aiqbench analysis
CipherGenome addresses the critical privacy gap in scaling genomic foundation models by enabling secure outsourcing of computation to untrusted cloud servers. By leveraging specific structural properties of Mixture-of-Experts architectures and module-LWE encryption, the protocol maintains inference accuracy while preventing sensitive nucleotide data from being recovered during processing. This approach effectively balances the computational demands of massive genome models with the strict confidentiality requirements of genomic research.
CipherGenome: Homomorphic Inference for Genomic Mixture-of-Experts
arXiv:2609.35883v1 Announce Type: cross Abstract: Genome foundation models are growing into sparse mixture-of-experts (MoE) networks whose expert weights no longer fit on the machines that hold the sequences, yet sending a private genome to rented accelerators exposes it: we show that a single server hosting one expert recovers the input nucleotides with 99.8% top-1 accuracy. We present CipherGenome, a protocol that keeps the embedding, attention and router of a 15.1B-parameter MoE genome model on a trusted thin client and outsources every expert projection, 95.8% of the parameters, to untrusted and possibly colluding GPU servers under module-LWE encryption. The design exploits three structural facts: expert layers are linear between two SwiGLU gates, expert weights are public, and GPU integer tensor cores can evaluate a ciphertext-weight product exactly modulo $2^{48}$ in a single GEMM. The client evaluates the nonlinearity exactly and re-encrypts with fresh secrets, so no polynomial approximation or bootstrapping is ever needed. On 72 windows from 12 bacterial genomes, encryption adds $2.54 \times 10^{-4}$ nats per token of KL divergence (95% CI upper bound $3.95 \times 10^{-4}$), below a pre-registered non-inferiority margin and indistinguishable from bf16 inference, while the same inversion attack falls to chance level. A reusable public hint cuts end-to-end latency by 3.54 times, wire compression reduces traffic 6.8 times, per-layer padding reduces routing leakage from 54.9% to 8.9% accuracy, and HE-compatible int4 experts remain non-inferior to their plaintext counterparts. Per expert and token, the server-side cost is more than six orders of magnitude below a CKKS baseline.
Abstract:Genome foundation models are growing into sparse mixture-of-experts (MoE) networks whose expert weights no longer fit on the machines that hold the sequences, yet sending a private genome to rented accelerators exposes it: we show that a single server hosting one expert recovers the input nucleotides with 99.8% top-1 accuracy. We present CipherGenome, a protocol that keeps the embedding, attention and router of a 15.1B-parameter MoE genome model on a trusted thin client and outsources every expert projection, 95.8% of the parameters, to untrusted and possibly colluding GPU servers under module-LWE encryption. The design exploits three structural facts: expert layers are linear between two SwiGLU gates, expert weights are public, and GPU integer tensor cores can evaluate a ciphertext-weight product exactly modulo $2^{48}$ in a single GEMM. The client evaluates the nonlinearity exactly and re-encrypts with fresh secrets, so no polynomial approximation or bootstrapping is ever needed. On 72 windows from 12 bacterial genomes, encryption adds $2.54 \times 10^{-4}$ nats per token of KL divergence (95% CI upper bound $3.95 \times 10^{-4}$), below a pre-registered non-inferiority margin and indistinguishable from bf16 inference, while the same inversion attack falls to chance level. A reusable public hint cuts end-to-end latency by 3.54 times, wire compression reduces traffic 6.8 times, per-layer padding reduces routing leakage from 54.9% to 8.9% accuracy, and HE-compatible int4 experts remain non-inferior to their plaintext counterparts. Per expert and token, the server-side cost is more than six orders of magnitude below a CKKS baseline.
Preprint. 19 pages
Cryptography and Security (cs.CR); Machine Learning (cs.LG); Genomics (q-bio.GN)
arXiv:2609.35883 [cs.CR]
(or arXiv:2609.35883v1 [cs.CR] for this version)
https://doi.org/10.48550/arXiv.2609.35883 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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Full text under the publisher's open licence · 348 words
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