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ETL with NVTabular

This notebook is created using the latest stable merlin-pytorch container.

Launch the docker container

docker run -it --gpus device=0 -p 8000:8000 -p 8001:8001 -p 8002:8002 -p 8888:8888 -v <path_to_data>:/workspace/data/  nvcr.io/nvidia/merlin/merlin-pytorch:22.XX

This script will mount your local data folder that includes your data files to /workspace/data directory in the merlin-pytorch docker container.

Overview

This notebook demonstrates how to use NVTabular to perform the feature engineering that is needed to model the YOOCHOOSE dataset which contains a collection of sessions from a retailer. Each session encapsulates the click events that the user performed in that session.

The dataset is available on Kaggle. You need to download it and copy to the DATA_FOLDER path. Note that we are only using the yoochoose-clicks.dat file.

First, let’s start by importing several libraries:

import os
import glob
import numpy as np
import gc

import cudf
import cupy
import nvtabular as nvt
from merlin.dag import ColumnSelector
from merlin.schema import Schema, Tags

/usr/local/lib/python3.8/dist-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm
/usr/local/lib/python3.8/dist-packages/merlin/dtypes/mappings/tf.py:52: UserWarning: Tensorflow dtype mappings did not load successfully due to an error: No module named 'tensorflow'
  warn(f"Tensorflow dtype mappings did not load successfully due to an error: {exc.msg}")

Avoid Numba low occupancy warnings:

from numba import config
config.CUDA_LOW_OCCUPANCY_WARNINGS = 0

Define Data Input and Output Paths

DATA_FOLDER = "/workspace/data/"
FILENAME_PATTERN = 'yoochoose-clicks.dat'
DATA_PATH = os.path.join(DATA_FOLDER, FILENAME_PATTERN)

OUTPUT_FOLDER = "./yoochoose_transformed"
OVERWRITE = False

Load and clean raw data

interactions_df = cudf.read_csv(DATA_PATH, sep=',', 
                                names=['session_id','timestamp', 'item_id', 'category'], 
                                dtype=['int', 'datetime64[s]', 'int', 'int'])

Remove repeated interactions within the same session

print("Count with in-session repeated interactions: {}".format(len(interactions_df)))
# Sorts the dataframe by session and timestamp, to remove consecutive repetitions
interactions_df.timestamp = interactions_df.timestamp.astype(int)
interactions_df = interactions_df.sort_values(['session_id', 'timestamp'])
past_ids = interactions_df['item_id'].shift(1).fillna()
session_past_ids = interactions_df['session_id'].shift(1).fillna()
# Keeping only no consecutive repeated in session interactions
interactions_df = interactions_df[~((interactions_df['session_id'] == session_past_ids) & (interactions_df['item_id'] == past_ids))]
print("Count after removed in-session repeated interactions: {}".format(len(interactions_df)))

Count with in-session repeated interactions: 33003944
Count after removed in-session repeated interactions: 28971543

Create new feature with the timestamp when the item was first seen

items_first_ts_df = interactions_df.groupby('item_id').agg({'timestamp': 'min'}).reset_index().rename(columns={'timestamp': 'itemid_ts_first'})
interactions_merged_df = interactions_df.merge(items_first_ts_df, on=['item_id'], how='left')
print(interactions_merged_df.head())

   session_id   timestamp    item_id  category  itemid_ts_first
0        7401  1396439960  214826816         0       1396321828
1        7402  1396780751  214613743         0       1396329089
2        7402  1396780780  214827011         0       1396735848
3        7402  1396780912  214821388         0       1396330458
4        7402  1396780991  214827011         0       1396735848

Let’s save the interactions_merged_df to disk to be able to use in the inference step.

interactions_merged_df.to_parquet(os.path.join(DATA_FOLDER, 'interactions_merged_df.parquet'))

# print the total number of unique items in the dataset
print(interactions_merged_df.item_id.nunique())

52739

# free gpu memory
del interactions_df, session_past_ids, items_first_ts_df
gc.collect()

518

Define a preprocessing workflow with NVTabular

NVTabular is a feature engineering and preprocessing library for tabular data designed to quickly and easily manipulate terabyte scale datasets used to train deep learning based recommender systems. It provides a high level abstraction to simplify code and accelerates computation on the GPU using the RAPIDS cuDF library.

NVTabular supports different feature engineering transformations required by deep learning (DL) models such as Categorical encoding and numerical feature normalization. It also supports feature engineering and generating sequential features.

More information about the supported features can be found here.

Feature engineering: Create and Transform items features

In this cell, we are defining three transformations ops:

    1. Encoding categorical variables using Categorify() op. We set start_index to 1 so that encoded null values start from 1 instead of 0 because we reserve 0 for padding the sequence features.

    1. Deriving temporal features from timestamp and computing their cyclical representation using a custom lambda function.

    1. Computing the item recency in days using a custom op. Note that item recency is defined as the difference between the first occurrence of the item in dataset and the actual date of item interaction.

For more ETL workflow examples, visit NVTabular example notebooks.

# Encodes categorical features as contiguous integers
cat_feats = ColumnSelector(['category', 'item_id']) >> nvt.ops.Categorify(start_index=1)

# create time features
session_ts = ColumnSelector(['timestamp'])
session_time = (
    session_ts >> 
    nvt.ops.LambdaOp(lambda col: cudf.to_datetime(col, unit='s')) >> 
    nvt.ops.Rename(name = 'event_time_dt')
)
sessiontime_weekday = (
    session_time >> 
    nvt.ops.LambdaOp(lambda col: col.dt.weekday) >> 
    nvt.ops.Rename(name ='et_dayofweek')
)

# Derive cyclical features: Define a custom lambda function 
def get_cycled_feature_value_sin(col, max_value):
    value_scaled = (col + 0.000001) / max_value
    value_sin = np.sin(2*np.pi*value_scaled)
    return value_sin

weekday_sin = sessiontime_weekday >> (lambda col: get_cycled_feature_value_sin(col+1, 7)) >> nvt.ops.Rename(name = 'et_dayofweek_sin')

# Compute Item recency: Define a custom Op 
class ItemRecency(nvt.ops.Operator):
    def transform(self, columns, gdf):
        for column in columns.names:
            col = gdf[column]
            item_first_timestamp = gdf['itemid_ts_first']
            delta_days = (col - item_first_timestamp) / (60*60*24)
            gdf[column + "_age_days"] = delta_days * (delta_days >=0)
        return gdf

    def compute_selector(
        self,
        input_schema: Schema,
        selector: ColumnSelector,
        parents_selector: ColumnSelector,
        dependencies_selector: ColumnSelector,
    ) -> ColumnSelector:
        self._validate_matching_cols(input_schema, parents_selector, "computing input selector")
        return parents_selector

    def column_mapping(self, col_selector):
        column_mapping = {}
        for col_name in col_selector.names:
            column_mapping[col_name + "_age_days"] = [col_name]
        return column_mapping

    @property
    def dependencies(self):
        return ["itemid_ts_first"]

    @property
    def output_dtype(self):
        return np.float64
    
recency_features = session_ts >> ItemRecency() 
# Apply standardization to this continuous feature
recency_features_norm = recency_features >> nvt.ops.LogOp() >> nvt.ops.Normalize(out_dtype=np.float32) >> nvt.ops.Rename(name='product_recency_days_log_norm')

time_features = (
    session_time +
    sessiontime_weekday +
    weekday_sin + 
    recency_features_norm
)

features = ColumnSelector(['session_id', 'timestamp']) + cat_feats + time_features

Define the preprocessing of sequential features

Once the item features are generated, the objective of this cell is to group interactions at the session level, sorting the interactions by time. We additionally truncate all sessions to first 20 interactions and filter out sessions with less than 2 interactions.

# Define Groupby Operator
groupby_features = features >> nvt.ops.Groupby(
    groupby_cols=["session_id"], 
    sort_cols=["timestamp"],
    aggs={
        'item_id': ["list", "count"],
        'category': ["list"],  
        'timestamp': ["first"],
        'event_time_dt': ["first"],
        'et_dayofweek_sin': ["list"],
        'product_recency_days_log_norm': ["list"]
        },
    name_sep="-")

# Truncate sequence features to first interacted 20 items 
SESSIONS_MAX_LENGTH = 20 


item_feat = groupby_features['item_id-list'] >> nvt.ops.TagAsItemID()
cont_feats = groupby_features['et_dayofweek_sin-list', 'product_recency_days_log_norm-list'] >> nvt.ops.AddMetadata(tags=[Tags.CONTINUOUS])


groupby_features_list =  item_feat + cont_feats + groupby_features['category-list']
groupby_features_truncated = groupby_features_list >> nvt.ops.ListSlice(-SESSIONS_MAX_LENGTH, pad=True)

# Calculate session day index based on 'event_time_dt-first' column
day_index = ((groupby_features['event_time_dt-first'])  >> 
             nvt.ops.LambdaOp(lambda col: (col - col.min()).dt.days +1) >> 
             nvt.ops.Rename(f = lambda col: "day_index") >>
             nvt.ops.AddMetadata(tags=[Tags.CATEGORICAL])
            )

# tag session_id column for serving with legacy api
sess_id = groupby_features['session_id'] >> nvt.ops.AddMetadata(tags=[Tags.CATEGORICAL])

# Select features for training 
selected_features = sess_id + groupby_features['item_id-count'] + groupby_features_truncated + day_index

# Filter out sessions with less than 2 interactions 
MINIMUM_SESSION_LENGTH = 2
filtered_sessions = selected_features >> nvt.ops.Filter(f=lambda df: df["item_id-count"] >= MINIMUM_SESSION_LENGTH)

Execute NVTabular workflow

Once we have defined the general workflow (filtered_sessions), we provide our cudf dataset to nvt.Dataset class which is optimized to split data into chunks that can fit in device memory and to handle the calculation of complex global statistics. Then, we execute the pipeline that fits and transforms data to get the desired output features.

dataset = nvt.Dataset(interactions_merged_df)
workflow = nvt.Workflow(filtered_sessions)
# Learn features statistics necessary of the preprocessing workflow
# The following will generate schema.pbtxt file in the provided folder and export the parquet files.
workflow.fit_transform(dataset).to_parquet(os.path.join(DATA_FOLDER, "processed_nvt"))

/usr/local/lib/python3.8/dist-packages/merlin/schema/tags.py:149: UserWarning: Compound tags like Tags.ITEM_ID have been deprecated and will be removed in a future version. Please use the atomic versions of these tags, like [<Tags.ITEM: 'item'>, <Tags.ID: 'id'>].
  warnings.warn(
/usr/local/lib/python3.8/dist-packages/merlin/schema/tags.py:149: UserWarning: Compound tags like Tags.ITEM_ID have been deprecated and will be removed in a future version. Please use the atomic versions of these tags, like [<Tags.ITEM: 'item'>, <Tags.ID: 'id'>].
  warnings.warn(

Let’s print the head of our preprocessed dataset. You can notice that now each example (row) is a session and the sequential features with respect to user interactions were converted to lists with matching length.

workflow.output_schema
name tags dtype is_list is_ragged properties.num_buckets properties.freq_threshold properties.max_size properties.start_index properties.cat_path properties.domain.min properties.domain.max properties.domain.name properties.embedding_sizes.cardinality properties.embedding_sizes.dimension properties.value_count.min properties.value_count.max
0 session_id (Tags.CATEGORICAL) DType(name='int64', element_type=<ElementType.... False False NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
1 item_id-count (Tags.CATEGORICAL) DType(name='int32', element_type=<ElementType.... False False NaN 0.0 0.0 1.0 .//categories/unique.item_id.parquet 0.0 52740.0 item_id 52741.0 512.0 NaN NaN
2 item_id-list (Tags.CATEGORICAL, Tags.ITEM, Tags.ITEM_ID, Ta... DType(name='int64', element_type=<ElementType.... True False NaN 0.0 0.0 1.0 .//categories/unique.item_id.parquet 0.0 52740.0 item_id 52741.0 512.0 20.0 20.0
3 et_dayofweek_sin-list (Tags.CONTINUOUS, Tags.LIST) DType(name='float32', element_type=<ElementTyp... True False NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 20.0 20.0
4 product_recency_days_log_norm-list (Tags.CONTINUOUS, Tags.LIST) DType(name='float32', element_type=<ElementTyp... True False NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 20.0 20.0
5 category-list (Tags.CATEGORICAL, Tags.LIST) DType(name='int64', element_type=<ElementType.... True False NaN 0.0 0.0 1.0 .//categories/unique.category.parquet 0.0 335.0 category 336.0 42.0 20.0 20.0
6 day_index (Tags.CATEGORICAL) DType(name='int64', element_type=<ElementType.... False False NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN

Save the preprocessing workflow

workflow.save(os.path.join(DATA_FOLDER, "workflow_etl"))

Export pre-processed data by day

In this example we are going to split the preprocessed parquet files by days, to allow for temporal training and evaluation. There will be a folder for each day and three parquet files within each day: train.parquet, validation.parquet and test.parquet.

P.s. It is worthwhile to note that the dataset has a single categorical feature (category), which, however, is inconsistent over time in the dataset. All interactions before day 84 (2014-06-23) have the same value for that feature, whereas many other categories are introduced afterwards. Thus for this example, we save only the last five days.

# read in the processed train dataset
sessions_gdf = cudf.read_parquet(os.path.join(DATA_FOLDER, "processed_nvt/part_0.parquet"))
sessions_gdf = sessions_gdf[sessions_gdf.day_index>=178]

print(sessions_gdf.head(3))

         session_id  item_id-count  \
6606147    11255549             12   
6606148    11255552              2   
6606149    11255553              2   

                                              item_id-list  \
6606147  [604, 878, 742, 90, 4777, 1583, 3446, 8083, 34...   
6606148  [184, 12288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...   
6606149  [7299, 1953, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...   

                                     et_dayofweek_sin-list  \
6606147  [-0.43388462, -0.43388462, -0.43388462, -0.433...   
6606148  [-0.43388462, -0.43388462, 0.0, 0.0, 0.0, 0.0,...   
6606149  [-0.781831, -0.781831, 0.0, 0.0, 0.0, 0.0, 0.0...   

                        product_recency_days_log_norm-list  \
6606147  [1.5241553, 1.5238751, 1.5239341, 1.5241631, 1...   
6606148  [-0.5330064, 1.521494, 0.0, 0.0, 0.0, 0.0, 0.0...   
6606149  [1.5338266, 1.5355074, 0.0, 0.0, 0.0, 0.0, 0.0...   

                                             category-list  day_index  
6606147  [3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 0, 0, 0, ...        178  
6606148  [2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...        178  
6606149  [7, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...        180  

from transformers4rec.utils.data_utils import save_time_based_splits
save_time_based_splits(data=nvt.Dataset(sessions_gdf),
                       output_dir=os.path.join(DATA_FOLDER, "preproc_sessions_by_day"),
                       partition_col='day_index',
                       timestamp_col='session_id', 
                      )

Creating time-based splits: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5/5 [00:00<00:00,  7.99it/s]

# free gpu memory
del  sessions_gdf
gc.collect()

474

That’s it! We created our sequential features, now we can go to the next notebook to train a PyTorch session-based model.