Relation Extraction in Biomedical Texts Based on Multi-Head Attention Model With Syntactic Dependency Feature: Modeling Study
Bibliographic record
Abstract
BACKGROUND: With the rapid expansion of biomedical literature, biomedical information extraction has attracted increasing attention from researchers. In particular, relation extraction between 2 entities is a long-term research topic. OBJECTIVE: This study aimed to perform 2 multiclass relation extraction tasks of Biomedical Natural Language Processing Workshop 2019 Open Shared Tasks: relation extraction of Bacteria-Biotope (BB-rel) task and binary relation extraction of plant seed development (SeeDev-binary) task. In essence, these 2 tasks are aimed at extracting the relation between annotated entity pairs from biomedical texts, which is a challenging problem. METHODS: Traditional research methods adopted feature- or kernel-based methods and achieved good performance. For these tasks, we propose a deep learning model based on a combination of several distributed features, such as domain-specific word embedding, part-of-speech embedding, entity-type embedding, distance embedding, and position embedding. The multi-head attention mechanism is used to extract the global semantic features of an entire sentence. Meanwhile, we introduced a dependency-type feature and the shortest dependency path connecting 2 candidate entities in the syntactic dependency graph to enrich the feature representation. RESULTS: score of our model is superior to that of other existing models and achieves state-of-the-art performance. CONCLUSIONS: We demonstrated that the multi-head attention mechanism can learn relevant syntactic and semantic features in different representation subspaces and different positions to extract comprehensive feature representation. Moreover, syntactic dependency features can improve the performance of the model by learning dependency relation between the entities in biomedical texts.
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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".