Merge pull request #149 from tigergraph/degree-cent

Degree cent
tigergraph · May 28, 2024 · 356c36f · 356c36f
2 parents ce724c0 + 090362c
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diff --git a/GDBMS_ALGO/centrality/degree_cent.gsql b/GDBMS_ALGO/centrality/degree_cent.gsql
@@ -1,70 +1,72 @@
 CREATE TEMPLATE QUERY GDBMS_ALGO.centrality.degree_cent(SET<STRING> v_type_set, SET<STRING> e_type_set, SET<STRING> reverse_e_type_set, BOOL in_degree = TRUE, BOOL out_degree = TRUE,
-  INT top_k=100, BOOL print_results = TRUE, STRING result_attribute = "",STRING file_path = "") SYNTAX V1 {
-
+  INT top_k=100, BOOL print_results = TRUE, STRING result_attribute = "",STRING file_path = "", BOOL normalize = TRUE) SYNTAX V1 {
     /*
-    First Author: <First Author Name>
-    First Commit Date:  <First Commit Date>
-
-    Recent Author: <Recent Commit Author Name>
-    Recent Commit Date: <Recent Commit Date>
+        First Author: <First Author Name>
+        First Commit Date:  <First Commit Date>
 
+        Recent Author: Rob Rossmiller
+        Recent Commit Date: 05/2024
 
-    Repository:
-        https://github.com/tigergraph/gsql-graph-algorithms/tree/master/algorithms/Centrality
 
-    Maturity:
-        Production
+        Repository:
+            https://github.com/tigergraph/gsql-graph-algorithms/tree/master/algorithms/Centrality
 
-    Description: 
-        Compute degree Centrality for each VERTEX.
-        for undirected graph, you only need to set e_type_set and indegree
+        Maturity:
+            Production
 
-    Publications:
-        NA
+        Description: 
+            Compute degree Centrality for each VERTEX.
+            for undirected graph, you only need to set e_type_set and indegree
 
-    TigerGraph Documentation:
-        https://docs.tigergraph.com/graph-ml/current/centrality-algorithms/degree-centrality
+        Publications:
+            NA
 
-    Parameters:
-        v_type_set:
-            vertex types to traverse
-        e_type_set:
-            edge types to traverse
-        reverse_e_type_set:
-            for indegree use
-        in_degree:
-            If True, count incoming relationships
-        out_degree:
-            If True, count outcoming relationships
-        top_k:
-            report only this many top scores
-        print_results:
-            If True, print the result
-        result_attribute:
-            attribute to write result to
-        file_path:
-            file to write CSV output to
+        TigerGraph Documentation:
+            https://docs.tigergraph.com/graph-ml/current/centrality-algorithms/degree-centrality
 
+        Parameters:
+            v_type_set:
+                vertex types to traverse
+            e_type_set:
+                edge types to traverse
+            reverse_e_type_set:
+                for indegree use
+            in_degree:
+                If True, count incoming relationships
+            out_degree:
+                If True, count outcoming relationships
+            top_k:
+                report only this many top scores
+            print_results:
+                If True, print the result
+            result_attribute:
+                attribute to write result to
+            file_path:
+                file to write CSV output to
+            normailize:
+                If True, return the normalized centrality. Default: True 
   */
 
   TYPEDEF TUPLE<VERTEX Vertex_ID, FLOAT score> Vertex_Score;
   HeapAccum<Vertex_Score>(top_k, score DESC) @@top_scores_heap;
-  SumAccum<INT> @sum_degree_score;
+  SumAccum<DOUBLE> @sum_degree_score;
   FILE f (file_path);
 
   all = {v_type_set};
   sll = SELECT s 
         FROM all:s
-        ACCUM IF in_degree THEN
-                 FOREACH edge_type in reverse_e_type_set DO
-                     s.@sum_degree_score+=s.outdegree(edge_type)
-                 END
-              END,
-              IF out_degree THEN
-                  FOREACH edge_type in e_type_set DO
-                      s.@sum_degree_score+=s.outdegree(edge_type)
-                  END
-              END;
+        ACCUM 
+            IF in_degree THEN
+                s.@sum_degree_score += s.outdegree(reverse_e_type_set)
+            END,
+            IF out_degree THEN
+                s.@sum_degree_score += s.outdegree(e_type_set)
+            END
+        POST-ACCUM 
+            IF normalize THEN
+                s.@sum_degree_score = s.@sum_degree_score / (all.size() - 1)
+            END;
+
   #Output
   IF file_path != "" THEN
       f.println("Vertex_ID", "Degree");

diff --git a/algorithms/Centrality/degree/unweighted/tg_degree_cent.gsql b/algorithms/Centrality/degree/unweighted/tg_degree_cent.gsql
@@ -1,70 +1,71 @@
-CREATE QUERY tg_degree_cent(SET<STRING> v_type_set, SET<STRING> e_type_set, SET<STRING> reverse_e_type_set, BOOL in_degree = TRUE, BOOL out_degree = TRUE,
-  INT top_k=100, BOOL print_results = TRUE, STRING result_attribute = "",STRING file_path = "") SYNTAX V1 {
-
+CREATE QUERY tg_degree_cent(SET<STRING> v_type_set, SET<STRING> e_type_set, SET<STRING> reverse_e_type_set, BOOL in_degree = TRUE, BOOL out_degree = TRUE, INT top_k=100, BOOL print_results = TRUE, STRING result_attribute = "",STRING file_path = "", BOOL normalize = TRUE) SYNTAX V1 {
     /*
-    First Author: <First Author Name>
-    First Commit Date:  <First Commit Date>
-
-    Recent Author: <Recent Commit Author Name>
-    Recent Commit Date: <Recent Commit Date>
+        First Author: <First Author Name>
+        First Commit Date:  <First Commit Date>
 
+        Recent Author: Rob Rossmiller
+        Recent Commit Date: 05/2024
 
-    Repository:
-        https://github.com/tigergraph/gsql-graph-algorithms/tree/master/algorithms/Centrality
 
-    Maturity:
-        Production
+        Repository:
+            https://github.com/tigergraph/gsql-graph-algorithms/tree/master/algorithms/Centrality
 
-    Description: 
-        Compute degree Centrality for each VERTEX.
-        for undirected graph, you only need to set e_type_set and indegree
+        Maturity:
+            Production
 
-    Publications:
-        NA
+        Description: 
+            Compute degree Centrality for each VERTEX.
+            for undirected graph, you only need to set e_type_set and indegree
 
-    TigerGraph Documentation:
-        https://docs.tigergraph.com/graph-ml/current/centrality-algorithms/degree-centrality
+        Publications:
+            NA
 
-    Parameters:
-        v_type_set:
-            vertex types to traverse
-        e_type_set:
-            edge types to traverse
-        reverse_e_type_set:
-            for indegree use
-        in_degree:
-            If True, count incoming relationships
-        out_degree:
-            If True, count outcoming relationships
-        top_k:
-            report only this many top scores
-        print_results:
-            If True, print the result
-        result_attribute:
-            attribute to write result to
-        file_path:
-            file to write CSV output to
+        TigerGraph Documentation:
+            https://docs.tigergraph.com/graph-ml/current/centrality-algorithms/degree-centrality
 
+        Parameters:
+            v_type_set:
+                vertex types to traverse
+            e_type_set:
+                edge types to traverse
+            reverse_e_type_set:
+                for indegree use
+            in_degree:
+                If True, count incoming relationships
+            out_degree:
+                If True, count outcoming relationships
+            top_k:
+                report only this many top scores
+            print_results:
+                If True, print the result
+            result_attribute:
+                attribute to write result to
+            file_path:
+                file to write CSV output to
+            normailize:
+                If True, return the normalized centrality. Default: True 
   */
 
   TYPEDEF TUPLE<VERTEX Vertex_ID, FLOAT score> Vertex_Score;
   HeapAccum<Vertex_Score>(top_k, score DESC) @@top_scores_heap;
-  SumAccum<INT> @sum_degree_score;
+  SumAccum<DOUBLE> @sum_degree_score;
   FILE f (file_path);
 
   all = {v_type_set};
   sll = SELECT s 
         FROM all:s
-        ACCUM IF in_degree THEN
-                 FOREACH edge_type in reverse_e_type_set DO
-                     s.@sum_degree_score+=s.outdegree(edge_type)
-                 END
-              END,
-              IF out_degree THEN
-                  FOREACH edge_type in e_type_set DO
-                      s.@sum_degree_score+=s.outdegree(edge_type)
-                  END
-              END;
+        ACCUM 
+            IF in_degree THEN
+                s.@sum_degree_score += s.outdegree(reverse_e_type_set)
+            END,
+            IF out_degree THEN
+                s.@sum_degree_score += s.outdegree(e_type_set)
+            END
+        POST-ACCUM 
+            IF normalize THEN
+                s.@sum_degree_score = s.@sum_degree_score / (all.size() - 1)
+            END;
+
   #Output
   IF file_path != "" THEN
       f.println("Vertex_ID", "Degree");

diff --git a/tests/README.md b/tests/README.md
@@ -0,0 +1,6 @@
+# Algorithm Testing
+
+[networkX](https://networkx.org/documentation/stable/reference/index.html) is used as
+the baseline for our tests where we can.
+
+A peculiarity to note about nx is that it counts self edges in undirected graphs as two separate edges. So, you'll see that some baselines use a modified version of the code that is found within nx. Take `run_degree_baseline_complete`, which generates the baseline for degree centrality on complete graphs. It uses the same code that can be found in `nx.centrality.degree_centrality` with the exception of subtracting a node's degree by one.
diff --git a/...elines/centrality/article_rank/Empty.json → ...seline/centrality/article_rank/Empty.json b/...elines/centrality/article_rank/Empty.json → ...seline/centrality/article_rank/Empty.json
diff --git a/...es/centrality/article_rank/Hub_Spoke.json → ...ne/centrality/article_rank/Hub_Spoke.json b/...es/centrality/article_rank/Hub_Spoke.json → ...ne/centrality/article_rank/Hub_Spoke.json
diff --git a/...lity/article_rank/Hub_Spoke_Directed.json → ...lity/article_rank/Hub_Spoke_Directed.json b/...lity/article_rank/Hub_Spoke_Directed.json → ...lity/article_rank/Hub_Spoke_Directed.json
diff --git a/...selines/centrality/article_rank/Line.json → ...aseline/centrality/article_rank/Line.json b/...selines/centrality/article_rank/Line.json → ...aseline/centrality/article_rank/Line.json
diff --git a/...entrality/article_rank/Line_Directed.json → ...entrality/article_rank/Line_Directed.json b/...entrality/article_rank/Line_Directed.json → ...entrality/article_rank/Line_Directed.json
diff --git a/...selines/centrality/article_rank/Ring.json → ...aseline/centrality/article_rank/Ring.json b/...selines/centrality/article_rank/Ring.json → ...aseline/centrality/article_rank/Ring.json
diff --git a/...entrality/article_rank/Ring_Directed.json → ...entrality/article_rank/Ring_Directed.json b/...entrality/article_rank/Ring_Directed.json → ...entrality/article_rank/Ring_Directed.json
diff --git a/...selines/centrality/article_rank/Tree.json → ...aseline/centrality/article_rank/Tree.json b/...selines/centrality/article_rank/Tree.json → ...aseline/centrality/article_rank/Tree.json
diff --git a/...entrality/article_rank/Tree_Directed.json → ...entrality/article_rank/Tree_Directed.json b/...entrality/article_rank/Tree_Directed.json → ...entrality/article_rank/Tree_Directed.json
diff --git a/...entrality/closeness_centrality/Empty.json → ...entrality/closeness_centrality/Empty.json b/...entrality/closeness_centrality/Empty.json → ...entrality/closeness_centrality/Empty.json
diff --git a/...ality/closeness_centrality/Hub_Spoke.json → ...ality/closeness_centrality/Hub_Spoke.json b/...ality/closeness_centrality/Hub_Spoke.json → ...ality/closeness_centrality/Hub_Spoke.json
diff --git a/...seness_centrality/Hub_Spoke_Directed.json → ...seness_centrality/Hub_Spoke_Directed.json b/...seness_centrality/Hub_Spoke_Directed.json → ...seness_centrality/Hub_Spoke_Directed.json
diff --git a/...centrality/closeness_centrality/Line.json → ...centrality/closeness_centrality/Line.json b/...centrality/closeness_centrality/Line.json → ...centrality/closeness_centrality/Line.json
diff --git a/...y/closeness_centrality/Line_Directed.json → ...y/closeness_centrality/Line_Directed.json b/...y/closeness_centrality/Line_Directed.json → ...y/closeness_centrality/Line_Directed.json
diff --git a/...centrality/closeness_centrality/Ring.json → ...centrality/closeness_centrality/Ring.json b/...centrality/closeness_centrality/Ring.json → ...centrality/closeness_centrality/Ring.json
diff --git a/...y/closeness_centrality/Ring_Directed.json → ...y/closeness_centrality/Ring_Directed.json b/...y/closeness_centrality/Ring_Directed.json → ...y/closeness_centrality/Ring_Directed.json
diff --git a/...centrality/closeness_centrality/Tree.json → ...centrality/closeness_centrality/Tree.json b/...centrality/closeness_centrality/Tree.json → ...centrality/closeness_centrality/Tree.json
diff --git a/...y/closeness_centrality/Tree_Directed.json → ...y/closeness_centrality/Tree_Directed.json b/...y/closeness_centrality/Tree_Directed.json → ...y/closeness_centrality/Tree_Directed.json
diff --git a/tests/data/baseline/centrality/degree_centrality/Complete.json b/tests/data/baseline/centrality/degree_centrality/Complete.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 1.1428571428571428}, {"Vertex_ID": "B", "score": 1.1428571428571428}, {"Vertex_ID": "C", "score": 1.1428571428571428}, {"Vertex_ID": "D", "score": 1.1428571428571428}, {"Vertex_ID": "E", "score": 1.1428571428571428}, {"Vertex_ID": "F", "score": 1.1428571428571428}, {"Vertex_ID": "G", "score": 1.1428571428571428}, {"Vertex_ID": "H", "score": 1.1428571428571428}]}]
diff --git a/...s/centrality/degree_centrality/Empty.json → ...e/centrality/degree_centrality/Empty.json b/...s/centrality/degree_centrality/Empty.json → ...e/centrality/degree_centrality/Empty.json
diff --git a/tests/data/baseline/centrality/degree_centrality/Hub_Spoke.json b/tests/data/baseline/centrality/degree_centrality/Hub_Spoke.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 1.0}, {"Vertex_ID": "B", "score": 0.05263157894736842}, {"Vertex_ID": "C", "score": 0.05263157894736842}, {"Vertex_ID": "D", "score": 0.05263157894736842}, {"Vertex_ID": "E", "score": 0.05263157894736842}, {"Vertex_ID": "F", "score": 0.05263157894736842}, {"Vertex_ID": "G", "score": 0.05263157894736842}, {"Vertex_ID": "H", "score": 0.05263157894736842}, {"Vertex_ID": "I", "score": 0.05263157894736842}, {"Vertex_ID": "J", "score": 0.05263157894736842}, {"Vertex_ID": "K", "score": 0.05263157894736842}, {"Vertex_ID": "L", "score": 0.05263157894736842}, {"Vertex_ID": "M", "score": 0.05263157894736842}, {"Vertex_ID": "N", "score": 0.05263157894736842}, {"Vertex_ID": "O", "score": 0.05263157894736842}, {"Vertex_ID": "P", "score": 0.05263157894736842}, {"Vertex_ID": "Q", "score": 0.05263157894736842}, {"Vertex_ID": "R", "score": 0.05263157894736842}, {"Vertex_ID": "S", "score": 0.05263157894736842}, {"Vertex_ID": "T", "score": 0.05263157894736842}]}]
diff --git a/tests/data/baseline/centrality/degree_centrality/Line.json b/tests/data/baseline/centrality/degree_centrality/Line.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 0.05263157894736842}, {"Vertex_ID": "B", "score": 0.10526315789473684}, {"Vertex_ID": "C", "score": 0.10526315789473684}, {"Vertex_ID": "D", "score": 0.10526315789473684}, {"Vertex_ID": "E", "score": 0.10526315789473684}, {"Vertex_ID": "F", "score": 0.10526315789473684}, {"Vertex_ID": "G", "score": 0.10526315789473684}, {"Vertex_ID": "H", "score": 0.10526315789473684}, {"Vertex_ID": "I", "score": 0.10526315789473684}, {"Vertex_ID": "J", "score": 0.10526315789473684}, {"Vertex_ID": "K", "score": 0.10526315789473684}, {"Vertex_ID": "L", "score": 0.10526315789473684}, {"Vertex_ID": "M", "score": 0.10526315789473684}, {"Vertex_ID": "N", "score": 0.10526315789473684}, {"Vertex_ID": "O", "score": 0.10526315789473684}, {"Vertex_ID": "P", "score": 0.10526315789473684}, {"Vertex_ID": "Q", "score": 0.10526315789473684}, {"Vertex_ID": "R", "score": 0.10526315789473684}, {"Vertex_ID": "S", "score": 0.10526315789473684}, {"Vertex_ID": "T", "score": 0.05263157894736842}]}]
diff --git a/tests/data/baseline/centrality/degree_centrality/Ring.json b/tests/data/baseline/centrality/degree_centrality/Ring.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 0.10526315789473684}, {"Vertex_ID": "B", "score": 0.10526315789473684}, {"Vertex_ID": "C", "score": 0.10526315789473684}, {"Vertex_ID": "D", "score": 0.10526315789473684}, {"Vertex_ID": "E", "score": 0.10526315789473684}, {"Vertex_ID": "F", "score": 0.10526315789473684}, {"Vertex_ID": "G", "score": 0.10526315789473684}, {"Vertex_ID": "H", "score": 0.10526315789473684}, {"Vertex_ID": "I", "score": 0.10526315789473684}, {"Vertex_ID": "J", "score": 0.10526315789473684}, {"Vertex_ID": "K", "score": 0.10526315789473684}, {"Vertex_ID": "L", "score": 0.10526315789473684}, {"Vertex_ID": "M", "score": 0.10526315789473684}, {"Vertex_ID": "N", "score": 0.10526315789473684}, {"Vertex_ID": "O", "score": 0.10526315789473684}, {"Vertex_ID": "P", "score": 0.10526315789473684}, {"Vertex_ID": "Q", "score": 0.10526315789473684}, {"Vertex_ID": "R", "score": 0.10526315789473684}, {"Vertex_ID": "S", "score": 0.10526315789473684}, {"Vertex_ID": "T", "score": 0.10526315789473684}]}]
diff --git a/tests/data/baseline/centrality/degree_centrality/Tree.json b/tests/data/baseline/centrality/degree_centrality/Tree.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 0.10526315789473684}, {"Vertex_ID": "B", "score": 0.15789473684210525}, {"Vertex_ID": "C", "score": 0.15789473684210525}, {"Vertex_ID": "D", "score": 0.15789473684210525}, {"Vertex_ID": "E", "score": 0.15789473684210525}, {"Vertex_ID": "F", "score": 0.15789473684210525}, {"Vertex_ID": "G", "score": 0.15789473684210525}, {"Vertex_ID": "H", "score": 0.15789473684210525}, {"Vertex_ID": "I", "score": 0.15789473684210525}, {"Vertex_ID": "J", "score": 0.10526315789473684}, {"Vertex_ID": "K", "score": 0.05263157894736842}, {"Vertex_ID": "L", "score": 0.05263157894736842}, {"Vertex_ID": "M", "score": 0.05263157894736842}, {"Vertex_ID": "N", "score": 0.05263157894736842}, {"Vertex_ID": "O", "score": 0.05263157894736842}, {"Vertex_ID": "P", "score": 0.05263157894736842}, {"Vertex_ID": "Q", "score": 0.05263157894736842}, {"Vertex_ID": "R", "score": 0.05263157894736842}, {"Vertex_ID": "S", "score": 0.05263157894736842}, {"Vertex_ID": "T", "score": 0.05263157894736842}]}]
diff --git a/tests/data/baseline/centrality/degree_centrality/in_degree/Hub_Spoke_Directed.json b/tests/data/baseline/centrality/degree_centrality/in_degree/Hub_Spoke_Directed.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 0.0}, {"Vertex_ID": "B", "score": 0.05263157894736842}, {"Vertex_ID": "C", "score": 0.05263157894736842}, {"Vertex_ID": "D", "score": 0.05263157894736842}, {"Vertex_ID": "E", "score": 0.05263157894736842}, {"Vertex_ID": "F", "score": 0.05263157894736842}, {"Vertex_ID": "G", "score": 0.05263157894736842}, {"Vertex_ID": "H", "score": 0.05263157894736842}, {"Vertex_ID": "I", "score": 0.05263157894736842}, {"Vertex_ID": "J", "score": 0.05263157894736842}, {"Vertex_ID": "K", "score": 0.05263157894736842}, {"Vertex_ID": "L", "score": 0.05263157894736842}, {"Vertex_ID": "M", "score": 0.05263157894736842}, {"Vertex_ID": "N", "score": 0.05263157894736842}, {"Vertex_ID": "O", "score": 0.05263157894736842}, {"Vertex_ID": "P", "score": 0.05263157894736842}, {"Vertex_ID": "Q", "score": 0.05263157894736842}, {"Vertex_ID": "R", "score": 0.05263157894736842}, {"Vertex_ID": "S", "score": 0.05263157894736842}, {"Vertex_ID": "T", "score": 0.05263157894736842}]}]
diff --git a/tests/data/baseline/centrality/degree_centrality/in_degree/Line_Directed.json b/tests/data/baseline/centrality/degree_centrality/in_degree/Line_Directed.json
@@ -0,0 +1 @@
+[{"top_scores": [{"Vertex_ID": "A", "score": 0.0}, {"Vertex_ID": "B", "score": 0.05263157894736842}, {"Vertex_ID": "C", "score": 0.05263157894736842}, {"Vertex_ID": "D", "score": 0.05263157894736842}, {"Vertex_ID": "E", "score": 0.05263157894736842}, {"Vertex_ID": "F", "score": 0.05263157894736842}, {"Vertex_ID": "G", "score": 0.05263157894736842}, {"Vertex_ID": "H", "score": 0.05263157894736842}, {"Vertex_ID": "I", "score": 0.05263157894736842}, {"Vertex_ID": "J", "score": 0.05263157894736842}, {"Vertex_ID": "K", "score": 0.05263157894736842}, {"Vertex_ID": "L", "score": 0.05263157894736842}, {"Vertex_ID": "M", "score": 0.05263157894736842}, {"Vertex_ID": "N", "score": 0.05263157894736842}, {"Vertex_ID": "O", "score": 0.05263157894736842}, {"Vertex_ID": "P", "score": 0.05263157894736842}, {"Vertex_ID": "Q", "score": 0.05263157894736842}, {"Vertex_ID": "R", "score": 0.05263157894736842}, {"Vertex_ID": "S", "score": 0.05263157894736842}, {"Vertex_ID": "T", "score": 0.05263157894736842}]}]
diff --git a/tests/data/baseline/centrality/degree_centrality/in_degree/Ring_Directed.json b/tests/data/baseline/centrality/degree_centrality/in_degree/Ring_Directed.json
@@ -0,0 +1 @@
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diff --git a/tests/data/baseline/centrality/degree_centrality/in_degree/Tree_Directed.json b/tests/data/baseline/centrality/degree_centrality/in_degree/Tree_Directed.json
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diff --git a/tests/data/baseline/centrality/degree_centrality/out_degree/Hub_Spoke_Directed.json b/tests/data/baseline/centrality/degree_centrality/out_degree/Hub_Spoke_Directed.json
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diff --git a/tests/data/baseline/centrality/degree_centrality/out_degree/Line_Directed.json b/tests/data/baseline/centrality/degree_centrality/out_degree/Line_Directed.json
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