Create Graph

The Scope allows you to create edges between the source nodes (Objects in the selection of the currently active Type) and target nodes (Objects referenced by the indicated path in the Scope).

Network  

All reported network measures per node read the same way: a higher value means more, e.g. more connected, more central, more influential. A value of 0 means the node is part of the graph but has no relevance to the measure. A non-existent value (-) means there was nothing to calculate for the node. Every entry below states what the node values mean (Primary, and Secondary when the algorithm reports a second value) and which summary figures the algorithm adds to the network overview (Statistic).

The graph follows from the configuration of the Scope. It is directed by default, and undirected when both directions are set. The graph is always one-mode: when nodes of one Type are connected because they share a node of another Type, that shared node acts as a collapsed intermediate node and does not become a node of the graph itself; the connection is projected between the two nodes as a single co-occurrence.

A projected (resolved) edge counts once: it is a single shared statement that is written in both directions. A direct Type-to-Type edge (native) sums its two directions, as each relationship is a statement in its own right, so a mutual edge counts stronger than a one-way edge. An edge can be unweighted, or weighted as a closeness or as a distance; how a weight is built and how each family of algorithms reads it is described in the Weight section below.

The currently available network algorithms are:

AlgorithmDescription
Connections
CountThe number of edges running from a node to other nodes, or their total edge length on a weighted graph. The most direct measure of activity: it counts connections, not their importance. More info.

Returns

Primary: The number of edges of the node, or their total edge length when weighted.

In an events network, the count ranks who took part in the most gatherings, before any question of how well-placed those gatherings were.

Shortest PathThe shortest path between one or a group of nodes (From) and any other node or a group of nodes (Target). More info.

Options

  • Centrality: weighs every node on these paths by betweenness centrality (absolute, relative, or normalised), showing which nodes the connection depends on.
  • Tolerance: (detour/slack) widens the centrality to near-shortest (ε-shortest) paths: a node is included when the best path via it is at most the tolerance longer than the shortest path (in weights, or steps when unweighted), showing which nodes the connection would run through if the shortest paths were unavailable. The tolerance applies when a Target is set.

Returns

Primary: The node's distance from the From selection: the length of the shortest path to it, in weights or steps when unweighted; From nodes report 0, nodes that are not reached report no value.
Secondary: With the centrality enabled, how strongly the connection depends on the node: the number of best routes between From and Target that run through it, or its betweenness for the paths from the From selection to the whole network when no Target is set.

In a correspondence network, the shortest path from a scholar to the court shows through whose hands a request most plausibly travelled; the tolerance adds who could have passed it on had a connection failed.

Literature
  • Dijkstra, E. W. (1959). 'A note on two problems in connexion with graphs'. Numerische Mathematik 1, 269-271.
  • Freeman, L. C. (1977). 'A set of measures of centrality based on betweenness'. Sociometry 40(1), 35-41.
  • Brandes, U. (2001). 'A faster algorithm for betweenness centrality'. Journal of Mathematical Sociology 25(2), 163-177.
Disjoint PathsThe largest set of routes between a selection of nodes (From) and another selection (Target) that share no edge: each route is an independent chain of documented relationships, so the count states how robust the connection between the two selections is and how many relationships must fail before it breaks (Menger's edge connectivity). Where Shortest Path finds the single best route, Disjoint Paths finds how many independent routes connect the selections. The number of routes depends only on which edges exist; among all largest sets, the reported one has the least total distance, so the routes shown are the most plausible representatives. More info.

Returns

Primary: The number of disjoint routes that run through the node; the From and Target nodes report the number of routes that start or end at them.
Secondary: The node's earliest step along a route, counted from the From side (a position, not a score).
Statistic: Paths: the number of independent routes between the selections. Distance: the total distance of that set of routes.

In a relationship network, disjoint paths show whether the contact between two milieus rests on a single go-between or on several independent chains of acquaintance.

Literature
  • Menger, K. (1927). 'Zur allgemeinen Kurventheorie'. Fundamenta Mathematicae 10, 96-115.
  • Ford, L. R. & Fulkerson, D. R. (1956). 'Maximal flow through a network'. Canadian Journal of Mathematics 8, 399-404.
  • Suurballe, J. W. & Tarjan, R. E. (1984). 'A quick method for finding shortest pairs of disjoint paths'. Networks 14(2), 325-336.
  • Bhandari, R. (1999). Survivable Networks: Algorithms for Diverse Routing. Kluwer Academic Publishers.
Katz PredictionScores nodes on the paths of every length between the node and the From selection, each path discounted the longer it is (attenuation). Where the other Link Prediction measures require directly shared connections, this prediction can identify nodes whose plausibility is based on longer paths only, shown by a high score with few or no shared connections. On a weighted graph a path multiplies the edge strengths along it, so a longer route over strong edges can outscore a short one over weak edges. More info

Options

  • Iterations: the maximum path length that is included.
  • Attenuation: how strongly longer paths are discounted; lower values keep the prediction local, higher values include more distant structure.
  • Mode: the plausibility scores as they are (absolute), or rescaled between 0 and 1 so the most plausible node is 1 (normalised).

Returns

Primary: The node's best plausibility score against the From selection; nodes with a documented connection score 0.
Secondary: The number of directly shared connections behind that best pair, which can be 0 when the plausibility is based on longer paths only.
Statistic: Candidates: the number of nodes scoring above 0. Best: the highest score found.

In a book network, Katz prediction can surface a printer and an author who share no acquaintances but sit in tightly interlinked circles, a connection worth checking the sources for.

Literature
  • Katz, L. (1953). 'A new status index derived from sociometric analysis'. Psychometrika 18(1), 39-43.
  • Liben-Nowell, D. & Kleinberg, J. (2007). 'The link-prediction problem for social networks'. Journal of the American Society for Information Science and Technology 58(7), 1019-1031.
Centrality - Distance
Closeness CentralityHow near a node is to the whole network: closeness weighs every node by its distances to all other nodes. More info.

Options

  • Mode: 1 divided by the summed distances, in which an unreachable node counts as a distance longer than any real path (absolute); or rescaled so 1 means directly connected to every other node, comparable across networks, where nodes in small disconnected parts rank low (normalised).

Returns

Primary: How near the node is to the whole network: higher means nearer.

In a travel or correspondence network, closeness centrality identifies from whom news could reach everyone in the fewest steps.

Literature
  • Bavelas, A. (1950). 'Communication patterns in task-oriented groups'. Journal of the Acoustical Society of America 22(6), 725-730.
  • Sabidussi, G. (1966). 'The centrality index of a graph'. Psychometrika 31(4), 581-603.
  • Wasserman, S. & Faust, K. (1994). Social Network Analysis: Methods and Applications. Cambridge University Press.
Closeness EccentricityHow near a node is to the farthest node it can reach. Eccentricity identifies the centre (highest values) and periphery of each connected part, but does not account for disconnection: use Closeness Centrality to compare across parts. More info.

Returns

Primary: 1 divided by the distance to the farthest node the node can reach.

In a travel network, eccentricity finds the natural centre: the place from which no destination is truly remote.

Literature
  • Hage, P. & Harary, F. (1995). 'Eccentricity and centrality in networks'. Social Networks 17(1), 57-63.
Betweenness CentralityThe number of times a node lies on the shortest paths between other nodes: bridges and gatekeepers, important for connecting others rather than being connected. More info.

Options

  • Mode: the plain path count (absolute), the share of all node pairs the node could sit between, comparable across networks (relative), or rescaled between 0 and 1 within this result (normalised).

Returns

Primary: The number of shortest paths between other nodes that run through the node.

In a book-trade network, betweenness centrality finds the agent through whom two otherwise separate circles of printers and buyers had to pass.

Literature
  • Freeman, L. C. (1977). 'A set of measures of centrality based on betweenness'. Sociometry 40(1), 35-41.
  • Brandes, U. (2001). 'A faster algorithm for betweenness centrality'. Journal of Mathematical Sociology 25(2), 163-177.
Centrality - Influence
Degree CentralityThe summed strength of a node's edges, per direction: how much of the network's documented activity attaches to the node directly. Unweighted, every edge counts as 1, so the values are the plain number of incoming and outgoing edges; on a weighted graph every edge counts by its strength, so a node with a few strong connections can outrank one with many weak ones. More info.

Options

  • Mode: the summed strengths as they are (absolute), or the incoming and outgoing sums each rescaled between 0 and 1 so the highest node is 1 (normalised).

Returns

Primary: The summed strength of the edges running to the node (in-degree).
Secondary: The summed strength of the edges running from the node (out-degree).

In a correspondence network, the in-degree ranks who received letters from the most correspondents and the out-degree who wrote the most widely; weighted, a sustained exchange counts for more than a single letter.

Literature
  • Freeman, L. C. (1979). 'Centrality in social networks: Conceptual clarification'. Social Networks 1(3), 215-239.
  • Opsahl, T., Agneessens, F. & Skvoretz, J. (2010). 'Node centrality in weighted networks: Generalizing degree and shortest paths'. Social Networks 32(3), 245-251.
Eigenvector CentralityThe influence of a node based on the influence of the nodes linking to it: a few well-placed connections can outweigh many marginal ones. On a directed graph only incoming edges pass on influence, so a node without incoming edges scores 0; use Katz Centrality when such nodes should still be ranked. More info.

Options

  • Iterations: the number of times the scores are passed on before the result is reported.

Returns

Primary: The node's influence, scaled so the most influential node is 1.
Statistic: Iterations: the number of iterations run. Change: how much the scores changed in the last iteration; near 0 means they have converged, a larger value means more iterations would still change them.

In a patronage network, a courtier with three well-placed patrons outranks a merchant with thirty ordinary contacts.

Literature
  • Bonacich, P. (1972). 'Factoring and weighting approaches to status scores and clique identification'. Journal of Mathematical Sociology 2(1), 113-120.
  • Bonacich, P. (1987). 'Power and centrality: A family of measures'. American Journal of Sociology 92(5), 1170-1182.
Katz CentralityEigenvector centrality in which every node keeps a base score, so nodes without incoming paths are still ranked; the attenuation factor discounts influence over longer paths. More info.

Options

  • Iterations: the maximum path length over which influence is passed on.
  • Attenuation: how strongly influence fades with every step; lower values keep the measure close to counting direct connections, higher values include the influence of the whole network.

Returns

Primary: The node's influence, scaled so the most influential node is 1.
Statistic: Iterations: the number run. Change: how much the scores still moved in the last iteration; near 0 means they have settled.

In a correspondence network, Katz centrality still ranks the peripheral figures: a copyist reached through a single chain of intermediaries keeps a score where eigenvector centrality would give none.

Literature
  • Katz, L. (1953). 'A new status index derived from sociometric analysis'. Psychometrika 18(1), 39-43.
PageRankThe importance of a node based on the number and quality of the edges leading to it: each node divides its own rank over its outgoing edges, so being linked by a selective, important node counts most. More info.

Options

  • Iterations: the number of times the rank is passed on.
  • Damping: the share of rank that follows the edges; the remainder is the base score every node keeps, which stops rank from pooling in closed loops.

Returns

Primary: The node's rank, on the scale of the original paper: a node without incoming edges keeps the base score of 1 minus the damping (0.15 by default), and the scores average around 1 over the network.
Statistic: Iterations: the number run. Change: how much the scores still moved in the last iteration; near 0 means they have settled.

In a citation or dedication network, PageRank ranks a work named by a few much-named works above one named often by works nobody names.

Literature
  • Brin, S. & Page, L. (1998). 'The anatomy of a large-scale hypertextual Web search engine'. Computer Networks and ISDN Systems 30(1-7), 107-117.
Hyperlink-Induced Topic Search (HITS)Two scores per node: authority (linked to by good hubs) and hub (linking to good authorities). Useful in directed networks, where outgoing and incoming edges mean different things. More info.

Options

  • Iterations: the number of times the two scores update each other.

Returns

Primary: The node's authority score, scaled so the highest is 1.
Secondary: The node's hub score, scaled so the highest is 1.
Statistic: Iterations: the number run. Change: how much the two scores changed in the last iteration; near 0 means they have converged.

In a correspondence network, HITS separates the great senders from the great receivers: the secretary who writes to every authority is a hub, the authority every hub writes to is an authority.

Literature
  • Kleinberg, J. M. (1999). 'Authoritative sources in a hyperlinked environment'. Journal of the ACM 46(5), 604-632.
Structure & Cohesion
Clustering CoefficientThe degree to which the neighbours of a node are also connected to each other. Both high and low values are informative: a well-connected node with a low coefficient brokers between groups that do not know each other. On a weighted graph a closed triangle counts by the strength of the node's edges into it (Barrat et al.), so a cluster bound together by strong edges weighs more. More info.

Returns

Primary: The node's coefficient: 0 means none of its neighbours are connected to each other, 1 means they form a complete cluster.
Statistic: Average: the mean coefficient over the analysed nodes, the overall clustering of the network.

In a relationship network, the clustering coefficient distinguishes a salon, where everyone knows everyone, from a patronage web that only stays together through its patron.

Literature
  • Watts, D. J. & Strogatz, S. H. (1998). 'Collective dynamics of "small-world" networks'. Nature 393, 440-442.
  • Barrat, A., Barthélemy, M., Pastor-Satorras, R. & Vespignani, A. (2004). 'The architecture of complex weighted networks'. Proceedings of the National Academy of Sciences (PNAS) 101(11), 3747-3752.
k-CoreThe deepest level k at which a node still belongs to a group in which every member has at least k edges: nodes with high core numbers are in the dense core of the network, nodes with low core numbers on the periphery. On a weighted graph the level is a summed edge strength instead of a count (the s-core), so a member kept in by a few strong edges ranks the same as one kept in by many weak edges. More info.

Returns

Primary: The node's core number, a strength level when weighted.
Secondary: The node's degree, or its summed edge strength when weighted.
Statistic: Degeneracy: the deepest core level of the network.

In an events network, the k-core peels the incidental attendees away layer by layer until the standing core of the scene remains.

Literature
  • Seidman, S. B. (1983). 'Network structure and minimum degree'. Social Networks 5(3), 269-287.
  • Batagelj, V. & Zaveršnik, M. (2003). 'An O(m) algorithm for cores decomposition of networks'. arXiv:cs/0310049.
  • Eidsaa, M. & Almaas, E. (2013). 'S-core network decomposition: A generalization of k-core analysis to weighted networks'. Physical Review E 88, 062819.
Articulation Points & BridgesThe nodes and edges that keep the network together: an articulation point is a node whose removal breaks a connected part into pieces, a bridge is an edge that does the same. Direction and weights are not used: the analysis concerns whether the structure is connected, not how strongly. More info.

Returns

Primary: The number of additional pieces the removal of the node would create; 0 means the network remains connected without it.
Secondary: The number of bridges connected to the node.
Statistic: Points: the number of articulation points in the network. Bridges: the number of bridges.

A single documented marriage binding two family networks together is an articulation point: a warning that everything said about their connection rests on a single relationship in the sources.

Literature
  • Hopcroft, J. & Tarjan, R. (1973). 'Algorithm 447: Efficient algorithms for graph manipulation'. Communications of the ACM 16(6), 372-378.
Connected ComponentsThe island of the network a node belongs to, to be consulted before comparing any distance or centrality across islands. The weak component ignores the direction of the edges; the strong component requires every member to reach every other following that direction, so the strong components are the circulation loops inside the weak islands, and the two coincide when every edge is mutual. More info.

Returns

Primary: The node's weak component. The components are numbered by size, 1 being the largest; like the community numbers, these numbers are identifiers, not scores.
Secondary: The node's strong component, numbered the same way.

Connected components tell whether the sources describe one connected world or several separate ones; in a correspondence network the strong components show between whom letters actually travelled both ways.

Literature
  • Tarjan, R. (1972). 'Depth-first search and linear graph algorithms'. SIAM Journal on Computing 1(2), 146-160.
BrokerageWhether a node's contacts are connected around it or only through it (Burt's structural holes). Effective size counts the contacts discounted by their redundancy: a node whose contacts all know each other has an effective size near 1, a node whose contacts are strangers to one another has an effective size of nearly its full number of contacts and is the broker. A node without edges has no ego network and reports no value. More info.

Returns

Primary: The node's effective size: higher means more brokerage.
Secondary: Burt's constraint, on the scale used in the literature; constraint is read inverted: a low value indicates the broker.
Statistic: Average Constraint: the mean constraint over the analysed nodes that have at least one edge.

In a trade network, the bookseller whose buyers and suppliers do not know one another scores a high effective size: every deal runs through the bookseller, and the sources on either side may never mention the other.

Literature
  • Burt, R. S. (1992). Structural Holes: The Social Structure of Competition. Harvard University Press.
  • Borgatti, S. P. (1997). 'Structural holes: Unpacking Burt's redundancy measures'. Connections 20(1), 35-38.
Community Detection
Every community analysis divides the network into communities: groups of nodes that belong together by the mode's own standard, stated per entry. All modes read the network undirected except Infomap and Statistical Inference, which read the direction of the edges themselves.

Options

  • Runs & Seed: every run after the first restarts the analysis with the nodes visited in a different order, and the best result by the mode's own quality is kept; the seed makes the random orders, and so the whole analysis, reproducible. At 0 runs the mode sets its own number: 10 for Label Propagation, which has to draw at random, 1 for the other modes, which choose the best step every time. Result determinism: with a single run of these other modes the seed has no effect: the division follows from the network and the settings alone, so two results only differ where the data or the settings differ, which makes them comparable across versions of a dataset. With more than one run, the runs that are not kept are still used: the modes that keep a best division also report how much the runs agreed on it, as each node's consensus (secondary value) and a figure over the whole network (statistic).
  • Significance: a quality score on its own is of limited value, because these measures score any network, including a random one. The setting compares the found quality with the same analysis on the set number of randomised networks, in which every node keeps its number of edges but all other structure is randomised; the resulting statistics report the mean and spread of the randomised qualities and the z-score and p of the found one, and a large z means the communities are actual structure, not a result of the edge counts alone.
  • Resolution: a higher resolution gives fewer, larger communities; a lower resolution more, smaller ones. 1 applies the measure as defined in the literature.
  • Size: how the size of a node's community is reported as the secondary value: absolute, relative, normalised, or not at all.

Returns

Primary: The community the node belongs to, numbered 1 up to the number of communities; the numbers are to be used as identifiers, not scores.
Secondary: The size of the node's community, as set by the Size option; with more than one run Modularity, Leiden, Leiden CPM and Label Propagation replace it with the node's consensus, how consistently the members of its community stay with it across the runs (1 when they are always in the same community, lower for a node between two circles). Statistical Inference and Infomap replace it as stated in their entries.
Statistic: Communities: the number found, reported by every mode. Consensus: with more than one run, the mean consensus over the nodes, how much the runs agreed on the division as a whole. Additional figures are specific to the mode and stated per entry.

Literature
  • Maslov, S. & Sneppen, K. (2002). 'Specificity and stability in topology of protein networks'. Science 296(5569), 910-913.
  • Lancichinetti, A. & Fortunato, S. (2012). 'Consensus clustering in complex networks'. Scientific Reports 2, 336.
ModularityDivides the network into communities in which edges are denser than expected by chance, with the classic Louvain search. Louvain can return communities that internally fall apart into disconnected pieces; it is included as an option for continuity and comparison, while Leiden is the recommended mode for modularity analyses. More info.

Returns

Statistic: Modularity: the achieved modularity, both as Newman defines it (roughly 0.3-0.7 signals clear community structure) and at the chosen resolution.

In a correspondence network, modularity divides the writers into circles that write mostly among themselves, the epistolary equivalent of schools and milieus.

Literature
  • Newman, M. E. J. & Girvan, M. (2004). 'Finding and evaluating community structure in networks'. Physical Review E 69, 026113.
  • Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. (2008). 'Fast unfolding of communities in large networks'. Journal of Statistical Mechanics: Theory and Experiment 2008(10), P10008.
  • Fortunato, S. & Barthélemy, M. (2007). 'Resolution limit in community detection'. Proceedings of the National Academy of Sciences (PNAS) 104(1), 36-41.
Leiden ModularityModularity with the improved Leiden search: every found community is guaranteed to be internally connected, and the search is repeated from its own result until the division no longer improves, on which the quality of the method is based. On the same network Leiden finds an equal or better division than Louvain, so it is preferred unless comparability with the classic modularity analysis is required. More info.

Returns

Statistic: Modularity: the achieved modularity, both as Newman defines it (roughly 0.3-0.7 signals clear community structure) and at the chosen resolution.

In a correspondence network, Leiden draws the same circles as modularity but guarantees each circle is actually connected, so no reported community consists of two unrelated groups.

Literature
  • Traag, V. A., Waltman, L. & van Eck, N. J. (2019). 'From Louvain to Leiden: guaranteeing well-connected communities'. Scientific Reports 9, 5233.
Leiden CPMThe Leiden search on the Constant Potts Model (CPM), which measures every community against the same fixed standard: an edge density, rather than the comparison of modularity with what would be expected by chance. This makes it resolution-limit-free: whether a small tight circle is recognised does not depend on how large the rest of the network is, where modularity merges small circles into their surroundings once the network grows. The resolution is read against the density of the whole network, so '1' requires a community to have the density of the network itself. More info.

Returns

Statistic: CPM: the achieved quality. Modularity: of the same division, for comparison. Absolute Resolution: the density threshold that results from the resolution, which is the resolution as stated in the literature and by other software.

In an events network spanning decades, the Constant Potts Model keeps recognising a small persistent circle of five regulars that modularity would merge into a larger period cluster.

Literature
  • Traag, V. A., Van Dooren, P. & Nesterov, Y. (2011). 'Narrow scope for resolution-limit-free community detection'. Physical Review E 84, 016114.
  • Traag, V. A., Waltman, L. & van Eck, N. J. (2019). 'From Louvain to Leiden: guaranteeing well-connected communities'. Scientific Reports 9, 5233.
Label PropagationEvery node repeatedly adopts the community most common among its neighbours until the labels no longer change: a node belongs where most of its connections belong. The method draws at random by design, so it always runs several times (the Runs setting) and keeps the division with the highest modularity. It remains practical when the network is too large for the other methods. More info.

Returns

Secondary: As it always runs several times, Label Propagation reports the node's consensus across those runs by default (see the shared Returns above), in place of the community size.
Statistic: Modularity: of the kept (best) division.

On a network of hundreds of thousands of records, label propagation still returns readable circles in the time the other modes need for a fraction of the data.

Literature
  • Raghavan, U. N., Albert, R. & Kumara, S. (2007). 'Near linear time algorithm to detect community structures in large-scale networks'. Physical Review E 76, 036106.
InfomapCommunities as the modules of a flow: Infomap follows a random walker over the network and groups the nodes where the walker lingers, judged by how well the modules compress a description of its movements (the map equation). It reads the direction of the edges, so it suits networks in which something actually moves in the direction of the edges; on a fully mutual network it reads the flow as undirected. More info.

Options

  • Teleportation: the share of steps the walker jumps to a random node instead of following an outgoing edge, required to prevent a directed flow from accumulating in dead ends; 0.15 is the rate of the original paper, and it applies to directed flow only.

Returns

Secondary: The node's visit rate instead of the community size: the share of the walker's steps spent at the node, its standing within the flow.
Statistic: Codelength: the description length of the walker's movements, in bits per step. Saving: the reduction in codelength by the modules compared to no modules, the evidence of this mode; a saving of 0 means no flow structure was found. Direction: whether the walker followed the direction of the edges or read the network undirected. Teleportation: the rate applied, on directed flow only.

In a travel or citation network, Infomap groups the places or works among which the traffic actually circulates, where the density based modes only see who is connected to whom.

Literature
  • Rosvall, M. & Bergstrom, C. T. (2008). 'Maps of random walks on complex networks reveal community structure'. Proceedings of the National Academy of Sciences (PNAS) 105(4), 1118-1123.
Statistical InferenceFits a stochastic block model, a statistical account of which groups of nodes connect to which, and keeps the division that best explains the network's edges. Where every other mode always produces a division and relies on randomised comparison networks to determine whether it is meaningful, statistical inference reports communities only where the evidence supports them (in a random network it would find none), weighing that evidence itself. More info.

The graph is read as directed, unless every edge is mutual and has the same strength in both directions. On a weighted graph the edges remain unchanged and the connection strengths are described in addition, per pair of groups. On a weighted graph, groups with stronger connections can be found on their strength alone, while weights without a pattern do not add groups and can remove the support for a weak group.

Options

  • Model: the kind of division the evidence is weighed for:
    • Planted Partition: ordinary communities, groups denser inside than between.
    • General: weighs every pair of groups on its own, so it also finds structure that is not shaped as communities, such as two sides that only ever connect to each other.
    • Nested: fits the general model on the nodes and then groups the communities themselves in turn, level upon level: circles within circles, which describes a large network more compactly than a single level of communities does.

    None of the three accounts for the number of connections of a node (the degree correction): they only consider how those connections are distributed across the groups, so a node with unusually many connections is read as an ordinary hub, not as a community of its own.

  • Samples: sweeps of a sampler around the best division, replacing the community size with the membership certainty per node; the sampler applies to the flat models only, so Nested does not use it.

Returns

Secondary: The size of the node's community; with Samples set, its membership certainty instead: the share of the sampled divisions that agree on its community, so a node between two circles is shown as uncertain rather than assigned to one of them without indication.
Statistic: Model: which model weighed the evidence. Description Length: how compactly the division explains the network (in 'natural units'/nats); on a weighted graph it can be below zero when the strengths are small, as results from a normalisation or a distance weight well above 1 (this is not an error, as only the differences between divisions are meaningful). Direction: whether the connections were fitted directed or undirected. Weights: stated on a weighted graph, as the strengths are described alongside the structure rather than counted as edges. Evidence: what the communities save over describing the network as a single community; at or below 0 the model found no communities to report; the single-community length is the same under every model, so the evidence compares across them. Levels: with Nested, the communities per level, from the node division up to the single top level. With Samples set: the number of sweeps run, the mean certainty over the nodes, and the acceptance rate of the sampler's merge-split moves.

Where every other mode divides a network of chance co-occurrences into "circles", statistical inference reports one community: the sources provide no evidence of any grouping.

Literature
  • Zhang, L. & Peixoto, T. P. (2020). 'Statistical inference of assortative community structures'. Physical Review Research 2, 043271.
  • Peixoto, T. P. (2014). 'Efficient Monte Carlo and greedy heuristic for the inference of stochastic block models'. Physical Review E 89, 012804.
  • Peixoto, T. P. (2014). 'Hierarchical block structures and the resolution limit of community detection'. Physical Review X 4, 011047.
  • Peixoto, T. P. (2017). 'Nonparametric Bayesian inference of the microcanonical stochastic block models'. Physical Review E 95, 012317.
  • Peixoto, T. P. (2018). 'Nonparametric weighted stochastic block models'. Physical Review E 97, 012306.
  • Peixoto, T. P. (2019). 'Bayesian stochastic blockmodeling'. In: P. Doreian, V. Batagelj & A. Ferligoj (eds.), Advances in Network Clustering and Blockmodeling, 289-332. Wiley.

Similarity  

With the support of vectors, it is possible to embed vectorised data that results from a machine learning model (e.g. large language models, computer vision, natural language processing) and use metrics for evaluating their similarity. The currently available similarity algorithms are:

AlgorithmDescription
Vector distanceThe distance between source and target vectors, so vectorised data from a machine learning (ML/AI) model can be compared: the nearer two vectors, the more alike the data behind them. A distance is read in reverse of the network measures above: a smaller value is a nearer, more similar pair.

Options

  • Approach: sets what the distance is measured between:
    • Connected: use the Scope to build a network between the vectors and measure only along its edges, so the distance reflects similarity where the network already connects the vectors; the target vector has to be last in the Scope selection. Weighting only applies to this approach, read as strength.
    • Disconnected: disregard the network and measure between the selected source and target vectors directly.
  • Calculate: the distance measure: Euclidean, the straight-line distance between the vectors, or Cosine, the angle between them regardless of their magnitude.
  • Mode: the summed distances as they are (absolute), each as its share of the summed distance over all nodes (relative), or rescaled between 0 and 1 within this result (normalised).

Returns

Primary: The node's summed distance to the target vectors, each weighted by its edge's strength when a weighted mode is set; a smaller value is nearer, more similar.

In a corpus of letters embedded by a language model, vector distance ranks which letters read most alike, surfacing near-duplicates and shared sources the catalogue never linked.

Literature
  • Salton, G., Wong, A. & Yang, C. S. (1975). 'A vector space model for automatic indexing'. Communications of the ACM 18(11), 613-620.
  • Mikolov, T., Sutskever, I., Chen, K., Corrado, G. & Dean, J. (2013). 'Distributed representations of words and phrases and their compositionality'. Advances in Neural Information Processing Systems 26, 3111-3119.

Export  

Export the computed graph for use in external applications. The graph provides:

  • Nodes with their name, nodegoat URI, Type, and weight.
  • Edges with their direction, weight, and time (using temporality (T) configured in the Scope).

The currently available export format is GEXF (Graph Exchange XML Format).

Weight  

When applicable to the algorithm you can indicate whether you want to make use of the graph's weight. A weight is the total edge length between two nodes and can be based on:

  • Duplicate edges becoming the one edge.
  • Weighting collapsed nodes and source/target nodes using the Conditions.
  • Combination of both.

A collapsed node shared by two nodes projects a single connection between them (see above); each such shared collapsed node adds 1 + (wa − 1) + (wb − 1) to the edge's weight (one for the shared node, plus each side's weight above the default of 1) so unweighted, the weight is the number of shared nodes.

The weight mode determines how the resulting weight should be applied:

ModeDescription
To ClosenessA higher weight is a nearer, stronger connection: edges add to a shorter total edge length.
To DistanceA higher weight is a farther, weaker connection: edges add to a longer total edge length.

The algorithms read a weight in one of two ways, since what a weight should count for depends on the algorithm's purpose:

ReadingDescription
As LengthSum the weights of the edges along a path, so a near connection is short and a far one long: unweighted an edge is 1 (a step), a closeness is reversed to (wmax + 1) − w against the highest weight in the graph, a distance is used as is. The best routes run over the shortest edges. Shortest Path, Disjoint Paths, Closeness, Eccentricity, Betweenness, and Count.
As StrengthWeigh every edge on its own, so a near connection is strong and a far one weak: unweighted an edge is 1, a closeness is used as is, a distance is reversed to 1 / w (not against the highest weight, as a single far outlier would then change every strength). A strength depends on its edge only, so adding an edge elsewhere does not change it. Community detection, the influence centralities (Degree Centrality included), Clustering Coefficient, k-Core, Brokerage, the prediction algorithms, and Vector Distance.

The reading applied by an analysis is reported with its run statistics.

The weights can also determine which edges are passed on to the algorithms, using the Weight Backbone setting described under Graph Verification below.

On the strength reading the weights can be normalised: every edge is weighed against the activity of its two nodes, so that a connection which is strong only because both its nodes are well-connected no longer dominates the graph. It only applies to the 'as strength' reading, the 'as length' reading remains unchanged, and it is disabled by default.

NormaliseDescription
Chance-Corrected (Association Strength)The edge against what the activity of its two nodes would produce by chance, so 1 is exactly expected, above 1 stronger than chance and below 1 weaker. The only one of the three that is not capped at 1, and the measure to prefer for co-occurrence (Van Eck & Waltman 2009).
Balanced (Cosine)The edge over the geometric mean of its two nodes' strength, which allows a sparsely connected node to connect strongly to a well-connected node; between 0 and 1.
Strict (Jaccard)The edge over the combined strength of its two nodes, which is the most demanding of the three: it never scores an edge higher than the balanced reading; between 0 and 1.

Graph Verification  

Two settings that do not measure the network but evaluate it: 'weight backbone' removes the edges that are explained by the activity of the data itself before an algorithm reads the graph, 'robustness' assesses how much of a result would remain if the sources had preserved slightly less. Both are disabled by default.

Weight Backbone  

Not every edge makes a statement: two nodes that share a collapsed node are formally connected, and a node with many edges will have some edges by chance alone. The backbone keeps only the edges that are stronger than the totals of their two nodes explain: every edge is read as a share of a node's total strength, and it is kept when that share is too large for a random split of that total across the node's edges to produce (the disparity filter).

It is sufficient for an edge to be significant to one of its two nodes, so an edge that is marginal to a well-connected node is kept when it is substantial to the other node, and a node with a single edge keeps it, as there is nothing to compare it to. The filter requires weights and is not applied without them; it applies before any algorithm runs, so the edge count of the run is the number of edges that remained.

Options

  • Level: the probability below which a share has to arise by chance for its edge to be kept. At 0 the filter is disabled and the graph remains complete; every level above 0 filters, the lowest level being the most demanding and a higher level keeping more edges. 0.05 is the common choice and keeps a tenth of the edges of a dense network or fewer: a large number of removed edges is the purpose of the filter, not a sign of an error. In a small network only few edges reach the level, so assess the removed edges before using the result further.

Returns

Statistic: Backbone: the level every edge was measured against. Edges: the number of edges removed by the filter, and the total number it received; the remaining edges are the edge count of the run.

In a network of people who attended the same events, the backbone drops the pairs who merely turn up in the same crowded events and keeps those who turn up together where few others do.

Literature
  • Serrano, M. Á., Boguñá, M. & Vespignani, A. (2009). 'Extracting the multiscale backbone of complex weighted networks'. Proceedings of the National Academy of Sciences (PNAS) 106(16), 6483-6488.

Robustness  

The sources are what survived, not what there was. Robustness assesses whether a result would remain if slightly more had been lost: it rebuilds the network without a randomly drawn tenth of its edges, runs the same analysis on it, and compares the resulting ranking with the ranking of the whole network.

It applies to the analyses that score every node, including the centralities; a community or a component is an identifier rather than a ranking, for which Significance and the consensus answer the same question. Only edges are removed and the weights keep the scale of the whole network, so every resample is compared over the same nodes on the same scale, and the reported results remain those of the whole network. Result determinism: these figures are an estimate based on resamples rather than a property of the network: for a given seed (when available in the algorithm) they are reproduced exactly, another seed changes them slightly, and more resamples stabilise them.

Options

  • Resamples: the number of times the analysis is run again on the network with a tenth of its edges removed. At 0 robustness is not assessed; 20 resamples are sufficient for verification.

Returns

Statistic: Resamples: the number of resamples run. Share: the share of edges removed in each resample. Agreement: how much of the ranking remained on average, as a rank correlation, 1 being a ranking that did not change at all. Lowest: the lowest agreement of the resamples, to consult when an argument is based on a single result.

In a correspondence network, a person whose brokerage rests on two surviving letters loses that standing as soon as a few connections fall away. A lower-end agreement of 0.6 then marks a finding that could reflect critically on the underlying sources.

Literature
  • Spearman, C. (1904). 'The proof and measurement of association between two things'. American Journal of Psychology 15(1), 72-101.
  • Costenbader, E. & Valente, T. W. (2003). 'The stability of centrality measures when networks are sampled'. Social Networks 25(4), 283-307.
  • Borgatti, S. P., Carley, K. M. & Krackhardt, D. (2006). 'On the robustness of centrality measures under conditions of imperfect data'. Social Networks 28(2), 124-136.

Network Statistics  

Every analysis concludes with the same overview of the network it ran on, in addition to the statistics of the algorithm itself, or of the options that generate the graph (stated in the entries above). The distance based figures (diameter, radius, average path length) count unweighted steps following the direction of the edges; the degree based figures (concentration, assortativity) count a node's edges in both directions together.

StatisticDescription
Average DegreeThe average number of edges per node.
Average Weighted DegreeThe average summed edge weight per node, based on the weights as provided.
Average Weighted Degree as LengthThe same average, over the weight the 'as length' reading gives each edge (see Weight): a closeness reversed against the highest weight, a distance as it is, either capped at a configured maximum. Stated only when it differs from the weights as provided.
Average Weighted Degree as StrengthThe same average, over the weight the 'as strength' reading gives each edge (see Weight): a closeness as provided, a distance turned into its reciprocal, either capped at a configured maximum, and a normalisation weighing it against the activity of its two nodes, which can lower the scale far below 1. Stated only when it differs from the weights as provided.
Degree ConcentrationHow unevenly the edges are spread over the nodes, as the Gini coefficient of their degrees: 0 when every node has the same number, towards 1 when a few nodes have nearly all of them. Useful for source criticism of the graph: it indicates a network shaped by only a few nodes.
Degree AssortativityWhether the well-connected nodes attach to each other or to sparsely connected ones, as the correlation between the degrees at the two ends of an edge (Newman 2002): above 0 they connect to each other as a core, below 0 each is at the centre of its own circle of nodes that have few other connections. Not stated when every node with edges has the same number of edges, as there is then nothing to correlate. More info.
DensityThe share of all possible edges that exist: 1 would mean every node is connected to every other.
ReciprocityThe share of edges that also run in the reverse direction: 1 means every edge is mutual and the network is effectively undirected.
DiameterThe longest shortest path in the network: how many steps the two most separated (still connected) nodes are apart.
RadiusThe steps needed from the best-placed node to its farthest reachable node; the centre of the network is at this depth.
Average Path LengthThe average number of steps between all pairs of connected nodes: the average separation of the nodes in the network.
Connected ComponentsThe number of islands the network falls into when the direction of the edges is ignored.
Largest ComponentThe number of nodes in the largest island: a number close to all nodes indicates one connected whole with a few separate fragments, far below it a substantial split.
Strongly Connected ComponentsThe number of groups within which every node can reach every other following the direction of the edges.
Largest Strong ComponentThe number of nodes in the largest such group; when every strong component is a single node, the network has no cycle at all.