
+ if threshold < 2:
+ raise nx.NetworkXError("The degree threshold must be >= 2")
+
+ degrees = G.in_degree if G.is_directed() else G.degree
+ # Group nodes based on degree threshold
+ high_degree_nodes = {n for n, d in degrees if d > threshold}
+ low_degree_nodes = G.nodes() - high_degree_nodes
+
+ auxiliary = {}
+ for node in G:
+ high_degree_nbrs = frozenset(high_degree_nodes & set(G[node]))
+ if high_degree_nbrs:
+ if high_degree_nbrs in auxiliary:
+ auxiliary[high_degree_nbrs].add(node)
+ else:
+ auxiliary[high_degree_nbrs] = {node}
+
+ if copy:
+ G = G.copy()
+
+ compressor_nodes = set()
+ for index, (high_degree_nodes, low_degree_nodes) in enumerate(auxiliary.items()):
+ low_degree_node_count = len(low_degree_nodes)
+ high_degree_node_count = len(high_degree_nodes)
+ old_edges = high_degree_node_count * low_degree_node_count
+ new_edges = high_degree_node_count + low_degree_node_count
+ if old_edges <= new_edges:
+ continue
+ compression_node = "".join(str(node) for node in high_degree_nodes)
+ if prefix:
+ compression_node = str(prefix) + compression_node
+ for node in low_degree_nodes:
+ for high_node in high_degree_nodes:
+ if G.has_edge(node, high_node):
+ G.remove_edge(node, high_node)
+
+ G.add_edge(node, compression_node)
+ for node in high_degree_nodes:
+ G.add_edge(compression_node, node)
+ compressor_nodes.add(compression_node)
+ return G, compressor_nodes
+
+
+def _snap_build_graph(
+ G,
+ groups,
+ node_attributes,
+ edge_attributes,
+ neighbor_info,
+ edge_types,
+ prefix,
+ supernode_attribute,
+ superedge_attribute,
+):
+ """
+ Build the summary graph from the data structures produced in the SNAP aggregation algorithm
+
+ Used in the SNAP aggregation algorithm to build the output summary graph and supernode
+ lookup dictionary. This process uses the original graph and the data structures to
+ create the supernodes with the correct node attributes, and the superedges with the correct
+ edge attributes
+
+ Parameters
+ ----------
+ G: networkx.Graph
+ the original graph to be summarized
+ groups: dict
+ A dictionary of unique group IDs and their corresponding node groups
+ node_attributes: iterable
+ An iterable of the node attributes considered in the summarization process
+ edge_attributes: iterable
+ An iterable of the edge attributes considered in the summarization process
+ neighbor_info: dict
+ A data structure indicating the number of edges a node has with the
+ groups in the current summarization of each edge type
+ edge_types: dict
+ dictionary of edges in the graph and their corresponding attributes recognized
+ in the summarization
+ prefix: string
+ The prefix to be added to all supernodes
+ supernode_attribute: str
+ The node attribute for recording the supernode groupings of nodes
+ superedge_attribute: str
+ The edge attribute for recording the edge types represented by superedges
+
+ Returns
+ -------
+ summary graph: Networkx graph
+ """
+ output = G.__class__()
+ node_label_lookup = {}
+ for index, group_id in enumerate(groups):
+ group_set = groups[group_id]
+ supernode = f"{prefix}{index}"
+ node_label_lookup[group_id] = supernode
+ supernode_attributes = {
+ attr: G.nodes[next(iter(group_set))][attr] for attr in node_attributes
+ }
+ supernode_attributes[supernode_attribute] = group_set
+ output.add_node(supernode, **supernode_attributes)
+
+ for group_id in groups:
+ group_set = groups[group_id]
+ source_supernode = node_label_lookup[group_id]
+ for other_group, group_edge_types in neighbor_info[
+ next(iter(group_set))
+ ].items():
+ if group_edge_types:
+ target_supernode = node_label_lookup[other_group]
+ summary_graph_edge = (source_supernode, target_supernode)
+
+ edge_types = [
+ dict(zip(edge_attributes, edge_type))
+ for edge_type in group_edge_types
+ ]
+
+ has_edge = output.has_edge(*summary_graph_edge)
+ if output.is_multigraph():
+ if not has_edge:
+ for edge_type in edge_types:
+ output.add_edge(*summary_graph_edge, **edge_type)
+ elif not output.is_directed():
+ existing_edge_data = output.get_edge_data(*summary_graph_edge)
+ for edge_type in edge_types:
+ if edge_type not in existing_edge_data.values():
+ output.add_edge(*summary_graph_edge, **edge_type)
+ else:
+ superedge_attributes = {superedge_attribute: edge_types}
+ output.add_edge(*summary_graph_edge, **superedge_attributes)
+
+ return output
+
+
+def _snap_eligible_group(G, groups, group_lookup, edge_types):
+ """
+ Determines if a group is eligible to be split.
+
+ A group is eligible to be split if all nodes in the group have edges of the same type(s)
+ with the same other groups.
+
+ Parameters
+ ----------
+ G: graph
+ graph to be summarized
+ groups: dict
+ A dictionary of unique group IDs and their corresponding node groups
+ group_lookup: dict
+ dictionary of nodes and their current corresponding group ID
+ edge_types: dict
+ dictionary of edges in the graph and their corresponding attributes recognized
+ in the summarization
+
+ Returns
+ -------
+ tuple: group ID to split, and neighbor-groups participation_counts data structure
+ """
+ nbr_info = {node: {gid: Counter() for gid in groups} for node in group_lookup}
+ for group_id in groups:
+ current_group = groups[group_id]
+
+ # build nbr_info for nodes in group
+ for node in current_group:
+ nbr_info[node] = {group_id: Counter() for group_id in groups}
+ edges = G.edges(node, keys=True) if G.is_multigraph() else G.edges(node)
+ for edge in edges:
+ neighbor = edge[1]
+ edge_type = edge_types[edge]
+ neighbor_group_id = group_lookup[neighbor]
+ nbr_info[node][neighbor_group_id][edge_type] += 1
+
+ # check if group_id is eligible to be split
+ group_size = len(current_group)
+ for other_group_id in groups:
+ edge_counts = Counter()
+ for node in current_group:
+ edge_counts.update(nbr_info[node][other_group_id].keys())
+
+ if not all(count == group_size for count in edge_counts.values()):
+ # only the nbr_info of the returned group_id is required for handling group splits
+ return group_id, nbr_info
+
+ # if no eligible groups, complete nbr_info is calculated
+ return None, nbr_info
+
+
+def _snap_split(groups, neighbor_info, group_lookup, group_id):
+ """
+ Splits a group based on edge types and updates the groups accordingly
+
+ Splits the group with the given group_id based on the edge types
+ of the nodes so that each new grouping will all have the same
+ edges with other nodes.
+
+ Parameters
+ ----------
+ groups: dict
+ A dictionary of unique group IDs and their corresponding node groups
+ neighbor_info: dict
+ A data structure indicating the number of edges a node has with the
+ groups in the current summarization of each edge type
+ edge_types: dict
+ dictionary of edges in the graph and their corresponding attributes recognized
+ in the summarization
+ group_lookup: dict
+ dictionary of nodes and their current corresponding group ID
+ group_id: object
+ ID of group to be split
+
+ Returns
+ -------
+ dict
+ The updated groups based on the split
+ """
+ new_group_mappings = defaultdict(set)
+ for node in groups[group_id]:
+ signature = tuple(
+ frozenset(edge_types) for edge_types in neighbor_info[node].values()
+ )
+ new_group_mappings[signature].add(node)
+
+ # leave the biggest new_group as the original group
+ new_groups = sorted(new_group_mappings.values(), key=len)
+ for new_group in new_groups[:-1]:
+ # Assign unused integer as the new_group_id
+ # ids are tuples, so will not interact with the original group_ids
+ new_group_id = len(groups)
+ groups[new_group_id] = new_group
+ groups[group_id] -= new_group
+ for node in new_group:
+ group_lookup[node] = new_group_id
+
+ return groups
+
+
+@nx._dispatchable(
+ node_attrs="[node_attributes]", edge_attrs="[edge_attributes]", returns_graph=True
+)
+def snap_aggregation(
+ G,
+ node_attributes,
+ edge_attributes=(),
+ prefix="Supernode-",
+ supernode_attribute="group",
+ superedge_attribute="types",
+):
+ """Creates a summary graph based on attributes and connectivity.
+
+ This function uses the Summarization by Grouping Nodes on Attributes
+ and Pairwise edges (SNAP) algorithm for summarizing a given
+ graph by grouping nodes by node attributes and their edge attributes
+ into supernodes in a summary graph. This name SNAP should not be
+ confused with the Stanford Network Analysis Project (SNAP).
+
+ Here is a high-level view of how this algorithm works:
+
+ 1) Group nodes by node attribute values.
+
+ 2) Iteratively split groups until all nodes in each group have edges
+ to nodes in the same groups. That is, until all the groups are homogeneous
+ in their member nodes' edges to other groups. For example,
+ if all the nodes in group A only have edge to nodes in group B, then the
+ group is homogeneous and does not need to be split. If all nodes in group B
+ have edges with nodes in groups {A, C}, but some also have edges with other
+ nodes in B, then group B is not homogeneous and needs to be split into
+ groups have edges with {A, C} and a group of nodes having
+ edges with {A, B, C}. This way, viewers of the summary graph can
+ assume that all nodes in the group have the exact same node attributes and
+ the exact same edges.
+
+ 3) Build the output summary graph, where the groups are represented by
+ super-nodes. Edges represent the edges shared between all the nodes in each
+ respective groups.
+
+ A SNAP summary graph can be used to visualize graphs that are too large to display
+ or visually analyze, or to efficiently identify sets of similar nodes with similar connectivity
+ patterns to other sets of similar nodes based on specified node and/or edge attributes in a graph.
+
+ Parameters
+ ----------
+ G: graph
+ Networkx Graph to be summarized
+ node_attributes: iterable, required
+ An iterable of the node attributes used to group nodes in the summarization process. Nodes
+ with the same values for these attributes will be grouped together in the summary graph.
+ edge_attributes: iterable, optional
+ An iterable of the edge attributes considered in the summarization process. If provided, unique
+ combinations of the attribute values found in the graph are used to
+ determine the edge types in the graph. If not provided, all edges
+ are considered to be of the same type.
+ prefix: str
+ The prefix used to denote supernodes in the summary graph. Defaults to 'Supernode-'.
+ supernode_attribute: str
+ The node attribute for recording the supernode groupings of nodes. Defaults to 'group'.
+ superedge_attribute: str
+ The edge attribute for recording the edge types of multiple edges. Defaults to 'types'.
+
+ Returns
+ -------
+ networkx.Graph: summary graph
+
+ Examples
+ --------
+ SNAP aggregation takes a graph and summarizes it in the context of user-provided
+ node and edge attributes such that a viewer can more easily extract and
+ analyze the information represented by the graph
+
+ >>> nodes = {
+ ... "A": dict(color="Red"),
+ ... "B": dict(color="Red"),
+ ... "C": dict(color="Red"),
+ ... "D": dict(color="Red"),
+ ... "E": dict(color="Blue"),
+ ... "F": dict(color="Blue"),
+ ... }
+ >>> edges = [
+ ... ("A", "E", "Strong"),
+ ... ("B", "F", "Strong"),
+ ... ("C", "E", "Weak"),
+ ... ("D", "F", "Weak"),
+ ... ]
+ >>> G = nx.Graph()
+ >>> for node in nodes:
+ ... attributes = nodes[node]
+ ... G.add_node(node, **attributes)
+ >>> for source, target, type in edges:
+ ... G.add_edge(source, target, type=type)
+ >>> node_attributes = ("color",)
+ >>> edge_attributes = ("type",)
+ >>> summary_graph = nx.snap_aggregation(
+ ... G, node_attributes=node_attributes, edge_attributes=edge_attributes
+ ... )
+
+ Notes
+ -----
+ The summary graph produced is called a maximum Attribute-edge
+ compatible (AR-compatible) grouping. According to [1]_, an
+ AR-compatible grouping means that all nodes in each group have the same
+ exact node attribute values and the same exact edges and
+ edge types to one or more nodes in the same groups. The maximal
+ AR-compatible grouping is the grouping with the minimal cardinality.
+
+ The AR-compatible grouping is the most detailed grouping provided by
+ any of the SNAP algorithms.
+
+ References
+ ----------
+ .. [1] Y. Tian, R. A. Hankins, and J. M. Patel. Efficient aggregation
+ for graph summarization. In Proc. 2008 ACM-SIGMOD Int. Conf.
+ Management of Data (SIGMOD’08), pages 567–580, Vancouver, Canada,
+ June 2008.
+ """
+ edge_types = {
+ edge: tuple(attrs.get(attr) for attr in edge_attributes)
+ for edge, attrs in G.edges.items()
+ }
+ if not G.is_directed():
+ if G.is_multigraph():
+ # list is needed to avoid mutating while iterating
+ edges = [((v, u, k), etype) for (u, v, k), etype in edge_types.items()]
+ else:
+ # list is needed to avoid mutating while iterating
+ edges = [((v, u), etype) for (u, v), etype in edge_types.items()]
+ edge_types.update(edges)
+
+ group_lookup = {
+ node: tuple(attrs[attr] for attr in node_attributes)
+ for node, attrs in G.nodes.items()
+ }
+ groups = defaultdict(set)
+ for node, node_type in group_lookup.items():
+ groups[node_type].add(node)
+
+ eligible_group_id, nbr_info = _snap_eligible_group(
+ G, groups, group_lookup, edge_types
+ )
+ while eligible_group_id:
+ groups = _snap_split(groups, nbr_info, group_lookup, eligible_group_id)
+ eligible_group_id, nbr_info = _snap_eligible_group(
+ G, groups, group_lookup, edge_types
+ )
+ return _snap_build_graph(
+ G,
+ groups,
+ node_attributes,
+ edge_attributes,
+ nbr_info,
+ edge_types,
+ prefix,
+ supernode_attribute,
+ superedge_attribute,
+ )