The prompt generator in TDI adds unneaded white space - this should f…

…ix that (#23) Co-authored-by: MATAN NINIO <[email protected]>
BiomedSciAI · Dec 4, 2024 · b6c491b · b6c491b
1 parent 459978e
commit b6c491b
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/mammal/examples/dti_bindingdb_kd/task.py b/mammal/examples/dti_bindingdb_kd/task.py
@@ -126,10 +126,10 @@ def data_preprocessing(
         ground_truth_value = sample_dict.get(ground_truth_key, None)
 
         sample_dict[ENCODER_INPUTS_STR] = (
-            f"<@TOKENIZER-TYPE=AA><MASK> \
-              <@TOKENIZER-TYPE=AA@MAX-LEN={target_max_seq_length}><MOLECULAR_ENTITY><MOLECULAR_ENTITY_GENERAL_PROTEIN><SEQUENCE_NATURAL_START>{target_sequence}<SEQUENCE_NATURAL_END> \
-              <@TOKENIZER-TYPE=SMILES@MAX-LEN={drug_max_seq_length}><MOLECULAR_ENTITY><MOLECULAR_ENTITY_SMALL_MOLECULE><SEQUENCE_NATURAL_START>{drug_sequence}<SEQUENCE_NATURAL_END> \
-              <EOS>"
+            "<@TOKENIZER-TYPE=AA><MASK>"
+            f"<@TOKENIZER-TYPE=AA@MAX-LEN={target_max_seq_length}><MOLECULAR_ENTITY><MOLECULAR_ENTITY_GENERAL_PROTEIN><SEQUENCE_NATURAL_START>{target_sequence}<SEQUENCE_NATURAL_END>"
+            f"<@TOKENIZER-TYPE=SMILES@MAX-LEN={drug_max_seq_length}><MOLECULAR_ENTITY><MOLECULAR_ENTITY_SMALL_MOLECULE><SEQUENCE_NATURAL_START>{drug_sequence}<SEQUENCE_NATURAL_END>"
+            "<EOS>"
         )
         tokenizer_op(
             sample_dict,