Gena LM-base (Manzo et al. 2025)

Overview

Gena LM-base (Manzo et al. 2025) as evaluated in the cited comparison.

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Evaluations and results

4 evaluations · 4 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Gena LM-base (Manzo et al. 2025)	Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025)	0.029 pearson-correlation unitless · higher Uncertainty: SE 0.227. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Gena LM-base on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'Hela (5241 SNPs)'
Configuration: Gena LM-base (Manzo et al. 2025)	Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025)	0.05 pearson-correlation unitless · higher Uncertainty: SE 0.033. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Gena LM-base on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'HepG2 (16,255 SNPs)'
Configuration: Gena LM-base (Manzo et al. 2025)	Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025)	0.077 pearson-correlation unitless · higher Uncertainty: SE 0.042. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Gena LM-base on K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'K562 (19,321 SNPs)'
Configuration: Gena LM-base (Manzo et al. 2025)	Protocol: Allelic reporter effect correlation in NPC (Manzo et al. 2025 Table 1) Dataset: NPC regulatory variant reporter data (Manzo et al. 2025)	0.024 pearson-correlation unitless · higher Uncertainty: SE 0.002. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Gena LM-base on NPC reporter variant effects regulatory-variant-20261009-protocol-manzo2025-npc-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'NPC (14,042 SNPs)'

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

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Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Original source · Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML

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Technical metadata and extraction receipts

Stable ID: regulatory-variant-20261009-config-manzo2025-gena-lm-base

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: Gena LM-base (Manzo et al. 2025)
foundation model eligible: true
parameters: Fine-tuned per cell line for enhancer versus control classification on 1 kb sequences (Table 2); variant effect is the log2 ratio of alternative to reference scores
source locator: Table 1 row 'Gena LM-base'; Table 2
missing metadata: version: reason: unreported; note: The table prints only the label 'Gena LM-base'; no release or checkpoint identifier.

Related records

configuration of: GENA-LM
system: Gena LM-base on HeLa reporter variant effects
system: Gena LM-base on HepG2 reporter variant effects
system: Gena LM-base on K562 reporter variant effects
system: Gena LM-base on NPC reporter variant effects