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Record W2805327676 · doi:10.31031/oabb.2018.01.000523

String Matching in DNA Databases

2018· article· en· W2805327676 on OpenAlexaff
Yangjun Chen

Bibliographic record

VenueOpen Access Biostatistics & Bioinformatics · 2018
Typearticle
Languageen
FieldComputer Science
TopicAlgorithms and Data Compression
Canadian institutionsUniversity of Winnipeg
Fundersnot available
KeywordsDatabaseString (physics)Computer scienceMatching (statistics)String searching algorithmDNAInformation retrievalComputational biologyBiologyPattern matchingArtificial intelligenceMathematicsPhysicsGeneticsTheoretical physicsStatistics

Abstract

fetched live from OpenAlex

The recent development of next-generation sequencing has changed the way we carry out the molecular biology and genomic studies. It has allowed us to sequence a DNA (Deoxyribonucleic acid) sequence at a significantly increased base coverage, as well as at a much faster rate [1]. This facilitates building an excellent platform for a whole genome sequencing, and for a variety of sequencing-based analyses, including gene expressions, mapping DNA-protein interactions, whole-transcriptome sequencing, and RNA (Ribonucleic acid) splicing profiles. For example, the RNA-Seq protocol [2], in which processed mRNA is converted to cDNA and then sequenced, is enabling the identification of previously unknown genes and alternative splice variants. The whole-genome sequencing of tumour cells can uncover previously unidentified cancer-initiating mutations.

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 imitation

Not 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.

metaresearch head score (Codex)0.004
metaresearch head score (Gemma)0.021
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Theoretical or conceptual · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.042
Threshold uncertainty score0.139

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0040.021
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0020.002
Bibliometrics0.0100.015
Science and technology studies0.0010.001
Scholarly communication0.0040.007
Open science0.0030.003
Research integrity0.0030.002
Insufficient payload (model declined to judge)0.0420.034

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.

Opus teacher head0.075
GPT teacher head0.394
Teacher spread0.319 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designTheoretical or conceptual
Domainnot available
GenreEmpirical

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".

Quick stats

Citations5
Published2018
Admission routes1
Has abstractyes

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