The Essential Steps in Data Preprocessing for Different Data Formats

Data preprocessing refines raw data for accurate analysis by handling missing values, normalizing and processing data.

"Garbage In, Garbage Out."

A concept every data analyst is familiar with. You can’t expect to gain any huge insights from a bad dataset. The input data’s quality dictates the output data’s quality.

This underscores the significance of data preprocessing. Data preprocessing is a collection of techniques and procedures to refine raw data into an analyzable format. The initial preprocessing steps can substantially influence the eventual insights or predictive accuracy, whether you're working with structured tabular data, intricate textual data, time-anchored temporal data, or even multimedia datasets. Here we want to provide an overview of the essential data preprocessing steps for exploratory analysis, tailored to these different data types, and how to effectively implement them to step up the foundation of any of your analysis.

You can find each of these snippets in a Hex notebook here.

Preprocessing Structured Data

Structured data, which you find in relational databases and spreadsheets, consists of clearly defined data types organized into columns and rows. Its tabular nature makes it a common starting point for many data analysis tasks. Preprocessing structured data usually requires handling missing data and converting data into the correct format for analysis.

Handling Missing Values

Null or missing values can distort statistical analyses and lead to biased machine learning model training. One common approach is imputation, where missing values are replaced with statistical measures, like mean or median.

import pandas as pd

data = pd.read_csv('data_file.csv')
data.fillna(data.mean(), inplace=True)

In this code, the pandas library reads a CSV file into a DataFrame, then the fillna method replaces missing values (NaN) with the mean of each column. Care should be taken when selecting the imputation strategy, as it can influence the subsequent data analysis outcomes. For datasets with a significant amount of missing data, understanding the nature and pattern of these missing values becomes crucial to avoid inadvertently introducing bias.

Data Normalization

Data normalization is a crucial preprocessing step, especially when features in the dataset have varying scales and ranges. Without normalization, features with larger scales can disproportionately influence the outcome of machine learning algorithms, especially those that rely on distance calculations such as k-means clustering or k-nearest neighbors.

This involves scaling all numeric variables to a standard range, typically between 0 and 1, ensuring that different features contribute equally to model training. Moreover, normalized data often leads to faster convergence during the training process and can improve the generalization capability of some models.

from sklearn.preprocessing import MinMaxScaler

scaler = MinMaxScaler()
data[['feature1', 'feature2']] = scaler.fit_transform(data[['feature1', 'feature2']])

Here, using the MinMaxScaler from scikit-learn, we scale 'feature1' and 'feature2' columns. The fit_transform function computes the minimum and maximum values of the columns and scales them accordingly.

One-hot Encoding

Handling categorical data is pivotal in the preprocessing pipeline as many machine learning models require numerical input features. Categorical variables, represented as text or discrete numbers, can introduce complexity due to their non-continuous nature and varied cardinalities.

One-hot encoding converts categorical variables into a format that can be provided to machine learning algorithms without losing the inherent categorical information. It represents each unique value of a categorical feature as a separate binary column. This ensures that no unintended ordinal relationships are introduced, as can happen with other encoding methods like label encoding.

data_encoded = pd.get_dummies(data, columns=['categorical_feature'])

The get_dummies function from pandas creates binary columns for each category in ‘categorical_feature' and populates them with ones and zeros based on the original data. By doing this, the transformed dataset retains the categorical information in a structure that's amenable to a wider array of algorithmic treatments without making unwarranted assumptions about the relationships between categories.

Feature Selection

Reducing dimensionality can lead to more efficient computation and can prevent overfitting. One common method is using correlation to eliminate redundant or irrelevant features through feature selection.

correlation_matrix = data.corr().abs()
upper_triangle = correlation_matrix.where(np.triu(np.ones(correlation_matrix.shape), k=1).astype(bool))
to_drop = [column for column in upper_triangle.columns if any(upper_triangle[column] > 0.95)]
data.drop(to_drop, axis=1, inplace=True)

This code computes a correlation matrix for the DataFrame and identifies pairs of features with a correlation greater than 0.95. Features from each high-correlation pair are then dropped, leaving behind a reduced set of features.

Preprocessing structured data involves tasks tailored to its tabular nature, addressing issues specific to columns and rows, and ensuring it's primed for rigorous, accurate analysis.

Preprocessing Textual Data

Textual data, often unstructured and derived from various sources like documents, social media, and websites, presents its unique challenges. Preprocessing this type of data is crucial to extract meaningful patterns and relationships and to perform advanced analytical techniques such as natural language processing.


Tokenization is a fundamental step in text preprocessing, especially for natural language processing (NLP) tasks. It involves dissecting a string or document into smaller units, such as words, phrases, symbols, or other meaningful elements called tokens. These tokens become the basic units for subsequent analysis and modeling. Precise tokenization is critical for understanding the context and meaning of the text, as it influences the accuracy of feature extraction and the performance of NLP models.

from nltk.tokenize import word_tokenize

text = "This is an example sentence."
tokens = word_tokenize(text)

Here, we use the word_tokenize function from the nltk (Natural Language Toolkit) library to split a given sentence into individual words or tokens. This function is sophisticated enough to separate words and punctuation, recognizing various intricacies of English grammar. It provides a foundation for further steps like stemming, lemmatization, and stopword removal, which refine the tokens for tasks such as sentiment analysis, topic modeling, or document classification.

Removing Stop Words

Stop words, like "and", "the", and "is", are common words that may not contribute meaningfully to text analysis. Removing them can improve analysis efficiency and focus.

from nltk.corpus import stopwords

filtered_tokens = [word for word in tokens if word.lower() not in stopwords.words('english')]

Here, we filter out stop words from our tokenized text using a predefined list of English stop words available in the nltk library.

Stemming and Lemmatization

Stemming and lemmatization condense words to their foundational forms. By doing so, they aid in achieving consistency in word representation, which can significantly enhance the performance of downstream tasks like text classification, topic modeling, and sentiment analysis.

While both stemming and lemmatization target word reduction, they follow different methodologies:

  • Stemming uses heuristic processes to clip off word suffixes, leading to a crude reduction, often producing non-real words.

  • Lemmatization employs linguistic rules, often using lexicon and morphological analysis, to return words to their base or dictionary form, ensuring the resultant word has a meaningful representation.

from nltk.stem import PorterStemmer, WordNetLemmatizer

stemmer = PorterStemmer()
lemmatizer = WordNetLemmatizer()

stemmed_tokens = [stemmer.stem(word) for word in filtered_tokens]
lemmatized_tokens = [lemmatizer.lemmatize(word) for word in filtered_tokens]

Using the PorterStemmer and WordNetLemmatizer classes from nltk, we transform our filtered tokens into their stemmed and lemmatized forms, respectively. The choice between stemming and lemmatization often hinges on the specific requirements of a task, the linguistic richness of the data, and the desired level of word normalization.

Text Vectorization

To analyze text using algorithms, we need to convert it into numerical format. TF-IDF (Term Frequency-Inverse Document Frequency) is a common method that represents text as vectors where each word's weight is adjusted by its frequency across documents.

from sklearn.feature_extraction.text import TfidfVectorizer

documents = ["This is a sample.", "This document is another example."]
vectorizer = TfidfVectorizer()
tfidf_matrix = vectorizer.fit_transform(documents)

Here, using TfidfVectorizer from scikit-learn, we convert a list of documents into a matrix of TF-IDF values, where each row represents a document and each column corresponds to a unique word in the entire corpus.

Preprocessing textual data involves tasks that transform human-readable content into structured, machine-analyzable formats, ready for in-depth data analysis or model training.

Preprocessing Temporal Data

Temporal data, characterized by its association with timestamps or chronological order, often arises in time series analysis, financial modeling, or event logging. Preprocessing for this type of data ensures that time-dependent relationships are effectively captured.

Parsing Date and Time

Converting string representations of dates and times into datetime objects simplifies subsequent time-based operations.

import pandas as pd

data = pd.DataFrame({'date': ['2023-01-01', '2023-01-02', '2023-01-03']})
data['date'] = pd.to_datetime(data['date'])

Here, we use pandas' to_datetime function to convert a column of date strings into datetime objects, allowing for easier time-based indexing and operations.

Handling Time Gaps

In time series data, missing timestamps can lead to inaccurate analysis. It's essential to identify and address these gaps.

full_date_range = pd.date_range(start=data['date'].min(), end=data['date'].max())
data = data.set_index('date').reindex(full_date_range).reset_index().rename(columns={'index': 'date'})

This code first creates a complete range of dates between the minimum and maximum dates in our dataset. It then reindexes the data based on this complete range, ensuring any missing dates are included as rows with NaN values.

Extracting Time-based Features

For certain analyses, it's beneficial to derive features such as the day of the week, month, or year.

data['year'] = data['date'].dt.year
data['month'] = data['date'].dt.month
data['day_of_week'] = data['date'].dt.dayofweek

Using the datetime accessor (dt) in pandas, we extract the year, month, and day of the week from each datetime object in our 'date' column and store them as separate features.

Resampling Time Series Data

For time series data analysis, the granularity or frequency at which data points are recorded can be pivotal. Often, raw time series data might be captured at an extremely detailed level, which, while informative, can also be overwhelming and computationally intensive to process.

Resampling offers a solution by allowing analysts and data scientists to adjust the time frame, enabling the examination of data at various levels of granularity, from milliseconds to years. This not only aids in revealing different patterns or behaviors in the data but also optimizes computational resources. The transformation can be accompanied by aggregation methods like sum, mean, or max to provide a consolidated view of the data over the newly defined intervals.

time_series_data = pd.DataFrame({'date': full_date_range, 'value': range(len(full_date_range))})
resampled_data = time_series_data.set_index('date').resample('M').mean()

In this snippet, we generate a sample time series DataFrame with a hypothetical set of dates and values. By utilizing the resample method from pandas, we transform the dataset's granularity to a monthly frequency, computing the average value for each month in the process. Resampling provides flexibility, and different functions can be applied based on the analytical goals, ensuring an appropriate representation of the underlying time series dynamics.

Lag Features

For predictive modeling of time series data, creating lag features (values from previous time steps) can be invaluable.

data['value_lag1'] = data['value'].shift(1)

By using the shift method, we create a new column where each entry is the value from the previous row (i.e., the previous time step).

Preprocessing temporal data necessitates an understanding of the sequential nature of the data and applying methods that respect and utilize this time-based ordering.

Preprocessing Image Data

Image data, consisting of pixels representing visual content, is widely used in domains like computer vision and medical imaging. Preprocessing for images ensures they are in a standardized format and augmented appropriately for better model generalization.

Loading and Resizing

Ensuring images have uniform dimensions is crucial, especially when batch processing or using convolutional neural networks (CNNs).

from PIL import Image

img_path = "path_to_image.jpg"
img =
img_resized = img.resize((224, 224))

Here, we use the Image class from the PIL (Python Imaging Library) to load an image from a given path. The resize method is then utilized to resize the image to a 224x224 pixel resolution.

Grayscale Conversion

In some analyses, color information might not be necessary. Converting images to grayscale can reduce dimensionality and computational overhead.

img_gray = img.convert("L")

Using the convert method with the "L" mode, we transform the loaded image into a grayscale version, retaining luminance and discarding color information.


Scaling pixel values to a range between 0 and 1 can help in stabilizing training and improving convergence in machine learning models.

import numpy as np

img_array = np.asarray(img_resized)
normalized_array = img_array / 255.0

After converting the image to a numpy array, we divide each pixel value by 255 (the maximum pixel value for an 8-bit image) to normalize the image data.

Edge Detection

Edges in an image represent areas where there are rapid changes in pixel intensity. Edge detection helps identify significant transitions in pixel intensity in an image and can be used as a feature extraction method in various applications. Detecting these edges can be useful for object recognition, segmentation, and other image analysis tasks. One popular method for edge detection is the Sobel operator.

import cv2

# Load the image using OpenCV
image_cv = cv2.imread(img_path, cv2.IMREAD_GRAYSCALE)

# Apply Sobel edge detection
sobel_x = cv2.Sobel(image_cv, cv2.CV_64F, 1, 0, ksize=3)
sobel_y = cv2.Sobel(image_cv, cv2.CV_64F, 0, 1, ksize=3)
sobel_edges = cv2.magnitude(sobel_x, sobel_y)

Here, we use the OpenCV library, a powerful tool for computer vision tasks. The Sobel function computes the gradient approximation of the image intensity for the x and y directions separately. The combined gradient magnitude, which represents the edges, is then computed using the magnitude function.

This edge-detected image can be used as input for further analysis or as a feature for machine learning tasks.

Getting Your Data Ready

The above might seem like laborious tasks before the fun starts. But really the shouldn’t be termed “preprocessing” as they are an integral part of the entire flow of data analysis. Without doing the above for whichever type of data you are analyzing, you will have poor results.

Starting with these, you end up with higher quality data which leads to higher quality analysis which leads to higher quality insights.

This is something we think a lot about at Hex, where we're creating a platform that makes it easy to build and share interactive data products which can help teams be more impactful. If this is is interesting, click below to get started, or to check out opportunities to join our team.