Datasets
The HIV dataset is used for neutralization prediction; other datasets address binding, binding sites and free-energy changes.
Task
antigen-antibody HIV neutralization prediction
Antibody neutralization classification is one of several distinct evaluations in the DeepInterAware paper.
Sources
DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captionsOverview
Metrics
AUROC, AUPRC and MCC are primary metrics for binding and neutralization classification.
Allowed inputs
Antibody–antigen pair representations.
Sources
DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captionsEvaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captionsSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: DeepInterAware | Task: antigen-antibody HIV neutralization prediction Dataset: HIV neutralization | 0.826 AUROC fraction · unknown Uncertainty: ±0.017 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepInterAware: antigen-antibody HIV neutralization prediction Sequence-based interface-aware model, antibody-unseen split Aggregation: Not reported DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Table 2, Ab Unseen section, DeepInterAware row, AUROC column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
The HIV dataset is used for neutralization prediction; other datasets address binding, binding sites and free-energy changes. The HIV neutralization table separates antibody-unseen evaluation; exact partition construction is delegated to Supporting Information §S1.1. AUROC, AUPRC and MCC are primary metrics for binding and neutralization classification. The HIV neutralization table compares DrugBAN, ESM2AbLang, ESM2AntiBERTy, ResPPI, PIPR, AbAgIntPre, MasonsCNN and DeepAAI. HIV pairs with antigen and antibody homology above 0.9 are filtered. Ab Unseen holds out 15% of antibodies; Ag Unseen holds out 20% of antigens. Ag&Ab Unseen additionally removes from training all pairs involving test antibodies. The other partner is deliberately shared in each single-partner holdout.
Sources (2)
DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data; deepinteraware-2025__ADVS-12-2412533-s001.pdf · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions; Supporting Information S1.1, HIV dataset and three neutralization scenariosRecorded 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 supported by sources
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- Ab Unseen, Ag Unseen and joint holdouts ask different transfer questions. Partner sharing is intentional in the single-partner scenarios and must remain visible in comparisons.
Sources (2)
DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data; deepinteraware-2025__ADVS-12-2412533-s001.pdf · Supporting Information S1.1, HIV dataset and three neutralization scenarios; Supporting Information S1.1 HIV; Table 2
Profile review details
Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.
Stable record: reported-task-45ead9a1eddf8dSpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | The HIV dataset is used for neutralization prediction; other datasets address binding, binding sites and free-energy changes.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Splits | The HIV neutralization table separates antibody-unseen evaluation; exact partition construction is delegated to Supporting Information §S1.1.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Metrics | AUROC, AUPRC and MCC are primary metrics for binding and neutralization classification.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Baselines | The HIV neutralization table compares DrugBAN, ESM2AbLang, ESM2AntiBERTy, ResPPI, PIPR, AbAgIntPre, MasonsCNN and DeepAAI.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Leakage controls | HIV pairs with antigen and antibody homology above 0.9 are filtered. Ab Unseen holds out 15% of antibodies; Ag Unseen holds out 20% of antigens. Ag&Ab Unseen additionally removes from training all pairs involving test antibodies. The other partner is deliberately shared in each single-partner holdout.Sources (2)DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data; deepinteraware-2025__ADVS-12-2412533-s001.pdf · Supporting Information S1.1, HIV dataset and three neutralization scenarios |
| Uncertainty | Each HIV scenario is repeated with five distinct random seeds and dataset splits. Supporting Information S1.1 calls the reported summaries means and variances; this wording is preserved rather than silently interpreting the table’s ± terms as 95% confidence intervals.Sources (2)DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data; deepinteraware-2025__ADVS-12-2412533-s001.pdf · Supporting Information S1.1 HIV; Table 2 |
| Entity type | Paper-specific computational evaluation protocol.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Organisms | HIV neutralization collection for this task.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Assays | Antibody neutralization outcomes; other paper tasks use distinct binding/free-energy labels.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Allowed inputs | Antibody–antigen pair representations.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
| Adaptation | Supervised antibody–antigen neutralization classification; the antibody-unseen test is identified separately from binding and transfer tasks.SourcesDeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions |
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. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data | version of record | Read source DOI: 10.1002/advs.202412533 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 1 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Keep the three held-out-entity regimes separate. Section S1 contains detailed split/hyperparameter information; no sequence-design or biological optimization material is part of this extraction.
Search and extraction details
primary comparison table screened
Searches
- "DeepInterAware" 2025
Evidence locations
- Table 2
- Experimental setting: model evaluation metrics
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets The HIV dataset is used for neutralization prediction; other datasets address binding, binding sites and free-energy changes. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits The HIV neutralization table separates antibody-unseen evaluation; exact partition construction is delegated to Supporting Information §S1.1. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised antibody–antigen neutralization classification; the antibody-unseen test is identified separately from binding and transfer tasks. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics AUROC, AUPRC and MCC are primary metrics for binding and neutralization classification. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines The HIV neutralization table compares DrugBAN, ESM2AbLang, ESM2AntiBERTy, ResPPI, PIPR, AbAgIntPre, MasonsCNN and DeepAAI. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls HIV pairs with antigen and antibody homology above 0.9 are filtered. Ab Unseen holds out 15% of antibodies; Ag Unseen holds out 20% of antigens. Ag&Ab Unseen additionally removes from training all pairs involving test antibodies. The other partner is deliberately shared in each single-partner holdout. Individual claims | DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data Supporting Information S1.1, HIV dataset and three neutralization scenarios Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls HIV pairs with antigen and antibody homology above 0.9 are filtered. Ab Unseen holds out 15% of antibodies; Ag Unseen holds out 20% of antigens. Ag&Ab Unseen additionally removes from training all pairs involving test antibodies. The other partner is deliberately shared in each single-partner holdout. Individual claims | deepinteraware-2025__ADVS-12-2412533-s001.pdf Supporting Information S1.1, HIV dataset and three neutralization scenarios Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved 2026-09-16; sha256:3c66d0d9561d744ca0e42a5d33c020719e6f46d7ed27e37a25c19c2bd8d89345 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: ADVS-12-2412533-s001.pdf |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
3 source records and release history
- DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Original source · version of record
- DeepInterAware: Deep Interaction Interface‐Aware Network for Improving Antigen‐Antibody Interaction Prediction from Sequence Data · Original source · version of record
- deepinteraware-2025__ADVS-12-2412533-s001.pdf · Original source · Retrieved 2026-09-16; sha256:3c66d0d9561d744ca0e42a5d33c020719e6f46d7ed27e37a25c19c2bd8d89345
Technical metadata and extraction receipts
Stable ID: reported-task-45ead9a1eddf8d
- areas
- molecular-interactions
- tasks
- antigen-antibody HIV neutralization prediction
- entity level
- task
- version
- Not reported
- task
- antigen-antibody HIV neutralization prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_table_screened; primary sources: expansion-p3-deepinteraware-2025; inspected locators: Table 2; Experimental setting: model evaluation metrics; searched queries: "DeepInterAware" 2025; gaps: Keep the three held-out-entity regimes separate. Section S1 contains detailed split/hyperparameter information; no sequence-design or biological optimization material is part of this extraction.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract
- 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 source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: deepinteraware-2025; source locator: Experimental Setting—Datasets; Model Evaluation Metrics; cached text lines 85–93; matching task comparison table/ablation captions; 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.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: HIV neutralization
- benchmark: DeepInterAware: antigen-antibody HIV neutralization prediction