Cerium: A Multi-GPU Framework for Terabyte-Scale Encrypted Inference

Fully Homomorphic Encryption (FHE) enables privacy-preserving Transformer inference, but long-sequence encrypted Transformers quickly exceed single-GPU memory capacity because encoded weights are already large and encrypted activations grow rapidly with sequence length. Multi-GPU execution therefore becomes unavoidable, yet scaling remains challenging because communication is jointly induced by application-level aggregation and encryption-level RNS coupling. Existing approaches either synchronize between devices frequently or replicate encrypted tensors across devices, leading to excessive communication and latency. We present AEGIS, an Application-Encryption Guided Inference System for scalable long-sequence encrypted Transformer inference on multi-GPU platforms. AEGIS derives device placement from ciphertext dependencies jointly induced by Transformer dataflow and CKKS polynomial coupling, co-locating modulus-coherent and token-coherent data so that communication is introduced only when application dependencies require it, while reordering polynomial operators to overlap the remaining collectives with computation. On 2048-token inputs, AEGIS reduces inter-GPU communication by up to 57.9% in feed-forward networks and 81.3% in self-attention versus prior state-of-the-art designs. On four GPUs, it achieves up to 96.62% scaling efficiency, 3.86x end-to-end speedup, and 69.1% per-device memory reduction. These results establish coordinated application-encryption parallelism as a practical foundation for scalable homomorphic Transformer inference.

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.

Fully Homomorphic Encryption (FHE) enables privacy-preserving machine learning but incurs extreme computational and memory overhead. These costs come not only from expensive low-level primitives, including Number Theoretic Transform (NTT), rotation, and key-switching, but also from inefficient ciphertext packing at the application level. Existing packing strategies typically preserve either neighboring data elements or feature grouping, but not both, leading to wasted ciphertext slots, excessive rotations, and inflated ciphertext counts. We propose FEnc2, a unified and principled fragment-based encoding framework for CKKS-based private convolutional neural network inference. FEnc2 optimizes slot utilization, rotation complexity, and ciphertext density through two components: 1)Conv-aware Encoding, which analytically selects an optimal fragment size to decouple spatial dependencies and jointly minimize inner-outer rotations across layers, and 2)Arch-aware Ct Compression, which restores ciphertext density after feature- or channel-reduction layers. Together, these transformations reshape encrypted workload structure and reduce homomorphic operations by one to two orders of magnitude. With full memory capacity utilized, i.e., at maximum batch size, FEnc2 achieves end-to-end latency speedups over the state-of-the-art Orion of up to 228.83x on GPU and 226.06x on CPU for LeNet on MNIST, and up to 4.55x on GPU and 9.43x on CPU for MobileNet on ImageNet. FEnc2 is hardware-agnostic yet architecturally transformative: by optimizing encrypted tensor layout before execution, it reduces ciphertext count and workload pressure on hardware, complementing primitive-level optimizations such as NTT and keyswitch accelerators. These results show that application-level data layout is a first-order architectural design dimension for encrypted inference and an important enabler for next-generation FHE systems.