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HEPrune: Fast Private Training of Deep Neural Networks With Encrypted Data Pruning
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Proposes HEPrune, an FHE-based encrypted data pruning framework for private DNN/MLP training, using an HE-friendly score, client-aided masking, and ciphertext-wise pruning to speed up encrypted training.
Problem
FHE-based private training of neural networks is very slow because every encrypted sample must go through repeated forward and backward passes; existing plaintext data pruning methods need costly non-linear and sorting operations under encryption and leave sparse ciphertexts.
Approach
Computes an FHE-friendly importance score (L1 error between prediction and label, via two subtractions and a max), offloads threshold selection to the client via client-aided masking to avoid homomorphic sorting, and merges sparse ciphertexts (ciphertext-wise pruning) so pruning actually removes ciphertexts.
Key results
- Pruning ratio 0.9 gives about 6.6x end-to-end speedup across five datasets with accuracy drop as small as 0.25% on Face Mask Detection; on CIFAR-10 the full pipeline reaches 6.55x speedup with 96.31% vs 96.57% accuracy for HETAL.
- On CIFAR-10 with 1% of data, the paper reports roughly 16x speedup with about 0.6% accuracy drop.
- Training from scratch on MNIST with a 3-layer MLP at 1% data gives 60.8x speedup but a 5.26% accuracy drop; 40-50% data matches or slightly exceeds full-data accuracy.
Measured effects reported in the paper
| What was changed | Where | Measured | Effect |
|---|---|---|---|
| Apply encrypted data pruning at p = 0.9 | HEPrune · MNIST | runtime (h): 276.75 -> 41.89 | Helped |
| Apply encrypted data pruning at p = 0.9 | HEPrune · CIFAR-10 | accuracy (%): 96.57±0.04 -> 96.31±0.06 | Hurt |
| Apply encrypted data pruning at p = 0.9 | HEPrune · CIFAR-10 | runtime (h): 293.3 -> 44.76 | Helped |
| Use naïve encrypted data pruning | HETAL on CIFAR-10 · CIFAR-10 | runtime (h): 293.3 -> 488.91 | Hurt |
| Add client-aided masking (ablation) | Prune Baseline on CIFAR-10 · CIFAR-10 | runtime (h): 488.91 -> 196.91 | Helped |
| Add HE-friendly score (ablation) | Client Aided on CIFAR-10 · CIFAR-10 | runtime (h): 196.91 -> 105.57 | Helped |
| Add HE-friendly score (ablation) | Client Aided on CIFAR-10 · CIFAR-10 | accuracy (%): 96.16±0.07 -> 96.31±0.06 | Helped |
| Add ciphertext-wise pruning (ablation) | HEFS on CIFAR-10 · CIFAR-10 | runtime (h): 105.57 -> 44.76 | Helped |
| Train with 1% of the data rather than the full dataset (ablation) | HEPrune · CIFAR-10 | accuracy drop (%): around 0.6% | Hurt |
| Train with 40% of the data rather than the full dataset (ablation) | HEPrune · CIFAR-10 | accuracy: without any loss of accuracy | No clear effect |
| Train with 1% of the data rather than the full dataset (ablation) | HEPrune, MLP from scratch · MNIST | accuracy (%): -5.26 | Hurt |
| Train with 40% of the data rather than the full dataset (ablation) | HEPrune, MLP from scratch · MNIST | accuracy (%): +0.03 | Helped |
Surprising findings
- Training on 40%-70% of CIFAR-10 yields slightly higher accuracy than full data.
- Naive plaintext pruning (prune baseline) increases total training time to 488.91 h versus 293.3 h for full-data HETAL.
Limitations
- Only simple MLP models were evaluated; CNNs and Transformers not covered.
- Experiments limited to relatively small datasets.
- Client participation is required for the masking step (client-aided), and meta-information like importance scores is sent to the client.
Experimental setup
Datasets: MNIST CIFAR-10 Face Mask Detection DermaMNIST SNIPS
Benchmarks: MNIST CIFAR-10 Face Mask Detection DermaMNIST SNIPS
Metrics: test accuracy end-to-end runtime (h) speedup
Baselines: HETAL Unencrypted training Prune Baseline FHESGD
Builds on: EL2N HETAL FHESGD CKKS dynamic data pruning
Closest papers by meaning
- CipherPrune: Efficient and Scalable Private Transformer Inference (ICLR 2025 · similarity 0.86)
- PrivCirNet: Efficient Private Inference via Block Circulant Transformation (NeurIPS 2024 · similarity 0.84)
- EncryptedLLM: Privacy-Preserving Large Language Model Inference via GPU-Accelerated Fully Homomorphic Encryption (ICML 2025 · similarity 0.83)
- FicGCN: Unveiling the Homomorphic Encryption Efficiency from Irregular Graph Convolutional Networks (ICML 2025 · similarity 0.83)
- Encryption-Friendly LLM Architecture (ICLR 2025 · similarity 0.83)
- DCT-CryptoNets: Scaling Private Inference in the Frequency Domain (ICLR 2025 · similarity 0.83)
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