Document BERTose IAR ambiguity input contract

README.md

@@ -44,7 +44,9 @@ No Hugging Face token is required for this BERTose IAR checkpoint now that the r
 
 ## Input
 
-Provide one WURCS glycan string or a CSV batch with a WURCS column. The resolver is intended for glycans that already contain uncertainty markers in WURCS form.
+Provide one WURCS glycan string or a CSV batch with `sample_id,wurcs`. The resolver is intended for glycans that already contain uncertainty markers in WURCS form.
+
+Free-text ambiguous glycan names are not parsed directly. Convert the name or IUPAC-condensed notation to WURCS first. If the structure is ambiguous, preserve that ambiguity in the WURCS string with WURCS-style uncertainty markers before running BERTose IAR.
 
 ## Output
 
@@ -52,6 +54,6 @@ Token-level ambiguity-resolution predictions with confidence scores. The compani
 
 ## Scope
 
-The resolver provides model-backed token updates and confidence values for ambiguous positions. It does not claim to reconstruct a final canonical WURCS string by itself, and it does not perform IUPAC-condensed to WURCS conversion.
+The resolver provides model-backed token updates and confidence values for ambiguous positions. It does not claim to reconstruct a final canonical WURCS string by itself, and it does not perform IUPAC-condensed/name-to-WURCS conversion.
 
 License metadata is currently `other`; update it when the final release license and citation text are chosen.

SHA256SUMS

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 ae468f4e8c06dc0c3848138a474dc43249aa6d14dfd0df8f58d68fcaad371152  ./checkpoints/bertose_iar_resolver.pt
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