CipherGenome: Homomorphic Inference for Genomic Mixture-of-Experts

arXiv:2609.35883 · cs.CR, cs.LG, q-bio.GN · Submitted 2026-09-27 · Read on arXiv

cs.CR, cs.LG, q-bio.GN

Submitted: 2026-09-27

Updated: 2026-10-01

Terminology

• Transformer — 16× in this paper · explained in 2 episodes
• Core — 15× in this paper · explained in 2 episodes
• Accuracy — 14× in this paper · explained in 1 episode
• Quantization — 13× in this paper · explained in 12 episodes
• Fidelity — 11× in this paper · explained in 2 episodes
• Foundation Model — 7× in this paper · explained in 3 episodes
• Embeddings — 4× in this paper · explained in 2 episodes
• In International Conference on Learning Representations — 4× in this paper
• Calibration — 3× in this paper · explained in 7 episodes
• Fine-Tuning — 3× in this paper · explained in 5 episodes
• Foundation Models — 3× in this paper · explained in 7 episodes
• Sparsity — 3× in this paper · explained in 4 episodes
• Adam — 2× in this paper · explained in 2 episodes
• Generative AI — 2× in this paper · explained in 2 episodes
• LoRA Fine-Tuning — 2× in this paper · explained in 3 episodes
• Mixture-of-Experts (MoE) — 2× in this paper · explained in 7 episodes
• Network and Distributed System Security Symposium — 2× in this paper
• Benchmark — 1× in this paper · explained in 2 episodes
• Elias — 1× in this paper · explained in 2 episodes
• Error Decomposition — 1× in this paper · explained in 3 episodes
• Meeting of the Association for Computational Linguistics — 1× in this paper
• Mixture of Experts — 1× in this paper · explained in 2 episodes
• Pruning — 1× in this paper · explained in 4 episodes
• SIGSAC Conference on Computer and Communications Security — 1× in this paper
• Trace — 1× in this paper · explained in 2 episodes

Sources

• TenSEAL: A Library for Encrypted Tensor Operations Using Homomorphic Encryption
• DeepSeek-V3 Technical Report
• Private LoRA Fine-tuning of Open-Source LLMs with Homomorphic Encryption
• Feasibility of Homomorphic Inference for a Genomic Foundation Model
• Mixtral of Experts
• Quantifying Memorization and Privacy Risks in Genomic Language Models
• Expert Selections In MoE Models Reveal (Almost) As Much As Text
• How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
• GLU Variants Improve Transformer
• SecMoE: Communication-Efficient Secure MoE Inference via Select-Then-Compute
• Stealing User Prompts from Mixture of Experts

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