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CipherPrune: Efficient and Scalable Private Transformer Inference
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Proposes CipherPrune, a private Transformer inference framework that progressively prunes tokens under encryption and assigns lower-degree polynomial approximations to less important tokens, cutting 2PC runtime by roughly 6.1x at 128 tokens and 10.6x at 512 tokens.
Problem
Private Transformer inference with cryptographic protocols (hybrid HE/MPC) has high latency and scales poorly with long token inputs, since attention cost grows quadratically with token count and high-degree polynomial non-linearities are expensive.
Approach
Input-adaptive, progressive token pruning computed on secret shares (importance scores from attention, comparison against learned thresholds, oblivious swaps to relocate pruned tokens), combined with encrypted polynomial reduction that uses low-degree polynomials for less important tokens, with thresholds learned jointly via a soft-mask gradient search that accounts for crypto cost.
Key results
- On BERT-Large, CipherPrune runs in 157.6 s vs 624.3 s for BOLT (about 3.9x faster) at 92.5% vs 92.4% accuracy.
- CipherPrune achieves about 6.1x speedup over BOLT for 128-token GPT2 inputs and about 10.6x at 512 tokens.
- Communication is reduced by 2.3 to 40.4x relative to prior works across BERT models.
Measured effects reported in the paper
| What was changed | Where | Measured | Effect |
|---|---|---|---|
| Use CipherPrune instead of BOLT | BERT Medium · BERT Medium | Time (s): 99.5 -> 43.6 | Helped |
| Use CipherPrune instead of BOLT | BERT Base · BERT Base | Time (s): 245.4 -> 79.1 | Helped |
| Use CipherPrune instead of BOLT | BERT Large · BERT Large | Time (s): 624.3 -> 157.6 | Helped |
| Use CipherPrune instead of BOLT | BERT models · BERT Medium, BERT Base, and BERT Large | Communication (GB): 14.3 -> 6.7; 25.7 -> 9.7; 67.9 -> 18.4 | Helped |
| Use CipherPrune instead of IRON | BERT models · BERT Medium, BERT Base, and BERT Large | Accuracy (%): 87.7±0.2 -> 87.4±0.2; 90.4±0.1 -> 90.1±0.2; 92.7±0.1 -> 92.5±0.1 | Hurt |
| Replace fixed 50% word elimination with adaptive, progressive token pruning (ablation) | CipherPrune† vs BOLT with W.E. · NLP tasks | Accuracy (%): +0.5% | Helped |
| Add progressive token pruning to adaptive token pruning (ablation) | CipherPrune† vs BOLT with W.E. · NLP tasks | Runtime speedup: 2.1× | Helped |
| Add polynomial reduction to token pruning (ablation) | CipherPrune · NLP tasks | Runtime speedup over BOLT: 6.1× | Helped |
| Add polynomial reduction to token pruning (ablation) | CipherPrune · NLP tasks | Accuracy | Hurt |
| Increase input length while using CipherPrune rather than BOLT without W.E. | GPT2 · 32 to 512 input tokens | Speedup: ~1.9× -> ~10.6× | Helped |
| Use a large α rather than a smaller α (ablation) | BERT-Base threshold settings · BERT-Base | Accuracy | Helped |
Limitations
- Pruning ratio and polynomial reduction thresholds require offline fine-tuning per model and task.
- Accuracy drops slightly with polynomial reduction compared to the pruning-only variant.
- Semi-honest threat model; the number of pruned tokens is revealed to both parties.
Experimental setup
Datasets: GLUE MNLI GLUE QNLI GLUE SST-2 GLUE MRPC
Benchmarks: GLUE MNLI GLUE QNLI GLUE SST-2 GLUE MRPC
Metrics: runtime (s) communication (GB) accuracy (%)
Baselines: IRON BOLT BOLT w/o W.E. BumbleBee MPCFormer PUMA
Builds on: BOLT IRON EzPC BFV
Closest papers by meaning
- Converting Transformers to Polynomial Form for Secure Inference Over Homomorphic Encryption (ICML 2024 · similarity 0.88)
- An Efficient Private GPT Never Autoregressively Decodes (ICML 2025 · similarity 0.87)
- Jaguar: Fast Private CNN Inference with Power-of-Two Homomorphic Arithmetic (NeurIPS 2026 · similarity 0.87)
- Nimbus: Secure and Efficient Two-Party Inference for Transformers (NeurIPS 2024 · similarity 0.87)
- United We Stand: Accelerating Privacy-Preserving Neural Inference by Conjunctive Optimization with Interleaved Nexus (AAAI 2024 · similarity 0.86)
- HEPrune: Fast Private Training of Deep Neural Networks With Encrypted Data Pruning (NeurIPS 2024 · similarity 0.86)
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