MNBC-ME identifies mobile elements and putative host species from metagenomic sequences
Bibliographic record
Abstract
These files provide supplementary data underlying the article: prok_Next150.fasta.gz: 13441246 150bp-long reads randomly generated from the prokaryotic test genomes, simulating reads sequenced by NextSeq (0.05 coverage) prok_Mi300.fasta.gz: 6723326 300bp-long reads randomly generated from the prokaryotic test genomes, simulating reads sequenced by MiSeq (0.05 coverage) prok_NanoND.fasta.gz: 371870 reads of normally distributed 1kb-10kb lengths randomly generated from the prokaryotic test genomes, simulating reads sequenced by Nanopore (0.05 coverage) plsdb_Next150.fasta.gz: 535249 150bp-long reads randomly generated from the test plasmids, simulating reads sequenced by NextSeq (0.05 coverage) plsdb_Mi300.fasta.gz: 271361 300bp-long reads randomly generated from the test plasmids, simulating reads sequenced by MiSeq (0.05 coverage) plsdb_NanoND.fasta.gz: 24226 reads of normally distributed 1kb-10kb lengths randomly generated from the test plasmids, simulating reads sequenced by Nanopore (0.05 coverage) virus_Next150.fasta.gz: 43381 150bp-long reads randomly generated from the viral test genomes, simulating reads sequenced by NextSeq (0.05 coverage) virus_Mi300.fasta.gz: 23004 300bp-long reads randomly generated from the viral test genomes, simulating reads sequenced by MiSeq (0.05 coverage) virus_NanoND.fasta.gz: 4885 reads of normally distributed 1kb-10kb lengths randomly generated from the viral test genomes, simulating reads sequenced by Nanopore (0.05 coverage) db_list.txt: List of 139052 prokaryotic, plasmidic and viral index filenames in the reference database, indicating the sequence accessions used to build the index files taxonomy.txt: Taxonomy file of the 139052 training sequences. Host taxa are given for plasmids. prok_training_and_test_sequences_list.txt: List of all 56107 prokaryotic training and test sequence accesions. plsdb_training_and_test_sequences_list.txt: List of all 72556 training and test plasmid accesions in the PLSDB database version 2024_05_31_v2 virus_training_and_test_sequences_list.txt: List of all 40353 training and test plasmid accesions in the Virus-Host database release 227
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.005 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.052 | 0.032 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".