This use case shows the steps to use SageMaker PCA with tdapiclient.
You can download the aws-usecases.zip file in the attachment as a reference. The pca folder in the zip file includes a Jupyter notebook file (ipynb) and a CSV file containing the dataset required to run this use case.
- Import necessary libraries.
import getpass from tdapiclient import create_tdapi_context, TDApiClient from teradataml import create_context, DataFrame, copy_to_sql,load_example_data, configure, LabelEncoder, valib,Retain import pandas as pd from teradatasqlalchemy.types import *
- Create the connection.
host = input("Host: ") username = input("Username: ") password = getpass.getpass("Password: ")
td_context = create_context(host=host, username=username, password=password)
- Create TDAPI context and TDApiClient object.
s3_bucket = input("S3 Bucket(Please provide just the bucket name, for example: test-bucket): ") access_id = input("Access ID:") access_key = getpass.getpass("Acess Key: ") region = input("AWS Region: ")
os.environ["AWS_ACCESS_KEY_ID"] = access_id os.environ["AWS_SECRET_ACCESS_KEY"] = access_key os.environ["AWS_REGION"] = region
tdapi_context = create_tdapi_context("aws", bucket_name=s3_bucket)
td_apiclient = TDApiClient(tdapi_context)
- Set up data.
- Read the breast cancer dataset.
data = pd.read_csv ("cancer_data.csv")
- Drop unnecessary columns.
data=data.drop(['Unnamed: 32'], axis=1)
- Rename columns for creating teradataml DataFrame.
data.rename(columns={'concave points_mean':'concave_points_mean', "concave points_se":"concave_points_se", "concave points_worst":"concave_points_worst"}, inplace=True)
- Insert the dataframe in the tables.
data_table = "cancer_data"
column_types = { "id":INTEGER, "diagnosis": CHAR(1), "radius_mean": FLOAT, "texture_mean": FLOAT, "perimeter_mean": FLOAT, "area_mean": FLOAT, "smoothness_mean": FLOAT , "compactness_mean": FLOAT , "concavity_mean": FLOAT , "concave_points_mean": FLOAT, "symmetry_mean": FLOAT , "fractal_dimension_mean": FLOAT, "radius_se": FLOAT , "texture_se": FLOAT , "perimeter_se": FLOAT , "area_se": FLOAT , "smoothness_se": FLOAT , "compactness_se": FLOAT , "concavity_se": FLOAT , "concave_points_se": FLOAT , "symmetry_se": FLOAT , "fractal_dimension_se": FLOAT , "radius_worst": FLOAT , "texture_worst": FLOAT , "perimeter_worst": FLOAT , "area_worst": FLOAT , "smoothness_worst": FLOAT , "compactness_worst": FLOAT , "concavity_worst": FLOAT , "concave_points_worst": FLOAT , "symmetry_worst": FLOAT , "fractal_dimension_worst": FLOAT }
copy_to_sql(df=data, table_name=data_table, if_exists="replace", types=column_types)
- Create a teradataml DataFrame using the table.
df = DataFrame(table_name=data_table)
- Read the breast cancer dataset.
- Prepare dataset.
- Encode the target column using label encoder.
from teradataml import LabelEncoder
rc = LabelEncoder(values=("M", 1), columns=["diagnosis"], default=0)
feature_columns_names= Retain(columns=["radius_mean", "texture_mean", "perimeter_mean", "area_mean", "smoothness_mean" , "compactness_mean" , "concavity_mean" , "concave_points_mean", "symmetry_mean" , "fractal_dimension_mean", "radius_se" , "texture_se" , "perimeter_se" , "area_se" , "smoothness_se" , "compactness_se" , "concavity_se" , "concave_points_se" , "symmetry_se" , "fractal_dimension_se" , "radius_worst" , "texture_worst" , "perimeter_worst" , "area_worst" , "smoothness_worst" , "compactness_worst" , "concavity_worst" , "concave_points_worst" , "symmetry_worst" , "fractal_dimension_worst" ])
configure.val_install_location = "alice" data = valib.Transform(data=df, label_encode=rc,index_columns="id",unique_index=True,retain=feature_columns_names)
df=data.result
- Drop unnecessary columns.
df=df.drop(["id","diagnosis"],axis=1)
- Create two samples of input data: sample 1 has 80% of total rows and sample 2 has 20% of total rows.
cancer_sample = df.sample(frac=[0.8, 0.2])
- Create train dataset from sample 1 by filtering on "sampleid" and drop "sampleid" column as it is not required for training model.
train = cancer_sample[cancer_sample.sampleid == "1"].drop("sampleid", axis = 1)
train
The output:radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean concave_points_mean symmetry_mean fractal_dimension_mean radius_se texture_se perimeter_se area_se smoothness_se compactness_se concavity_se concave_points_se symmetry_se fractal_dimension_se radius_worst texture_worst perimeter_worst area_worst smoothness_worst compactness_worst concavity_worst concave_points_worst symmetry_worst fractal_dimension_worst 18.08 21.84 117.4 1024.0 0.07371 0.08642 0.1103 0.05778 0.177 0.0534 0.6362 1.305 4.312 76.36 0.00553 0.05296 0.0611 0.01444 0.0214 0.005036 19.76 24.7 129.1 1228.0 0.08822 0.1963 0.2535 0.09181 0.2369 0.06558 18.05 16.15 120.2 1006.0 0.1065 0.2146 0.1684 0.108 0.2152 0.06673 0.9806 0.5505 6.311 134.8 0.00794 0.05839 0.04658 0.0207 0.02591 0.007054 22.39 18.91 150.1 1610.0 0.1478 0.5634 0.3786 0.2102 0.3751 0.1108 19.07 24.81 128.3 1104.0 0.09081 0.219 0.2107 0.09961 0.231 0.06343 0.9811 1.666 8.83 104.9 0.006548 0.1006 0.09723 0.02638 0.05333 0.007646 24.09 33.17 177.4 1651.0 0.1247 0.7444 0.7242 0.2493 0.467 0.1038 16.17 16.07 106.3 788.5 0.0988 0.1438 0.06651 0.05397 0.199 0.06572 0.1745 0.489 1.349 14.91 0.00451 0.01812 0.01951 0.01196 0.01934 0.003696 16.97 19.14 113.1 861.5 0.1235 0.255 0.2114 0.1251 0.3153 0.0896 15.3 25.27 102.4 732.4 0.1082 0.1697 0.1683 0.08751 0.1926 0.0654 0.439 1.012 3.498 43.5 0.005233 0.03057 0.03576 0.01083 0.01768 0.002967 20.27 36.71 149.3 1269.0 0.1641 0.611 0.6335 0.2024 0.4027 0.09876 14.5 10.89 94.28 640.7 0.1101 0.1099 0.08842 0.05778 0.1856 0.06402 0.2929 0.857 1.928 24.19 0.003818 0.01276 0.02882 0.012 0.0191 0.002808 15.7 15.98 102.8 745.5 0.1313 0.1788 0.256 0.1221 0.2889 0.08006 15.04 16.74 98.73 689.4 0.09883 0.1364 0.07721 0.06142 0.1668 0.06869 0.372 0.8423 2.304 34.84 0.004123 0.01819 0.01996 0.01004 0.01055 0.003237 16.76 20.43 109.7 856.9 0.1135 0.2176 0.1856 0.1018 0.2177 0.08549 8.196 16.84 51.71 201.9 0.086 0.05943 0.01588 0.005917 0.1769 0.06503 0.1563 0.9567 1.094 8.205 0.008968 0.01646 0.01588 0.005917 0.02574 0.002582 8.964 21.96 57.26 242.2 0.1297 0.1357 0.0688 0.02564 0.3105 0.07409 16.26 21.88 107.5 826.8 0.1165 0.1283 0.1799 0.07981 0.1869 0.06532 0.5706 1.457 2.961 57.72 0.01056 0.03756 0.05839 0.01186 0.04022 0.006187 17.73 25.21 113.7 975.2 0.1426 0.2116 0.3344 0.1047 0.2736 0.07953 9.042 18.9 60.07 244.5 0.09968 0.1972 0.1975 0.04908 0.233 0.08743 0.4653 1.911 3.769 24.2 0.009845 0.0659 0.1027 0.02527 0.03491 0.007877 10.06 23.4 68.62 297.1 0.1221 0.3748 0.4609 0.1145 0.3135 0.1055
- Create test dataset from sample 2 by filtering on "sampleid" and drop "sampleid" column as it is not required for scoring.
test = cancer_sample[cancer_sample.sampleid == "2"].drop("sampleid", axis = 1)
test
The output:radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean concave_points_mean symmetry_mean fractal_dimension_mean radius_se texture_se perimeter_se area_se smoothness_se compactness_se concavity_se concave_points_se symmetry_se fractal_dimension_se radius_worst texture_worst perimeter_worst area_worst smoothness_worst compactness_worst concavity_worst concave_points_worst symmetry_worst fractal_dimension_worst 18.31 20.58 120.8 1052.0 0.1068 0.1248 0.1569 0.09451 0.186 0.05941 0.5449 0.9225 3.218 67.36 0.006176 0.01877 0.02913 0.01046 0.01559 0.002725 21.86 26.2 142.2 1493.0 0.1492 0.2536 0.3759 0.151 0.3074 0.07863 15.1 22.02 97.26 712.8 0.09056 0.07081 0.05253 0.03334 0.1616 0.05684 0.3105 0.8339 2.097 29.91 0.004675 0.0103 0.01603 0.009222 0.01095 0.001629 18.1 31.69 117.7 1030.0 0.1389 0.2057 0.2712 0.153 0.2675 0.07873 19.8 21.56 129.7 1230.0 0.09383 0.1306 0.1272 0.08691 0.2094 0.05581 0.9553 1.186 6.487 124.4 0.006804 0.03169 0.03446 0.01712 0.01897 0.004045 25.73 28.64 170.3 2009.0 0.1353 0.3235 0.3617 0.182 0.307 0.08255 15.3 25.27 102.4 732.4 0.1082 0.1697 0.1683 0.08751 0.1926 0.0654 0.439 1.012 3.498 43.5 0.005233 0.03057 0.03576 0.01083 0.01768 0.002967 20.27 36.71 149.3 1269.0 0.1641 0.611 0.6335 0.2024 0.4027 0.09876 10.29 27.61 65.67 321.4 0.0903 0.07658 0.05999 0.02738 0.1593 0.06127 0.2199 2.239 1.437 14.46 0.01205 0.02736 0.04804 0.01721 0.01843 0.004938 10.84 34.91 69.57 357.6 0.1384 0.171 0.2 0.09127 0.2226 0.08283 9.268 12.87 61.49 248.7 0.1634 0.2239 0.0973 0.05252 0.2378 0.09502 0.4076 1.093 3.014 20.04 0.009783 0.04542 0.03483 0.02188 0.02542 0.01045 10.28 16.38 69.05 300.2 0.1902 0.3441 0.2099 0.1025 0.3038 0.1252 11.04 16.83 70.92 373.2 0.1077 0.07804 0.03046 0.0248 0.1714 0.0634 0.1967 1.387 1.342 13.54 0.005158 0.009355 0.01056 0.007483 0.01718 0.002198 12.41 26.44 79.93 471.4 0.1369 0.1482 0.1067 0.07431 0.2998 0.07881 13.61 24.98 88.05 582.7 0.09488 0.08511 0.08625 0.04489 0.1609 0.05871 0.4565 1.29 2.861 43.14 0.005872 0.01488 0.02647 0.009921 0.01465 0.002355 16.99 35.27 108.6 906.5 0.1265 0.1943 0.3169 0.1184 0.2651 0.07397 14.03 21.25 89.79 603.4 0.0907 0.06945 0.01462 0.01896 0.1517 0.05835 0.2589 1.503 1.667 22.07 0.007389 0.01383 0.007302 0.01004 0.01263 0.002925 15.33 30.28 98.27 715.5 0.1287 0.1513 0.06231 0.07963 0.2226 0.07617 14.64 15.24 95.77 651.9 0.1132 0.1339 0.09966 0.07064 0.2116 0.06346 0.5115 0.7372 3.814 42.76 0.005508 0.04412 0.04436 0.01623 0.02427 0.004841 16.34 18.24 109.4 803.6 0.1277 0.3089 0.2604 0.1397 0.3151 0.08473
- Encode the target column using label encoder.
- Create PCA SageMaker instance through tdapiclient.
exec_role_arn = "arn:aws:iam::076782961461:role/service-role/AmazonSageMaker-ExecutionRole-20210112T215668"
pca = td_apiclient.PCA( role=exec_role_arn, instance_count=1, instance_type="ml.m5.xlarge", feature_dim=30, num_components=20, subtract_mean=True, mini_batch_size=20 )
- Covert teradataml DataFrame to NumPy ndarray and store it as PCA RecordSet object.
train_set=pca.record_set(train.get_values().astype('float32'))
- Start training using RecordSet object.
pca.fit(train_set)
- Create Serializer and Deserializer, so predictor can handle CSV input and output.
from sagemaker.serializers import CSVSerializer from sagemaker.deserializers import CSVDeserializer csv_ser = CSVSerializer() csv_dser = CSVDeserializer()
predictor = pca.deploy("aws-endpoint", sagemaker_kw_args={"instance_type": "ml.m5.large", "initial_instance_count": 1, "serializer": csv_ser, "deserializer": csv_dser})
- Try prediction integration using teradataml DataFrame and the predictor object created in previous step.
- Confirm that predictor is correctly configured for accepting csv input.
print(predictor.cloudObj.accept)
The output:('text/csv',)
- Try prediction with UDF and Client options.Prediction with Client option:
output = predictor.predict(test, mode="client",content_type='csv')
output
The output:[['{"projections": [{"projection": [0.003895685076713562', ' 0.0061229318380355835', ' -0.0047997236251831055', ' 0.004468563944101334', ' 0.010653555393218994', ' -0.016420233994722366', ' -0.008977413177490234', ' 0.03230781853199005', ' -0.10400402545928955', ' 0.17058533430099487', ' -0.053495049476623535', ' -0.3316737413406372', ' -0.23530852794647217', ' 0.17611587047576904', ' 0.27698516845703125', ' -1.7408714294433594', ' 1.8240509033203125', ' 5.520957946777344', ' -42.47268295288086', ' -280.5753173828125]}', ' {"projection": [-0.0140230692923069', ' -0.015108399093151093', ' 0.006812885403633118', ' 0.10005844384431839', ' 0.01633429527282715', ' 0.16064375638961792', ' 0.025818675756454468', ' -0.07550624012947083', ' 0.35952305793762207', ' -0.3493649363517761', ' -0.7519358992576599', ' -0.9317904710769653', ' 1.6834189891815186', ' 3.1111135482788086', ' 4.511608123779297', ' 2.9455032348632812', ' 7.4655609130859375', ' 69.96951293945312', ' 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Prediction with UDF option:output = predictor.predict(test, mode="UDF",content_type='csv')
output
The output:radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean concave_points_mean symmetry_mean fractal_dimension_mean radius_se texture_se perimeter_se area_se smoothness_se compactness_se concavity_se concave_points_se symmetry_se fractal_dimension_se radius_worst texture_worst perimeter_worst area_worst smoothness_worst compactness_worst concavity_worst concave_points_worst symmetry_worst fractal_dimension_worst Output 11.26 19.96 73.72 394.1 0.0802 0.1181 0.09274 0.05588 0.2595 0.06233 0.4866 1.905 2.877 34.68 0.01574 0.08262 0.08099 0.03487 0.03418 0.006517 11.86 22.33 78.27 437.6 0.1028 0.1843 0.1546 0.09314 0.2955 0.07009 {"projections": [{"projection": [0.03280608355998993, 0.04537193104624748, 0.022922128438949585, -0.04075419902801514, -0.002420380711555481, 0.06853789836168289, 0.07840818166732788, -0.012627199292182922, -0.059899359941482544, 0.07341676950454712, 0.32374298572540283, 0.39884722232818604, 0.5078041553497314, 1.8295392990112305, 1.9261531829833984, 0.6402130126953125, -0.379180908203125, 23.91823387145996, 9.325920104980469, -531.2207641601562]}]} 14.54 27.54 96.73 658.8 0.1139 0.1595 0.1639 0.07364 0.2303 0.07077 0.37 1.033 2.879 32.55 0.005607 0.0424 0.04741 0.0109 0.01857 0.005466 17.46 37.13 124.1 943.2 0.1678 0.6577 0.7026 0.1712 0.4218 0.1341 {"projections": [{"projection": [-0.0009193867444992065, 0.0017432048916816711, -0.02580226957798004, 0.031872328370809555, 0.013675473630428314, 0.046332910656929016, 0.04852712154388428, -0.08409607410430908, 0.10175716876983643, 0.10230475664138794, 0.03288924694061279, 0.5122510194778442, -0.933474063873291, 1.1933152675628662, -1.9981422424316406, 3.7658538818359375, 18.38623046875, -12.721473693847656, -31.42217254638672, 39.1029052734375]}]} 17.19 22.07 111.6 928.3 0.09726 0.08995 0.09061 0.06527 0.1867 0.0558 0.4203 0.7383 2.819 45.42 0.004493 0.01206 0.02048 0.009875 0.01144 0.001575 21.58 29.33 140.5 1436.0 0.1558 0.2567 0.3889 0.1984 0.3216 0.0757 {"projections": [{"projection": [0.024966612458229065, 0.00318821519613266, 0.011346578598022461, 0.013895014300942421, -0.035234734416007996, -0.04609498381614685, 0.022311151027679443, 0.04100880026817322, 0.0029187798500061035, 0.07415980100631714, 0.023444533348083496, -0.466349720954895, -0.44150519371032715, 0.7395851612091064, -0.10807037353515625, 1.4590539932250977, -0.01204681396484375, -30.102813720703125, -61.1049690246582, 600.102783203125]}]} 16.26 21.88 107.5 826.8 0.1165 0.1283 0.1799 0.07981 0.1869 0.06532 0.5706 1.457 2.961 57.72 0.01056 0.03756 0.05839 0.01186 0.04022 0.006187 17.73 25.21 113.7 975.2 0.1426 0.2116 0.3344 0.1047 0.2736 0.07953 {"projections": [{"projection": [-0.011844988912343979, -0.02179451286792755, -0.010386645793914795, 0.008400904946029186, 0.021189682185649872, 0.05686948448419571, 0.03128334879875183, 0.07214194536209106, -0.10330820083618164, 0.22019651532173157, 0.26925790309906006, 0.1362295150756836, -0.3018451929092407, 0.7699693441390991, 4.445920944213867, 0.6706113815307617, 1.6569290161132812, 4.774696350097656, 95.55809020996094, 155.3846435546875]}]} 12.8 17.46 83.05 508.3 0.08044 0.08895 0.0739 0.04083 0.1574 0.0575 0.3639 1.265 2.668 30.57 0.005421 0.03477 0.04545 0.01384 0.01869 0.004067 13.74 21.06 90.72 591.0 0.09534 0.1812 0.1901 0.08296 0.1988 0.07053 {"projections": [{"projection": [-0.0067559704184532166, 0.014604754745960236, 0.01802411675453186, -0.010528565384447575, 0.006629347801208496, 0.016444597393274307, -0.05062919855117798, 0.03539012372493744, 0.04209035634994507, -0.0821576714515686, 0.025034427642822266, 0.1480346918106079, 0.20329409837722778, 0.7110903263092041, 1.1703987121582031, -3.158243179321289, -0.9195556640625, 8.130979537963867, 25.84123992919922, -340.67529296875]}]} 13.56 13.9 88.59 561.3 0.1051 0.1192 0.0786 0.04451 0.1962 0.06303 0.2569 0.4981 2.011 21.03 0.005851 0.02314 0.02544 0.00836 0.01842 0.002918 14.98 17.13 101.1 686.6 0.1376 0.2698 0.2577 0.0909 0.3065 0.08177 {"projections": [{"projection": [-0.0014752037823200226, -0.0001922324299812317, -0.022153660655021667, 0.004760150797665119, 0.005818486213684082, 0.005189649760723114, 0.018100589513778687, -0.007178470492362976, -0.011704623699188232, -0.061644792556762695, -0.01568889617919922, 0.24525690078735352, -0.3842885494232178, 0.44938480854034424, -0.03153419494628906, -10.148139953613281, -1.5808181762695312, -8.009380340576172, 20.58032989501953, -231.72698974609375]}]} 15.78 22.91 105.7 782.6 0.1155 0.1752 0.2133 0.09479 0.2096 0.07331 0.552 1.072 3.598 58.63 0.008699 0.03976 0.0595 0.0139 0.01495 0.005984 20.19 30.5 130.3 1272.0 0.1855 0.4925 0.7356 0.2034 0.3274 0.1252 {"projections": [{"projection": [0.01153247058391571, 0.0015450343489646912, -0.015420198440551758, 0.03970148414373398, 0.00606585294008255, -0.06252686679363251, -0.04455491900444031, 0.0688396692276001, -0.032323360443115234, 0.432451069355011, -0.34291768074035645, -0.024285316467285156, -0.05630701780319214, -0.05635809898376465, 3.764974594116211, 0.5162458419799805, 5.687568664550781, -4.091133117675781, -98.36248779296875, 384.857666015625]}]} 19.45 19.33 126.5 1169.0 0.1035 0.1188 0.1379 0.08591 0.1776 0.05647 0.5959 0.6342 3.797 71.0 0.004649 0.018 0.02749 0.01267 0.01365 0.00255 25.7 24.57 163.1 1972.0 0.1497 0.3161 0.4317 0.1999 0.3379 0.0895 {"projections": [{"projection": [-0.003980252891778946, -0.010626271367073059, -0.006792634725570679, -0.008252562023699284, -0.017011135816574097, -0.08394775539636612, -0.004725664854049683, -0.02420821785926819, 0.012678205966949463, 0.2570701241493225, -0.06448578834533691, -0.7454780340194702, 0.19521880149841309, 1.0544383525848389, 1.7985343933105469, -1.3808135986328125, -10.75503158569336, -35.819427490234375, -137.74705505371094, 1183.744873046875]}]} 14.5 10.89 94.28 640.7 0.1101 0.1099 0.08842 0.05778 0.1856 0.06402 0.2929 0.857 1.928 24.19 0.003818 0.01276 0.02882 0.012 0.0191 0.002808 15.7 15.98 102.8 745.5 0.1313 0.1788 0.256 0.1221 0.2889 0.08006 {"projections": [{"projection": [-0.0006802044808864594, 0.0011173263192176819, -0.0009288638830184937, 0.010933362878859043, -0.012361034750938416, 0.012531246989965439, 0.027433812618255615, 0.04611416161060333, 0.01518857479095459, -0.024760305881500244, 0.03486478328704834, 0.038599371910095215, 0.06981098651885986, -1.8400537967681885, 0.7896766662597656, -11.008148193359375, -5.187385559082031, -10.673084259033203, 57.32084655761719, -139.78204345703125]}]} 15.5 21.08 102.9 803.1 0.112 0.1571 0.1522 0.08481 0.2085 0.06864 1.37 1.213 9.424 176.5 0.008198 0.03889 0.04493 0.02139 0.02018 0.005815 23.17 27.65 157.1 1748.0 0.1517 0.4002 0.4211 0.2134 0.3003 0.1048 {"projections": [{"projection": [0.013529270887374878, 0.011912591755390167, 0.015189513564109802, -0.003150681033730507, -0.01537679135799408, 0.014327986165881157, -0.038580626249313354, 0.02162991464138031, -0.010568737983703613, -0.08091932535171509, 0.19230222702026367, 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- Confirm that predictor is correctly configured for accepting csv input.
- Clean up.
predictor.cloudObj.delete_model() predictor.cloudObj.delete_endpoint() remove_tdapi_context(tdapi_context)