Reduction of Supervision for Biomedical Knowledge Discovery

Knowledge discovery 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 and time-consuming and hinders scalability when exploring new domains. In this context, our study addresses the challenge of identifying semantic relationships between biomedical entities (e.g., diseases, proteins) 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 biomedical benchmark datasets explores the effectiveness of the methods. Our approach tackles a central issue in knowledge discovery: balancing performance with minimal supervision. By gradually decreasing supervision, we assess the robustness of pointwise binary classification 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, suggesting an encouraging direction toward adaptable knowledge discovery systems, representing progress in creating data-efficient methodologies for extracting useful insights when annotated data is limited.

Enhancing Biomedical Knowledge Discovery for Diseases: An End-To-End Open-Source Framework

The ever-growing volume of biomedical publications creates a critical need for efficient knowledge discovery. In this context, we introduce an open-source end-to-end framework designed to construct knowledge around specific diseases directly from raw text. To facilitate research in disease-related knowledge discovery, we create two annotated datasets focused on Rett syndrome and Alzheimer's disease, enabling the identification of semantic relations between biomedical entities. Extensive benchmarking explores various ways to represent relations and entity representations, offering insights into optimal modeling strategies for semantic relation detection and highlighting language models' competence in knowledge discovery. We also conduct probing experiments using different layer representations and attention scores to explore transformers' ability to capture semantic relations.