HTCNN: High-Throughput Batch CNN Inference with Homomorphic Encryption

Homomorphic Encryption (HE) technology allows for processing encrypted data, breaking through data isolation barriers and providing a promising solution for privacy-preserving computation. The integration of HE technology into Convolutional Neural Network (CNN) inference shows potential in addressing privacy issues in identity verification, medical imaging diagnosis, and various other applications. The CKKS HE algorithm stands out as a popular option for homomorphic CNN inference due to its capability to handle real number computations. However, challenges such as computational delays and resource overhead present significant obstacles to the practical implementation of homomorphic CNN inference, largely due to the complex nature of HE operations. In addition, current methods for speeding up homomorphic CNN inference primarily address individual images or large batches of input images, lacking a solution for efficiently processing a moderate number of input images with fast homomorphic inference capabilities. In response to these challenges, we introduce a novel leveled homomorphic CNN inference scheme aimed at reducing latency and improving throughput using the CKKS scheme. Our proposed inference strategy involves mapping multiple inputs to a set of ciphertext by exploiting the sliding window properties of convolutions to utilize CKKS's inherent Single-Instruction-Multiple-Data (SIMD) capability. To mitigate the delay associated with homomorphic CNN inference, we introduce optimization techniques, including mask-weight merging, rotation multiplexing, stride convolution segmentation, and folding rotations. The efficacy of our homomorphic inference scheme is demonstrated through evaluations carried out on the MNIST and CIFAR-10 datasets. Specifically, results from the MNIST dataset on a single CPU thread show that inference for 163 images can be completed in 10.4 seconds with an accuracy of 98.95%, which is a 6.9× throughput improvement over state-of-the-art works. Comparative analysis with existing methodologies highlights the superior performance of our proposed inference scheme in terms of latency, throughput, communication overhead, and memory utilization. © 2025 IEEE.