GeNet (main database, Peres da Silva et al. 2024)
Configuration of GeNet: Extended to a capacity similar to MetageNN and trained on the same main-database training set; majority vote and 0.5 probability cutoff.
Overview
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Evaluations and results
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Protocol: Database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024) · Dataset: ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
Sorted by Inference throughput (reads classified per second with four CPUs) (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 | Inference throughput (reads classified per second with four CPUs) | Reference storage size (database or index (model weights for MetageNN and GeNet) built from the 516-genome main database) |
|---|---|---|
| GeNet (main database, Peres da Silva et al. 2024)Evaluation | 134 | 0.758 |
All 2 result rows with coverage, uncertainty and sources
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Original source · BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261012-metagenn-config-genet
- areas
- microbes-communities
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- GeNet
- foundation model eligible
- false
- parameters
- Extended to a capacity similar to MetageNN and trained on the same main-database training set; majority vote and 0.5 probability cutoff
- source locator
- Results 'MetageNN presents a higher F1 score than GeNet...' Baselines and Experimental setup; Methods 'Databases'
- access reuse
- Tool run by the article's authors; the trained MetageNN model is not linked from the article
- missing metadata
- version: reason: unreported; note: No tool versions are given
- review
- method: source-hash-verification; scope-review; reviewer: claude; reviewer note: Separate Claude review agent (rev-mlvb), independent of the extracting agent; no human review claimed; date: 2026-10-12; artifact sha256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11022314/fullTextXML; note: Checked against the re-downloaded article XML (SHA-256 matches).
- provenance note
- GeNet as run by the MetageNN authors with the 516-genome main database.