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.
Fully homomorphic encryption (FHE) supports only additions and multiplications, so FHE-only neural-network inference typically replaces ReLU with polynomials fitted over empirical activation intervals. Such interval fitting often requires higher-degree polynomials to control activation error, incurring homomorphic evaluation costs, while classification is determined by the final logit decision. We revisit ReLU replacement from a decision-aware perspective: given a trained single-hidden-layer ReLU MLP and a specified calibration set, can an HE-friendly low-degree polynomial replace ReLU without retraining while preserving calibration-set decisions? We focus on quadratic replacement, the lowest-degree choice that retains a genuine per-unit nonlinearity. For calibration sets positive-margin separable in the lifted space, we formulate quadratic replacement as a linear separation problem, yielding necessary and sufficient conditions for calibration-lossless replacement and a constructive algorithm for the coefficients. When the positive-margin condition fails -- typically due to a few misclassified calibration samples -- we extend the same geometric framework via reduced convex hulls and Lagrangian-dual soft-margin relaxations, which bound the influence of any single sample, converting the problem into smaller convex quadratic programs that yield approximately feasible coefficients with high empirical agreement on calibration-set decisions. In particular, at the maximal weight cap $μ=1$, the reduced-convex-hull relaxation reduces to the convex-hull separation of the strictly separable case; the relaxation thus continuously extends the exact theory. Under CKKS, the quadratic replacement matches plaintext top-1 accuracy on multiple benchmarks, running 3.7--4.1$\times$ faster than Remez-7 in the activation module and 1.18--1.68$\times$ faster end-to-end.