Dummy node logic

config/config.yaml

@@ -45,7 +45,7 @@ container_registry:
 algorithms:
       - name: "pathlinker"
         params:
-              include: true
+              include: false
               run1:
                   k: range(100,201,100)
 
@@ -56,10 +56,11 @@ algorithms:
                   b: [5, 6]
                   w: np.linspace(0,5,2)
                   d: [10]
+                  dummy_mode: ["terminals"] 
 
       - name: "omicsintegrator2"
         params:
-              include: true
+              include: false
               run1:
                   b: [4]
                   g: [0]
@@ -69,26 +70,26 @@ algorithms:
 
       - name: "meo"
         params:
-              include: true
+              include:  false
               run1:
                   max_path_length: [3]
                   local_search: ["Yes"]
                   rand_restarts: [10]
 
       - name: "mincostflow"
         params:
-              include: true
+              include: false
               run1:
                   flow: [1] # The flow must be an int
                   capacity: [1]
 
       - name: "allpairs"
         params:
-              include: true
+              include: false
 
       - name: "domino"
         params:
-              include: true
+              include: false
               run1:
                   slice_threshold: [0.3]
                   module_threshold: [0.05]
@@ -101,6 +102,7 @@ datasets:
     -
       # Labels can only contain letters, numbers, or underscores
       label: data0
+      # To run OmicsIntegrator1 with dummy nodes, add the dummy.txt file to node_files
       node_files: ["node-prizes.txt", "sources.txt", "targets.txt"]
       # DataLoader.py can currently only load a single edge file, which is the primary network
       edge_files: ["network.txt"]
@@ -173,4 +175,4 @@ analysis:
         # 'euclidean', 'manhattan', 'cosine'
         metric: 'euclidean'
       evaluation:
-        include: true
+        include: true

input/README.md

@@ -18,6 +18,31 @@ C	2.5		True	True
 D	1.9	True	True	True
 ```
 
+##### OmicsIntegrator1: Dummy Nodes
+There are 4 dummy mode possibilities:
+ 1. terminals -> connect the dummy node to all nodes that have been assigned prizes 
+ 2. all ->  connect the dummy node to all nodes in the interactome i.e. full set of nodes in graph
+ 3. others -> connect the dummy node to all nodes that are not terminal nodes i.e. nodes w/o prizes
+ 4. file -> custom nodes - connect the dummy node to a specific list of nodes provided in a file
+To support the `file` dummy node logic as part of OmicsIntegrator1, you can either add a seperate `dummy.txt` file (and add this to the `node_files` argument in `config.yaml `) or add a `dummy` column node attribute to a file that contains `NODEID`, `prize`, `source`, etc. 
+
+If adding a seperate `dummy.txt` file:
+Make a file with the name `dummy.txt` and list the dummy nodes, each seperated by a new line. Example:
+```
+A
+B
+C
+```
+
+If adding the `dummy` column node attribute, then add the dummy column and specify boolean values for the `dummy` attribute:
+```
+NODEID	prize	sources	targets	dummy
+A	1.0		True	True    True
+B	3.3	True	True	
+C	2.5		True	True
+D	1.9	True	True	True
+```
+
 A secondary format provides only a list of node identifiers and uses the filename as the node attribute, as in the example `sources.txt`.
 This format may be deprecated.
 

input/dummy.txt

@@ -0,0 +1 @@
+A