Dummy node logic

config/config.yaml

@@ -56,6 +56,7 @@ algorithms:
                   b: [5, 6]
                   w: np.linspace(0,5,2)
                   d: [10]
+                  dummy_mode: ["terminals"]
 
       - name: "omicsintegrator2"
         params:
@@ -69,7 +70,7 @@ algorithms:
 
       - name: "meo"
         params:
-              include: true
+              include:  true
               run1:
                   max_path_length: [3]
                   local_search: ["Yes"]
@@ -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

config/egfr.yaml

@@ -33,6 +33,7 @@ algorithms:
           - 0.1
         mu:
           - 0.008
+        dummy_mode: ["file"]
   -
     name: omicsintegrator2
     params:

input/README.md

@@ -11,13 +11,21 @@ All other columns specify additional node attributes such as prizes.
 Any nodes that are listed in a node file but are not present in one or more edges in the edge file will be removed.
 For example:
 ```
-NODEID	prize	sources	targets	active
-A	1.0		True	True
-B	3.3	True		True
+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
 ```
 
+##### 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. 
+
 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

input/node-prizes.txt

@@ -1,3 +1,3 @@
-NODEID	prize	active
+NODEID	prize	active	dummy
 A	2	true
 C	5.7	true

input/tps-egfr-prizes.txt

@@ -1,4 +1,4 @@
-NODEID	prize	sources	targets	active
+NODEID	prize	sources	targets	active	dummy
 1433Z_HUMAN	1.041379133		True	True
 41_HUMAN	3.389112802		True	True
 4ET_HUMAN	2.569973509		True	True
@@ -181,7 +181,7 @@ EF1A1_HUMAN	3.774750081		True	True
 EF1B_HUMAN	0.768939794		True	True
 EF1D_HUMAN	1.240472409		True	True
 EFNB2_HUMAN	2.222686177		True	True
-EGF_HUMAN	10	True		True
+EGF_HUMAN	10	True		True	True
 EGFR_HUMAN	6.787874699		True	True
 EGLN1_HUMAN	1.876580206		True	True
 EIF3B_HUMAN	2.048949271		True	True

spras/omicsintegrator1.py

@@ -47,7 +47,7 @@ def write_conf(filename=Path('config.txt'), w=None, b=None, d=None, mu=None, noi
 
 """
 class OmicsIntegrator1(PRM):
-    required_inputs = ['prizes', 'edges']
+    required_inputs = ['prizes', 'edges', 'dummy_nodes']
 
     @staticmethod
     def generate_inputs(data, filename_map):
@@ -83,13 +83,23 @@ def generate_inputs(data, filename_map):
                         columns=['Interactor1','Interactor2','Weight','Direction'],
                         header=['protein1','protein2','weight','directionality'])
 
+        # creates the dummy_nodes file
+        if 'dummy' in data.node_table.columns:
+            dummy_df = data.node_table[data.node_table['dummy'] == True]
+            # save as list of dummy nodes
+            dummy_df.to_csv(filename_map['dummy_nodes'], index=False, columns=['NODEID'], header=None)
+        else:
+            # create empty dummy file
+            with open(filename_map['dummy_nodes'], mode='w'):
+                pass
+
 
     # TODO add parameter validation
     # TODO add support for knockout argument
     # TODO add reasonable default values
     # TODO document required arguments
     @staticmethod
-    def run(edges=None, prizes=None, dummy_mode=None, mu_squared=None, exclude_terms=None,
+    def run(edges=None, prizes=None, dummy_nodes=None, dummy_mode=None, mu_squared=None, exclude_terms=None,
             output_file=None, noisy_edges=None, shuffled_prizes=None, random_terminals=None,
             seed=None, w=None, b=None, d=None, mu=None, noise=None, g=None, r=None, container_framework="docker"):
         """
@@ -118,6 +128,19 @@ def run(edges=None, prizes=None, dummy_mode=None, mu_squared=None, exclude_terms
         bind_path, prize_file = prepare_volume(prizes, work_dir)
         volumes.append(bind_path)
 
+        # 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
+
+        # add dummy node file to the volume if dummy_mode is not None and it is 'file'
+        if dummy_mode == 'file':
+            if dummy_nodes is None:
+                raise ValueError("dummy_nodes file is required when dummy_mode is set to 'file'")
+            bind_path, dummy_file = prepare_volume(dummy_nodes, work_dir)
+            volumes.append(bind_path)
+
         out_dir = Path(output_file).parent
         # Omics Integrator 1 requires that the output directory exist
         out_dir.mkdir(parents=True, exist_ok=True)
@@ -139,9 +162,16 @@ def run(edges=None, prizes=None, dummy_mode=None, mu_squared=None, exclude_terms
                    '--outpath', mapped_out_dir,
                    '--outlabel', 'oi1']
 
+        # add the dummy mode argument
+        if dummy_mode is not None and dummy_mode:
+            # for custom dummy modes, add the file
+            if dummy_mode == 'file':
+                command.extend(['--dummy', dummy_file])
+            # else pass in the dummy_mode and let oi1 handle it
+            else:
+                command.extend(['--dummy', dummy_mode])
+
         # Add optional arguments
-        if dummy_mode is not None:
-            command.extend(['--dummyMode', str(dummy_mode)])
         if mu_squared is not None and mu_squared:
             command.extend(['--musquared'])
         if exclude_terms is not None and exclude_terms: