CipherGenome: Homomorphic Inference for Genomic Mixture-of-Experts

Genome foundation models are most useful where sequences are generated, yet the largest models need datacenter accelerators and a place to send private DNA. We ask whether a 15-billion-parameter genome mixture-of-experts (MoE) model can instead run on volunteers' web browsers, with the experts spread across many untrusted devices, without changing its predictions and without revealing the sequence to any single device. We build a system in which a trusted coordinator runs attention and routing while browser workers run every expert feed-forward network through hand-written WebGPU kernels, and we protect the expert inputs with real-valued Lagrange coded computing: each worker receives only a Gaussian-padded share, computes the expert's linear maps, and the coordinator decodes from any two of three workers. On GenomeOcean-MoE (8 experts, top-2 routing, 24 layers), the browser path matches native llama.cpp at every quantization level, the distributed path stays at the BF16 numerical noise floor (KL 0.0036 nats per token), and an unfitted latency model predicts decode time within 0.74% (median) under emulated wide-area links. We first show that plaintext expert inputs are not private: a probe recovers the token from a single vector at every depth, and one worker can identify the source genome from 300 unordered tokens with 92% accuracy. With coded experts, an adaptive attacker trained on shares falls to the most-frequent-token baseline, one worker's information about each token is bounded below one bit per forward pass, and the fidelity cost stays below the BF16 noise floor; in Chrome, coded decoding runs at 220 to 376 ms per token, depending on how much of the routing is hidden, and continues without replicas when a worker fails.

Large Language Models (LLMs) are increasingly served on shared accelerators where an adversary with read access to device memory can observe KV caches and hidden states, threatening prompt privacy for open-source models. Cryptographic protections such as MPC and FHE offer strong guarantees but remain one to two orders of magnitude too slow for interactive inference, while static obfuscation schemes break under multi-run statistical attacks once the model is known. We present GELO (Good-Enough LLM Obfuscation), a lightweight protocol for privacy-preserving inference that limits information leakage from untrusted accelerator observations by hiding hidden states with fresh, per-batch invertible mixing. For each offloaded projection, the TEE samples a random matrix $A$, forms $U = AH$, offloads $U$ and weights W to the accelerator, and then applies $A^{-1}$ on return, so that $A^{-1}((AH)W ) = HW$ and outputs are unchanged. Because mixing is never reused across batches, the attacker faces only a single-batch blind source separation problem. We analyse information leakage and introduce two practical defences: (i) non-orthogonal mixing to mask Gram matrices, and (ii) orthogonal mixing augmented with a small fraction of high-energy "shield" vectors that pollute higher-order statistics. On Llama-2 7B, GELO preserves float32 outputs exactly, closely matches low-precision baselines, and shows about $20$--$30\%$ compute-side overhead in a controlled offload microbenchmark; an unoptimized remote prototype is dominated by transport overhead, motivating deeper serving-engine integration. GELO resists ICA/BSS and anchor-assisted attacks; a 60M-parameter transformer-based unmixing attack also fails under strong mixing and shielding.

Fully homomorphic encryption (FHE) allows a server to run a language model directly on encrypted user prompts, but current approaches remain prohibitively slow. Ciphertexts natively support only addition, multiplication, and rotation, and multiplications may be composed only to a bounded depth before a costly bootstrapping operation is required to continue. Every nonlinearity must therefore be approximated by an iterative method; each iteration increasing the number of multiplications. A higher iteration count buys precision but exhausts the available depth more frequently and thus triggers more bootstraps, which dominate latency. We introduce Homomorphic Encryption-Aware Training (HEAT), a fine-tuning method that makes the per-nonlinearity iteration counts learnable, enabling them and the model weights to co-adapt during training. HEAT optimizes iterations with respect to the task objective, allowing the model to adapt to approximation errors encountered during inference without architectural changes or retraining from scratch. We further relate iteration count to quantization bit width and bound, at fixed weights, the gap between our objective and quantization-aware training. On encrypted GPT-2 decoding, HEAT reduces iterations by $3.1\times$, bootstraps by $1.6\times$, and end-to-end latency by $1.4\times$, while improving decode agreement over the calibrated encrypted baseline.