Leveraging AI for Pathology Reports in Cancer Research

By Sumona Bose

March 13, 2024

Introduction

Cedars-Sinai investigators have elected the potential of artificial intelligence (AI) to work on the intricate landscape of cancer patients’ medical records. They particularly focused on pathology reports. These reports, integral to diagnostic and prognostic processes, contain vital assessments by pathologists on tumour samples. Unlike structured electronic health record (EHR) data, these text-based reports offer a wealth of information that can be efficiently extracted and analysed by advanced large language models (LLMs). This is an innovative approach for integrating AI in pathology reports.

The initiative centers around the cancer genome atlas (TCGA), a pivotal resource in oncology research, housing diverse data sets from cancer patients nationwide. This dataset not only facilitates cancer research but also serves as a benchmark for developing and refining AI models tailored to analyse and interpret pathology reports effectively.

The Significance of Pathology Reports in Cancer Research

The convergence of enhanced optical character recognition (OCR) technologies and sophisticated natural language processing (NLP) techniques underscores the need for benchmark datasets. By leveraging these advancements, the team successfully transformed thousands of pathology reports into a machine-readable format, enabling precise cancer-type classification with remarkable accuracy. This milestone dataset promises to catalyse advancements in cancer research, benefiting various stakeholders from research clinicians to clinical NLP experts. Is this pathbreaking for future cancer research?

TCGA Potential in Oncology Research

The TCGA pathology report corpus serves as a valuable resource for researchers conducting analyses in the realm of cancer research. From cancer-subtype classification to survival prediction and named entity recognition, the text within these reports offers a wealth of information that can significantly enhance prognostic accuracy and data extraction. Clinical researchers can develop robust tools to apply to private patient data, either focusing on specific cancer types or adopting a pan-cancer approach.

Expanding Insights Through TCGA’s Multifaceted Patient Data

This multi-dimensional dataset opens up avenues for conducting multimodal analyses, enhancing the performance of various downstream tasks. Despite its strengths, the TCGA dataset does have multiple limitations. These include the absence of clinical notes or symptom timelines and potential outdated terminology in reports. The lack of varying lengths of survival follow-up based on cancer type can also be a challenge for medical records. There is the underrepresentation of certain cancer types like skin cutaneous melanoma (SKCM). Addressing these limitations through advanced OCR techniques present  opportunities for future research and development. Figure 1 illustrates the process of how patient data-sets are sorted according to distributive categories and studied according to cancer type. The vast data collection and analysis improves the reliable nature of the process.

Figure thumbnail gr1
Figure 1: (A) Distribution of patients remaining in the dataset after data selection, OCR, and post-processing, presented per cancer type. (B) Distribution of number of lines removed per report during the final post-processing step of matched regular expression removal.

Conclusion

The TCGA pathology report corpus offers a rich resource for cancer research, enabling advanced analyses and model development. Considerations for data limitations and evolving oncological classifications highlight areas for refinement in leveraging this dataset for future research endeavours.

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