Secure similar patients query with homomorphically evaluated thresholds
Bibliographic record
Abstract
Patient-centric precision medicine requires the analysis of large volumes of genomic data to tailor treatments and medications based on individual-level characteristics. Because the amount of data held by a single institution is limited, researchers may want access to genomic data held by other institutions. Owing to the inherent privacy implications of genomic data, performing comparisons on encrypted data is preferable in certain settings. The Similar patient query (SPQ) is an application that enables a secure search across genomic databases for patients with similar genetic makeup. Query results can be used to draw meaningful conclusions regarding suitable therapies. However, existing protocols either reveal intermediate computations, such as similarity scores, which can lead to membership-inference attacks, or they realize the ideal Boolean output (similar/not similar) through multiple protocol rounds, requiring the database owners to stay online throughout. This paper introduces a two-party privacy-preserving approach to perform SPQs across encrypted genomic databases based on secure function extensions of additively homomorphic encryption. In contrast to related works, our scheme enables secure computation of genomic data similarity without an external party in a single round. This is achieved for more than 1000 positions of a genome in a single public key operation of 256-bit security level in the integer factorization setting.
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 | 0.004 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.003 | 0.007 |
| Open science | 0.002 | 0.006 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 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".