Pushing Forward Multi-Secret-Key Homomorphic Encryption for Private Average Aggregation

Federated Learning enables multiple clients to train a shared model while keeping their local datasets isolated. However, the exchanged model updates may still leak sensitive information, making private aggregation a central building block in practical deployments, especially in the cross-silo setting. Homomorphic Encryption naturally fits the client--aggregator communication pattern of Federated Learning, but conventional single-key deployments rely on strong non-collusion assumptions. Multiparty Homomorphic Encryption removes this limitation, although recent attacks under restricted decryption access require large-variance smudging noise during collaborative decryption, which significantly increases ciphertext size and implementation complexity. In this work, we propose lightweight multi-secret-key protocols for private average aggregation based on RLWE-based Homomorphic Encryption. Our construction departs from the usual multiparty blueprint by avoiding the generation of a collective public key. Instead, each client encrypts its update under its own secret key, while the resulting ciphertexts remain compatible with homomorphic aggregation and collaborative decryption. By explicitly tracking and cancelling the ciphertext noise during decryption, the protocol removes the need for large $λ$-dependent smudging noise. We instantiate the construction with both exact BFV-based and approximate CKKS-based variants, prove its security in the semi-honest model against an adversary corrupting the aggregator and up to $L-1$ clients, and compare its communication and runtime performance with state-of-the-art MHE-based aggregation. Our results show that the proposed approach substantially reduces ciphertext expansion and online cost, while preserving practical homomorphic aggregation performance.

HEAT: Faster Fully Homomorphic Inference via Approximations-Weights Co-Adaptation

Fully homomorphic encryption (FHE) allows a server to run a language model directly on encrypted user prompts, but current approaches remain prohibitively slow. Ciphertexts natively support only addition, multiplication, and rotation, and multiplications may be composed only to a bounded depth before a costly bootstrapping operation is needed to continue. Every nonlinearity must therefore be approximated by an iterative method, and each iteration uses multiplications. A higher iteration count buys precision but exhausts the available depth faster and triggers more bootstraps, which dominate latency. Existing approaches fix the iteration counts uniformly across the model rather than tailoring them to each site's error tolerance. We introduce Homomorphic Encryption-Aware Training (HEAT), a fine-tuning method that makes the per-nonlinearity iteration counts learnable, enabling them and the model weights to co-adapt during training. HEAT optimizes iterations with respect to the task objective, allowing the model to adapt to approximation errors encountered during inference without architectural changes or retraining from scratch. On encrypted GPT-2 decoding, HEAT reduces iterations by $3.1\times$, bootstraps by $1.6\times$, and end-to-end latency by $1.4\times$, while improving decode agreement over the calibrated baseline.

SecureDrive-FL: Joint Differential Privacy and Gradient-Aware Selective Homomorphic Encryption for Federated Driver Monitoring

Federated Learning (FL) enables privacy-aware distributed training, yet gradient updates remain exploitable: Man-in-the-Middle (MitM) interception exposes updates in transit, while model poisoning corrupts global convergence. We first introduce GASHE (Gradient-Aware Selective Homomorphic Encryption), a novel selective encryption strategy that dynamically identifies and encrypts only the gradient components exceeding a DP-calibrated sensitivity threshold, rather than encrypting all parameters uniformly as in static layer-based or full-parameter CKKS schemes. Building on GASHE, we introduce SecureDrive-FL, a federated driver monitoring framework that couples DP-SGD with GASHE to create the first closed-loop DP+HE privacy pipeline: DP-SGD calibration parameters directly derive the GASHE encryption mask, unifying training-time privacy and communication-time confidentiality. Evaluated on a ten-class distracted driver classification task under non-IID federated splits, SecureDrive-FL matches DP-SGD alone's poisoning resistance (73.6% vs. 74.0% accuracy, 3.9% Attack Success Rate for both) while additionally withstanding MitM interception, where DP-SGD alone collapses to near-random accuracy (78.2% vs. 10.4%), all under only approx. 8--10% additional runtime overhead relative to DP-SGD alone---under DP-SGD noise injection with per-round privacy parameter epsilon_0=4.

GoldenRetriever: Non-Interactive Homomorphic Encrypted Retrieval for Privacy-Preserving RAG

Retrieval-Augmented Generation (RAG) enhances large language models by incorporating external knowledge, but existing pipelines typically operate on plaintext data, raising significant privacy concerns. Prior work on privacy-preserving retrieval leverages cryptographic techniques such as homomorphic encryption (HE) and private information retrieval (PIR), but often relies on interactive protocols or ranking-based selection mechanisms that incur high latency and potential information leakage. In this paper, we propose a practical non-interactive encrypted retrieval framework for RAG based on threshold selection. Instead of performing expensive top-$k$ ranking under encryption, our approach selects documents whose similarity scores exceed a predefined threshold, reducing computational complexity from quadratic to linear in the corpus size. We implement this design using CKKS-based homomorphic computation, enabling fully encrypted similarity evaluation and document selection without revealing query content, intermediate scores, or selected indices. To bridge the gap between approximate encrypted computation and discrete token reconstruction, we introduce a precision-stable mask polarization method that ensures accurate recovery of selected documents. Experiments on standard retrieval benchmarks demonstrate that our approach achieves competitive retrieval effectiveness while significantly reducing latency compared to ranking-based encrypted methods. These results highlight threshold-based selection as a practical foundation for scalable and secure RAG systems.

MOSAIC-FL, a micro-service based privacy-preserving framework with application to genomics

Security and privacy are primordial requirements for Federated Learning (FL), especially in fields such as healthcare and genomics where sensitive information has to be analyzed. Our FL framework is designed to address these challenges while proposing a modular, flexible and micro-service architecture. More precisely, it integrates an efficient gRPC communication layer and a Finite State Machine to ensure robust component synchronization and threat detection, while relying on a fault-tolerant secure aggregation protocol using a Threshold variant of the CKKS homomorphic cryptosystem. This allows blind model aggregation by an orchestration server, requiring a minimum of $t$-out-of-$N$ active clients for decryption while minimizing communication overhead thanks to both cryptographic and network protocols. We ensure IND-CPA-D security through noise flooding and mitigate the recent key-recovery attack on synchronized decryptors by renewing the collective key material at every round. We demonstrate the framework's effectiveness through diverse use cases, ranging from standard image recognition (EMNIST) to complex genomic classification including breast cancer subtyping on TCGA, evaluating system performance across different threshold values and model scales.

ATLAS: Automated Approximation of Transformers for Efficient Homomorphic Inference in One Hour

Fully homomorphic encryption (FHE) lets a server run inference on encrypted data with strong privacy guarantees, but running a Transformer under FHE is expensive. Its non-linear operations, such as softmax, normalization, and activation, must be replaced with polynomial approximations that the CKKS scheme supports, and the depth of these approximations dominates inference cost. Existing FHE Transformers use hand-tuned approximation settings, such as iteration count and polynomial degree, applied uniformly across layers, models, and tasks. Hand-tuning is slow and error-prone. Even a single uniform setting has about $10^7$ choices, and manual search cannot exploit layer-wise variation. AutoFHE, the only automated method with multi-objective search, targets ReLU-only CNNs and needs full fine-tuning per candidate, which is too costly for Transformers. Per-layer settings also push the search space to about $10^{85}$ for BERT and ViT and $10^{228}$ for LLaMA3, beyond both manual and fine-tuning-based search. We present ATLAS, a training-free framework that automates this search by treating each layer's approximation setting as a multi-objective optimization over latency and accuracy. The problem is hard: the decision space is large (96 or 256 variables), each configuration takes 70 to 1,000 seconds to evaluate even in cleartext, and 85 to 90 percent of configurations are invalid. ATLAS handles this with a two-stage optimization strategy and a surrogate model, completing the search in about one hour. Compared to an iterative softmax baseline, ATLAS cuts multiplicative depth and end-to-end latency by about 35 percent with little accuracy loss, and works across encoder-only, decoder-only, and vision Transformers, complementing parallel work on packing and matrix multiplication.

PRISM: Sensitivity-Aware PolynoMial PRuning for EffIcient Neural Network Encryption

Structured pruning is essential for making neural network inference feasible under homomorphic encryption (HE), yet its impact on model reliability has remained unexplored. This paper presents a systematic reliability characterization of pruned CKKS-encrypted neural networks and introduces Polynomial-Sensitivity-Aware Pruning (PSAP), a structured pruning method that is inherently reliability-aware. PSAP scores filters jointly by weight magnitude, polynomial activation sensitivity, and rotation cost, which concentrates pruning in fault-tolerant regions. Across two architectures, two datasets, two numerical representations, and five bit-error rates (40 full-model and 108 per-layer experiments), PSAP-pruned models limit catastrophic (>10 pp accuracy drop) layers to at most two versus 5--14 for magnitude-pruned baselines, reducing worst-case vulnerability by up to 29 times under int32 bit-flip injection. Direct CKKS encrypted fault injection indicates a safe operating boundary near BER~ 10^{-5}, supporting int32 injection as a conservative reliability proxy. The fault-critical structural layers account for only 1.1% of parameters, enabling selective hardening at minimal overhead. These reliability gains are obtained alongside competitive efficiency: PSAP reduces Halevi--Shoup rotations by up to 45.2\% on ResNet-32, and an adaptive mixed-degree allocation scheme lowers multiplicative depth from 66 to 56 levels, enabling leveled inference without bootstrapping.

Layer-Parallel Inference Reduces Encrypted Nonlinear Depth in Transformers

Fully homomorphic encryption (FHE) enables computation on encrypted data, but practical encrypted Transformer inference is bottlenecked by the sequential composition of many nonlinear blocks. We study whether Structured Newton Layer Parallelism (SNLP) can make this inter-layer composition more FHE-friendly: each Transformer block still requires polynomial approximations for operations such as softmax and RMSNorm, but SNLP reduces the layerwise sequential nonlinear depth from L stages to a small number of solver iterations plus linear structured corrections. Using a simulation framework based on Chebyshev polynomial approximations, we measure error accumulation under sequential versus SNLP inference across 8 models and 4 architecture families. On a 0.5B IDN-trained model, SNLP reduces symbolic bootstraps from 53 to 20 (2.65x) with only +1.2% perplexity degradation, while lowering error amplification (1.36x vs. 1.42x). Across all tested models, SNLP has lower amplification than sequential inference. Ablations show that softmax approximation dominates the error budget and CKKS arithmetic noise is negligible in our setting, suggesting that SNLP is complementary to block-level FHE-friendly operator design rather than a replacement for it.

Arbitrary Reduction of Validation Error for AI Decision Tests using Homomorphic AI and Repetition Codes

This paper presents new results and breakthrough obtained with the HbHAI techniques (Hash-based Homomorphic Artificial Intelligence) proposed in \cite{filiol0,sepp}. HbHAI is based on a novel class of key-dependent hash functions that naturally preserve most similarity properties, most AI algorithms rely on. It enables to analyse and process data in its cryptographically secure form while using existing native AI algorithms without modification, with unprecedented performances compared to existing homomorphic encryption schemes and most notably compared to the same processing on corresponding plaintext data. Two major results have been obtained further. First we enable to reduce the compression rate up to a factor of 10 thus allowing to process massive datasets while reducing the computation time and the energy footprint in the same order. Second, we show how it is possible to arbitrarily reduce the final validation error of AI-based decision tests by using repetition error-correcting codes.

TGHE: Template-based Graph Homomorphic Encryption for Privacy-Preserving GNN Inference in Edge-Cloud Systems

Existing homomorphic encryption (HE)-based GNN systems adopt a graph-centric paradigm that couples per-query cost to global graph size, limiting evaluations to at most ~20k nodes and making them incompatible with dynamic, large-scale financial graphs. We propose TGHE (Template-based Graph Homomorphic Encryption), an ego-centric framework that resolves this by exploiting a template phenomenon: local computation trees in transaction graphs converge into a small set of structural shapes. TGHE canonicalizes ego-graphs at the edge and packs structurally identical trees into shared CKKS ciphertexts for SIMD-parallel encrypted inference, with two long-tail optimizers (Approximate Template Fitting and Topology Collapse) ensuring full SIMD coverage. On DGraphFin (3.7M nodes, 4.3M edges), TGHE-Collapse achieves a 66.9x speedup over the sequential encrypted baseline with less than 0.002 AUC loss.

Hybrid privacy-aware semantic search: SVD-truncated document geometry and CKKS-encrypted query reranking under a restricted threat model

Semantic search creates an asymmetric disclosure problem: query embeddings may reveal user intent, while returning exact provider vectors distributes reusable representations. We evaluate a deliberately restricted hybrid design. A public corpus-fitted SVD basis and PQ index support client-side candidate selection; candidate IDs are disclosed, while the projected query is encrypted with CKKS. A block-SIMD kernel scores 100 plaintext provider vectors and returns one ciphertext. At 672 dimensions, median server time falls from 1689.1 to 224.5 ms and response size by a factor of 99.5; provider-only saturation reaches 25.99 requests/s with 16 workers. In a frozen post-exploratory revision-analysis subset, disjoint from validation and containing 3,235 canonical BEIR queries, five of six collections satisfy a +/-0.002 nDCG@10 equivalence rule between actual CKKS and plaintext reranking of the same shortlist, while ArguAna is inconclusive. Projection controls favor SVD over random and coordinate truncation. Leakage audits show that disclosed candidate sets are highly linkable and reproduce part of the exact neighbourhood, while public PQ reveals approximate corpus geometry. The design therefore conditionally hides numerical query slots, but does not provide semantic-query, document, unlinkability, circuit, or access-pattern privacy.

Homomorphic Encryptions for Privacy Preserving Vision

Legal requirements might prevent organizations from sharing sensitive data like medical or financial details of consumers which prevents them from leveraging cloud based ML-as-a-service solutions provided by third party providers, which are quickly gaining popularity these days. In this project, we aim to perform inference tasks in Computer Vision in a privacy-preserving manner, i.e, by only looking at encrypted data. Recent advances in fully homomorphic encryption make this possible. A fully homomorphic encryption allows an arbitrary sequence of additive and multiplicative operations to be performed on encrypted data directly. Applying homomorphic encryptions to CNNs requires modifying the conventional CNN layers, so that they adhere to the encryption scheme. Our aim was to explore the best methods to create CNNs which can classify encrypted images directly. We used Microsoft SEAL for performing homomorphic encryption. The performance of these "encryption based CNNs" should be comparable with baseline accuracies of the same CNNs trained on unencrypted data, and the aim was to achieve as low of a hit on inference-time performance as possible. We successfully obtained minimal drop in classification accuracy for various datasets. We used MNIST as our baseline, which is popularly used in related research work and then explored more complex datasets like Kuzushiji MNIST, Fashion-MNIST and CIFAR-10 as a part of our contribution. Additionally, we also added support for more complex operations on top of TenSEAL, like processing colored images (multi-channel input), applying multiple convolutional layers and performing average pooling.

Detecting and Understanding Vulnerabilities in Fully Homomorphic Encryption Frameworks

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.

FEnc$^2$: Unifying Data Packing for Efficient Private Inference via Convolution and Architecture-Aware Fragment Encoding

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.

Preserving Data Privacy in Learning Causal Structure with Fully Homomorphic Encryption

Preserving data privacy is an important topic in structural data management and data mining. However, the issue of privacy leakage in distributed causal structure learning is a persistent challenge, especially in cases where data transmission and computation are required. In this paper, we propose a method based on fully homomorphic encryption (FHE) that performs calculations on ciphertexts, keeping data encrypted in transition and computation. Nevertheless, adopting FHE to causal structure learning is challenging due to the high computation cost and limited support on division as well as logarithm operations in FHE. To tackle this challenge, we propose a series of novel techniques including (i) circuit simplification for better efficiency, (ii) approximation of division and logarithm through Newton-Raphson Reciprocal and Taylor expansion, and (iii) a batching technique with SIMD-acceleration to enhance the whole learning process. Additionally, our method can be easily extended beyond FHE by demonstration of its portability to support differential privacy. Empirical results show that our method achieves high consistency and comparable causal structure with the plaintext version in the datasets tested. Last, our method is efficient and practical to complete learning causal structures in tens of minutes even under the privacy protection of FHE.

Decision-Aware Quadratic ReLU Replacement for HE-Friendly Inference

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.

Privacy-Preserving Federated Learning via Differential Privacy and Homomorphic Encryption for Cardiovascular Disease Risk Modeling

Protecting sensitive health data while enabling collaborative analysis is a central challenge in healthcare. Traditional machine learning (ML) requires institutions to pool anonymized patient records, centralizing analytical development and privacy risks at a single site. Privacy-enhancing technologies (PETs), including Differential Privacy (DP) and Homomorphic Encryption (HE), can mitigate these risks. However, they are mainly studied in conventional data-sharing settings and often introduce trade-offs, including reduced model utility, higher computational cost, and increased implementation complexity. Federated Learning (FL) reduces data centralization by enabling institutions to train models locally and share only model updates. Nevertheless, FL does not eliminate privacy risks, as shared parameters or gradients may still reveal sensitive information. Integrating DP or HE into FL can strengthen privacy guarantees, yet their comparative performance and deployment implications in real-world healthcare settings remain unclear. We systematically evaluated DP and HE integration in FL under real-world conditions, comparing them with standard FL and centralized ML (cML) to quantify privacy-utility trade-offs in multi-institutional settings. Using nationwide Swedish healthcare data, we evaluated cardiovascular disease risk prediction using logistic regression (LR) and neural network (NN) learners. FL with HE achieved performance comparable to cML but introduced measurable cryptographic overhead, particularly in the NN implementation. FL with DP incurred lower computational cost; however, LR was more sensitive to calibrated noise than the NN, resulting in greater performance degradation. Our findings provide practical guidance for deploying privacy-preserving FL in fragmented healthcare systems.