Document Retrieval for Precision Medicine Using a Deep Learning Ensemble Method
Bibliographic record
Abstract
BACKGROUND: With the development of biomedicine, the number of biomedical documents has increased rapidly bringing a great challenge for researchers trying to retrieve the information they need. Information retrieval aims to meet this challenge by searching relevant documents from abundant documents based on the given query. However, sometimes the relevance of search results needs to be evaluated from multiple aspects in specific retrieval tasks, thereby increasing the difficulty of biomedical information retrieval. OBJECTIVE: This study aimed to find a more systematic method for retrieving relevant scientific literature for a given patient. METHODS: In the initial retrieval stage, we supplemented query terms through query expansion strategies and applied query boosting to obtain an initial ranking list of relevant documents. In the re-ranking phase, we employed a text classification model and relevance matching model to evaluate documents from different dimensions and then combined the outputs through logistic regression to re-rank all the documents from the initial ranking list. RESULTS: The proposed ensemble method contributed to the improvement of biomedical retrieval performance. Compared with the existing deep learning-based methods, experimental results showed that our method achieved state-of-the-art performance on the data collection provided by the Text Retrieval Conference 2019 Precision Medicine Track. CONCLUSIONS: In this paper, we proposed a novel ensemble method based on deep learning. As shown in the experiments, the strategies we used in the initial retrieval phase such as query expansion and query boosting are effective. The application of the text classification model and relevance matching model better captured semantic context information and improved retrieval performance.
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 | 0.003 | 0.005 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.005 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| 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".