Boosting Performance and Memory Efficiency with PyArrow and Pandas for Clinical Trial Data

1. Introduction

In the world of data analysis and manipulation, efficiency and memory usage play crucial roles, especially when dealing with large datasets. Clinical trials generate vast amounts of data, making it imperative to employ tools that optimize both processing time and memory utilization. One such strategy involves combining the power of Pandas and PyArrow, two popular Python libraries for data manipulation and in-memory columnar storage, respectively.

In this blog, we'll delve into how PyArrow can be integrated with Pandas to enhance both processing speed and memory efficiency while analyzing a clinical trial dataset.

Create Dummy Clinical Dataset

Let's start by considering a sample clinical trial dataset, which consists of various attributes such as patient identifiers, demographic information, treatment details, medical measurements, and more. This dataset comprises meaningful columns that simulate the kind of data encountered in clinical trials. Here's how the dataset is generated using NumPy and Pandas:

import pandas as pd
import numpy as np

# Generating a sample dataset with 20 columns meaningful for clinical trials
np.random.seed(42)
num_rows = 100000
num_columns = 20

# Generating columns with meaningful names related to clinical trials
data = {
    'Patient_ID': np.arange(1, num_rows + 1),  # Unique identifier for each patient
    'Age': np.random.randint(18, 80, num_rows),  # Age of the patient
    'Sex': np.random.choice(['Male', 'Female'], num_rows),  # Gender of the patient
    'Treatment': np.random.choice(['Drug A', 'Drug B', 'Placebo'], num_rows),  # Treatment administered
    'Blood_Pressure': np.random.randint(80, 180, num_rows),  # Blood pressure reading
    'Cholesterol': np.random.randint(120, 300, num_rows),  # Cholesterol level
    'BMI': np.random.uniform(18, 40, num_rows),  # Body Mass Index
    'Heart_Rate': np.random.randint(60, 100, num_rows),  # Heart rate
    'Diabetes': np.random.choice(['Yes', 'No'], num_rows),  # Presence of diabetes
    'Smoker': np.random.choice(['Smoker', 'Non-Smoker'], num_rows),  # Smoking status
    'Family_History': np.random.choice(['Yes', 'No'], num_rows),  # Family history of conditions
    'Adverse_Event': np.random.choice(['Mild', 'Moderate', 'Severe', 'None'], num_rows),  # Adverse events experienced
    'Lab_Result_1': np.random.uniform(0, 10, num_rows),  # Laboratory result 1
    'Lab_Result_2': np.random.uniform(50, 150, num_rows),  # Laboratory result 2
    'Lab_Result_3': np.random.uniform(1, 20, num_rows),  # Laboratory result 3
    'Efficacy_Score': np.random.uniform(0, 100, num_rows),  # Efficacy score of treatment
    'Visit_1': np.random.choice(['Completed', 'Missed'], num_rows),  # Visit status
    'Visit_2': np.random.choice(['Completed', 'Missed'], num_rows),  # Visit status
    'Visit_3': np.random.choice(['Completed', 'Missed'], num_rows),  # Visit status
    'Follow_Up_Status': np.random.choice(['Ongoing', 'Completed'], num_rows)  # Follow-up status
}

df = pd.DataFrame(data)

# Display the first few rows of the DataFrame
df.head()

Integrating PyArrow with Pandas

To leverage the benefits of both Pandas and PyArrow, we'll first create a Pandas DataFrame from the clinical trial data, and then convert this DataFrame into a PyArrow Table. This step allows us to utilize the advanced memory layout optimization and columnar storage offered by PyArrow. Here's how it's done:

# Import required libraries
import pandas as pd
import pyarrow as pa

# Create pandas DataFrame from the clinical trial data
pandas_df = pd.DataFrame(df)

# Convert pandas DataFrame to pyarrow Table
pyarrow_table = pa.Table.from_pandas(pandas_df)

Measuring Memory Usage

One of the primary advantages of using PyArrow is its efficient memory utilization, particularly when working with large datasets. To visualize this benefit, we'll compare the memory usage of the Pandas DataFrame and the PyArrow Table:

# Calculate memory usage for Pandas DataFrame and PyArrow Table
pandas_memory_usage = pandas_df.memory_usage(deep=True).sum() / (1024 * 1024)
pyarrow_memory_usage = pyarrow_table.nbytes / (1024 * 1024)

# Create a memory usage comparison graph
plt.figure(figsize=(6, 4))
plt.bar(['Pandas', 'PyArrow'], [pandas_memory_usage, pyarrow_memory_usage], color=['blue', 'orange'])
plt.ylabel('Memory Usage (MB)')
plt.title('Memory Usage Comparison: Pandas vs. PyArrow')
plt.show()

The Benefits: Speed and Memory Efficiency

The integration of PyArrow with Pandas presents two significant benefits: improved processing speed and enhanced memory efficiency.

Processing Speed: PyArrow's columnar storage format optimizes data access and retrieval. This leads to faster query execution times, as the data of each column is stored together, reducing the amount of data read from memory. In scenarios like clinical trials, where complex analyses and querying are common, this acceleration in processing speed can significantly improve productivity.

Memory Efficiency: PyArrow employs highly efficient compression algorithms and storage techniques, which reduce the memory footprint of the dataset. This becomes increasingly crucial when working with large clinical trial datasets that might not fit entirely in memory. By minimizing memory usage, PyArrow allows for the manipulation of larger datasets without causing memory-related bottlenecks.

Conclusion

In this blog, I have explored how the integration of PyArrow with Pandas can lead to a substantial improvement in processing speed and memory efficiency when dealing with large clinical trial datasets. By capitalizing on PyArrow's columnar storage and advanced memory optimization techniques, analysts and researchers can perform complex analyses more swiftly and manage larger datasets without compromising memory limitations. The combined power of Pandas and PyArrow opens up new possibilities for insightful exploration and data-driven decision-making in the realm of clinical trials and beyond

Comments

[Finarb Analytics Consulting]

Interesting read! If you would like to explore more on how leading CRO's like IQVIA are using a data driven approach to clinical trials, Finarb is organizing a webinar on Sep 28th, with IQVIA to delve into specific use cases where data & AI is advancing clinical trials at various stages. Find more about the webinar and use cases that will be discussed here dev.to/finarbanalytics/webinar-a-d...