Identifying interaction sentences from biological literature using automatically extracted patterns
Bibliographic record
Abstract
An important task in information retrieval is to identify sentences that contain important relationships between key concepts. In this work, we propose a novel approach to automatically extract sentence patterns that contain interactions involving concepts of molecular biology. A pattern is defined in this work as a sequence of specialized Part-of-Speech (POS) tags that capture the structure of key sentences in the scientific literature. Each candidate sentence for the classification task is encoded as a POS array and then aligned to a collection of pre-extracted patterns. The quality of the alignment is expressed as a pairwise alignment score. The most innovative component of this work is the use of a Genetic Algorithm (GA) to maximize the classification performance of the alignment scoring scheme. The system achieves an F-score of 0.834 in identifying sentences which describe interactions between biological entities. This performance is mostly affected by the quality of the preprocessing steps such as term identification and POS tagging.
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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 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.010 | 0.006 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.003 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".