Update create_diffusion_dataset.py

create_diffusion_dataset.py

@@ -6,6 +6,8 @@ import json
 import random
 from collections import defaultdict, Counter
 
+LIMIT_CANDIDATE_PROTEINS = 5000
+
 class ProteinNetworkConversationDataset:
     def __init__(self, filename: str):
         """
@@ -101,7 +103,7 @@ class ProteinNetworkConversationDataset:
         print(f"Found {len(candidate_proteins)} proteins with degree {min_connections}-{max_connections}")
         
         neighborhoods = []
-        for protein in candidate_proteins[:500]:  # Limit for processing
+        for protein in candidate_proteins[:LIMIT_CANDIDATE_PROTEINS]:  # Limit for processing
             neighborhood = self.extract_neighborhood(protein, interactions, max_size=10)
             if len(neighborhood['proteins']) >= 3:  # Minimum viable network
                 neighborhoods.append(neighborhood)