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CKKS Bootstrapping

When a ciphertext is created, it has a fixed multiplication count called a level. When two cipehrtexts are multiplied, the resulting ciphertext will have the level reduced by one compared to the input ciphertexts. A ciphertext with level 0 can no longer be multiplied. It is possible to reset this level to a higher value by the bootstrapping operation.

Regular Bootstrap

The Bootstrapping operation requires the bootstrap key. The bootstrap key incorporates every single fixed rotation key that is needed by the bootstrap operation. Because of this, the bootstrap key is quite large (about 12.3GB).

from desilofhe import Engine

engine = Engine(use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
bootstrap_key = engine.create_bootstrap_key(secret_key, stage_count=3)

message = [-1, 0, 1]
ciphertext = engine.encrypt(message, public_key, level=0)
bootstrapped = engine.bootstrap(
    ciphertext, relinearization_key, conjugation_key, bootstrap_key
)

Small Bootstrap Key

Alternatively, the bootstrapping operation can be performed using the rotation key and the small bootstrap key instead of the bootstrapping key. This approach reduces memory usage to around 3.8GB but makes the operation slower.

from desilofhe import Engine

engine = Engine(use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
rotation_key = engine.create_rotation_key(secret_key)
small_bootstrap_key = engine.create_small_bootstrap_key(secret_key)

message = [-1, 0, 1]
ciphertext = engine.encrypt(message, public_key, level=0)
bootstrapped = engine.bootstrap(
    ciphertext,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
)

bootstrapped_stage_count_5 = engine.bootstrap(
    ciphertext,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
    stage_count=5,
)

Benchmark

Here are the benchmarks of the bootstrapping operation. The experiments were performed on an Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz for the CPU measurements and an NVIDIA GeForce RTX 5090 for the GPU measurements. These values are the averages of 10 runs.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 103.576 43.935 31.667 2.422
Small 4 66.286 27.947 19.814 1.621
Small 5 66.098 26.751 18.845 1.499
Medium 3 30.534 12.784 9.860 0.723
Medium 4 25.265 10.231 7.871 0.585
Medium 5 23.741 9.676 7.231 0.550
Large 3 27.901 11.898 9.601 0.704
Large 4 24.348 10.211 8.158 0.612
Large 5 21.952 8.876 6.938 0.540

Bootstrap To 14 Levels

The original parameter set for bootstrapping leaves 10 levels after 3 stages. To overcome this, a new parameter set has been introduced to have 14 levels after the bootstrapping operation. Due to the limitations of the new parameter set, the only supported stage count is 3.

from desilofhe import Engine

engine = Engine(use_bootstrap_to_14_levels=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
bootstrap_key = engine.create_bootstrap_key(secret_key)

message = [-1, 0, 1]
ciphertext = engine.encrypt(message, public_key, level=0)
bootstrapped = engine.bootstrap(
    ciphertext, relinearization_key, conjugation_key, bootstrap_key
)

Small Bootstrap Key

The small boostrap key can also be used for this parameter set.

from desilofhe import Engine

engine = Engine(use_bootstrap_to_14_levels=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
rotation_key = engine.create_rotation_key(secret_key)
small_bootstrap_key = engine.create_small_bootstrap_key(secret_key)

message = [-1, 0, 1]
ciphertext = engine.encrypt(message, public_key, level=0)
bootstrapped = engine.bootstrap(
    ciphertext,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
)

Benchmark

Here are the benchmarks of the bootstrapping operation to 14 levels. The experiments were performed on an Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz for the CPU measurements and an NVIDIA GeForce RTX 5090 for the GPU measurements. These values are the averages of 10 runs.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 128.663 53.768 38.903 2.648
Medium 3 37.597 15.653 12.453 0.780
Large 3 33.732 14.571 11.857 0.761

Compact Representation

Here are the benchmarks of the bootstrapping operation to 14 levels using the compact representation. The experiments were performed on an Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz for the CPU measurements and an NVIDIA GeForce RTX 5090 for the GPU measurements. These values are the averages of 10 runs.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 96.820 41.575 29.676 2.440
Medium 3 29.001 12.017 9.370 0.696
Large 3 26.245 11.263 9.127 0.688

Sparse Bootstrap

The bootstrapping operation is faster with a reduced slot_count. The sparse bootstrapping operation can be done with either a bootstrap key or a small bootstrap key.

Bootstrap Key

from desilofhe import Engine

engine = Engine(slot_count=1024, use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
bootstrap_key = engine.create_bootstrap_key(secret_key, stage_count=3)

message = [-1, 0, 1, 0] * 256
ciphertext = engine.encrypt(message, public_key, level=0)
bootstrapped = engine.bootstrap(
    ciphertext, relinearization_key, conjugation_key, bootstrap_key
)

Small Bootstrap Key

from desilofhe import Engine

engine = Engine(slot_count=1024, use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
rotation_key = engine.create_rotation_key(secret_key)
small_bootstrap_key = engine.create_small_bootstrap_key(secret_key)

message = [-1, 0, 1, 0] * 256
ciphertext = engine.encrypt(message, public_key, level=0)
bootstrapped = engine.bootstrap(
    ciphertext,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
    stage_count=1,
)

Benchmark

Here are the benchmarks of the sparse bootstrapping operation. The experiments were performed on an Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz for the CPU measurements and an NVIDIA GeForce RTX 5090 for the GPU measurements. These values are the averages of 10 runs.

Slot
Count		 Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
32 Small 1 40.939 15.817 11.287 0.702
32 Small 2 30.597 12.426 8.820 0.565
32 Medium 1 27.247 10.853 8.025 0.529
32 Medium 2 25.596 10.118 7.346 0.488
32 Large 1 26.732 10.851 8.135 0.527
1024 Small 2 65.276 26.217 18.302 1.165
1024 Small 3 46.940 18.205 12.952 0.846
1024 Small 4 43.523 16.964 12.020 0.825
1024 Medium 2 28.699 11.951 9.054 0.632
1024 Medium 3 25.617 10.222 7.640 0.530
1024 Medium 4 23.844 9.620 7.126 0.512
1024 Large 2 27.579 11.412 8.985 0.616
1024 Large 3 24.704 10.051 7.687 0.532

Lossy Bootstap

The lossy bootstrap operation is faster while sacrificing some precision. The resulting significant figures below the decimal is about halved. In general, the regular bootstrapping is the recommended method, but depending on the precision requirements this method could also be useful. The lossy bootstrapping operation can be done with either a lossy bootstrap key or a small bootstrap key. The lossy bootstrapping operation is not supported for the bootstrap to 14 levels parameter set.

Lossy Bootstrap Key

from desilofhe import Engine

engine = Engine(use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
lossy_bootstrap_key = engine.create_lossy_bootstrap_key(
    secret_key, stage_count=3
)

message = [-1, 0, 1]
ciphertext = engine.encrypt(message, public_key, level=3)
bootstrapped = engine.lossy_bootstrap(
    ciphertext, relinearization_key, conjugation_key, lossy_bootstrap_key
)

Small Bootstrap Key

from desilofhe import Engine

engine = Engine(use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
rotation_key = engine.create_rotation_key(secret_key)
small_bootstrap_key = engine.create_small_bootstrap_key(secret_key)

message = [-1, 0, 1]
ciphertext_level_3 = engine.encrypt(message, public_key, level=3)
bootstrapped = engine.lossy_bootstrap(
    ciphertext_level_3,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
)

ciphertext_level_5 = engine.encrypt(message, public_key, level=5)
bootstrapped_stage_count_5 = engine.lossy_bootstrap(
    ciphertext_level_5,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
    stage_count=5,
)

Benchmark

Here are the benchmarks of the lossy bootstrapping operation. The experiments were performed on an Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz for the CPU measurements and an NVIDIA GeForce RTX 5090 for the GPU measurements. These values are the averages of 10 runs.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 80.174 34.116 24.705 2.140
Small 4 54.537 22.900 16.349 1.447
Small 5 56.380 22.884 16.296 1.326
Medium 3 24.450 10.145 7.756 0.589
Medium 4 20.422 8.408 6.419 0.494
Medium 5 20.545 8.087 6.080 0.459
Large 3 22.222 9.489 7.581 0.583
Large 4 19.739 8.429 6.676 0.509
Large 5 18.540 7.566 5.858 0.456

Lossy bootstrapping is optimized for ciphertexts that contain only real values.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 72.628 33.699 23.179 2.013
Small 4 47.709 20.558 14.787 1.315
Small 5 50.619 20.842 14.892 1.197
Medium 3 18.279 7.632 5.948 0.464
Medium 4 14.905 6.150 4.753 0.360
Medium 5 14.930 6.037 4.497 0.337
Large 3 16.323 7.056 5.789 0.451
Large 4 14.316 6.148 5.010 0.378
Large 5 13.081 5.385 4.270 0.326

Sign Bootstrap

The sign bootstrapping operation is a variant of the lossy bootstrap that enables bootstrapping of sign values, i.e., -1 and 1, with higher precision. Although this is applicable only to sign values, the resulting ciphertext achieves roughly three times more significant digits. By efficiently reducing the noise of sign values, this operation facilitates fast and high-precision comparison functions such as min and max. The sign bootstrapping can be performed with either a small bootstrap key or a lossy bootstrap key. The sign bootstrapping operation is not supported for the bootstrap to 14 levels parameter set.

Sign Bootstrap with Lossy Bootstrap Key

from desilofhe import Engine

engine = Engine(use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
lossy_bootstrap_key = engine.create_lossy_bootstrap_key(
    secret_key, stage_count=3
)

message = [-1, 1]
ciphertext = engine.encrypt(message, public_key, level=3)
bootstrapped = engine.sign_bootstrap(
    ciphertext, relinearization_key, conjugation_key, lossy_bootstrap_key
)

Small Bootstrap Key

from desilofhe import Engine

engine = Engine(use_bootstrap=True)
secret_key = engine.create_secret_key()
public_key = engine.create_public_key(secret_key)
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
rotation_key = engine.create_rotation_key(secret_key)
small_bootstrap_key = engine.create_small_bootstrap_key(secret_key)

message = [-1, 1]
ciphertext_level_3 = engine.encrypt(message, public_key, level=3)
bootstrapped = engine.sign_bootstrap(
    ciphertext_level_3,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
)

ciphertext_level_5 = engine.encrypt(message, public_key, level=5)
bootstrapped_stage_count_5 = engine.sign_bootstrap(
    ciphertext_level_5,
    relinearization_key,
    conjugation_key,
    rotation_key,
    small_bootstrap_key,
    stage_count=5,
)

Benchmark

Here are the benchmarks of the sign bootstrapping operation. The experiments were performed on an Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz for the CPU measurements and an NVIDIA GeForce RTX 5090 for the GPU measurements. These values are the averages of 10 runs.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 78.827 34.179 24.825 2.134
Small 4 53.524 22.790 16.341 1.431
Small 5 54.988 22.973 16.325 1.337
Medium 3 24.488 10.150 7.772 0.588
Medium 4 20.310 8.484 6.449 0.488
Medium 5 20.269 8.145 6.077 0.462
Large 3 22.412 9.531 7.602 0.594
Large 4 20.224 8.373 6.674 0.507
Large 5 18.211 7.500 5.847 0.448

Sign bootstrapping is optimized for ciphertexts that contain only real values.

Key
Size		 Stage
Count		 Runtime (s)
1 Thread
4 Threads
16 Threads
GPU
Small 3 72.748 33.052 23.141 2.010
Small 4 48.586 20.592 14.801 1.306
Small 5 50.297 20.894 14.933 1.201
Medium 3 18.325 7.711 5.962 0.463
Medium 4 14.911 6.117 4.740 0.359
Medium 5 14.930 5.947 4.500 0.334
Large 3 16.072 7.078 5.775 0.451
Large 4 14.303 6.160 4.998 0.380
Large 5 13.148 5.451 4.282 0.327

Comparison of Bootstrapping Error for Sign Messages

The following shows the average error observed when bootstrapping sign messages (i.e., -1 and 1) using the regular, lossy, and sign bootstrapping methods, respectively.

Regular
Bootstrap		 Lossy
Bootstrap		 Sign
Bootstrap
Average error 8.03008e-4 1.60562e-3 1.98124e-08
Precision 10.3 bits 9.3 bits 25.6 bits

Precision of Bootstrapping

The following represents the precision of the bootstrapping operation. It is the average of the bootstrapping error measured over messages uniformly distributed in the interval [-1, 1]. When evaluating the precision of the sign bootstrapping, we use only the sign values (i.e., -1 and 1).

Average error Precision
Bootstrap 6.72878e-07 20.5 bits
Bootstrap to 14 Levels 7.29874e-06 17.1 bits
Sparse Bootstrap 2.59681e-07 21.9 bits
Lossy Bootstrap 4.01552e-4 11.3 bits
Sign Bootstrap 1.98124e-08 25.6 bits

The errors were measured with the following code.

Bootstrap 
import numpy as np
from desilofhe import Engine

engine = Engine(use_bootstrap=True)

secret_key = engine.create_secret_key()
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
bootstrap_key = engine.create_bootstrap_key(secret_key)

message = np.linspace(-1, 1, engine.slot_count)

ciphertext = engine.encrypt(message, secret_key)
bootstrapped = engine.bootstrap(
    ciphertext, relinearization_key, conjugation_key, bootstrap_key
)
decrypted = engine.decrypt(bootstrapped, secret_key)

average_noise = np.mean(abs(message - decrypted))
print(f"Bootstrap Average Noise :{average_noise}")
print(f"Bootstrap Average Noise (Bits) :{np.log2(average_noise)}")
Bootstrap to 14 Levels 
import numpy as np
from desilofhe import Engine

engine = Engine(use_bootstrap_to_14_levels=True)

secret_key = engine.create_secret_key()
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
bootstrap_key = engine.create_bootstrap_key(secret_key)

message = np.linspace(-1, 1, engine.slot_count)

ciphertext = engine.encrypt(message, secret_key)
bootstrapped = engine.bootstrap(
    ciphertext, relinearization_key, conjugation_key, bootstrap_key
)
decrypted = engine.decrypt(bootstrapped, secret_key)

average_noise = np.mean(abs(message - decrypted))
print(f"BootstrapTo14Levels Average Noise :{average_noise}")
print(f"BootstrapTo14Levels Average Noise (Bits) :{np.log2(average_noise)}")
Sparse Bootstrap 
import numpy as np
from desilofhe import Engine

engine = Engine(slot_count=1024, use_bootstrap=True)

secret_key = engine.create_secret_key()
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
bootstrap_key = engine.create_bootstrap_key(secret_key)

message = np.linspace(-1, 1, engine.slot_count)

ciphertext = engine.encrypt(message, secret_key)
bootstrapped = engine.bootstrap(
    ciphertext, relinearization_key, conjugation_key, bootstrap_key
)
decrypted = engine.decrypt(bootstrapped, secret_key)

average_noise = np.mean(abs(message - decrypted))
print(f"SparseBootstrap Average Noise :{average_noise}")
print(f"SparseBootstrap Average Noise (Bits) :{np.log2(average_noise)}")
Lossy Bootstrap 
import numpy as np
from desilofhe import Engine

engine = Engine(use_bootstrap=True)

secret_key = engine.create_secret_key()
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
lossy_bootstrap_key = engine.create_lossy_bootstrap_key(secret_key)

message = np.linspace(-1, 1, engine.slot_count)

ciphertext = engine.encrypt(message, secret_key)
bootstrapped = engine.lossy_bootstrap(
    ciphertext, relinearization_key, conjugation_key, lossy_bootstrap_key
)
decrypted = engine.decrypt(bootstrapped, secret_key)

average_noise = np.mean(abs(message - decrypted))
print(f"Lossy Bootstrap Average Noise :{average_noise}")
print(f"Lossy Bootstrap Average Noise (Bits) :{np.log2(average_noise)}")
Sign Bootstrap 
import numpy as np
from desilofhe import Engine

engine = Engine(use_bootstrap=True)

secret_key = engine.create_secret_key()
relinearization_key = engine.create_relinearization_key(secret_key)
conjugation_key = engine.create_conjugation_key(secret_key)
lossy_bootstrap_key = engine.create_lossy_bootstrap_key(secret_key)

message = [-1, 1] * (engine.slot_count // 2)

ciphertext = engine.encrypt(message, secret_key)
bootstrapped = engine.sign_bootstrap(
    ciphertext, relinearization_key, conjugation_key, lossy_bootstrap_key
)
decrypted = engine.decrypt(bootstrapped, secret_key)

average_noise = np.mean(abs(message - decrypted))
print(f"Sign Bootstrap Average Noise :{average_noise}")
print(f"Sign Bootstrap Average Noise (Bits) :{np.log2(average_noise)}")