TAPE Transformer (ATOM3D baseline)

Stable ID: atom3d-method-rao-et-al-2019

areas

molecular-interactions

source locator

Table 4, column([Rao et al., 2019])

missing metadata

checkpoint revision: unreported; parameters: unextracted

source label

[Rao et al., 2019]

source identity

status: resolved; label form: bracketed_citation; display name: TAPE Transformer (ATOM3D baseline); identity: TAPE Transformer; configuration: RES uses the accuracy reported in the TAPE paper. MSP uses the public TAPE implementation with a modified head, trained by the ATOM3D authors.; basis: ATOM3D §5.1 describes the comparison as 'the TAPE model [Rao et al., 2019], a transformer architecture that operates on protein sequence', and App. F.3 names 'the transformer architecture TAPE'. The RES value 0.30 also equals the Transformer held-out-family accuracy in TAPE Table 1. That match corroborates the text; it is not the basis of the identity.; source ids: evidence-expansion-atom3d-92656c20; evidence-expansion-evidence-discovery-final-tape-6ee0c3e6; source locator: ATOM3D arXiv:2012.04035v4 §5.1 and Table 4, p.7; App. F.3 and F.4 with footnote 9, p.24; Table 8 RES and MSP rows, p.28. TAPE arXiv:1906.08230v1 Table 1 and Architectures and Training, p.6.; known details: label: RES value; value: Taken from TAPE's reported language-modelling accuracy on held-out Pfam families, which ATOM3D treats as a sequence-only counterpart of RES. Table 8 marks it as trained on different data.; source ids: evidence-expansion-atom3d-92656c20; evidence-expansion-evidence-discovery-final-tape-6ee0c3e6; source locator: ATOM3D App. F.3, p.24; Table 8, p.28; TAPE Table 1, p.6; label: MSP; value: Public TAPE implementation with its sequence-to-sequence head modified to predict the effect of mutations at given positions.; source ids: evidence-expansion-atom3d-92656c20; source locator: ATOM3D App. F.4, p.24; unknown: label: MSP initial weights; note: ATOM3D does not say whether MSP training started from pretrained TAPE weights.; label: Checkpoint; note: No checkpoint or implementation revision is identified.; original name: [Rao et al., 2019]; original description: TAPE, a transformer over protein sequence, as the ATOM3D text describes it.; review: method: automated_source_review; date: 2026-09-24; note: AI-assisted review against the cited primary sources. No human scientific review. Values, locators and comparison conditions are unchanged.

• family: TAPE Transformer
• model: TAPE Transformer (ATOM3D baseline) on ATOM3D MSP: Mutation stability prediction
• model: TAPE Transformer (ATOM3D baseline) on ATOM3D RES: Residue identity
• subject: TAPE Transformer (ATOM3D baseline): family TAPE Transformer