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SpeciesLM_Embeddings.plus.euclidean_distance (TraitGym)

SpeciesLM scored as 'Euclidean distance of embeddings' in TraitGym.

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2 evaluations · 2 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')
SpeciesLM_Embeddings.plus.euclidean_distance (TraitGym)Evaluation	TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls	0.327 (best in column)
SpeciesLM_Embeddings.plus.euclidean_distance (TraitGym)Evaluation	TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls	0.135

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: SpeciesLM_Embeddings.plus.euclidean_distance (TraitGym)	Protocol: TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Complex traits, matched 9 controls	0.135 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.005358835398246915 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpeciesLM_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9 lit-genomics-20261011-traitgym-protocol-complex-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · complex_traits_matched_9/AUPRC_by_chrom_weighted_average/all/SpeciesLM_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se')
Configuration: SpeciesLM_Embeddings.plus.euclidean_distance (TraitGym)	Protocol: TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average Dataset: TraitGym Mendelian traits, matched 9 controls	0.327 AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') unitless · higher Uncertainty: SE 0.02851404689024901 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpeciesLM_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9 lit-genomics-20261011-traitgym-protocol-mendelian-traits-matched-9-zero-shot Aggregation: Not reported TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/SpeciesLM_Embeddings.plus.euclidean_distance.csv, column 'score' (standard error in column 'se')

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · Original source · Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-traitgym-config-specieslm-embeddings-plus-euclidean-distance

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: SpeciesLM_Embeddings.plus.euclidean_distance
foundation model eligible: true
parameters: johahi/specieslm-metazoa-upstream-k6; Euclidean distance of embeddings
access reuse: Public weights or score files (paper Appendix B.1)
source locator: File name 'SpeciesLM_Embeddings.plus.euclidean_distance.csv'; config/models.csv; paper Table S5
version: johahi/specieslm-metazoa-upstream-k6

Related records

configuration of: SpeciesLM
system: SpeciesLM_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
system: SpeciesLM_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9

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