remove network stats print

stracquadaniolab · Aug 21, 2024 · 9deb656 · 9deb656
1 parent eb96cd3
commit 9deb656
Show file tree

Hide file tree

Showing 5 changed files with 14 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -127,8 +127,16 @@ docker pull ghcr.io/stracquadaniolab/gnn-suite:latest
     models = ["gcn", "gat", ..., "new_model"]
     ```
 
-
-
+## FAQ
+In case:
+```groovy
+Command error:
+  .command.sh: line 2: ../gnn-suite/bin/plot.py: Permission denied
+```
+Give permission to run:
+```groovy
+ chmod +x /home/<path>/code/gnn-suite/bin/plot.py
+```
 ## Paper
 
 - Forthcoming

diff --git a/bin/gnn.py b/bin/gnn.py
@@ -391,7 +391,7 @@ def run(
     )
 
     # Print network statistics
-    print_network_statistics(data)
+    # print_network_statistics(data)
 
     # Determine the device to use for computation
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

diff --git a/bin/plot.py b/bin/plot.py
diff --git a/bin/split_data.py b/bin/split_data.py
diff --git a/conf/string.config b/conf/string.config
@@ -3,9 +3,9 @@ params {
   resultsDir = "${baseDir}/results/"
   networkFile = "${baseDir}/data/entrez_stringhc.tsv"
   geneFile = "${baseDir}/data/entrez_fpancanall_nstringhc_lbailey.csv"
-  epochs = [300]
-  models = ["gcn2", "gcn", "gat", "gat3h", "hgcn", "phgcn", "sage", "gin", "gtn"]
-  replicates = 10
+  epochs = [100]
+  models = ["gcn",]
+  replicates = 3
   verbose_interval = 1
   dropout = 0.2
   alpha = 0.1