Extracting biomarkers from PDF files using traditional approaches presents several challenges:

1. Complex Formatting: PDF files are designed for visual presentation, not for data extraction. They can contain complex layouts with tables, images, and varying fonts, making it difficult for traditional text extraction tools to accurately parse and extract information.

2. Non-Standardization: Biomarker information in PDFs may not follow a standardized format. Different sources might use varied terminologies, abbreviations, and structures to represent the same data, complicating the extraction process.

3. Data Embedded in Images: Often, important data in PDFs, such as graphs or charts, is embedded as images. Traditional text extraction methods cannot interpret these images, requiring additional steps like optical character recognition (OCR) and image analysis.

4. Contextual Understanding: Understanding the context in which a biomarker is mentioned is crucial. Traditional methods may extract the text but fail to capture the context, like whether a biomarker value is within a normal range or associated with a specific condition.

5. Data Integrity and Accuracy: Ensuring the integrity and accuracy of the extracted data is a significant challenge. Minor errors in extraction can lead to significant misunderstandings, especially in a sensitive field like healthcare.

6. Scalability and Efficiency: Manually extracting data from PDFs is time-consuming and not feasible for large-scale studies. Automated traditional methods might not scale well or may require extensive customization for different types of PDFs.

7. Compliance and Privacy Concerns: Handling medical data requires compliance with regulations like HIPAA. Ensuring that the extraction process is secure and compliant is challenging, especially when dealing with patient-sensitive information.

We employ advanced techniques such as OCR, machine learning, natural language processing and Large Language Models to overcome these challenges, offering more sophisticated, accurate, and efficient means of extracting biomarker data from PDF files without having to customize or train the AI for each type of PDF that we extract data from.