result · source checked
0.54 Adjusted Rand Index
GenePT-w · Adjusted Rand Index · Aorta single-cell dataset
- Tested model
- GenePT-w
- Task or benchmark
- Cell-type structure in frozen embeddings
- Dataset
- Aorta single-cell dataset
- Procedure
- k-means on pretrained cell embeddings; agreement with original cell-type labels.
- Evaluation
- GenePT-w: Cell-type structure in frozen embeddings
- Evidence
- Author-reported evaluation · source checkedGenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT · Table 2, Aorta / Cell type row, GenePT-w ARI column
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: needs review. Source checked does not mean independently reproduced.
Evaluation results
Release 2026-09-16-d74d282221a9 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| GenePT-w: Cell-type structure in frozen embeddings Model: GenePT-w · Benchmark: Cell-type structure in frozen embeddings · Dataset: Aorta single-cell dataset k-means on pretrained cell embeddings; agreement with original cell-type labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.54 Adjusted Rand Index Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedGenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT · Table 2, Aorta / Cell type row, GenePT-w ARI column Source checking is not independent reproduction. |
Sources and history
Release 2026-09-16-d74d282221a9 · Record review: source checked
- GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT · Original source · PMC archival version PMC10614824.2
Technical metadata and extraction receipts
Stable ID: lit-b3-011
- areas
- cells-tissues
- tasks
- Cell-type structure in frozen embeddings
- printed value
- 0.54
- numeric value
- 0.54
- metric
- Adjusted Rand Index
- metric direction
- unknown
- unit
- unitless
- uncertainty
- Not reported
- source locator
- Table 2, Aorta / Cell type row, GenePT-w ARI column
- review
- method: independent_ai_table_review; reviewer: Codex omics research agent; independent source-table review, not human review; reviewed at: 2026-09-16T10:44:03.399274+00:00; notes: First Cell type row belongs to Aorta, not preceding Phenotype row or later organs. ARI is first in each three-metric method block, not AMI/ASW. Source check verifies central value and table context, not experiment reproduction or all metadata.; evidence: {"table_xml_id": "T6", "row_cells": ["", "Cell type", "0.21", "0.31", "−0.04", "0.47", "0.64", "0.18", "0.54", "0.60", "0.03", "0.31", "0.47", "0.04"], "selected_cell_zero_based": 8, "selected_cell_xml": "<td align=\"center\" valign=\"top\" rowspan=\"1\" colspan=\"1\">\n<bold>0.54</bold>\n</td>", "caption": "Assessing the Association Between Different Latent Cell Representations and Biological Annotations.This analysis involves datasets representing cells from circulatory systems (Aorta and Artery), bone tissues (Bones, Myeloid), the Pancreas, and immune cells collected from healthy individuals and patients with Multiple Sclerosis. We utilized pretrained Geneformer and scGPT embeddings for this task. The Adjusted Rand Index (ARI) and Adjusted Mutual Information (AMI) were computed to compare the labels derived from k-means clustering with the true annotations of the original samples (higher values indicate better alignment); the Average Silhouette Width (ASW) was calculated using the true annotations of original samples to assess the cohesion and separation of the clusters."}; artifact sha256: 230a2ec55458d9243eaeeebf3244df7409eb02d47f4b809ee56a06dcb6fdd047; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10614824/fullTextXML
- legacy id
- lit-b3-011
- legacy row
- id: lit-b3-011; paper id: genept-2024; domain id: cells-tissues; task: Cell-type structure in frozen embeddings; model: GenePT-w; model version: Not reported; dataset: Aorta single-cell dataset; dataset version: Not reported; split: Not reported; metric: Adjusted Rand Index; value: 0.54; unit: unitless; uncertainty: Not reported; protocol: k-means on pretrained cell embeddings; agreement with original cell-type labels.; source locator: Table 2, Aorta / Cell type row, GenePT-w ARI column; source url: https://pmc.ncbi.nlm.nih.gov/articles/PMC10614824/; evaluation origin: author_reported; reviewed utc: 2026-09-15T23:29:32Z
- missing metadata
- model version: not_reported_in_legacy_extract; dataset version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract; uncertainty: not_reported_in_legacy_extract