Reduction of supervision for biomedical knowledge discovery

Abstract

Abstract Background Knowledge discovery in scientific literature is hindered by the increasing volume of publications and the scarcity of extensive annotated data. To tackle the challenge of information overload, it is essential to employ automated methods for knowledge extraction and processing. Finding the right balance between the level of supervision and the effectiveness of models poses a significant challenge. While supervised techniques generally result in better performance, they have the major drawback of demanding labeled data. This requirement is labor-intensive, time-consuming, and hinders scalability when exploring new domains. Methods and Results In this context, our study addresses the challenge of identifying semantic relationships between biomedical entities (e.g., diseases, proteins, medications) in unstructured text while minimizing dependency on supervision. We introduce a suite of unsupervised algorithms based on dependency trees and attention mechanisms and employ a range of pointwise binary classification methods. Transitioning from weakly supervised to fully unsupervised settings, we assess the methods’ ability to learn from data with noisy labels. The evaluation on four biomedical benchmark datasets explores the effectiveness of the methods, demonstrating their potential to enable scalable knowledge discovery systems less reliant on annotated datasets. Conclusion Our approach tackles a central issue in knowledge discovery: balancing performance with minimal supervision which is crucial to adapting models to varied and changing domains. This study also investigates the use of pointwise binary classification techniques within a weakly supervised framework for knowledge discovery. By gradually decreasing supervision, we assess the robustness of these techniques in handling noisy labels, revealing their capability to shift from weakly supervised to entirely unsupervised scenarios. Comprehensive benchmarking offers insights into the effectiveness of these techniques, examining how unsupervised methods can reliably capture complex relationships in biomedical texts. These results suggest an encouraging direction toward scalable, adaptable knowledge discovery systems, representing progress in creating data-efficient methodologies for extracting useful insights when annotated data is limited.

Keywords

• Knowledge discovery
• Relation extraction
• Unsupervised learning
• Weakly supervised learning
• Biomedical text