Strengths and considerations
- Species holdout directly tests genus retrieval beyond the reference species.
Sources
BarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60
Task
unseen-species genus classification
Genus classification tests whether frozen DNA-barcode embeddings transfer to species absent from the reference partition.
Sources
BarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60At a glance
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.
| Property | Description and evidence |
|---|---|
| Datasets | DNA barcodes organized into Seen and Unseen species partitions, with genus labels.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Splits | One-nearest-neighbour genus prediction uses the Seen training subset as reference and the Unseen species partition as queries.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Metrics | Genus-level classification accuracy with cosine-similarity nearest-neighbour retrieval.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Baselines | BLAST and several DNA language-model embeddings are compared in the paper.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Leakage controls | Unseen species are excluded from the reference partition; this task is distinct from fine-tuned closed-world species classification.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Entity type | Paper-specific computational evaluation protocol.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Organisms | Seen and Unseen species partitions with genus-level labels.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Assays | DNA barcode sequence/taxonomic annotations.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Allowed inputs | DNA barcodes represented as frozen model embeddings.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
| Adaptation | One-nearest-neighbour retrieval from Seen training examples; no task-head training for this genus task.SourcesBarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
BarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60Evaluation methodology
DNA barcodes organized into Seen and Unseen species partitions, with genus labels. One-nearest-neighbour genus prediction uses the Seen training subset as reference and the Unseen species partition as queries. Genus-level classification accuracy with cosine-similarity nearest-neighbour retrieval. BLAST and several DNA language-model embeddings are compared in the paper. Unseen species are excluded from the reference partition; this task is distinct from fine-tuned closed-world species classification. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
BarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60Recorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| BarcodeBERT (4–4-4): unseen-species genus classification Configuration: BarcodeBERT (4–4-4)Task: unseen-species genus classificationDataset: DNA barcodes of unseen species genus-level nearest-neighbor probe on species unseen in training Author-reported evaluation · Evaluation metadata: needs review | ||
| 78.5% accuracy Unit: percent · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedBarcodeBERT: transformers for biodiversity analyses · Table 1, BarcodeBERT (4–4-4) row, unseen-species genus-level 1-NN Acc (%) column Source checking is not 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 |
|---|---|---|
| BarcodeBERT: transformers for biodiversity analyses | journal full text in PMC | Read source DOI: 10.1093/bioadv/vbag054 |
What is still missing
- Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder.
Search and extraction details
primary comparison table screened
Searches
- "BarcodeBERT" unseen species
Evidence locations
- Table 1 and footnotes
- Section 3.1.2 Data partitioning
Strengths and limitations
Limitations and conditions
- Species exclusion establishes the task split, not complete exclusion from every comparator’s pretraining corpus.
Sources
BarcodeBERT: transformers for biodiversity analyses · Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60
Profile review details
Task-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced.
Stable record: reported-task-4a54ce01b5a855Evidence 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.
18 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 | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: DNA barcodes represented as frozen model embeddings.","Evaluation: One-nearest-neighbour retrieval from Seen training examples; no task-head training for this genus task.","Readout: Genus-level classification accuracy with cosine-similarity nearest-neighbour retrieval."] Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets DNA barcodes organized into Seen and Unseen species partitions, with genus labels. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits One-nearest-neighbour genus prediction uses the Seen training subset as reference and the Unseen species partition as queries. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation One-nearest-neighbour retrieval from Seen training examples; no task-head training for this genus task. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Genus-level classification accuracy with cosine-similarity nearest-neighbour retrieval. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines BLAST and several DNA language-model embeddings are compared in the paper. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Unseen species are excluded from the reference partition; this task is distinct from fine-tuned closed-world species classification. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | BarcodeBERT: transformers for biodiversity analyses Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60 Version: journal full text in PMC | unreported automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- BarcodeBERT: transformers for biodiversity analyses · Original source · journal full text in PMC
- BarcodeBERT: transformers for biodiversity analyses · Original source · journal full text in PMC
Technical metadata and extraction receipts
Stable ID: reported-task-4a54ce01b5a855
- areas
- dna-genomes
- tasks
- unseen-species genus classification
- entity level
- task
- version
- Not reported
- task
- unseen-species genus classification
- 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-barcodebert-2026; inspected locators: Table 1 and footnotes; Section 3.1.2 Data partitioning; searched queries: "BarcodeBERT" unseen species; gaps: Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder.; 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: barcodebert-2026; source locator: Experimental setup §§4.1.1–4.1.4; Table 1; cached text lines 35–50, 60; 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.