Secure Genomic String Search with Parallel Homomorphic Encryption
Bibliographic record
Abstract
Fully homomorphic encryption (FHE) cryptographic systems enable limitless computations over encrypted data, providing solutions to many of today’s data security problems. While effective FHE platforms can address modern data security concerns in unsecure environments, the extended execution time for these platforms hinders their broader application. This project aims to enhance FHE systems through an efficient parallel framework, specifically building upon the existing torus FHE (TFHE) system chillotti2016faster. The TFHE system was chosen for its superior bootstrapping computations and precise results for countless Boolean gate evaluations, such as AND and XOR. Our first approach was to expand upon the gate operations within the current system, shifting towards algebraic circuits, and using graphics processing units (GPUs) to manage cryptographic operations in parallel. Then, we implemented this GPU-parallel FHE framework into a needed genomic data operation, specifically string search. We utilized popular string distance metrics (hamming distance, edit distance, set maximal matches) to ascertain the disparities between multiple genomic sequences in a secure context with all data and operations occurring under encryption. Our experimental data revealed that our GPU implementation vastly outperforms the former method, providing a 20-fold speedup for any 32-bit Boolean operation and a 14.5-fold increase for multiplications.This paper introduces unique enhancements to existing FHE cryptographic systems using GPUs and additional algorithms to quicken fundamental computations. Looking ahead, the presented framework can be further developed to accommodate more complex, real-world applications.
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".