BioCite: A Deep Learning-based Citation Linkage Framework for Biomedical Research Articles
Bibliographic record
Abstract
Research papers reflect scientific advances.Citations are widely used in research publications to support the new findings and show their benefits, while also regulating the information flow to make the contents clearer for the audience.A citation in a research article refers to the information's source, but not the specific text span from that source article.In biomedical research articles, this task is challenging as the same chemical or biological component can be represented in multiple ways in different papers from various domains.This paper suggests a mechanism for linking citing sentences in a publication with cited sentences in referenced sources.The framework presented here pairs the citing sentence with all of the sentences in the reference text, and then tries to retrieve the semantically equivalent pairs.These semantically related sentences from the reference paper are chosen as the cited statements.This effort involves designing a citation linkage framework utilizing sequential and tree-structured siamese deep learning models.This paper also provides a method to create an automatically generated corpus for such a task.
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 | 0.002 | 0.008 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.008 | 0.007 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.004 |
| Open science | 0.003 | 0.003 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.005 | 0.002 |
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".