Task

TAPE Remote Homology Detection

The TAPE remote protein-homology classification task evaluates a trained protein representation.

Sources

songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references

10 evaluations · 10 results

Overview

Datasets

SCOP 1.75 domains with fold labels and held-out superfamilies.

Sources

tape primary benchmark evidence · Appendix A.1

Metrics

Top-1 class accuracy.

Sources

songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references

Allowed inputs

Protein sequence with a remote-homology class.

Sources

songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references

Evaluation procedure diagram

How it worksEvaluation procedure

Conceptual procedure. Task variants and protocol versions retain their separate scoring conditions.

Sources (2)

songlab-cal/tape official source; tape primary benchmark evidence · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Evaluation scope and datasetMetric and reported setup

Remote homology in original TAPE Table 2

accuracy (fraction) · Higher values are better.

TAPE Remote Homology Detection · SCOP1.75 fold-level test

Evidence origin: Author-reported evaluation, Independent external evaluation.

tape primary benchmark evidence · Results on downstream supervised tasks; Table2,p.7,row1(No pretraining/Transformer),columnRemote homology; Table2,p.7,row2(No pretraining/LSTM),columnRemote homology; Table2,p.7,row3(No pretraining/ResNet),columnRemote homology; Table2,p.7,row4(Self-supervised pretraining/Transformer),columnRemote homology; Table2,p.7,row5(Self-supervised pretraining/LSTM),columnRemote homology; Table2,p.7,row6(Self-supervised pretraining/ResNet),columnRemote homology; Table2,p.7,row7(Supervised pretraining/Bepler supervised LSTM),columnRemote homology; Table2,p.7,row8(Self-supervised pretraining/UniRep mLSTM),columnRemote homology; Table2,p.7,row9(One-hot baseline/One-hot),columnRemote homology; Table2,p.7,row10(Task-specific alignment/HMM baseline/Alignment),columnRemote homology

Same task split and supervised downstream architecture within this paper. Input information differs for alignment/HMM features; pretraining regimes are explicit. Do not pool scores across tasks or with later TAPE implementations. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.

Comparison details and limitations

Held-out evolutionary groups; fold-level classification into 1,195 folds

Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Find a tested model or method

Showing 10 of 10 matching rows.

Zoom to observed range

Tested configuration

00.250.50.751

Reported score

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation methodology

SCOP 1.75 protein domains are grouped by evolutionary hierarchy; entire superfamilies are held out for fold-level classification. Holding out superfamilies tests remote homologues without transferring examples from the same superfamily between train and test.

Sources

tape primary benchmark evidence · Section 3 task definitions; Appendix A.1.1–A.1.5

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

TAPE

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Run instructions

No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Distinct sequence, residue and protein-level tasks avoid relying on language-model perplexity as a proxy for transfer.
Sources
songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references

Limitations and conditions

The original TAPE paper and the later PyTorch implementation are distinct versions. Preserve the task split and implementation; pretraining exposure is separate from supervised sequence-identity filtering.
Sources
tape primary benchmark evidence · Section 3; Appendix A.1; Tables 1–2

Profile review details

Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction.

Stable record: discovery-benchmark-tape-remote-homology-detection

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	SCOP 1.75 domains with fold labels and held-out superfamilies. Sources tape primary benchmark evidence · Appendix A.1
Splits	SCOP 1.75 protein domains are grouped by evolutionary hierarchy; entire superfamilies are held out for fold-level classification. Sources tape primary benchmark evidence · Section 3 task definitions; Appendix A.1.1–A.1.5
Metrics	Top-1 class accuracy. Sources songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references
Baselines	Task leaderboard comparisons include Transformer, LSTM, UniRep, ResNet, Bepler and one-hot baselines; alignment-augmented references appear where applicable. Sources songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references
Leakage controls	Holding out superfamilies tests remote homologues without transferring examples from the same superfamily between train and test. Sources tape primary benchmark evidence · Section 3 task definitions; Appendix A.1.1–A.1.5
Uncertainty	The original paper reports point estimates in its task result tables. Methods and task appendices do not define a suite-wide repeated-seed or bootstrap interval; individual later evaluations must supply their own uncertainty. · Not reported in inspected sources Sources tape primary benchmark evidence · Section 3; Appendix A.1; Tables 1–2
Entity type	Constituent benchmark task: TAPE Remote Homology Detection Sources songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references
Organisms	SCOP protein-domain collection across organisms; the evaluated label is structural fold, not species. Sources tape primary benchmark evidence · Section 3 task definitions; Appendix A.1.1–A.1.5
Assays	Protein structure/homology annotations and experimental fluorescence/stability measurements. Sources songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references
Allowed inputs	Protein sequence with a remote-homology class. Sources songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references
Adaptation	Unsupervised pretraining followed by supervised downstream training; the README warns that downstream hyperparameters require task-specific tuning. Sources songlab-cal/tape official source · Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references

Applicable tests and references

Applicability is distinct from a completed evaluation.

Profile-HMM sequence search · proposed

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.

Paper or primary resource	Version	Reference
Evaluating Protein Transfer Learning with TAPE	1906.08230v1	Read source

Search and extraction details

complete tables extracted

Searches

TAPE protein representation learning benchmark Rao 2019 table 1 2 original paper

Evidence locations

Original arXiv v1 Table 2, p.7; Table S1, p.14; Appendix A.2

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

23 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual procedure. Task variants and protocol versions retain their separate scoring conditions. Individual claims	tape primary benchmark evidence Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1906.08230v1 Retrieved: 2026-09-16T20:23:48.238777+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `6ee0c3e6e870635cba8fa67e0a4abc5598c0ab2a10ba127a46b67ac450ae0168` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram caption Conceptual procedure. Task variants and protocol versions retain their separate scoring conditions. Individual claims	songlab-cal/tape official source Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6d345c2b2bbf52cd32cf179325c222afd92aec7e Retrieved: 2026-09-16T10:31:32.443187+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `b28c74fe3cd6b69a8ba6d84891d0539e54dfef882abd5ed4d11ed0b029bb477a` Hash scope: Hash scope not separately documented; inspect source record
Diagram steps Allowed inputs: Protein sequence with a remote-homology class. Splits: SCOP 1.75 protein domains are grouped by evolutionary hierarchy; entire superfamilies are held out for fold-level classification. Metrics: Top-1 class accuracy. Individual claims	tape primary benchmark evidence Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1906.08230v1 Retrieved: 2026-09-16T20:23:48.238777+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `6ee0c3e6e870635cba8fa67e0a4abc5598c0ab2a10ba127a46b67ac450ae0168` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Allowed inputs: Protein sequence with a remote-homology class. Splits: SCOP 1.75 protein domains are grouped by evolutionary hierarchy; entire superfamilies are held out for fold-level classification. Metrics: Top-1 class accuracy. Individual claims	songlab-cal/tape official source Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6d345c2b2bbf52cd32cf179325c222afd92aec7e Retrieved: 2026-09-16T10:31:32.443187+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `b28c74fe3cd6b69a8ba6d84891d0539e54dfef882abd5ed4d11ed0b029bb477a` Hash scope: Hash scope not separately documented; inspect source record
Diagram title Evaluation procedure Individual claims	tape primary benchmark evidence Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1906.08230v1 Retrieved: 2026-09-16T20:23:48.238777+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `6ee0c3e6e870635cba8fa67e0a4abc5598c0ab2a10ba127a46b67ac450ae0168` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluation procedure Individual claims	songlab-cal/tape official source Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; Section 3 task definitions; Appendix A.1.1–A.1.5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 6d345c2b2bbf52cd32cf179325c222afd92aec7e Retrieved: 2026-09-16T10:31:32.443187+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `b28c74fe3cd6b69a8ba6d84891d0539e54dfef882abd5ed4d11ed0b029bb477a` Hash scope: Hash scope not separately documented; inspect source record
Datasets SCOP 1.75 domains with fold labels and held-out superfamilies. Individual claims	tape primary benchmark evidence Original source ↗ Appendix A.1 Version: 1906.08230v1 Retrieved: 2026-09-16T20:23:48.238777+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `6ee0c3e6e870635cba8fa67e0a4abc5598c0ab2a10ba127a46b67ac450ae0168` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits SCOP 1.75 protein domains are grouped by evolutionary hierarchy; entire superfamilies are held out for fold-level classification. Individual claims	tape primary benchmark evidence Original source ↗ Section 3 task definitions; Appendix A.1.1–A.1.5 Version: 1906.08230v1 Retrieved: 2026-09-16T20:23:48.238777+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `6ee0c3e6e870635cba8fa67e0a4abc5598c0ab2a10ba127a46b67ac450ae0168` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Unsupervised pretraining followed by supervised downstream training; the README warns that downstream hyperparameters require task-specific tuning. Individual claims	songlab-cal/tape official source Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references Version: 6d345c2b2bbf52cd32cf179325c222afd92aec7e Retrieved: 2026-09-16T10:31:32.443187+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `b28c74fe3cd6b69a8ba6d84891d0539e54dfef882abd5ed4d11ed0b029bb477a` Hash scope: Hash scope not separately documented; inspect source record
Metrics Top-1 class accuracy. Individual claims	songlab-cal/tape official source Original source ↗ Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references Version: 6d345c2b2bbf52cd32cf179325c222afd92aec7e Retrieved: 2026-09-16T10:31:32.443187+00:00	source checked automated source review · 2026-09-16 Audit details Primary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `b28c74fe3cd6b69a8ba6d84891d0539e54dfef882abd5ed4d11ed0b029bb477a` Hash scope: Hash scope not separately documented; inspect source record

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Release 2026-09-29-06401fd5b220 · Record review: discovered

3 source records and release history

songlab-cal/tape official source · Original source · 6d345c2b2bbf52cd32cf179325c222afd92aec7e
tape primary benchmark evidence · Original source · 1906.08230v1
Evaluating Protein Transfer Learning with TAPE · Original source · 1906.08230v1

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Technical metadata and extraction receipts

Stable ID: discovery-benchmark-tape-remote-homology-detection

areas: protein-function
entity level: task
scope note: Specialist molecular or omics evaluation; protocol details require review before numerical comparison.
task: Remote Homology Detection
version: Not reported
comparison panels: id: tape-2019-table2-remote-homology-detection; title: Remote homology in original TAPE Table 2; protocol id: discovery-benchmark-tape-remote-homology-detection; dataset id: paper-dataset-b84068b24ba74c6f4a; metric: accuracy; unit: fraction; direction: higher; result ids: paper-result-903d5d36162835d916; paper-result-e3595d7ae7d4b30746; paper-result-f0df0b60fea8d2cbd8; paper-result-eaedde3a911fefd0f0; paper-result-5cba527e65eec40f91; paper-result-5514a0ebdd6e527021; paper-result-5a6fc3ad0ed3cd1c6e; paper-result-b8ae4a359f201ae45f; paper-result-6067a3c9fb922d3c81; paper-result-6de41027c29faf11f2; source ids: evidence-discovery-final-tape; source locator: Results on downstream supervised tasks; Table2,p.7,row1(No pretraining/Transformer),columnRemote homology; Table2,p.7,row2(No pretraining/LSTM),columnRemote homology; Table2,p.7,row3(No pretraining/ResNet),columnRemote homology; Table2,p.7,row4(Self-supervised pretraining/Transformer),columnRemote homology; Table2,p.7,row5(Self-supervised pretraining/LSTM),columnRemote homology; Table2,p.7,row6(Self-supervised pretraining/ResNet),columnRemote homology; Table2,p.7,row7(Supervised pretraining/Bepler supervised LSTM),columnRemote homology; Table2,p.7,row8(Self-supervised pretraining/UniRep mLSTM),columnRemote homology; Table2,p.7,row9(One-hot baseline/One-hot),columnRemote homology; Table2,p.7,row10(Task-specific alignment/HMM baseline/Alignment),columnRemote homology; context: Held-out evolutionary groups; fold-level classification into 1,195 folds; caveats: Same task split and supervised downstream architecture within this paper. Input information differs for alignment/HMM features; pretraining regimes are explicit. Do not pool scores across tasks or with later TAPE implementations. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_tables_extracted; primary sources: evidence-expansion-evidence-discovery-final-tape-6ee0c3e6; inspected locators: Original arXiv v1 Table 2, p.7; Table S1, p.14; Appendix A.2; searched queries: TAPE protein representation learning benchmark Rao 2019 table 1 2 original paper; gaps: None recorded; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
historical missing metadata: dataset release: unextracted; metric implementation: unextracted; split manifest: unextracted; version: unextracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-songlab-cal-tape; source locator: Pinned README: compatibility notice; Evaluating a Downstream Model; Data; task leaderboards; README task-specific leaderboard and data-source references; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.

Related records

parent: TAPE
part of: TAPE
applicable to: Profile-HMM sequence search
subject: TAPE Remote Homology Detection: links:part_of:discovery-benchmark-tape
benchmark: TAPE Unirep: SCOP1.75 fold-level test
benchmark: TAPE LSTM: SCOP1.75 fold-level test
benchmark: ResNet (no pretraining): SCOP1.75 fold-level test
benchmark: TAPE Transformer: SCOP1.75 fold-level test
benchmark: Transformer (no pretraining): SCOP1.75 fold-level test
benchmark: Alignment: SCOP1.75 fold-level test
benchmark: TAPE One Hot: SCOP1.75 fold-level test
benchmark: TAPE Bepler: SCOP1.75 fold-level test
benchmark: TAPE ResNet: SCOP1.75 fold-level test
benchmark: LSTM (no pretraining): SCOP1.75 fold-level test
subject: TAPE Remote Homology Detection: part of TAPE

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