EFFECTIVE BIO-EVENT EXTRACTION USING TRIGGER WORDS AND SYNTACTIC DEPENDENCIES
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.
Bibliographic record
Abstract
The scientific literature is the main source for comprehensive, up-to-date biological knowledge. Automatic extraction of this knowledge facilitates core biological tasks, such as database curation and knowledge discovery. We present here a linguistically inspired, rule-based and syntax-driven methodology for biological event extraction. We rely on a dictionary of trigger words to detect and characterize event expressions and syntactic dependency based heuristics to extract their event arguments. We refine and extend our prior work to recognize speculated and negated events. We show that heuristics based on syntactic dependencies, used to identify event arguments, extend naturally to also identify speculation and negation scope. In the BioNLP’09 Shared Task on Event Extraction, our system placed third in the Core Event Extraction Task (F-score of 0.4462), and first in the Speculation and Negation Task (F-score of 0.4252). Of particular interest is the extraction of complex regulatory events, where it scored second place. Our system significantly outperformed other participating systems in detecting speculation and negation. These results demonstrate the utility of a syntax-driven approach. In this article, we also report on our more recent work on supervised learning of event trigger expressions and discuss event annotation issues, based on our corpus analysis.
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 imitationNot 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.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it