Enable to simplify multiple-relation edges to a single edge

This can either be done manually when calling 'simplify.network' or automatically at network creation via a new network configuration parameter 'simplify.multiple.relations'. Signed-off-by: Thomas Bock <bockthom@cs.uni-saarland.de>
se-sic · Feb 9, 2024 · 2105ea8 · 2105ea8
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diff --git a/README.md b/README.md
@@ -654,6 +654,10 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
 - `simplify`
     * Perform edge contraction to retrieve a simplified network
     * [`TRUE`, *`FALSE`*]
+- `simplify.multiple.relations`
+    * Whether the simplified network should contract edges of multiple relations into a single edge or not (if not, there will be one edge for each relation, resulting in possibly more than one edge between a pair of vertices)
+    * **Note** This parameter does not take effect if ``simplify = FALSE``!
+    * [`TRUE`, *`FALSE`*]
 - `skip.threshold`
     * The upper bound for total amount of edges to build for a subset of the data, i.e., not building any edges for the subset exceeding the limit
     * any positive integer

diff --git a/util-conf.R b/util-conf.R
@@ -18,7 +18,7 @@
 ## Copyright 2020-2021 by Christian Hechtl <hechtl@cs.uni-saarland.de>
 ## Copyright 2017 by Felix Prasse <prassefe@fim.uni-passau.de>
 ## Copyright 2017-2019 by Thomas Bock <bockthom@fim.uni-passau.de>
-## Copyright 2021, 2023 by Thomas Bock <bockthom@cs.uni-saarland.de>
+## Copyright 2021, 2023-2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
 ## Copyright 2018 by Barbara Eckl <ecklbarb@fim.uni-passau.de>
 ## Copyright 2018-2019 by Jakob Kronawitter <kronawij@fim.uni-passau.de>
 ## Copyright 2019 by Anselm Fehnker <fehnker@fim.uni-passau.de>
@@ -863,6 +863,12 @@ NetworkConf = R6::R6Class("NetworkConf", inherit = Conf,
                 allowed = c(TRUE, FALSE),
                 allowed.number = 1
             ),
+            simplify.multiple.relations = list(
+               default = FALSE,
+               type = "logical",
+               allowed = c(TRUE, FALSE),
+               allowed.number = 1
+           ),
             skip.threshold = list(
                 default = Inf,
                 type = "numeric",

diff --git a/util-networks.R b/util-networks.R
@@ -15,7 +15,7 @@
 ## Copyright 2017 by Raphael Nömmer <noemmer@fim.uni-passau.de>
 ## Copyright 2017-2018 by Christian Hechtl <hechtl@fim.uni-passau.de>
 ## Copyright 2017-2019 by Thomas Bock <bockthom@fim.uni-passau.de>
-## Copyright 2021, 2023 by Thomas Bock <bockthom@cs.uni-saarland.de>
+## Copyright 2021, 2023-2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
 ## Copyright 2018 by Barbara Eckl <ecklbarb@fim.uni-passau.de>
 ## Copyright 2018-2019 by Jakob Kronawitter <kronawij@fim.uni-passau.de>
 ## Copyright 2020 by Anselm Fehnker <anselm@muenster.de>
@@ -1260,7 +1260,8 @@ construct.network.from.edge.list = function(vertices, edge.list, network.conf, d
 
     ## transform multiple edges to edge weights
     if (network.conf$get.value("simplify")) {
-        net = simplify.network(net)
+        net = simplify.network(net,
+                               simplify.multiple.relations = network.conf$get.value("simplify.multiple.relations"))
     }
 
     logging::logdebug("construct.network.from.edge.list: finished.")
@@ -1536,16 +1537,19 @@ add.attributes.to.network = function(network, type = c("vertex", "edge"), attrib
 #' @param network the given network
 #' @param remove.multiple whether to contract multiple edges between the same pair of vertices [default: TRUE]
 #' @param remove.loops whether to remove loops [default: TRUE]
+#' @param simplify.multiple.relations whether to combine edges of multiple relations into
+#'        one simplified edge [default: FALSE]
 #'
 #' @return the simplified network
-simplify.network = function(network, remove.multiple = TRUE, remove.loops = TRUE) {
+simplify.network = function(network, remove.multiple = TRUE, remove.loops = TRUE,
+                            simplify.multiple.relations = FALSE) {
     logging::logdebug("simplify.network: starting.")
     logging::loginfo("Simplifying network.")
 
     ## save network attributes, otherwise they get lost
     network.attributes = igraph::get.graph.attribute(network)
 
-    if (length(unique(igraph::get.edge.attribute(network, "relation"))) > 1) {
+    if (!simplify.multiple.relations && length(unique(igraph::get.edge.attribute(network, "relation"))) > 1) {
         ## data frame of the network
         edge.data = igraph::as_data_frame(network, what = "edges")
         vertex.data = igraph::as_data_frame(network, what = "vertices")
@@ -1587,17 +1591,20 @@ simplify.network = function(network, remove.multiple = TRUE, remove.loops = TRUE
 #' @param networks the list of networks
 #' @param remove.multiple whether to contract multiple edges between the same pair of vertices [default: TRUE]
 #' @param remove.loops whether to remove loops [default: TRUE]
+#' @param simplify.multiple.relations whether to combine edges of multiple relations into
+#'                                    one simplified edge [default: FALSE]
 #'
 #' @return the simplified networks
-simplify.networks = function(networks, remove.multiple = TRUE, remove.loops = TRUE) {
+simplify.networks = function(networks, remove.multiple = TRUE, remove.loops = TRUE,
+                             simplify.multiple.relations = FALSE) {
     logging::logdebug("simplify.networks: starting.")
     logging::loginfo(
         "Simplifying networks (names = [%s]).",
         paste(names(networks), collapse = ", ")
     )
 
     nets = parallel::mclapply(networks, simplify.network, remove.multiple = remove.multiple,
-                              remove.loops = remove.loops)
+                              remove.loops = remove.loops, simplify.multiple.relations = simplify.multiple.relations)
 
     logging::logdebug("simplify.networks: finished.")
     return(nets)