ComputeFHE: A Privacy-Preserving General-Purpose Computation Library
Authors: Faris Serdar Tasel, Efe Ciftci
Organizations: Department of Computer Engineering, Çankaya University, Ankara, Turkey · Computer Programming Program, Çankaya University, Ankara, Turkey
Fully Homomorphic Encryption (FHE) enables computations to be performed directly on encrypted data while preserving data confidentiality. However, its practical applications remain limited by high computational costs and development complexity. This paper presents ComputeFHE, an open-source C++ library that facilitates the development of privacy-preserving applications based on the TFHE cryptosystem. The library provides encrypted integer and fixed-point data types together with arithmetic, logical, comparison, conditional, and oblivious array-access operations which allow developers to implement algorithms using a familiar imperative programming paradigm. ComputeFHE supports both conventional TFHE arithmetic based on standard two-input logic gates and an optimized Arithmetic Logic Unit (ALU) architecture utilizing FHE-friendly logic primitives. Experimental results demonstrate significant reductions in the number of required bootstrapping operations, achieving performance improvements of up to 3.9x for selected operations. In addition, the library includes a simulation mode that enables testing, debugging, and complexity analysis without performing actual cryptographic computations while providing circuit complexity and bootstrapping costs. Built on top of OpenFHE, ComputeFHE offers a practical and accessible framework for developing and evaluating privacy-preserving algorithms and applications.
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) enables inference on private data without revealing it to the server, but evaluating an entire input under FHE is expensive. We study \emph{selective homomorphic inference}, where only a sensitive region of interest (ROI) is encrypted, and computations independent of that region are performed in plaintext. Selective evaluation produces the same output as full FHE on the same model, without retraining. Its efficiency depends on how quickly encrypted dependencies spread through the network. For small encrypted ROIs, locality-preserving architectures can achieve order-of-magnitude homomorphic-evaluation speedups, whereas architectures with early global mixing provide essentially no speedup. These results identify locality as the key architectural property governing the benefit of selective homomorphic inference.
Fully homomorphic encryption (FHE) allows computations to be performed directly on encrypted data without decryption, offering strong privacy guarantees for sensitive data analysis. This capability is important for privacy-sensitive applications like secure cloud computing, finance, and healthcare. The complexity of FHE schemes, however, has hindered their practical adoption. To make FHE accessible to a broader range of developers, a new generation of specialized frameworks has emerged to translate high-level FHE programs into complex FHE operations, introducing a new programming paradigm. However, the inherent complexity of FHE frameworks makes them prone to incorrect implementation logic. Unlike mere crashes, logic bugs in these frameworks can silently corrupt encrypted computation, potentially leading to severe financial losses and security vulnerabilities in FHE-enhanced applications. In this work, we introduce HERTA, the first automated testing tool tailored for FHE frameworks. HERTA leverages metamorphic testing to uncover deep-seated implementation bugs and vulnerabilities across the multi-layered FHE software stack. To that end, we design a set of novel metamorphic relations (MRs) derived specifically from FHE semantics. These MRs stress the most challenging aspects of the pipeline, enabling automated correctness testing without the need for a manual ground truth. Our evaluation of HERTA on 3 leading industry frameworks discovered 21 previously unknown bugs, several of which have already been confirmed and fixed by developers. Furthermore, our hazard analysis reveals the critical security impact these bugs pose to the integrity and availability of FHE-based services.