Frozen protein embeddings, input-audit records and label files for the paper ProtCompass: Biological Information and Predictive Utility in Protein Representations (anonymous submission to ICLR 2027). Protein encoders are usually evaluated by structural probing, downstream prediction and concept erasure. These measurements can mix signal learned by the encoder with information that is already present in the input or that the evaluation adds. ProtCompass separates these sources. It audits which inputs each encoder actually reads, compares structural probe scores with non-learned descriptions of the same inputs, compares downstream scores with simple sequence baselines, and controls…
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