OptiPrime: Optimizing Private Inference through Protocol-Hardware Co-design

Privacy-preserving machine learning (PPML) has become increasingly important in applications where sensitive data must remain confidential. Homomorphic Encryption (HE) enables computation directly on encrypted data, allowing neural network inference without revealing raw inputs. While prior works have largely focused on inference over a single encrypted image, batch processing of encrypted inputs lags behind, despite being critical for high-throughput inference scenarios and training-oriented workloads. In this work, we address this gap by developing optimized algorithms for batched HE-friendly neural networks. We also introduced a pipeline architecture designed to maximize resource efficiency for different batch size execution. We implemented these algorithms and evaluated our work using HE-friendly ResNet-20 and ResNet-34 models on encrypted CIFAR-10 and CIFAR-100 datasets, respectively. For ResNet-20, our approach achieves an amortized inference time of 8.86 seconds per image when processing a batch of 512 encrypted images, with a peak memory usage of 98.96 GB. These results represent a 1.78x runtime improvement and a 3.74x reduction in memory usage compared to the state-of-the-art design. For the deeper ResNet-34 model, we achieve an amortized inference time of 28.14 on a batch of 256 encrypted images using 246.78GB of RAM

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.

Institutions may benefit from collaborative inference on time-series data. In settings where privacy is necessary, multi-party computation (MPC) is a straightforward approach to providing strong guarantees, yet it remains prohibitively expensive and scales poorly with modern transformer architectures. Vertical Federated Learning (VFL) offers efficiency but suffers from privacy leakage at the embedding level, and securing the entire VFL model head via MPC remains prohibitively slow and communication-heavy for larger models. To enable practical, secure inference at scale, we propose "Public/Private Hybrid Head-VFL" (PPHH-VFL). This hybrid architecture splits the model head into an efficient plaintext public head and a secure, lightweight MPC private head. By applying adversarial training to the public embeddings, we mitigate privacy leakage; concurrently, the small private head securely preserves the flow of sensitive information needed for high downstream utility. Empirical evaluations on models ranging up to 86 million parameters demonstrate that PPHH-VFL accelerates inference by up to six orders of magnitude compared to end-to-end MPC. Compared to a standard VFL+MPC baseline, our approach scales significantly better, achieving a speedup of up to 44.4x in WAN and a 91.2x reduction in communication costs (dropping from 1.7 GB to 19 MB per batch), while simultaneously improving downstream classification accuracy by 2.50% and regression RMSE by 40.7%.