Task

Held-out-clade classification

Held-out-clade classification asks how well sequence-based classification works when a defined taxonomic group is absent from training.

Sources

BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.

0 evaluations · 0 results

Overview

Datasets

No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.

inapplicable

Metrics

Classification accuracy or other declared label metrics at the target rank; results at different taxonomic ranks are not interchangeable.

Allowed inputs

Labelled reference sequences and a taxonomically held-out query set; exact rank and reference-library membership are protocol-specific.

Sources

BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

Evaluation procedure diagram

How it worksConceptual evaluation workflow

Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.

Sources

BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Results

All evaluations

0 evaluations · 0 results. Different protocols are not a single leaderboard.

Applied filters: All linked evaluations

No evaluations linked in this release.

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Choosing an evaluation

Specify both the taxonomic level that is withheld and the level that is predicted. BarcodeBERT’s unseen-species genus probe illustrates why these differ: species can be unseen while their genera remain represented. A benchmark must document which reference sequences and labels remain available before interpreting a result as taxonomic generalisation.

Sources

BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

Task scope

This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.

Sources

BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

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

Explicit taxonomic holdout distinguishes close-reference matching from transfer to less familiar sequences.
Sources
BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

Limitations and conditions

Unseen-species performance within known genera is not evidence for classifying entirely novel genera.
Sources
BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

Profile review details

Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.

Stable record: catalog-task-heldout-clade

Specifications

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.

Data, procedure and scoring
Property	Description and evidence
Entity type	Task guide; concrete protocol identities remain separate. Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Allowed inputs	Labelled reference sequences and a taxonomically held-out query set; exact rank and reference-library membership are protocol-specific. Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Metrics	Classification accuracy or other declared label metrics at the target rank; results at different taxonomic ranks are not interchangeable. Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction
Baselines	The BarcodeBERT protocol includes nearest-neighbour evaluation of sequence representations. A proposed alternative comparator is not a completed result. Sources BarcodeBERT: transformers for biodiversity analyses · Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction

Applicable tests and references

Applicability is distinct from a completed evaluation.

Kraken2 · 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. 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

Historical gaps recorded on 2026-09-17

Table does not give uncertainty for each genus accuracy; BLAST is an alignment reference, not a pretrained encoder.

Search and extraction details

broad task primary protocol linked

Searches

"BarcodeBERT" unseen species

Evidence locations

Table 1 and footnotes
Section 3.1.2 Data partitioning

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.

17 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 task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Choose held-out and predicted ranks Construct reference and query sets Apply the declared classifier or probe Score at the specified taxonomic rank Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Conceptual evaluation workflow Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Entity type Task guide; concrete protocol identities remain separate. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Allowed inputs Labelled reference sequences and a taxonomically held-out query set; exact rank and reference-library membership are protocol-specific. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims	BarcodeBERT: transformers for biodiversity analyses Original source ↗ Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558051+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.6.value` Source artifact SHA-256: `493f9fe70b483780ba76d51ccf217d3ca83539c82b89917fd3ccebe2b6eb831d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

View linked audit checks and correction history

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

6 source records and release history

ProkBERT official resource · Original source · Not reported
METAGENE-1 official resource · Original source · Not reported
Evo 2 official resource · Original source · Not reported
Kraken2 official resource · Original source · Not reported
BarcodeBERT: transformers for biodiversity analyses · Original source · journal full text in PMC
BarcodeBERT: transformers for biodiversity analyses · Original source · journal full text in PMC

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Technical metadata and extraction receipts

Stable ID: catalog-task-heldout-clade

areas: microbes-communities
entity level: task
version: Not reported
task: Held-out-clade classification
scope note: Hold clades out of downstream fitting and reference databases; evaluate known ancestor labels or unknown-taxon detection, and audit pretraining overlap separately.
benchmark research: review date: 2026-09-17; status: broad_task_primary_protocol_linked; 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_yet_extracted
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: barcodebert-2026; source locator: Methods: dataset partition and 1-NN probing; Results: unseen-species genus prediction; ambiguities: None recorded

Related records

applicable to: Kraken2

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