Datasets
HPA field-of-view and single-cell image tasks.
Task
protein localization classification
Protein-localization classification evaluates frozen microscopy-image representations using Human Protein Atlas tasks.
Sources
Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results tableOverview
Metrics
F1 for protein-localization classification; cell-line accuracy and Cell Painting metrics are separate tasks.
Allowed inputs
Field-of-view or single-cell images, depending on the task setting.
Sources
Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results tableEvaluation 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
Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results tablelimited source coverage · 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: Cell-DINO ViT-L | Task: protein localization classification Dataset: HPA-FoV | 65.5% F1 percent · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCell-DINO ViT-L: protein localization classification Self-supervised microscopy embedding pre-trained on HPA-FoV; downstream protein-localization classifier. Dataset-specific pretraining; the paper does not claim a general-purpose foundation model that generalizes beyond these benchmarks. Aggregation: Not reported Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Table 2, HPA-FoV section, Cell-DINO row, PL 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
HPA field-of-view and single-cell image tasks. The Kaggle field-of-view evaluation uses five folds to choose and average class thresholds. F1 for protein-localization classification; cell-line accuracy and Cell Painting metrics are separate tasks. The paper includes nearest-neighbour, linear and MLP-based evaluations; these are distinct classifier settings. Routine HPA train/validation analysis and Kaggle public-test generalization are different settings; per-class thresholds are selected on validation folds rather than inferred from the public score.
Sources
Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results tableRecorded 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
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- Field-of-view challenge ensembling, single-cell classification and nearest-neighbor evaluation use different classifiers and protocols. Their scores should not be merged into one interchangeable result.
Sources (2)
Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy; cell-dino-2025__pcbi.1013828.s001.pdf · Methods: Training and evaluation protocol on HPA datasets; Tables 1–3 and 6; S1 Text
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-7621fa1be55362Specifications
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 | HPA field-of-view and single-cell image tasks.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Splits | The Kaggle field-of-view evaluation uses five folds to choose and average class thresholds.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Metrics | F1 for protein-localization classification; cell-line accuracy and Cell Painting metrics are separate tasks.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Baselines | The paper includes nearest-neighbour, linear and MLP-based evaluations; these are distinct classifier settings.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Leakage controls | Routine HPA train/validation analysis and Kaggle public-test generalization are different settings; per-class thresholds are selected on validation folds rather than inferred from the public score.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Uncertainty | The protein-localization tables report point F1 or challenge scores. The HPA evaluation methods and S1 Text do not define repeated-seed confidence intervals or an uncertainty estimator for these values; comparisons between protocols retain their distinct classifiers and label access. · Not reported in inspected sourcesSources (2)Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy; cell-dino-2025__pcbi.1013828.s001.pdf · Methods: Training and evaluation protocol on HPA datasets; Tables 1–3 and 6; S1 Text |
| Entity type | Paper-specific computational evaluation protocol.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Organisms | Human Protein Atlas cells.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Assays | Microscopy images with protein-localization labels.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Allowed inputs | Field-of-view or single-cell images, depending on the task setting.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
| Adaptation | Frozen-feature nearest-neighbour/linear/MLP evaluation regimes are distinct; threshold selection uses folds.SourcesCell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table |
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 |
|---|---|---|
| Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy | version of record | Read source DOI: 10.1371/journal.pcbi.1013828 |
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.
- Table 2 architectures and pretraining datasets differ; HPA-FoV and HPA-SC are separate protocols.
- Do not attach Cell Painting MoA AUPRC to protein localization.
- Table 6 ensembling is five MLPs with threshold/prediction averaging; not the base frozen model alone.
Search and extraction details
primary comparison table screened
Searches
- "PMC12826486"
Evidence locations
- Tables 2 and 6
- Methods: Kaggle evaluation protocol
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.
19 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 | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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
| Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 HPA field-of-view and single-cell image tasks. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 Kaggle field-of-view evaluation uses five folds to choose and average class thresholds. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 Frozen-feature nearest-neighbour/linear/MLP evaluation regimes are distinct; threshold selection uses folds. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 F1 for protein-localization classification; cell-line accuracy and Cell Painting metrics are separate tasks. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 paper includes nearest-neighbour, linear and MLP-based evaluations; these are distinct classifier settings. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 Routine HPA train/validation analysis and Kaggle public-test generalization are different settings; per-class thresholds are selected on validation folds rather than inferred from the public score. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table 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 |
| Uncertainty The protein-localization tables report point F1 or challenge scores. The HPA evaluation methods and S1 Text do not define repeated-seed confidence intervals or an uncertainty estimator for these values; comparisons between protocols retain their distinct classifiers and label access. Individual claims | Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy Methods: Training and evaluation protocol on HPA datasets; Tables 1–3 and 6; S1 Text Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record | unreported 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 |
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
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Original source · version of record
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy · Original source · version of record
- cell-dino-2025__pcbi.1013828.s001.pdf · Original source · Retrieved 2026-09-16; sha256:e19d3d5c8d9dc1abcaf699c571349d869a1a7fa8e293660f49f67819f4b4d283
Technical metadata and extraction receipts
Stable ID: reported-task-7621fa1be55362
- areas
- cells-tissues
- tasks
- protein localization classification
- entity level
- task
- version
- Not reported
- task
- protein localization 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-cell-dino-2025; inspected locators: Tables 2 and 6; Methods: Kaggle evaluation protocol; searched queries: "PMC12826486"; gaps: Table 2 architectures and pretraining datasets differ; HPA-FoV and HPA-SC are separate protocols.; Do not attach Cell Painting MoA AUPRC to protein localization.; Table 6 ensembling is five MLPs with threshold/prediction averaging; not the base frozen model alone.; 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; split: 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: cell-dino-2025; source locator: Methods: Training and evaluation protocol on HPA datasets; Kaggle evaluation protocol; cached text lines 46, 86–94; task metric definitions and corresponding results table; 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: HPA-FoV
- benchmark: Cell-DINO ViT-L: protein localization classification