Dummy node logic

config/config.yaml

@@ -42,10 +42,13 @@ container_registry:
 # then myAlg will be run on (a=1,b=0.5),(a=1,b=0.75),(a=2,b=0.5), and (a=2,b=0,75). Pretty neat, but be
 # careful: too many parameters might make your runs take a long time.
 
+# TODO: where does the dummy node argument go?
+# i.e. where do i set dummy_mode = all, etc.
+
 algorithms:
       - name: "pathlinker"
         params:
-              include: true
+              include: false
               run1:
                   k: range(100,201,100)
 
@@ -56,10 +59,11 @@ 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 +73,26 @@ 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]
@@ -100,37 +104,24 @@ algorithms:
 datasets:
     -
       # Labels can only contain letters, numbers, or underscores
-      label: data0
-      node_files: ["node-prizes.txt", "sources.txt", "targets.txt"]
+      label: hivtest2
+      node_files: ["modified_prize_05.txt"]
       # DataLoader.py can currently only load a single edge file, which is the primary network
-      edge_files: ["network.txt"]
+      edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
       # Placeholder
       other_files: []
       # Relative path from the spras directory
       data_dir: "input"
-    -
-      label: data1
-      # Reuse some of the same sources file as 'data0' but different network and targets
-      node_files: ["node-prizes.txt", "sources.txt", "alternative-targets.txt"]
-      edge_files: ["alternative-network.txt"]
-      other_files: []
-      # Relative path from the spras directory
-      data_dir: "input"
 
-gold_standards:
-    -
-      # Labels can only contain letters, numbers, or underscores
-      label: gs0
-      node_files: ["gs_nodes0.txt"]
-      # edge_files: [] TODO: later iteration
-      data_dir: "input"
-      # List of dataset labels to compare with the specific gold standard dataset
-      dataset_labels: ["data0"]
-    -
-      label: gs1
-      node_files: ["gs_nodes1.txt"]
-      data_dir: "input"
-      dataset_labels: ["data1", "data0"]
+# gold_standards:
+#     -
+#       # Labels can only contain letters, numbers, or underscores
+#       label: gs0
+#       node_files: ["gs_nodes0.txt"]
+#       # edge_files: [] TODO: later iteration
+#       data_dir: "input"
+#       # List of dataset labels to compare with the specific gold standard dataset
+#       dataset_labels: ["data0"]
 
 # If we want to reconstruct then we should set run to true.
 # TODO: if include is true above but run is false here, algs are not run.
@@ -173,4 +164,4 @@ analysis:
         # 'euclidean', 'manhattan', 'cosine'
         metric: 'euclidean'
       evaluation:
-        include: true
+        include: false

input/dummy-1.txt

@@ -0,0 +1,55 @@
+UBAC2_HUMAN
+H37_HUMAN
+PHF3_HUMAN
+DDX52_HUMAN
+HNRPK_HUMAN
+Q5T5H1_HUMAN
+ZC11A_HUMAN
+TCPG_HUMAN
+2A5E_HUMAN
+CPNE2_HUMAN
+HEYL_HUMAN
+CAMP1_HUMAN
+SVEP1_HUMAN
+SPRL1_HUMAN
+C9JFD3_HUMAN
+THAP5_HUMAN
+NCOR1_HUMAN
+SKIL_HUMAN
+A8YXX4_HUMAN
+CO4A2_HUMAN
+ZBTB3_HUMAN
+MORC4_HUMAN
+HIPK3_HUMAN
+ZN200_HUMAN
+TGFR1_HUMAN
+Q2TU89_HUMAN
+SUMO2_HUMAN
+UBC9_HUMAN
+AXIN1_HUMAN
+RS27_HUMAN
+UBP25_HUMAN
+RN111_HUMAN
+CBX4_HUMAN
+B4E127_HUMAN
+G4XH65_HUMAN
+CPNE1_HUMAN
+HDAC1_HUMAN
+RNF4_HUMAN
+SETB1_HUMAN
+SMAD2_HUMAN
+TRI62_HUMAN
+FAF1_HUMAN
+EF1G_HUMAN
+AHNK_HUMAN
+LRP1_HUMAN
+UIMC1_HUMAN
+B3KWV4_HUMAN
+CDC27_HUMAN
+RB_HUMAN
+ZMYM2_HUMAN
+WWP1_HUMAN
+RU17_HUMAN
+HIPK1_HUMAN
+ZZEF1_HUMAN
+SMAD4_HUMAN

input/dummy.txt

@@ -0,0 +1,86 @@
+NODEID	prize	sources	dummy	active
+1433Z_HUMAN	1.041379133		True	True
+41_HUMAN	3.389112802		True	True
+4ET_HUMAN	2.569973509		True	True
+A8K1N6_HUMAN	1.948221966		True	True
+A9CQZ4_HUMAN	0.421460919		True	True
+AAGAB_HUMAN	0.906857382		True	True
+ABCF1_HUMAN	1.662535462		True	True
+ABI1_HUMAN	2.262002188		True	True
+ABI2_HUMAN	6.039545959		True	True
+ABLM1_HUMAN	1.851877252		True	True
+ACACA_HUMAN	1.413801552		True	True
+ACAP2_HUMAN	2.26361378		True	True
+ACINU_HUMAN	5.059742801		True	True
+ACK1_HUMAN	4.634804389		True	True
+ACLY_HUMAN	0.924296287		True	True
+ACTB_HUMAN	6.332977709		True	True
+ADAT1_HUMAN	0.15086641		True	True
+ADCY6_HUMAN	0.213467876		True	True
+ADDA_HUMAN	2.023396633		True	True
+ADNP_HUMAN	1.863304115		True	True
+AFAD_HUMAN	5.746711895		True	True
+AFTIN_HUMAN	1.428578311		True	True
+AHNK_HUMAN	1.03846887		True	True
+AKA10_HUMAN	1.256166574		True	True
+AKA11_HUMAN	0.927725859		True	True
+AKA12_HUMAN	0.839912266		True	True
+AKAP1_HUMAN	1.744860335		True	True
+AKAP2_HUMAN	1.596611866		True	True
+AMOT_HUMAN	1.79256998		True	True
+ANS1A_HUMAN	2.76115098		True	True
+ANXA2_HUMAN	1.709856841		True	True
+AP3D1_HUMAN	4.077699923		True	True
+APC1_HUMAN	0.888837295		True	True
+AR6P4_HUMAN	0.701112743		True	True
+AR6P6_HUMAN	2.695059469		True	True
+ARHG5_HUMAN	7.044363255		True	True
+ARHG7_HUMAN	3.809839832		True	True
+ARHGB_HUMAN	2.260010614		True	True
+ARIP4_HUMAN	0.270475986		True	True
+ARMX3_HUMAN	0.11573305		True	True
+ARP8_HUMAN	1.094787599		True	True
+ASPM_HUMAN	0.369667496		True	True
+AT133_HUMAN	1.627668371		True	True
+AT1A1_HUMAN	2.904315518		True	True
+AT2B1_HUMAN	2.165602139		True	True
+ATRX_HUMAN	0.701149125		True	True
+ATX2L_HUMAN	4.425369048		True	True
+AZI1_HUMAN	1.861521522		True	True
+B2L13_HUMAN	1.614443902		True	True
+B4DGC6_HUMAN	0.752406932		True	True
+B4DM10_HUMAN	0.474391755		True	True
+B4DQA8_HUMAN	0.12336285		True	True
+B4DQQ2_HUMAN	0.509838368		True	True
+B4DSL6_HUMAN	1.401622791		True	True
+B4DZC2_HUMAN	0.736249376		True	True
+BACH_HUMAN	0.409715682		True	True
+BACH2_HUMAN	0.942291628		True	True
+BAD_HUMAN	0.390261342		True	True
+BAG6_HUMAN	0.406028443		True	True
+BAP18_HUMAN	2.420530962		True	True
+BARD1_HUMAN	0.113513875		True	True
+BAZ1B_HUMAN	0.714778368		True	True
+BAZ2A_HUMAN	1.358383434		True	True
+BBX_HUMAN	1.196178614		True	True
+BCAR1_HUMAN	5.368797237		True	True
+BCLF1_HUMAN	3.268307286		True	True
+BCS1_HUMAN	1.435079955		True	True
+BIG3_HUMAN	0.978095454		True	True
+BMS1_HUMAN	1.398231144		True	True
+BORG1_HUMAN	0.8309547		True	True
+BORG4_HUMAN	0.908661259		True	True
+BRAP_HUMAN	0.507219767		True	True
+BRD2_HUMAN	1.88956051		True	True
+BRD3_HUMAN	0.351886484		True	True
+BUD13_HUMAN	1.407446196		True	True
+BZW2_HUMAN	0.610443432		True	True
+C170B_HUMAN	0.887656818		True	True
+C2CD5_HUMAN	0.319586924		True	True
+CA052_HUMAN	1.950626165		True	True
+CA172_HUMAN	0.676879108		True	True
+CAAP1_HUMAN	0.46595922		True	True
+CAF1B_HUMAN	0.356408629		True	True
+CALM_HUMAN	0.977490284		True	True
+CALX_HUMAN	1.062601393		True	True
+CAV1_HUMAN	0.258171175		True	True