Homomorphic Encryption

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

The applications of Generative Artificial Intelligence (GenAI) and their intersections with data-driven fields, such as healthcare, finance, transportation, and information security, have led to significant improvements in service efficiency and low latency. However, this synergy raises serious concerns regarding the security of large language models (LLMs) and their potential impact on the privacy of companies and users' data. Many technology companies that incorporate LLMs in their services with a certain level of command and control bear a risk of data exposure and secret divulgence caused by insecure LLM pipelines, making them vulnerable to multiple attacks such as data poisoning, prompt injection, and model theft. Although several security techniques (input/output sanitization, decentralized learning, access control management, and encryption) were implemented to reduce this risk, there is still an imminent risk of quantum computing attacks, which are expected to break existing encryption algorithms, hence, retrieving secret keys, encrypted sensitive data, and decrypting encrypted models. In this extensive work, we integrate the Post-Quantum Cryptography (PQC) based Lattice-based Homomorphic Encryption (HE) main functions in the LLM's inference pipeline to secure some of its layers against data privacy attacks. We modify the inference pipeline of the transformer architecture for the LLAMA-3 model while injecting the main homomorphic encryption operations provided by the concrete-ml library. We demonstrate high text generation accuracies (up to 98%) with reasonable latencies (237 ms) on an i9 CPU, reaching up to 80 tokens per second, which proves the feasibility and validity of our work while running a FHE-secured LLAMA-3 inference model. Further experiments and analysis are discussed to justify models' text generation latencies and behaviours.

Fully homomorphic encryption (FHE) has recently attracted significant attention as both a cryptographic primitive and a systems challenge. Given the latest advances in accelerated computing, FHE presents a promising opportunity for progress, with applications ranging from machine learning to information security. We target the most computationally intensive operation in deep neural networks from a hardware perspective, matrix multiplication (matmul), and adapt it for execution on AMD GPUs. We propose a new optimized method that improves the runtime and complexity of ciphertext matmul by using FIDESlib, a recent open-source FHE library designed specifically for GPUs. By exploiting sparsity in both operands, our sparse matmul implementation outperforms its CPU counterpart by up to $3.0\times$ and reduces the time complexity from cubic to semi-linear, demonstrating an improvement over existing FHE matmul implementations.

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.

Iris-based biometric identification is increasingly recognized for its significant accuracy and long-term stability compared to other biometric modalities such as fingerprints or facial features. However, all biometric modalities are highly sensitive data that raise serious privacy and security concerns, particularly in decentralized and untrusted environments. While Fully Homomorphic Encryption (FHE) has emerged as a promising solution for protecting sensitive data during computation, existing privacy-preserving iris recognition systems face significant performance limitations that hinder their practical deployment. This paper investigates the performance challenges of the current landscape of privacy-preserving iris recognition systems using FHE. Based on these insights, we outline a scalable privacy-preserving framework that aligns with all the requirements specified in the ISO/IEC 24745 standard. Leveraging the Open Iris library, our approach starts with robust iris segmentation, followed by normalization and feature extraction using Gabor filters to generate iris codes. We then apply binary masking to filter out unreliable regions and perform matching using Hamming distance on encrypted iris codes. The accuracy and performance of our proposed privacy-preserving framework is evaluated on the CASIA-Iris-Thousand dataset. Results show that our privacy-preserving framework yields very similar accuracy to the cleartext equivalent, but a much higher computational overhead with respect to pairwise iris template comparisons, of $\sim 120\,000 \times$. This points towards the need for the deployment of two-level schemes in the context of scalable $1-N$ template comparisons.

With the rapid advancement of AI technology, we have seen more and more concerns on data privacy, leading to some cutting-edge research on machine learning with encrypted computation. Fully Homomorphic Encryption (FHE) is a crucial technology for privacy-preserving computation, while it struggles with continuous non-polynomial functions, as it operates on discrete integers and supports only addition and multiplication. Spiking Neural Networks (SNNs), which use discrete spike signals, naturally complement FHE's characteristics. In this paper, we introduce FHE-DiCSNN, a framework built on the TFHE scheme, utilizing the discrete nature of SNNs for secure and efficient computations. By leveraging bootstrapping techniques, we successfully implement Leaky Integrate-and-Fire (LIF) neuron models on ciphertexts, allowing SNNs of arbitrary depth. Our framework is adaptable to other spiking neuron models, offering a novel approach to homomorphic evaluation of SNNs. Additionally, we integrate convolutional methods inspired by CNNs to enhance accuracy and reduce the simulation time associated with random encoding. Parallel computation techniques further accelerate bootstrapping operations. Experimental results on the MNIST and FashionMNIST datasets validate the effectiveness of FHE-DiCSNN, with a loss of less than 3% compared to plaintext, respectively, and computation times of under 1 second per prediction. We also apply the model into real medical image classification problems and analyze the parameter optimization and selection.

We present mmFHE, the first system that executes the entire cloud-side mmWave sensing pipeline including the DSP and ML inference under fully homomorphic encryption (FHE). mmFHE encrypts range profiles on an edge device after lightweight plaintext preprocessing and executes the entire mmWave signal-processing and ML inference pipeline homomorphically on a semi-honest cloud that operates exclusively on ciphertexts. At the core of mmFHE is a library of seven composable, data-oblivious FHE kernels that replace standard DSP routines with fixed arithmetic circuits for different application-specific pipelines. We demonstrate this approach on two representative tasks: vital-sign monitoring and gesture recognition. We formally prove two cryptographic guarantees for any pipeline assembled from this library: input privacy and data obliviousness. These guarantees effectively neutralize various supervised and unsupervised privacy attacks on raw data, including re-identification and data-dependent privacy leakage. Evaluation on three public radar datasets shows that encryption introduces negligible error versus the plaintext pipeline, with 84.5% gesture accuracy (vs. 84.7%). End-to-end cloud GPU latency is 1.21 s per 10 s vital-sign window and 5.76 s per 3 s gesture window. These results establish the initial feasibility of end-to-end mmWave sensing under FHE on commodity hardware.

Modern cloud inference creates a two sided privacy problem where users reveal sensitive inputs to providers, while providers must execute proprietary model weights inside potentially leaky execution environments. Fully homomorphic encryption (FHE) offers cryptographic guarantees but remains prohibitively expensive for modern architectures. We argue that progress requires co-design where specializing FHE schemes/compilers for the static structure of inference circuits, while simultaneously constraining inference architectures to reduce dominant homomorphic cost drivers. We outline a meet in the middle agenda and concrete optimization targets on both axes.

Federated learning (FL) enables collaborative training of machine learning models without sharing sensitive client data, making it a cornerstone for privacy-critical applications. However, FL faces the dual challenge of ensuring learning quality and robust privacy protection while keeping resource consumption low, particularly when using computationally expensive techniques such as homomorphic encryption (HE). In this work, we enhance an FL process that preserves privacy using HE by integrating it with synthetic data generation and an interleaving strategy. Specifically, our solution, named Alternating Federated Learning (Alt-FL), consists of alternating between local training with authentic data (authentic rounds) and local training with synthetic data (synthetic rounds) and transferring the encrypted and plaintext model parameters on authentic and synthetic rounds (resp.). Our approach improves learning quality (e.g., model accuracy) through datasets enhanced with synthetic data, preserves client data privacy via HE, and keeps manageable encryption and decryption costs through our interleaving strategy. We evaluate our solution against data leakage attacks, such as the DLG attack, demonstrating robust privacy protection. Also, Alt-FL provides 13.4% higher model accuracy and decreases HE-related costs by up to 48% with respect to Selective HE.

Encrypted AI using fully homomorphic encryption (FHE) enables inference directly over encrypted queries, providing strong privacy guarantees. However, its computational and memory overheads have limited practical deployment. Custom FHE accelerators improve performance, but rely on advanced manufacturing technologies that limit their accessibility. GPUs offer a more widely available alternative, yet achieving ASIC-class performance on GPUs is challenging. Large models such as LLMs compound these challenges by requiring optimized kernels, terabyte-scale memory management, and efficient execution across multiple devices. We present Cerium, a multi-GPU framework for large-scale FHE inference. Cerium combines a domain-specific language, an optimizing compiler, and a runtime system to automatically generate optimized GPU kernels, compress plaintext data, manage terabyte-scale memory footprints, and optimize multi-GPU communication. Implemented on NVIDIA GPUs, Cerium outperforms expert-written GPU libraries by up to 2.25x and achieves performance competitive with state-of-the-art FHE ASICs, matching the CraterLake ASIC. It is the first GPU system to execute CKKS bootstrapping in under 10 milliseconds, achieving 7.5 milliseconds, and is the first to demonstrate encrypted inference for BERT-Base and Llama3-8B prefill in 8 seconds and 43 seconds, respectively. The Cerium framework is open-source and available at https://github.com/CMU-CAOS/Cerium

In contemporary cloud-based services, protecting users' sensitive data and ensuring the confidentiality of the server's model are critical. Fully homomorphic encryption (FHE) enables inference directly on encrypted inputs, but its practicality is hindered by expensive bootstrapping and inefficient approximations of non-linear activations. We introduce Safhire, a hybrid inference framework that executes linear layers under encryption on the server while offloading non- linearities to the client in plaintext. This design eliminates bootstrapping, supports exact activations, and significantly reduces computation cost. To safeguard model confidentiality despite client access to intermediate outputs, Safhire applies randomized shuffling, which obfuscates intermediate values and makes it practically impossible for a client to reconstruct the model. To further reduce inference latency, Safhire incorporates advanced optimizations such as fast ciphertext packing and partial extraction. Evaluations on multiple standard models and datasets show that Safhire achieves up to 7.6x and 7.4x lower inference latency than Orion and Concrete-ML, respectively, which are two state-of-the-art FHE baselines, with manageable communication overhead and comparable accuracy. These results underline the practicality of our hybrid FHE inference scheme.