1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358
|
#------------------------------------------------------------------------------
# cython: cdivision=True
# cython: boundscheck=False
# cython: wraparound=False
#
# Authors: Danny Sullivan <dbsullivan23@gmail.com>
# Tom Dupre la Tour <tom.dupre-la-tour@m4x.org>
# Arthur Mensch <arthur.mensch@m4x.org
#
# License: BSD 3 clause
"""
SAG and SAGA implementation
WARNING: Do not edit .pyx file directly, it is generated from .pyx.tp
"""
cimport numpy as np
import numpy as np
from libc.math cimport fabs, exp, log
from libc.time cimport time, time_t
from ._sgd_fast cimport LossFunction
from ._sgd_fast cimport Log, SquaredLoss
from ..utils._seq_dataset cimport SequentialDataset32, SequentialDataset64
from libc.stdio cimport printf
np.import_array()
cdef extern from "_sgd_fast_helpers.h":
bint skl_isfinite64(double) nogil
cdef extern from "_sgd_fast_helpers.h":
bint skl_isfinite32(float) nogil
cdef inline double fmax64(double x, double y) nogil:
if x > y:
return x
return y
cdef inline float fmax32(float x, float y) nogil:
if x > y:
return x
return y
cdef double _logsumexp64(double* arr, int n_classes) nogil:
"""Computes the sum of arr assuming arr is in the log domain.
Returns log(sum(exp(arr))) while minimizing the possibility of
over/underflow.
"""
# Use the max to normalize, as with the log this is what accumulates
# the less errors
cdef double vmax = arr[0]
cdef double out = 0.0
cdef int i
for i in range(1, n_classes):
if vmax < arr[i]:
vmax = arr[i]
for i in range(n_classes):
out += exp(arr[i] - vmax)
return log(out) + vmax
cdef float _logsumexp32(float* arr, int n_classes) nogil:
"""Computes the sum of arr assuming arr is in the log domain.
Returns log(sum(exp(arr))) while minimizing the possibility of
over/underflow.
"""
# Use the max to normalize, as with the log this is what accumulates
# the less errors
cdef float vmax = arr[0]
cdef float out = 0.0
cdef int i
for i in range(1, n_classes):
if vmax < arr[i]:
vmax = arr[i]
for i in range(n_classes):
out += exp(arr[i] - vmax)
return log(out) + vmax
cdef class MultinomialLogLoss64:
cdef double _loss(self, double* prediction, double y, int n_classes,
double sample_weight) nogil:
r"""Multinomial Logistic regression loss.
The multinomial logistic loss for one sample is:
loss = - sw \sum_c \delta_{y,c} (prediction[c] - logsumexp(prediction))
= sw (logsumexp(prediction) - prediction[y])
where:
prediction = dot(x_sample, weights) + intercept
\delta_{y,c} = 1 if (y == c) else 0
sw = sample_weight
Parameters
----------
prediction : pointer to a np.ndarray[double] of shape (n_classes,)
Prediction of the multinomial classifier, for current sample.
y : double, between 0 and n_classes - 1
Indice of the correct class for current sample (i.e. label encoded).
n_classes : integer
Total number of classes.
sample_weight : double
Weight of current sample.
Returns
-------
loss : double
Multinomial loss for current sample.
Reference
---------
Bishop, C. M. (2006). Pattern recognition and machine learning.
Springer. (Chapter 4.3.4)
"""
cdef double logsumexp_prediction = _logsumexp64(prediction, n_classes)
cdef double loss
# y is the indice of the correct class of current sample.
loss = (logsumexp_prediction - prediction[int(y)]) * sample_weight
return loss
cdef void _dloss(self, double* prediction, double y, int n_classes,
double sample_weight, double* gradient_ptr) nogil:
r"""Multinomial Logistic regression gradient of the loss.
The gradient of the multinomial logistic loss with respect to a class c,
and for one sample is:
grad_c = - sw * (p[c] - \delta_{y,c})
where:
p[c] = exp(logsumexp(prediction) - prediction[c])
prediction = dot(sample, weights) + intercept
\delta_{y,c} = 1 if (y == c) else 0
sw = sample_weight
Note that to obtain the true gradient, this value has to be multiplied
by the sample vector x.
Parameters
----------
prediction : pointer to a np.ndarray[double] of shape (n_classes,)
Prediction of the multinomial classifier, for current sample.
y : double, between 0 and n_classes - 1
Indice of the correct class for current sample (i.e. label encoded)
n_classes : integer
Total number of classes.
sample_weight : double
Weight of current sample.
gradient_ptr : pointer to a np.ndarray[double] of shape (n_classes,)
Gradient vector to be filled.
Reference
---------
Bishop, C. M. (2006). Pattern recognition and machine learning.
Springer. (Chapter 4.3.4)
"""
cdef double logsumexp_prediction = _logsumexp64(prediction, n_classes)
cdef int class_ind
for class_ind in range(n_classes):
gradient_ptr[class_ind] = exp(prediction[class_ind] -
logsumexp_prediction)
# y is the indice of the correct class of current sample.
if class_ind == y:
gradient_ptr[class_ind] -= 1.0
gradient_ptr[class_ind] *= sample_weight
def __reduce__(self):
return MultinomialLogLoss64, ()
cdef class MultinomialLogLoss32:
cdef float _loss(self, float* prediction, float y, int n_classes,
float sample_weight) nogil:
r"""Multinomial Logistic regression loss.
The multinomial logistic loss for one sample is:
loss = - sw \sum_c \delta_{y,c} (prediction[c] - logsumexp(prediction))
= sw (logsumexp(prediction) - prediction[y])
where:
prediction = dot(x_sample, weights) + intercept
\delta_{y,c} = 1 if (y == c) else 0
sw = sample_weight
Parameters
----------
prediction : pointer to a np.ndarray[float] of shape (n_classes,)
Prediction of the multinomial classifier, for current sample.
y : float, between 0 and n_classes - 1
Indice of the correct class for current sample (i.e. label encoded).
n_classes : integer
Total number of classes.
sample_weight : float
Weight of current sample.
Returns
-------
loss : float
Multinomial loss for current sample.
Reference
---------
Bishop, C. M. (2006). Pattern recognition and machine learning.
Springer. (Chapter 4.3.4)
"""
cdef float logsumexp_prediction = _logsumexp32(prediction, n_classes)
cdef float loss
# y is the indice of the correct class of current sample.
loss = (logsumexp_prediction - prediction[int(y)]) * sample_weight
return loss
cdef void _dloss(self, float* prediction, float y, int n_classes,
float sample_weight, float* gradient_ptr) nogil:
r"""Multinomial Logistic regression gradient of the loss.
The gradient of the multinomial logistic loss with respect to a class c,
and for one sample is:
grad_c = - sw * (p[c] - \delta_{y,c})
where:
p[c] = exp(logsumexp(prediction) - prediction[c])
prediction = dot(sample, weights) + intercept
\delta_{y,c} = 1 if (y == c) else 0
sw = sample_weight
Note that to obtain the true gradient, this value has to be multiplied
by the sample vector x.
Parameters
----------
prediction : pointer to a np.ndarray[float] of shape (n_classes,)
Prediction of the multinomial classifier, for current sample.
y : float, between 0 and n_classes - 1
Indice of the correct class for current sample (i.e. label encoded)
n_classes : integer
Total number of classes.
sample_weight : float
Weight of current sample.
gradient_ptr : pointer to a np.ndarray[float] of shape (n_classes,)
Gradient vector to be filled.
Reference
---------
Bishop, C. M. (2006). Pattern recognition and machine learning.
Springer. (Chapter 4.3.4)
"""
cdef float logsumexp_prediction = _logsumexp32(prediction, n_classes)
cdef int class_ind
for class_ind in range(n_classes):
gradient_ptr[class_ind] = exp(prediction[class_ind] -
logsumexp_prediction)
# y is the indice of the correct class of current sample.
if class_ind == y:
gradient_ptr[class_ind] -= 1.0
gradient_ptr[class_ind] *= sample_weight
def __reduce__(self):
return MultinomialLogLoss32, ()
cdef inline double _soft_thresholding64(double x, double shrinkage) nogil:
return fmax64(x - shrinkage, 0) - fmax64(- x - shrinkage, 0)
cdef inline float _soft_thresholding32(float x, float shrinkage) nogil:
return fmax32(x - shrinkage, 0) - fmax32(- x - shrinkage, 0)
def sag64(SequentialDataset64 dataset,
np.ndarray[double, ndim=2, mode='c'] weights_array,
np.ndarray[double, ndim=1, mode='c'] intercept_array,
int n_samples,
int n_features,
int n_classes,
double tol,
int max_iter,
str loss_function,
double step_size,
double alpha,
double beta,
np.ndarray[double, ndim=2, mode='c'] sum_gradient_init,
np.ndarray[double, ndim=2, mode='c'] gradient_memory_init,
np.ndarray[bint, ndim=1, mode='c'] seen_init,
int num_seen,
bint fit_intercept,
np.ndarray[double, ndim=1, mode='c'] intercept_sum_gradient_init,
double intercept_decay,
bint saga,
bint verbose):
"""Stochastic Average Gradient (SAG) and SAGA solvers.
Used in Ridge and LogisticRegression.
Reference
---------
Schmidt, M., Roux, N. L., & Bach, F. (2013).
Minimizing finite sums with the stochastic average gradient
https://hal.inria.fr/hal-00860051/document
(section 4.3)
Defazio, A., Bach, F., Lacoste-Julien, S. (2014),
SAGA: A Fast Incremental Gradient Method With Support
for Non-Strongly Convex Composite Objectives
https://arxiv.org/abs/1407.0202
"""
# the data pointer for x, the current sample
cdef double *x_data_ptr = NULL
# the index pointer for the column of the data
cdef int *x_ind_ptr = NULL
# the number of non-zero features for current sample
cdef int xnnz = -1
# the label value for current sample
# the label value for curent sample
cdef double y
# the sample weight
cdef double sample_weight
# helper variable for indexes
cdef int f_idx, s_idx, feature_ind, class_ind, j
# the number of pass through all samples
cdef int n_iter = 0
# helper to track iterations through samples
cdef int sample_itr
# the index (row number) of the current sample
cdef int sample_ind
# the maximum change in weights, used to compute stopping criteria
cdef double max_change
# a holder variable for the max weight, used to compute stopping criteria
cdef double max_weight
# the start time of the fit
cdef time_t start_time
# the end time of the fit
cdef time_t end_time
# precomputation since the step size does not change in this implementation
cdef double wscale_update = 1.0 - step_size * alpha
# vector of booleans indicating whether this sample has been seen
cdef bint* seen = <bint*> seen_init.data
# helper for cumulative sum
cdef double cum_sum
# the pointer to the coef_ or weights
cdef double* weights = <double * >weights_array.data
# the pointer to the intercept_array
cdef double* intercept = <double * >intercept_array.data
# the pointer to the intercept_sum_gradient
cdef double* intercept_sum_gradient = \
<double * >intercept_sum_gradient_init.data
# the sum of gradients for each feature
cdef double* sum_gradient = <double*> sum_gradient_init.data
# the previously seen gradient for each sample
cdef double* gradient_memory = <double*> gradient_memory_init.data
# the cumulative sums needed for JIT params
cdef np.ndarray[double, ndim=1] cumulative_sums_array = \
np.empty(n_samples, dtype=np.float64, order="c")
cdef double* cumulative_sums = <double*> cumulative_sums_array.data
# the index for the last time this feature was updated
cdef np.ndarray[int, ndim=1] feature_hist_array = \
np.zeros(n_features, dtype=np.int32, order="c")
cdef int* feature_hist = <int*> feature_hist_array.data
# the previous weights to use to compute stopping criteria
cdef np.ndarray[double, ndim=2] previous_weights_array = \
np.zeros((n_features, n_classes), dtype=np.float64, order="c")
cdef double* previous_weights = <double*> previous_weights_array.data
cdef np.ndarray[double, ndim=1] prediction_array = \
np.zeros(n_classes, dtype=np.float64, order="c")
cdef double* prediction = <double*> prediction_array.data
cdef np.ndarray[double, ndim=1] gradient_array = \
np.zeros(n_classes, dtype=np.float64, order="c")
cdef double* gradient = <double*> gradient_array.data
# Intermediate variable that need declaration since cython cannot infer when templating
cdef double val
# Bias correction term in saga
cdef double gradient_correction
# the scalar used for multiplying z
cdef double wscale = 1.0
# return value (-1 if an error occurred, 0 otherwise)
cdef int status = 0
# the cumulative sums for each iteration for the sparse implementation
cumulative_sums[0] = 0.0
# the multipliative scale needed for JIT params
cdef np.ndarray[double, ndim=1] cumulative_sums_prox_array
cdef double* cumulative_sums_prox
cdef bint prox = beta > 0 and saga
# Loss function to optimize
cdef LossFunction loss
# Wether the loss function is multinomial
cdef bint multinomial = False
# Multinomial loss function
cdef MultinomialLogLoss64 multiloss
if loss_function == "multinomial":
multinomial = True
multiloss = MultinomialLogLoss64()
elif loss_function == "log":
loss = Log()
elif loss_function == "squared":
loss = SquaredLoss()
else:
raise ValueError("Invalid loss parameter: got %s instead of "
"one of ('log', 'squared', 'multinomial')"
% loss_function)
if prox:
cumulative_sums_prox_array = np.empty(n_samples,
dtype=np.float64, order="c")
cumulative_sums_prox = <double*> cumulative_sums_prox_array.data
else:
cumulative_sums_prox = NULL
with nogil:
start_time = time(NULL)
for n_iter in range(max_iter):
for sample_itr in range(n_samples):
# extract a random sample
sample_ind = dataset.random(&x_data_ptr, &x_ind_ptr, &xnnz,
&y, &sample_weight)
# cached index for gradient_memory
s_idx = sample_ind * n_classes
# update the number of samples seen and the seen array
if seen[sample_ind] == 0:
num_seen += 1
seen[sample_ind] = 1
# make the weight updates
if sample_itr > 0:
status = lagged_update64(weights, wscale, xnnz,
n_samples, n_classes,
sample_itr,
cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox,
sum_gradient,
x_ind_ptr,
False,
n_iter)
if status == -1:
break
# find the current prediction
predict_sample64(x_data_ptr, x_ind_ptr, xnnz, weights, wscale,
intercept, prediction, n_classes)
# compute the gradient for this sample, given the prediction
if multinomial:
multiloss._dloss(prediction, y, n_classes, sample_weight,
gradient)
else:
gradient[0] = loss._dloss(prediction[0], y) * sample_weight
# L2 regularization by simply rescaling the weights
wscale *= wscale_update
# make the updates to the sum of gradients
for j in range(xnnz):
feature_ind = x_ind_ptr[j]
val = x_data_ptr[j]
f_idx = feature_ind * n_classes
for class_ind in range(n_classes):
gradient_correction = \
val * (gradient[class_ind] -
gradient_memory[s_idx + class_ind])
if saga:
weights[f_idx + class_ind] -= \
(gradient_correction * step_size
* (1 - 1. / num_seen) / wscale)
sum_gradient[f_idx + class_ind] += gradient_correction
# fit the intercept
if fit_intercept:
for class_ind in range(n_classes):
gradient_correction = (gradient[class_ind] -
gradient_memory[s_idx + class_ind])
intercept_sum_gradient[class_ind] += gradient_correction
gradient_correction *= step_size * (1. - 1. / num_seen)
if saga:
intercept[class_ind] -= \
(step_size * intercept_sum_gradient[class_ind] /
num_seen * intercept_decay) + gradient_correction
else:
intercept[class_ind] -= \
(step_size * intercept_sum_gradient[class_ind] /
num_seen * intercept_decay)
# check to see that the intercept is not inf or NaN
if not skl_isfinite64(intercept[class_ind]):
status = -1
break
# Break from the n_samples outer loop if an error happened
# in the fit_intercept n_classes inner loop
if status == -1:
break
# update the gradient memory for this sample
for class_ind in range(n_classes):
gradient_memory[s_idx + class_ind] = gradient[class_ind]
if sample_itr == 0:
cumulative_sums[0] = step_size / (wscale * num_seen)
if prox:
cumulative_sums_prox[0] = step_size * beta / wscale
else:
cumulative_sums[sample_itr] = \
(cumulative_sums[sample_itr - 1] +
step_size / (wscale * num_seen))
if prox:
cumulative_sums_prox[sample_itr] = \
(cumulative_sums_prox[sample_itr - 1] +
step_size * beta / wscale)
# If wscale gets too small, we need to reset the scale.
if wscale < 1e-9:
if verbose:
with gil:
print("rescaling...")
status = scale_weights64(
weights, &wscale, n_features, n_samples, n_classes,
sample_itr, cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox, sum_gradient, n_iter)
if status == -1:
break
# Break from the n_iter outer loop if an error happened in the
# n_samples inner loop
if status == -1:
break
# we scale the weights every n_samples iterations and reset the
# just-in-time update system for numerical stability.
status = scale_weights64(weights, &wscale, n_features,
n_samples,
n_classes, n_samples - 1,
cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox, sum_gradient, n_iter)
if status == -1:
break
# check if the stopping criteria is reached
max_change = 0.0
max_weight = 0.0
for idx in range(n_features * n_classes):
max_weight = fmax64(max_weight, fabs(weights[idx]))
max_change = fmax64(max_change,
fabs(weights[idx] -
previous_weights[idx]))
previous_weights[idx] = weights[idx]
if ((max_weight != 0 and max_change / max_weight <= tol)
or max_weight == 0 and max_change == 0):
if verbose:
end_time = time(NULL)
with gil:
print("convergence after %d epochs took %d seconds" %
(n_iter + 1, end_time - start_time))
break
elif verbose:
printf('Epoch %d, change: %.8f\n', n_iter + 1,
max_change / max_weight)
n_iter += 1
# We do the error treatment here based on error code in status to avoid
# re-acquiring the GIL within the cython code, which slows the computation
# when the sag/saga solver is used concurrently in multiple Python threads.
if status == -1:
raise ValueError(("Floating-point under-/overflow occurred at epoch"
" #%d. Scaling input data with StandardScaler or"
" MinMaxScaler might help.") % n_iter)
if verbose and n_iter >= max_iter:
end_time = time(NULL)
print(("max_iter reached after %d seconds") %
(end_time - start_time))
return num_seen, n_iter
def sag32(SequentialDataset32 dataset,
np.ndarray[float, ndim=2, mode='c'] weights_array,
np.ndarray[float, ndim=1, mode='c'] intercept_array,
int n_samples,
int n_features,
int n_classes,
double tol,
int max_iter,
str loss_function,
double step_size,
double alpha,
double beta,
np.ndarray[float, ndim=2, mode='c'] sum_gradient_init,
np.ndarray[float, ndim=2, mode='c'] gradient_memory_init,
np.ndarray[bint, ndim=1, mode='c'] seen_init,
int num_seen,
bint fit_intercept,
np.ndarray[float, ndim=1, mode='c'] intercept_sum_gradient_init,
double intercept_decay,
bint saga,
bint verbose):
"""Stochastic Average Gradient (SAG) and SAGA solvers.
Used in Ridge and LogisticRegression.
Reference
---------
Schmidt, M., Roux, N. L., & Bach, F. (2013).
Minimizing finite sums with the stochastic average gradient
https://hal.inria.fr/hal-00860051/document
(section 4.3)
Defazio, A., Bach, F., Lacoste-Julien, S. (2014),
SAGA: A Fast Incremental Gradient Method With Support
for Non-Strongly Convex Composite Objectives
https://arxiv.org/abs/1407.0202
"""
# the data pointer for x, the current sample
cdef float *x_data_ptr = NULL
# the index pointer for the column of the data
cdef int *x_ind_ptr = NULL
# the number of non-zero features for current sample
cdef int xnnz = -1
# the label value for current sample
# the label value for curent sample
cdef float y
# the sample weight
cdef float sample_weight
# helper variable for indexes
cdef int f_idx, s_idx, feature_ind, class_ind, j
# the number of pass through all samples
cdef int n_iter = 0
# helper to track iterations through samples
cdef int sample_itr
# the index (row number) of the current sample
cdef int sample_ind
# the maximum change in weights, used to compute stopping criteria
cdef float max_change
# a holder variable for the max weight, used to compute stopping criteria
cdef float max_weight
# the start time of the fit
cdef time_t start_time
# the end time of the fit
cdef time_t end_time
# precomputation since the step size does not change in this implementation
cdef float wscale_update = 1.0 - step_size * alpha
# vector of booleans indicating whether this sample has been seen
cdef bint* seen = <bint*> seen_init.data
# helper for cumulative sum
cdef float cum_sum
# the pointer to the coef_ or weights
cdef float* weights = <float * >weights_array.data
# the pointer to the intercept_array
cdef float* intercept = <float * >intercept_array.data
# the pointer to the intercept_sum_gradient
cdef float* intercept_sum_gradient = \
<float * >intercept_sum_gradient_init.data
# the sum of gradients for each feature
cdef float* sum_gradient = <float*> sum_gradient_init.data
# the previously seen gradient for each sample
cdef float* gradient_memory = <float*> gradient_memory_init.data
# the cumulative sums needed for JIT params
cdef np.ndarray[float, ndim=1] cumulative_sums_array = \
np.empty(n_samples, dtype=np.float32, order="c")
cdef float* cumulative_sums = <float*> cumulative_sums_array.data
# the index for the last time this feature was updated
cdef np.ndarray[int, ndim=1] feature_hist_array = \
np.zeros(n_features, dtype=np.int32, order="c")
cdef int* feature_hist = <int*> feature_hist_array.data
# the previous weights to use to compute stopping criteria
cdef np.ndarray[float, ndim=2] previous_weights_array = \
np.zeros((n_features, n_classes), dtype=np.float32, order="c")
cdef float* previous_weights = <float*> previous_weights_array.data
cdef np.ndarray[float, ndim=1] prediction_array = \
np.zeros(n_classes, dtype=np.float32, order="c")
cdef float* prediction = <float*> prediction_array.data
cdef np.ndarray[float, ndim=1] gradient_array = \
np.zeros(n_classes, dtype=np.float32, order="c")
cdef float* gradient = <float*> gradient_array.data
# Intermediate variable that need declaration since cython cannot infer when templating
cdef float val
# Bias correction term in saga
cdef float gradient_correction
# the scalar used for multiplying z
cdef float wscale = 1.0
# return value (-1 if an error occurred, 0 otherwise)
cdef int status = 0
# the cumulative sums for each iteration for the sparse implementation
cumulative_sums[0] = 0.0
# the multipliative scale needed for JIT params
cdef np.ndarray[float, ndim=1] cumulative_sums_prox_array
cdef float* cumulative_sums_prox
cdef bint prox = beta > 0 and saga
# Loss function to optimize
cdef LossFunction loss
# Wether the loss function is multinomial
cdef bint multinomial = False
# Multinomial loss function
cdef MultinomialLogLoss32 multiloss
if loss_function == "multinomial":
multinomial = True
multiloss = MultinomialLogLoss32()
elif loss_function == "log":
loss = Log()
elif loss_function == "squared":
loss = SquaredLoss()
else:
raise ValueError("Invalid loss parameter: got %s instead of "
"one of ('log', 'squared', 'multinomial')"
% loss_function)
if prox:
cumulative_sums_prox_array = np.empty(n_samples,
dtype=np.float32, order="c")
cumulative_sums_prox = <float*> cumulative_sums_prox_array.data
else:
cumulative_sums_prox = NULL
with nogil:
start_time = time(NULL)
for n_iter in range(max_iter):
for sample_itr in range(n_samples):
# extract a random sample
sample_ind = dataset.random(&x_data_ptr, &x_ind_ptr, &xnnz,
&y, &sample_weight)
# cached index for gradient_memory
s_idx = sample_ind * n_classes
# update the number of samples seen and the seen array
if seen[sample_ind] == 0:
num_seen += 1
seen[sample_ind] = 1
# make the weight updates
if sample_itr > 0:
status = lagged_update32(weights, wscale, xnnz,
n_samples, n_classes,
sample_itr,
cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox,
sum_gradient,
x_ind_ptr,
False,
n_iter)
if status == -1:
break
# find the current prediction
predict_sample32(x_data_ptr, x_ind_ptr, xnnz, weights, wscale,
intercept, prediction, n_classes)
# compute the gradient for this sample, given the prediction
if multinomial:
multiloss._dloss(prediction, y, n_classes, sample_weight,
gradient)
else:
gradient[0] = loss._dloss(prediction[0], y) * sample_weight
# L2 regularization by simply rescaling the weights
wscale *= wscale_update
# make the updates to the sum of gradients
for j in range(xnnz):
feature_ind = x_ind_ptr[j]
val = x_data_ptr[j]
f_idx = feature_ind * n_classes
for class_ind in range(n_classes):
gradient_correction = \
val * (gradient[class_ind] -
gradient_memory[s_idx + class_ind])
if saga:
weights[f_idx + class_ind] -= \
(gradient_correction * step_size
* (1 - 1. / num_seen) / wscale)
sum_gradient[f_idx + class_ind] += gradient_correction
# fit the intercept
if fit_intercept:
for class_ind in range(n_classes):
gradient_correction = (gradient[class_ind] -
gradient_memory[s_idx + class_ind])
intercept_sum_gradient[class_ind] += gradient_correction
gradient_correction *= step_size * (1. - 1. / num_seen)
if saga:
intercept[class_ind] -= \
(step_size * intercept_sum_gradient[class_ind] /
num_seen * intercept_decay) + gradient_correction
else:
intercept[class_ind] -= \
(step_size * intercept_sum_gradient[class_ind] /
num_seen * intercept_decay)
# check to see that the intercept is not inf or NaN
if not skl_isfinite32(intercept[class_ind]):
status = -1
break
# Break from the n_samples outer loop if an error happened
# in the fit_intercept n_classes inner loop
if status == -1:
break
# update the gradient memory for this sample
for class_ind in range(n_classes):
gradient_memory[s_idx + class_ind] = gradient[class_ind]
if sample_itr == 0:
cumulative_sums[0] = step_size / (wscale * num_seen)
if prox:
cumulative_sums_prox[0] = step_size * beta / wscale
else:
cumulative_sums[sample_itr] = \
(cumulative_sums[sample_itr - 1] +
step_size / (wscale * num_seen))
if prox:
cumulative_sums_prox[sample_itr] = \
(cumulative_sums_prox[sample_itr - 1] +
step_size * beta / wscale)
# If wscale gets too small, we need to reset the scale.
if wscale < 1e-9:
if verbose:
with gil:
print("rescaling...")
status = scale_weights32(
weights, &wscale, n_features, n_samples, n_classes,
sample_itr, cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox, sum_gradient, n_iter)
if status == -1:
break
# Break from the n_iter outer loop if an error happened in the
# n_samples inner loop
if status == -1:
break
# we scale the weights every n_samples iterations and reset the
# just-in-time update system for numerical stability.
status = scale_weights32(weights, &wscale, n_features,
n_samples,
n_classes, n_samples - 1,
cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox, sum_gradient, n_iter)
if status == -1:
break
# check if the stopping criteria is reached
max_change = 0.0
max_weight = 0.0
for idx in range(n_features * n_classes):
max_weight = fmax32(max_weight, fabs(weights[idx]))
max_change = fmax32(max_change,
fabs(weights[idx] -
previous_weights[idx]))
previous_weights[idx] = weights[idx]
if ((max_weight != 0 and max_change / max_weight <= tol)
or max_weight == 0 and max_change == 0):
if verbose:
end_time = time(NULL)
with gil:
print("convergence after %d epochs took %d seconds" %
(n_iter + 1, end_time - start_time))
break
elif verbose:
printf('Epoch %d, change: %.8f\n', n_iter + 1,
max_change / max_weight)
n_iter += 1
# We do the error treatment here based on error code in status to avoid
# re-acquiring the GIL within the cython code, which slows the computation
# when the sag/saga solver is used concurrently in multiple Python threads.
if status == -1:
raise ValueError(("Floating-point under-/overflow occurred at epoch"
" #%d. Scaling input data with StandardScaler or"
" MinMaxScaler might help.") % n_iter)
if verbose and n_iter >= max_iter:
end_time = time(NULL)
print(("max_iter reached after %d seconds") %
(end_time - start_time))
return num_seen, n_iter
cdef int scale_weights64(double* weights, double* wscale,
int n_features,
int n_samples, int n_classes, int sample_itr,
double* cumulative_sums,
double* cumulative_sums_prox,
int* feature_hist,
bint prox,
double* sum_gradient,
int n_iter) nogil:
"""Scale the weights with wscale for numerical stability.
wscale = (1 - step_size * alpha) ** (n_iter * n_samples + sample_itr)
can become very small, so we reset it every n_samples iterations to 1.0 for
numerical stability. To be able to scale, we first need to update every
coefficients and reset the just-in-time update system.
This also limits the size of `cumulative_sums`.
"""
cdef int status
status = lagged_update64(weights, wscale[0], n_features,
n_samples, n_classes, sample_itr + 1,
cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox,
sum_gradient,
NULL,
True,
n_iter)
# if lagged update succeeded, reset wscale to 1.0
if status == 0:
wscale[0] = 1.0
return status
cdef int scale_weights32(float* weights, float* wscale,
int n_features,
int n_samples, int n_classes, int sample_itr,
float* cumulative_sums,
float* cumulative_sums_prox,
int* feature_hist,
bint prox,
float* sum_gradient,
int n_iter) nogil:
"""Scale the weights with wscale for numerical stability.
wscale = (1 - step_size * alpha) ** (n_iter * n_samples + sample_itr)
can become very small, so we reset it every n_samples iterations to 1.0 for
numerical stability. To be able to scale, we first need to update every
coefficients and reset the just-in-time update system.
This also limits the size of `cumulative_sums`.
"""
cdef int status
status = lagged_update32(weights, wscale[0], n_features,
n_samples, n_classes, sample_itr + 1,
cumulative_sums,
cumulative_sums_prox,
feature_hist,
prox,
sum_gradient,
NULL,
True,
n_iter)
# if lagged update succeeded, reset wscale to 1.0
if status == 0:
wscale[0] = 1.0
return status
cdef int lagged_update64(double* weights, double wscale, int xnnz,
int n_samples, int n_classes, int sample_itr,
double* cumulative_sums,
double* cumulative_sums_prox,
int* feature_hist,
bint prox,
double* sum_gradient,
int* x_ind_ptr,
bint reset,
int n_iter) nogil:
"""Hard perform the JIT updates for non-zero features of present sample.
The updates that awaits are kept in memory using cumulative_sums,
cumulative_sums_prox, wscale and feature_hist. See original SAGA paper
(Defazio et al. 2014) for details. If reset=True, we also reset wscale to
1 (this is done at the end of each epoch).
"""
cdef int feature_ind, class_ind, idx, f_idx, lagged_ind, last_update_ind
cdef double cum_sum, grad_step, prox_step, cum_sum_prox
for feature_ind in range(xnnz):
if not reset:
feature_ind = x_ind_ptr[feature_ind]
f_idx = feature_ind * n_classes
cum_sum = cumulative_sums[sample_itr - 1]
if prox:
cum_sum_prox = cumulative_sums_prox[sample_itr - 1]
if feature_hist[feature_ind] != 0:
cum_sum -= cumulative_sums[feature_hist[feature_ind] - 1]
if prox:
cum_sum_prox -= cumulative_sums_prox[feature_hist[feature_ind] - 1]
if not prox:
for class_ind in range(n_classes):
idx = f_idx + class_ind
weights[idx] -= cum_sum * sum_gradient[idx]
if reset:
weights[idx] *= wscale
if not skl_isfinite64(weights[idx]):
# returning here does not require the gil as the return
# type is a C integer
return -1
else:
for class_ind in range(n_classes):
idx = f_idx + class_ind
if fabs(sum_gradient[idx] * cum_sum) < cum_sum_prox:
# In this case, we can perform all the gradient steps and
# all the proximal steps in this order, which is more
# efficient than unrolling all the lagged updates.
# Idea taken from scikit-learn-contrib/lightning.
weights[idx] -= cum_sum * sum_gradient[idx]
weights[idx] = _soft_thresholding64(weights[idx],
cum_sum_prox)
else:
last_update_ind = feature_hist[feature_ind]
if last_update_ind == -1:
last_update_ind = sample_itr - 1
for lagged_ind in range(sample_itr - 1,
last_update_ind - 1, -1):
if lagged_ind > 0:
grad_step = (cumulative_sums[lagged_ind]
- cumulative_sums[lagged_ind - 1])
prox_step = (cumulative_sums_prox[lagged_ind]
- cumulative_sums_prox[lagged_ind - 1])
else:
grad_step = cumulative_sums[lagged_ind]
prox_step = cumulative_sums_prox[lagged_ind]
weights[idx] -= sum_gradient[idx] * grad_step
weights[idx] = _soft_thresholding64(weights[idx],
prox_step)
if reset:
weights[idx] *= wscale
# check to see that the weight is not inf or NaN
if not skl_isfinite64(weights[idx]):
return -1
if reset:
feature_hist[feature_ind] = sample_itr % n_samples
else:
feature_hist[feature_ind] = sample_itr
if reset:
cumulative_sums[sample_itr - 1] = 0.0
if prox:
cumulative_sums_prox[sample_itr - 1] = 0.0
return 0
cdef int lagged_update32(float* weights, float wscale, int xnnz,
int n_samples, int n_classes, int sample_itr,
float* cumulative_sums,
float* cumulative_sums_prox,
int* feature_hist,
bint prox,
float* sum_gradient,
int* x_ind_ptr,
bint reset,
int n_iter) nogil:
"""Hard perform the JIT updates for non-zero features of present sample.
The updates that awaits are kept in memory using cumulative_sums,
cumulative_sums_prox, wscale and feature_hist. See original SAGA paper
(Defazio et al. 2014) for details. If reset=True, we also reset wscale to
1 (this is done at the end of each epoch).
"""
cdef int feature_ind, class_ind, idx, f_idx, lagged_ind, last_update_ind
cdef float cum_sum, grad_step, prox_step, cum_sum_prox
for feature_ind in range(xnnz):
if not reset:
feature_ind = x_ind_ptr[feature_ind]
f_idx = feature_ind * n_classes
cum_sum = cumulative_sums[sample_itr - 1]
if prox:
cum_sum_prox = cumulative_sums_prox[sample_itr - 1]
if feature_hist[feature_ind] != 0:
cum_sum -= cumulative_sums[feature_hist[feature_ind] - 1]
if prox:
cum_sum_prox -= cumulative_sums_prox[feature_hist[feature_ind] - 1]
if not prox:
for class_ind in range(n_classes):
idx = f_idx + class_ind
weights[idx] -= cum_sum * sum_gradient[idx]
if reset:
weights[idx] *= wscale
if not skl_isfinite32(weights[idx]):
# returning here does not require the gil as the return
# type is a C integer
return -1
else:
for class_ind in range(n_classes):
idx = f_idx + class_ind
if fabs(sum_gradient[idx] * cum_sum) < cum_sum_prox:
# In this case, we can perform all the gradient steps and
# all the proximal steps in this order, which is more
# efficient than unrolling all the lagged updates.
# Idea taken from scikit-learn-contrib/lightning.
weights[idx] -= cum_sum * sum_gradient[idx]
weights[idx] = _soft_thresholding32(weights[idx],
cum_sum_prox)
else:
last_update_ind = feature_hist[feature_ind]
if last_update_ind == -1:
last_update_ind = sample_itr - 1
for lagged_ind in range(sample_itr - 1,
last_update_ind - 1, -1):
if lagged_ind > 0:
grad_step = (cumulative_sums[lagged_ind]
- cumulative_sums[lagged_ind - 1])
prox_step = (cumulative_sums_prox[lagged_ind]
- cumulative_sums_prox[lagged_ind - 1])
else:
grad_step = cumulative_sums[lagged_ind]
prox_step = cumulative_sums_prox[lagged_ind]
weights[idx] -= sum_gradient[idx] * grad_step
weights[idx] = _soft_thresholding32(weights[idx],
prox_step)
if reset:
weights[idx] *= wscale
# check to see that the weight is not inf or NaN
if not skl_isfinite32(weights[idx]):
return -1
if reset:
feature_hist[feature_ind] = sample_itr % n_samples
else:
feature_hist[feature_ind] = sample_itr
if reset:
cumulative_sums[sample_itr - 1] = 0.0
if prox:
cumulative_sums_prox[sample_itr - 1] = 0.0
return 0
cdef void predict_sample64(double* x_data_ptr, int* x_ind_ptr, int xnnz,
double* w_data_ptr, double wscale,
double* intercept, double* prediction,
int n_classes) nogil:
"""Compute the prediction given sparse sample x and dense weight w.
Parameters
----------
x_data_ptr : pointer
Pointer to the data of the sample x
x_ind_ptr : pointer
Pointer to the indices of the sample x
xnnz : int
Number of non-zero element in the sample x
w_data_ptr : pointer
Pointer to the data of the weights w
wscale : double
Scale of the weights w
intercept : pointer
Pointer to the intercept
prediction : pointer
Pointer to store the resulting prediction
n_classes : int
Number of classes in multinomial case. Equals 1 in binary case.
"""
cdef int feature_ind, class_ind, j
cdef double innerprod
for class_ind in range(n_classes):
innerprod = 0.0
# Compute the dot product only on non-zero elements of x
for j in range(xnnz):
feature_ind = x_ind_ptr[j]
innerprod += (w_data_ptr[feature_ind * n_classes + class_ind] *
x_data_ptr[j])
prediction[class_ind] = wscale * innerprod + intercept[class_ind]
cdef void predict_sample32(float* x_data_ptr, int* x_ind_ptr, int xnnz,
float* w_data_ptr, float wscale,
float* intercept, float* prediction,
int n_classes) nogil:
"""Compute the prediction given sparse sample x and dense weight w.
Parameters
----------
x_data_ptr : pointer
Pointer to the data of the sample x
x_ind_ptr : pointer
Pointer to the indices of the sample x
xnnz : int
Number of non-zero element in the sample x
w_data_ptr : pointer
Pointer to the data of the weights w
wscale : float
Scale of the weights w
intercept : pointer
Pointer to the intercept
prediction : pointer
Pointer to store the resulting prediction
n_classes : int
Number of classes in multinomial case. Equals 1 in binary case.
"""
cdef int feature_ind, class_ind, j
cdef float innerprod
for class_ind in range(n_classes):
innerprod = 0.0
# Compute the dot product only on non-zero elements of x
for j in range(xnnz):
feature_ind = x_ind_ptr[j]
innerprod += (w_data_ptr[feature_ind * n_classes + class_ind] *
x_data_ptr[j])
prediction[class_ind] = wscale * innerprod + intercept[class_ind]
def _multinomial_grad_loss_all_samples(
SequentialDataset64 dataset,
np.ndarray[double, ndim=2, mode='c'] weights_array,
np.ndarray[double, ndim=1, mode='c'] intercept_array,
int n_samples, int n_features, int n_classes):
"""Compute multinomial gradient and loss across all samples.
Used for testing purpose only.
"""
cdef double* weights = <double * >weights_array.data
cdef double* intercept = <double * >intercept_array.data
cdef double *x_data_ptr = NULL
cdef int *x_ind_ptr = NULL
cdef int xnnz = -1
cdef double y
cdef double sample_weight
cdef double wscale = 1.0
cdef int i, j, class_ind, feature_ind
cdef double val
cdef double sum_loss = 0.0
cdef MultinomialLogLoss64 multiloss = MultinomialLogLoss64()
cdef np.ndarray[double, ndim=2] sum_gradient_array = \
np.zeros((n_features, n_classes), dtype=np.double, order="c")
cdef double* sum_gradient = <double*> sum_gradient_array.data
cdef np.ndarray[double, ndim=1] prediction_array = \
np.zeros(n_classes, dtype=np.double, order="c")
cdef double* prediction = <double*> prediction_array.data
cdef np.ndarray[double, ndim=1] gradient_array = \
np.zeros(n_classes, dtype=np.double, order="c")
cdef double* gradient = <double*> gradient_array.data
with nogil:
for i in range(n_samples):
# get next sample on the dataset
dataset.next(&x_data_ptr, &x_ind_ptr, &xnnz,
&y, &sample_weight)
# prediction of the multinomial classifier for the sample
predict_sample64(x_data_ptr, x_ind_ptr, xnnz, weights, wscale,
intercept, prediction, n_classes)
# compute the gradient for this sample, given the prediction
multiloss._dloss(prediction, y, n_classes, sample_weight, gradient)
# compute the loss for this sample, given the prediction
sum_loss += multiloss._loss(prediction, y, n_classes, sample_weight)
# update the sum of the gradient
for j in range(xnnz):
feature_ind = x_ind_ptr[j]
val = x_data_ptr[j]
for class_ind in range(n_classes):
sum_gradient[feature_ind * n_classes + class_ind] += \
gradient[class_ind] * val
return sum_loss, sum_gradient_array
|