Identifying Personalised Treatments and Clinical Trials for Precision Medicine using Semantic Search with Thalia
Bibliographic record
Abstract
This paper reports the main methods applied in our submission to TREC 2017 Precision Medicine Track. The goal of this challenge was to retrieve documents containing potential treatments and clinical trials for specific patient characteristics. Our main strategy involved using a semantic search engine called Thalia (Text mining for Highlighting, Aggregating and Linking Information in Articles), which allows the recognition of diseases and genes mentioned in text. The recognition of named entities and its linking to concepts in ontologies facilitates more accurate retrieval than just relying on plain textual search and matching. We also highlight the different strategies applied when querying Thalia in the context of this Precision Medicine challenge, which aimed to support different use cases (i.e. more focused or broader searches).
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 | 0.015 | 0.048 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.013 | 0.007 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.006 | 0.005 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.013 | 0.004 |
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".