@@ -1,8 +0,0 @@ | |||||
# Revisiting Time Series Outlier Detection: Definitions and Benchmarks | |||||
## Benchmark Directions | |||||
* Step1: Follow the instructions in main page to intall the package | |||||
* Step2: Go to the sub-directories (realworld\_data or synthetic) to see the detailed instruction for running the benchmarking pipelines. | |||||
@@ -1,51 +0,0 @@ | |||||
# Revisiting Time Series Outlier Detection:Definitions and Benchmarks | |||||
This branch is the source code of experiment part of our paper. We provide everything needed when running the experiments: Dataset, Dataset Generator, Pipeline json, Python script, runner and the result (in "./result") we get from the experiments. | |||||
## Resources | |||||
* Paper: Under review | |||||
## Datasets | |||||
To get the dataset, please go to "data/script" to run all of the python scripts. They will download and preprocess the data automatically into "data/" folder. | |||||
## Pipeline | |||||
This Pipeline json files are organized by different settings of algorithms. | |||||
## Runner | |||||
To run a pipeline, you can generate your own pipeline json file from script. | |||||
```python | |||||
sh build_pipelines.sh | |||||
``` | |||||
Then run the pipeline with run\_pipeline.py (Below is the example for running IForest on GECCO dataset) | |||||
```python | |||||
python run_pipeline.py --pipeline_path pipelines/simple/pyod_iforest_0.01.json --data_path ./data/water_quality.csv | |||||
``` | |||||
Or you can directly use the pipelines we have generated in /pipelines with bash script: | |||||
```python | |||||
sh run.sh | |||||
``` | |||||
## Cite this Work: | |||||
If you find this work useful, you may cite this work: | |||||
``` | |||||
@misc{lai2020tods, | |||||
title={TODS: An Automated Time Series Outlier Detection System}, | |||||
author={Kwei-Harng Lai and Daochen Zha and Guanchu Wang and Junjie Xu and Yue Zhao and Devesh Kumar and Yile Chen and Purav Zumkhawaka and Minyang Wan and Diego Martinez and Xia Hu}, | |||||
year={2020}, | |||||
eprint={2009.09822}, | |||||
archivePrefix={arXiv}, | |||||
primaryClass={cs.DB} | |||||
} | |||||
``` | |||||
*Please refer master branch of TODS for details of running pipelines. |
@@ -1,26 +0,0 @@ | |||||
#!/bin/bash | |||||
if [ ! -d "./pipelines/simple" ]; then | |||||
mkdir -p ./pipelines/simple | |||||
fi | |||||
if [ ! -d "./pipelines/subseq" ]; then | |||||
mkdir -p ./pipelines/subseq | |||||
fi | |||||
python pipeline_construction/pipeline_construction_simple.py | |||||
python pipeline_construction/pipeline_construction_subseq.py | |||||
data="swan_sf creditcard web_attack water_quality" | |||||
for d in $data | |||||
do | |||||
if [ ! -d "./pipelines/AE/$d" ]; then | |||||
mkdir -p ./pipelines/AE/$d | |||||
fi | |||||
if [ ! -d "./pipelines/RNN_LSTM/$d" ]; then | |||||
mkdir -p ./pipelines/RNN_LSTM/$d | |||||
fi | |||||
python pipeline_construction/neural/build_AE_pipeline.py "./data/"$d".csv" | |||||
python pipeline_construction/neural/build_RNNLSTM_pipeline.py "./data/"$d".csv" | |||||
done | |||||
@@ -1,43 +0,0 @@ | |||||
import pandas as pd | |||||
import numpy as np | |||||
import os | |||||
import requests | |||||
def preprocess_web_attack(): | |||||
def get_data(): | |||||
link="http://205.174.165.80/CICDataset/CIC-IDS-2017/Dataset/MachineLearningCSV.zip" | |||||
r = requests.get(link) | |||||
with open('./raw_data/cicids.zip', 'wb') as f: | |||||
f.write(r.content) | |||||
os.system("unzip ./raw_data/cicids.zip -d ./raw_data") | |||||
os.system("mv ./raw_data/MachineLearningCSV/Thursday-WorkingHours-Morning-WebAttacks.pcap_ISCX.csv ./raw_data/cicids.csv") | |||||
os.system("rm -r MachineLearningCSV") | |||||
os.system("rm cicids.zip") | |||||
if get_data == True: | |||||
get_data() | |||||
#df = pd.read_csv("./raw_data/MachineLearningCSV/Thursday-WorkingHours-Morning-WebAttacks.pcap_ISCX.csv") | |||||
df = pd.read_csv("./raw_data/cicids.csv") | |||||
df.replace([float('inf'), 'Infinity',''], np.nan, inplace=True) | |||||
df = df.dropna() | |||||
#df = df.sample(frac=0.05, replace=False, random_state=1) | |||||
df[' Timestamp'] = pd.to_datetime(df[' Timestamp'], infer_datetime_format=True) | |||||
df = df.sort_values(by=[' Timestamp']) | |||||
# drop nan and str columns | |||||
drop_cols = list(df.columns)[0:5] | |||||
drop_cols = list(df.columns)[0:5] | |||||
drop_cols.append(list(df.columns)[6]) | |||||
df = df.drop(columns=drop_cols) | |||||
# relabeing and put label in the first column | |||||
df[' Label'] = df[' Label'].map({'BENIGN':"0", "Web Attack Brute Force": "1","Web Attack Sql Injection": "1", "Web Attack XSS": "1"}) | |||||
cols = df.columns.tolist() | |||||
cols = cols[-1:] + cols[:-1] | |||||
df = df[cols] | |||||
df.to_csv("../web_attack.csv", index=False, encoding='utf-8') | |||||
if __name__ == "__main__": | |||||
preprocess_web_attack() |
@@ -1,28 +0,0 @@ | |||||
import pandas as pd | |||||
import os | |||||
import requests | |||||
def preprocess_creditcard(): | |||||
def get_data(): | |||||
link="https://www.openml.org/data/get_csv/1673544/phpKo8OWT" | |||||
r = requests.get(link) | |||||
with open('./raw_data/openml_creditcard.csv', 'wb') as f: | |||||
f.write(r.content) | |||||
get_data() | |||||
df = pd.read_csv("./raw_data/openml_creditcard.csv") | |||||
# drop nan and str columns | |||||
df = df.dropna() | |||||
#df = df.drop(columns=['Time']) | |||||
cols = df.columns.tolist() | |||||
cols = cols[-1:] + cols[:-1] | |||||
df = df[cols] | |||||
#df['Class'] = df['Class'].map({0:"nominal", 1: "anomaly"}) | |||||
#df = df.sample(frac=0.025, replace=False, random_state=1) | |||||
df = df.sort_values(by=['Time']) | |||||
df = df.drop(columns=['Time']) | |||||
df['Class'] = df['Class'].str.replace(r'\'', '').astype(int) | |||||
df.to_csv("../creditcard.csv", index=False, encoding='utf-8') | |||||
if __name__ == "__main__": | |||||
preprocess_creditcard() |
@@ -1,31 +0,0 @@ | |||||
import pandas as pd | |||||
import os | |||||
import requests | |||||
def preprocess_gecco(): | |||||
def get_data(): | |||||
link="https://ndownloader.figshare.com/articles/12451142/versions/1" | |||||
r = requests.get(link) | |||||
with open('./raw_data/gecco.zip', 'wb') as f: | |||||
f.write(r.content) | |||||
os.system("unzip ./raw_data/gecco.zip -d ./raw_data") | |||||
os.system("rm ./raw_data/*.pdf ./raw_data/4_ResourcePackage_GECCO_Industrial_Challenge_2018.zip") | |||||
get_data() | |||||
df = pd.read_csv("./raw_data/1_gecco2018_water_quality.csv") | |||||
# drop nan and str columns | |||||
df = df.dropna() | |||||
df = df.drop(columns=['Time', df.columns[0]]) | |||||
cols = df.columns.tolist() | |||||
cols = cols[-1:] + cols[:-1] | |||||
df = df[cols] | |||||
df['EVENT'] = df['EVENT'].map({False:"0", True: "1"}) | |||||
df = df.rename(columns={"EVENT": "label"}) | |||||
#df['Class'] = df['Class'].map({0:"nominal", 1: "anomaly"}) | |||||
#df = df.sample(frac=0.025, replace=False, random_state=1) | |||||
#df = df.sort_values(by=['Time']) | |||||
#df = df.drop(columns=['Time']) | |||||
df.to_csv("../water_quality.csv", index=False, encoding='utf-8') | |||||
if __name__ == "__main__": | |||||
preprocess_gecco() |
@@ -1,44 +0,0 @@ | |||||
import pandas as pd | |||||
import os | |||||
import requests | |||||
def get_data(): | |||||
link="https://bitbucket.org/gsudmlab/mvtsdata_toolkit/downloads/petdataset_01.zip" | |||||
r = requests.get(link) | |||||
with open('./swan_sf.zip', 'wb') as f: | |||||
f.write(r.content) | |||||
os.system("unzip swan_sf.zip") | |||||
def read_labeled_data(): | |||||
dir_path = "./petdataset_01" | |||||
files = os.listdir(dir_path) | |||||
inlier = [] | |||||
label = {} | |||||
for f in files: | |||||
#if "csv" not in f and "NF" not in f: | |||||
if "csv" not in f: | |||||
continue | |||||
label = f.split("lab[")[1].split("]")[0] | |||||
#print(label) | |||||
f_path = os.path.join(dir_path, f) | |||||
df = pd.read_csv(f_path, header=0, sep='\t') | |||||
df['label'] = label | |||||
inlier.append(df) | |||||
df = pd.concat(inlier, axis=0, ignore_index=True) | |||||
df = df.sort_values(by=['Timestamp']) | |||||
drop_cols = [col for col in df.columns if "label" in col or "loc" in col or "Timestamp" in col][:-1] | |||||
df = df.drop(columns=drop_cols) | |||||
df.reset_index(drop=True, inplace=True) | |||||
df = df.fillna(method='ffill') | |||||
df = df.dropna(axis="columns") | |||||
df['label'].replace({"NF":0, "C":1, "B":1, "M":1, "X":1}, inplace=True) | |||||
df['IS_TMFI'].replace({True:1, False:0}, inplace=True) | |||||
cols = df.columns.tolist() | |||||
cols = cols[-1:] + cols[:-1] | |||||
df = df[cols] | |||||
df.to_csv("../swan_sf.csv", index=False) | |||||
if __name__ == "__main__": | |||||
get_data() | |||||
read_labeled_data() | |||||
os.system("rm -rf swan_sf.zip petdataset_01") |
@@ -1,78 +0,0 @@ | |||||
import sys | |||||
import pandas as pd | |||||
dataset = sys.argv[1] | |||||
data_name = dataset.split("/")[-1].split(".")[0] | |||||
df = pd.read_csv(dataset) | |||||
feature_dim = len(df.columns) - 1 # take off label | |||||
from d3m import index | |||||
from d3m.metadata.base import ArgumentType | |||||
from d3m.metadata.pipeline import Pipeline, PrimitiveStep | |||||
for cont_rate in [0.01, 0.05, 0.1, 0.15, 0.2, 0.25]: | |||||
# Creating pipeline | |||||
pipeline_description = Pipeline() | |||||
pipeline_description.add_input(name='inputs') | |||||
# Step 0: dataset_to_dataframe | |||||
step_0 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.dataset_to_dataframe')) | |||||
step_0.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='inputs.0') | |||||
step_0.add_output('produce') | |||||
pipeline_description.add_step(step_0) | |||||
# Step 1: column_parser | |||||
step_1 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.column_parser')) | |||||
step_1.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_1.add_output('produce') | |||||
pipeline_description.add_step(step_1) | |||||
# Step 2: extract_columns_by_semantic_types(attributes) | |||||
step_2 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_2.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
step_2.add_output('produce') | |||||
step_2.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/Attribute']) | |||||
pipeline_description.add_step(step_2) | |||||
# Step 3: extract_columns_by_semantic_types(targets) | |||||
step_3 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_3.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_3.add_output('produce') | |||||
step_3.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/TrueTarget']) | |||||
pipeline_description.add_step(step_3) | |||||
attributes = 'steps.2.produce' | |||||
targets = 'steps.3.produce' | |||||
# Step 4: processing | |||||
step_4 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.timeseries_processing.transformation.axiswise_scaler')) | |||||
step_4.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference=attributes) | |||||
step_4.add_output('produce') | |||||
pipeline_description.add_step(step_4) | |||||
# Step 5: algorithm` | |||||
step_5 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.detection_algorithm.pyod_ae')) | |||||
step_5.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.4.produce') | |||||
step_5.add_hyperparameter(name='hidden_neurons', argument_type=ArgumentType.VALUE, data=[feature_dim, 32, 16, 32, feature_dim]) | |||||
step_5.add_hyperparameter(name='contamination', argument_type=ArgumentType.VALUE, data=cont_rate) | |||||
step_5.add_output('produce') | |||||
pipeline_description.add_step(step_5) | |||||
# Step 6: Predictions | |||||
step_6 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.construct_predictions')) | |||||
step_6.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.5.produce') | |||||
step_6.add_argument(name='reference', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
step_6.add_output('produce') | |||||
pipeline_description.add_step(step_6) | |||||
# Final Output | |||||
pipeline_description.add_output(name='output predictions', data_reference='steps.6.produce') | |||||
# Output to json | |||||
data = pipeline_description.to_json() | |||||
with open('./pipelines/AE/'+data_name+'/ae_pipeline_'+str(cont_rate)+'.json', 'w') as f: | |||||
f.write(data) | |||||
print(data) | |||||
@@ -1,78 +0,0 @@ | |||||
import sys | |||||
import pandas as pd | |||||
dataset = sys.argv[1] | |||||
data_name = dataset.split("/")[-1].split(".")[0] | |||||
df = pd.read_csv(dataset) | |||||
feature_dim = len(df.columns) - 1 # take off label | |||||
from d3m import index | |||||
from d3m.metadata.base import ArgumentType | |||||
from d3m.metadata.pipeline import Pipeline, PrimitiveStep | |||||
for cont_rate in [0.01, 0.05, 0.1, 0.15, 0.2, 0.25]: | |||||
# Creating pipeline | |||||
pipeline_description = Pipeline() | |||||
pipeline_description.add_input(name='inputs') | |||||
# Step 0: dataset_to_dataframe | |||||
step_0 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.dataset_to_dataframe')) | |||||
step_0.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='inputs.0') | |||||
step_0.add_output('produce') | |||||
pipeline_description.add_step(step_0) | |||||
# Step 1: column_parser | |||||
step_1 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.column_parser')) | |||||
step_1.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_1.add_output('produce') | |||||
pipeline_description.add_step(step_1) | |||||
# Step 2: extract_columns_by_semantic_types(attributes) | |||||
step_2 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_2.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
step_2.add_output('produce') | |||||
step_2.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/Attribute']) | |||||
pipeline_description.add_step(step_2) | |||||
# Step 3: extract_columns_by_semantic_types(targets) | |||||
step_3 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_3.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_3.add_output('produce') | |||||
step_3.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/TrueTarget']) | |||||
pipeline_description.add_step(step_3) | |||||
attributes = 'steps.2.produce' | |||||
targets = 'steps.3.produce' | |||||
# Step 4: processing | |||||
step_4 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.timeseries_processing.transformation.axiswise_scaler')) | |||||
step_4.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference=attributes) | |||||
step_4.add_output('produce') | |||||
pipeline_description.add_step(step_4) | |||||
# Step 5: algorithm` | |||||
step_5 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.detection_algorithm.LSTMODetector')) | |||||
step_5.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.4.produce') | |||||
step_5.add_hyperparameter(name='feature_dim', argument_type=ArgumentType.VALUE, data=feature_dim) | |||||
step_5.add_hyperparameter(name='contamination', argument_type=ArgumentType.VALUE, data=cont_rate) | |||||
step_5.add_output('produce') | |||||
pipeline_description.add_step(step_5) | |||||
# Step 6: Predictions | |||||
step_6 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.construct_predictions')) | |||||
step_6.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.5.produce') | |||||
step_6.add_argument(name='reference', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
step_6.add_output('produce') | |||||
pipeline_description.add_step(step_6) | |||||
# Final Output | |||||
pipeline_description.add_output(name='output predictions', data_reference='steps.6.produce') | |||||
# Output to json | |||||
data = pipeline_description.to_json() | |||||
with open('./pipelines/RNN_LSTM/'+data_name+'/rnnlstm_pipeline_'+str(cont_rate)+'.json', 'w') as f: | |||||
f.write(data) | |||||
print(data) | |||||
@@ -1,183 +0,0 @@ | |||||
import uuid | |||||
import random | |||||
from d3m.metadata.pipeline import Pipeline | |||||
from axolotl.algorithms.base import PipelineSearchBase | |||||
from axolotl.utils import schemas as schemas_utils | |||||
primitive_python_paths = { # pragma: no cover | |||||
'data_processing': [ | |||||
#'d3m.primitives.tods.data_processing.time_interval_transform', | |||||
#'d3m.primitives.tods.data_processing.categorical_to_binary', | |||||
#'d3m.primitives.tods.data_processing.column_filter', | |||||
#'d3m.primitives.tods.data_processing.timestamp_validation', | |||||
#'d3m.primitives.tods.data_processing.duplication_validation', | |||||
#'d3m.primitives.tods.data_processing.continuity_validation', | |||||
], | |||||
'timeseries_processing': [ | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.axiswise_scaler', | |||||
#'d3m.primitives.tods.timeseries_processing.subsequence_segmentation', | |||||
'd3m.primitives.tods.timeseries_processing.transformation.standard_scaler', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.power_transformer', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.quantile_transformer', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.moving_average_transform', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.simple_exponential_smoothing', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.holt_smoothing', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.holt_winters_exponential_smoothing', | |||||
#'d3m.primitives.tods.timeseries_processing.decomposition.time_series_seasonality_trend_decomposition', | |||||
], | |||||
'feature_analysis': [ | |||||
#'d3m.primitives.tods.feature_analysis.auto_correlation', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_median', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_g_mean', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_abs_energy', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_abs_sum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_h_mean', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_maximum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_minimum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean_abs', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean_abs_temporal_derivative', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean_temporal_derivative', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_median_abs_deviation', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_kurtosis', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_skew', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_std', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_var', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_variation', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_vec_sum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_willison_amplitude', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_zero_crossing', | |||||
#'d3m.primitives.tods.feature_analysis.spectral_residual_transform', | |||||
#'d3m.primitives.tods.feature_analysis.fast_fourier_transform', | |||||
#'d3m.primitives.tods.feature_analysis.discrete_cosine_transform', | |||||
#'d3m.primitives.tods.feature_analysis.non_negative_matrix_factorization', | |||||
#'d3m.primitives.tods.feature_analysis.bk_filter', | |||||
#'d3m.primitives.tods.feature_analysis.hp_filter', | |||||
#'d3m.primitives.tods.feature_analysis.truncated_svd', | |||||
#'d3m.primitives.tods.feature_analysis.wavelet_transform', | |||||
#'d3m.primitives.tods.feature_analysis.trmf', | |||||
], | |||||
'detection_algorithm': [ | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_ae', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_vae', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_cof', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_sod', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_abod', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_hbos', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_iforest', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_lof', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_knn', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_ocsvm', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_loda', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_cblof', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_sogaal', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_mogaal', | |||||
'd3m.primitives.tods.detection_algorithm.matrix_profile', | |||||
'd3m.primitives.tods.detection_algorithm.AutoRegODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.LSTMODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.AutoRegODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.PCAODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.KDiscordODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.deeplog', | |||||
#'d3m.primitives.tods.detection_algorithm.telemanom', | |||||
], | |||||
'contamination': [0.01, 0.05, 0.1, 0.15, 0.2, 0.25], | |||||
} | |||||
def _generate_pipeline(combinations): | |||||
from d3m import index | |||||
from d3m.metadata.base import ArgumentType | |||||
from d3m.metadata.pipeline import Pipeline, PrimitiveStep | |||||
piplines = [] | |||||
for combination in combinations: | |||||
# Creating pipeline | |||||
pipeline_description = Pipeline() | |||||
pipeline_description.add_input(name='inputs') | |||||
# The first three steps are fixed | |||||
# Step 0: dataset_to_dataframe | |||||
step_0 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.dataset_to_dataframe')) | |||||
step_0.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='inputs.0') | |||||
step_0.add_output('produce') | |||||
pipeline_description.add_step(step_0) | |||||
# Step 1: column_parser | |||||
step_1 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.column_parser')) | |||||
step_1.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_1.add_output('produce') | |||||
pipeline_description.add_step(step_1) | |||||
# Step 2: extract_columns_by_semantic_types(attributes) | |||||
step_2 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_2.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
step_2.add_output('produce') | |||||
step_2.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/Attribute']) | |||||
pipeline_description.add_step(step_2) | |||||
# Step 3: extract_columns_by_semantic_types(targets) | |||||
step_3 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_3.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_3.add_output('produce') | |||||
step_3.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/TrueTarget']) | |||||
pipeline_description.add_step(step_3) | |||||
attributes = 'steps.2.produce' | |||||
targets = 'steps.3.produce' | |||||
tods_step_4 = PrimitiveStep(primitive=index.get_primitive(combination[0])) | |||||
tods_step_4.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference=attributes) | |||||
#tods_step_4.add_hyperparameter(name='window_size', argument_type=ArgumentType.VALUE, data=10) | |||||
#tods_step_4.add_hyperparameter(name='step', argument_type=ArgumentType.VALUE, data=1) | |||||
tods_step_4.add_output('produce') | |||||
pipeline_description.add_step(tods_step_4) | |||||
tods_step_5= PrimitiveStep(primitive=index.get_primitive(combination[1])) | |||||
tods_step_5.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.4.produce') | |||||
tods_step_5.add_output('produce') | |||||
tods_step_5.add_hyperparameter(name='contamination', argument_type=ArgumentType.VALUE, data=combination[2]) | |||||
pipeline_description.add_step(tods_step_5) | |||||
# Finalize the pipeline | |||||
final_step = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.construct_predictions')) | |||||
final_step.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.5.produce') | |||||
final_step.add_argument(name='reference', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
final_step.add_output('produce') | |||||
pipeline_description.add_step(final_step) | |||||
pipeline_description.add_output(name='output predictions', data_reference='steps.6.produce') | |||||
data = pipeline_description.to_json() | |||||
#with open('../pipelines/'+str(combination[1].split(".")[-1])+'_'+str(combination[2])+".json", 'w') as f: | |||||
with open('./pipelines/simple/'+str(combination[1].split(".")[-1])+'_'+str(combination[2])+".json", 'w') as f: | |||||
f.write(data) | |||||
pipeline_description.id = str(uuid.uuid4()) | |||||
pipeline_description.created = Pipeline().created | |||||
piplines.append(pipeline_description) | |||||
return piplines | |||||
def _generate_pipelines(primitive_python_paths, cpu_count=40): # pragma: no cover | |||||
""" | |||||
Args: | |||||
primitive_python_paths: a list of primitive Python paths for algorithms | |||||
Returns: | |||||
the pipline description json | |||||
""" | |||||
import itertools | |||||
import multiprocessing as mp | |||||
#components = ['data_processing', 'timeseries_processing', 'feature_analysis', 'detection_algorithm'] | |||||
components = ['timeseries_processing', 'detection_algorithm', 'contamination'] | |||||
combinations = itertools.product(*(primitive_python_paths[k] for k in components)) | |||||
return _generate_pipeline(combinations) | |||||
if __name__ == "__main__": | |||||
combinations = _generate_pipelines(primitive_python_paths) | |||||
print(combinations) |
@@ -1,183 +0,0 @@ | |||||
import uuid | |||||
import random | |||||
from d3m.metadata.pipeline import Pipeline | |||||
from axolotl.algorithms.base import PipelineSearchBase | |||||
from axolotl.utils import schemas as schemas_utils | |||||
primitive_python_paths = { # pragma: no cover | |||||
'data_processing': [ | |||||
#'d3m.primitives.tods.data_processing.time_interval_transform', | |||||
#'d3m.primitives.tods.data_processing.categorical_to_binary', | |||||
#'d3m.primitives.tods.data_processing.column_filter', | |||||
#'d3m.primitives.tods.data_processing.timestamp_validation', | |||||
#'d3m.primitives.tods.data_processing.duplication_validation', | |||||
#'d3m.primitives.tods.data_processing.continuity_validation', | |||||
], | |||||
'timeseries_processing': [ | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.axiswise_scaler', | |||||
'd3m.primitives.tods.timeseries_processing.subsequence_segmentation', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.standard_scaler', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.power_transformer', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.quantile_transformer', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.moving_average_transform', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.simple_exponential_smoothing', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.holt_smoothing', | |||||
#'d3m.primitives.tods.timeseries_processing.transformation.holt_winters_exponential_smoothing', | |||||
#'d3m.primitives.tods.timeseries_processing.decomposition.time_series_seasonality_trend_decomposition', | |||||
], | |||||
'feature_analysis': [ | |||||
#'d3m.primitives.tods.feature_analysis.auto_correlation', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_median', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_g_mean', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_abs_energy', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_abs_sum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_h_mean', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_maximum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_minimum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean_abs', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean_abs_temporal_derivative', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_mean_temporal_derivative', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_median_abs_deviation', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_kurtosis', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_skew', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_std', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_var', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_variation', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_vec_sum', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_willison_amplitude', | |||||
#'d3m.primitives.tods.feature_analysis.statistical_zero_crossing', | |||||
#'d3m.primitives.tods.feature_analysis.spectral_residual_transform', | |||||
#'d3m.primitives.tods.feature_analysis.fast_fourier_transform', | |||||
#'d3m.primitives.tods.feature_analysis.discrete_cosine_transform', | |||||
#'d3m.primitives.tods.feature_analysis.non_negative_matrix_factorization', | |||||
#'d3m.primitives.tods.feature_analysis.bk_filter', | |||||
#'d3m.primitives.tods.feature_analysis.hp_filter', | |||||
#'d3m.primitives.tods.feature_analysis.truncated_svd', | |||||
#'d3m.primitives.tods.feature_analysis.wavelet_transform', | |||||
#'d3m.primitives.tods.feature_analysis.trmf', | |||||
], | |||||
'detection_algorithm': [ | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_ae', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_vae', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_cof', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_sod', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_abod', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_hbos', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_iforest', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_lof', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_knn', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_ocsvm', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_loda', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_cblof', | |||||
'd3m.primitives.tods.detection_algorithm.pyod_sogaal', | |||||
#'d3m.primitives.tods.detection_algorithm.pyod_mogaal', | |||||
#'d3m.primitives.tods.detection_algorithm.matrix_profile', | |||||
#'d3m.primitives.tods.detection_algorithm.AutoRegODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.LSTMODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.AutoRegODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.PCAODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.KDiscordODetector', | |||||
#'d3m.primitives.tods.detection_algorithm.deeplog', | |||||
#'d3m.primitives.tods.detection_algorithm.telemanom', | |||||
], | |||||
'contamination': [0.01, 0.05, 0.1, 0.15, 0.2, 0.25], | |||||
} | |||||
def _generate_pipeline(combinations): | |||||
from d3m import index | |||||
from d3m.metadata.base import ArgumentType | |||||
from d3m.metadata.pipeline import Pipeline, PrimitiveStep | |||||
piplines = [] | |||||
for combination in combinations: | |||||
# Creating pipeline | |||||
pipeline_description = Pipeline() | |||||
pipeline_description.add_input(name='inputs') | |||||
# The first three steps are fixed | |||||
# Step 0: dataset_to_dataframe | |||||
step_0 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.dataset_to_dataframe')) | |||||
step_0.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='inputs.0') | |||||
step_0.add_output('produce') | |||||
pipeline_description.add_step(step_0) | |||||
# Step 1: column_parser | |||||
step_1 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.column_parser')) | |||||
step_1.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_1.add_output('produce') | |||||
pipeline_description.add_step(step_1) | |||||
# Step 2: extract_columns_by_semantic_types(attributes) | |||||
step_2 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_2.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
step_2.add_output('produce') | |||||
step_2.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/Attribute']) | |||||
pipeline_description.add_step(step_2) | |||||
# Step 3: extract_columns_by_semantic_types(targets) | |||||
step_3 = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.extract_columns_by_semantic_types')) | |||||
step_3.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.0.produce') | |||||
step_3.add_output('produce') | |||||
step_3.add_hyperparameter(name='semantic_types', argument_type=ArgumentType.VALUE, | |||||
data=['https://metadata.datadrivendiscovery.org/types/TrueTarget']) | |||||
pipeline_description.add_step(step_3) | |||||
attributes = 'steps.2.produce' | |||||
targets = 'steps.3.produce' | |||||
tods_step_4 = PrimitiveStep(primitive=index.get_primitive(combination[0])) | |||||
tods_step_4.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference=attributes) | |||||
tods_step_4.add_hyperparameter(name='window_size', argument_type=ArgumentType.VALUE, data=10) | |||||
tods_step_4.add_hyperparameter(name='step', argument_type=ArgumentType.VALUE, data=1) | |||||
tods_step_4.add_output('produce') | |||||
pipeline_description.add_step(tods_step_4) | |||||
tods_step_5= PrimitiveStep(primitive=index.get_primitive(combination[1])) | |||||
tods_step_5.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.4.produce') | |||||
tods_step_5.add_output('produce') | |||||
tods_step_5.add_hyperparameter(name='contamination', argument_type=ArgumentType.VALUE, data=combination[2]) | |||||
pipeline_description.add_step(tods_step_5) | |||||
# Finalize the pipeline | |||||
final_step = PrimitiveStep(primitive=index.get_primitive('d3m.primitives.tods.data_processing.construct_predictions')) | |||||
final_step.add_argument(name='inputs', argument_type=ArgumentType.CONTAINER, data_reference='steps.5.produce') | |||||
final_step.add_argument(name='reference', argument_type=ArgumentType.CONTAINER, data_reference='steps.1.produce') | |||||
final_step.add_output('produce') | |||||
pipeline_description.add_step(final_step) | |||||
pipeline_description.add_output(name='output predictions', data_reference='steps.6.produce') | |||||
data = pipeline_description.to_json() | |||||
#with open('../pipelines/'+str(combination[1].split(".")[-1])+'_'+str(combination[2])+".json", 'w') as f: | |||||
with open('./pipelines/subseq/'+str(combination[1].split(".")[-1])+'_subseq_'+str(combination[2])+".json", 'w') as f: | |||||
f.write(data) | |||||
pipeline_description.id = str(uuid.uuid4()) | |||||
pipeline_description.created = Pipeline().created | |||||
piplines.append(pipeline_description) | |||||
return piplines | |||||
def _generate_pipelines(primitive_python_paths, cpu_count=40): # pragma: no cover | |||||
""" | |||||
Args: | |||||
primitive_python_paths: a list of primitive Python paths for algorithms | |||||
Returns: | |||||
the pipline description json | |||||
""" | |||||
import itertools | |||||
import multiprocessing as mp | |||||
#components = ['data_processing', 'timeseries_processing', 'feature_analysis', 'detection_algorithm'] | |||||
components = ['timeseries_processing', 'detection_algorithm', 'contamination'] | |||||
combinations = itertools.product(*(primitive_python_paths[k] for k in components)) | |||||
return _generate_pipeline(combinations) | |||||
if __name__ == "__main__": | |||||
combinations = _generate_pipelines(primitive_python_paths) | |||||
print(combinations) |
@@ -1 +0,0 @@ | |||||
{"id": "9913179f-f470-49fa-b373-a53603341cf7", "schema": "https://metadata.datadrivendiscovery.org/schemas/v0/pipeline.json", "created": "2021-06-01T20:36:06.644888Z", "inputs": [{"name": "inputs"}], "outputs": [{"data": "steps.6.produce", "name": "output predictions"}], "steps": [{"type": "PRIMITIVE", "primitive": {"id": "c78138d9-9377-31dc-aee8-83d9df049c60", "version": "0.3.0", "python_path": "d3m.primitives.tods.data_processing.dataset_to_dataframe", "name": "Extract a DataFrame from a Dataset"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "inputs.0"}}, "outputs": [{"id": "produce"}]}, {"type": "PRIMITIVE", "primitive": {"id": "81235c29-aeb9-3828-911a-1b25319b6998", "version": "0.6.0", "python_path": "d3m.primitives.tods.data_processing.column_parser", "name": "Parses strings into their types"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "steps.0.produce"}}, "outputs": [{"id": "produce"}]}, {"type": "PRIMITIVE", "primitive": {"id": "a996cd89-ddf0-367f-8e7f-8c013cbc2891", "version": "0.4.0", "python_path": "d3m.primitives.tods.data_processing.extract_columns_by_semantic_types", "name": "Extracts columns by semantic type"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "steps.1.produce"}}, "outputs": [{"id": "produce"}], "hyperparams": {"semantic_types": {"type": "VALUE", "data": ["https://metadata.datadrivendiscovery.org/types/Attribute"]}}}, {"type": "PRIMITIVE", "primitive": {"id": "a996cd89-ddf0-367f-8e7f-8c013cbc2891", "version": "0.4.0", "python_path": "d3m.primitives.tods.data_processing.extract_columns_by_semantic_types", "name": "Extracts columns by semantic type"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "steps.0.produce"}}, "outputs": [{"id": "produce"}], "hyperparams": {"semantic_types": {"type": "VALUE", "data": ["https://metadata.datadrivendiscovery.org/types/TrueTarget"]}}}, {"type": "PRIMITIVE", "primitive": {"id": "642de2e7-5590-3cab-9266-2a53c326c461", "version": "0.0.1", "python_path": "d3m.primitives.tods.timeseries_processing.transformation.axiswise_scaler", "name": "Axis_wise_scale"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "steps.2.produce"}}, "outputs": [{"id": "produce"}]}, {"type": "PRIMITIVE", "primitive": {"id": "67e7fcdf-d645-3417-9aa4-85cd369487d9", "version": "0.0.1", "python_path": "d3m.primitives.tods.detection_algorithm.pyod_ae", "name": "TODS.anomaly_detection_primitives.AutoEncoder"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "steps.4.produce"}}, "outputs": [{"id": "produce"}], "hyperparams": {"hidden_neurons": {"type": "VALUE", "data": [29, 32, 16, 32, 29]}, "contamination": {"type": "VALUE", "data": 0.01}}}, {"type": "PRIMITIVE", "primitive": {"id": "2530840a-07d4-3874-b7d8-9eb5e4ae2bf3", "version": "0.3.0", "python_path": "d3m.primitives.tods.data_processing.construct_predictions", "name": "Construct pipeline predictions output"}, "arguments": {"inputs": {"type": "CONTAINER", "data": "steps.5.produce"}, "reference": {"type": "CONTAINER", "data": "steps.1.produce"}}, "outputs": [{"id": "produce"}]}], "digest": "d42e26f9c3f72aaaf3935c651f6a54ef95dad4e3185d48eaed8001593aed3f43"} |
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