Task

TAPE Contact Prediction

The TAPE protein residue-contact prediction 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

ProteinNet structural data with CASP12 test targets.

Sources

tape primary benchmark evidence · Appendix A.1

Metrics

Precision at L/5 for medium- and long-range contacts.

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 residue-contact target derived from ProteinNet.

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

Contact prediction in original TAPE Table 2

precision at L/5 (fraction) · Higher values are better.

TAPE Contact Prediction · ProteinNet CASP12

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

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

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

CASP12 test, 30% sequence-identity partition; medium/long-range contacts

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

ProteinNet training/validation partitions filtered at 30% sequence identity; the held-out evaluation uses CASP12 targets. Sequence-identity filtering and the CASP12 target set define the supervised generalization boundary.

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-contact-prediction

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	ProteinNet structural data with CASP12 test targets. Sources tape primary benchmark evidence · Appendix A.1
Splits	ProteinNet training/validation partitions filtered at 30% sequence identity; the held-out evaluation uses CASP12 targets. Sources tape primary benchmark evidence · Section 3 task definitions; Appendix A.1.1–A.1.5
Metrics	Precision at L/5 for medium- and long-range contacts. 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	Sequence-identity filtering and the CASP12 target set define the supervised generalization boundary. 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 Contact Prediction 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	Mixed-organism ProteinNet/CASP protein structures; organism identity is not the partitioning key. 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 residue-contact target derived from ProteinNet. 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

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 residue-contact target derived from ProteinNet. Splits: ProteinNet training/validation partitions filtered at 30% sequence identity; the held-out evaluation uses CASP12 targets. Metrics: Precision at L/5 for medium- and long-range contacts. 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 residue-contact target derived from ProteinNet. Splits: ProteinNet training/validation partitions filtered at 30% sequence identity; the held-out evaluation uses CASP12 targets. Metrics: Precision at L/5 for medium- and long-range contacts. 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 ProteinNet structural data with CASP12 test targets. 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 ProteinNet training/validation partitions filtered at 30% sequence identity; the held-out evaluation uses CASP12 targets. 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 Precision at L/5 for medium- and long-range contacts. 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-contact-prediction

areas: protein-function
entity level: task
scope note: Specialist molecular or omics evaluation; protocol details require review before numerical comparison.
task: Contact Prediction
version: Not reported
comparison panels: id: tape-2019-table2-contact-prediction; title: Contact prediction in original TAPE Table 2; protocol id: discovery-benchmark-tape-contact-prediction; dataset id: paper-dataset-b2114365a5517543b7; metric: precision at L/5; unit: fraction; direction: higher; result ids: paper-result-db4756024c9a9b11a9; paper-result-82ef40ee0784b9d645; paper-result-62b3b957e3f7390e67; paper-result-0c4a6be02b3815342f; paper-result-d161cb7797686a25fc; paper-result-0311b73601922d0209; paper-result-e4f7b63768be9c9e2c; paper-result-8ea9c35dce1fcd6959; paper-result-ea124a67c83fa7bf99; paper-result-a4faa27255330fb9f2; source ids: evidence-discovery-final-tape; source locator: Results on downstream supervised tasks; Table2,p.7,row1(No pretraining/Transformer),columnContact prediction; Table2,p.7,row2(No pretraining/LSTM),columnContact prediction; Table2,p.7,row3(No pretraining/ResNet),columnContact prediction; Table2,p.7,row4(Self-supervised pretraining/Transformer),columnContact prediction; Table2,p.7,row5(Self-supervised pretraining/LSTM),columnContact prediction; Table2,p.7,row6(Self-supervised pretraining/ResNet),columnContact prediction; Table2,p.7,row7(Supervised pretraining/Bepler supervised LSTM),columnContact prediction; Table2,p.7,row8(Self-supervised pretraining/UniRep mLSTM),columnContact prediction; Table2,p.7,row9(One-hot baseline/One-hot),columnContact prediction; Table2,p.7,row10(Task-specific alignment/HMM baseline/Alignment),columnContact prediction; context: CASP12 test, 30% sequence-identity partition; medium/long-range contacts; 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
subject: TAPE Contact Prediction: links:part_of:discovery-benchmark-tape
benchmark: Alignment: ProteinNet CASP12
benchmark: LSTM (no pretraining): ProteinNet CASP12
benchmark: TAPE Bepler: ProteinNet CASP12
benchmark: TAPE Unirep: ProteinNet CASP12
benchmark: TAPE Transformer: ProteinNet CASP12
benchmark: Transformer (no pretraining): ProteinNet CASP12
benchmark: TAPE LSTM: ProteinNet CASP12
benchmark: ResNet (no pretraining): ProteinNet CASP12
benchmark: TAPE ResNet: ProteinNet CASP12
benchmark: TAPE One Hot: ProteinNet CASP12
subject: TAPE Contact Prediction: part of TAPE

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