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Record W2054145206 · doi:10.1145/1148170.1148336

Concept-based biomedical text retrieval

2006· article· en· W2054145206 on OpenAlex
Ming Zhong

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

Venuenot available
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicBiomedical Text Mining and Ontologies
Canadian institutionsYork University
Fundersnot available
KeywordsComputer scienceInformation retrievalSet (abstract data type)Text retrievalArtificial intelligence

Abstract

fetched live from OpenAlex

One challenging problem for biomedical text retrieval is to find accurate synonyms or name variants for biomedical entities. In this paper, we propose a new concept-based approach to tackle this problem. In this approach, a set of concepts instead of keywords will be extracted from a query first. Then these concepts will be used for retrieval purpose. The experiment results show that the proposed approach can boost the retrieval performance and it generates very good results on 2005 TREC Genomics data sets.

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.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.381
Threshold uncertainty score0.331

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

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 head0.009
GPT teacher head0.253
Teacher spread0.244 · 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

Quick stats

Citations27
Published2006
Admission routes1
Has abstractyes

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Same topicBiomedical Text Mining and OntologiesFrench-language works237,207