Biomedical entity linking (BioEL) is the process of connecting entities referenced in documents to entries in biomedical databases such as the Unified Medical Language System (UMLS) or Medical Subject Headings (MeSH). The study objective was to comprehensively evaluate nine recent state-of-the-art biomedical entity linking models under a unified framework. We compare these models along axes of (1) accuracy, (2) speed, (3) ease of use, (4) generalization, and (5) adaptability to new ontologies and datasets. We additionally quantify the impact of various preprocessing choices such as abbreviation detection. Systematic evaluation reveals several notable gaps in current methods. In particular, current methods struggle to correctly link genes and proteins and often have difficulty effectively incorporating context into linking decisions. To expedite future development and baseline testing, we release our unified evaluation framework and all included models on GitHub at https://github.com/davidkartchner/biomedical-entity-linking

Meta-analysis of randomized clinical trials (RCTs) plays a crucial role in evidence-based medicine but can be labor-intensive and error-prone. This study explores the use of large language models to enhance the efficiency of aggregating results from randomized clinical trials (RCTs) at scale. We perform a detailed comparison of the performance of these models in zero-shot prompt-based information extraction from a diverse set of RCTs to traditional manual annotation methods. We analyze the results for two different meta-analyses aimed at drug repurposing in cancer therapy pharmacovigilience in chronic myeloid leukemia. Our findings reveal that the best model for the two demonstrated tasks, ChatGPT can generally extract correct information and identify when the desired information is missing from an article. We additionally conduct a systematic error analysis, documenting the prevalence of diverse error types encountered during the process of prompt-based information extraction.

We study the problem of learning neural text classifiers without using any labeled data, but only easy-to-provide rules as multiple weak supervision sources. This problem is challenging because rule-induced weak labels are often noisy and incomplete. To address these two challenges, we design a label denoiser, which estimates the source reliability using a conditional soft attention mechanism and then reduces label noise by aggregating rule-annotated weak labels. The denoised pseudo labels then supervise a neural classifier to predicts soft labels for unmatched samples, which address the rule coverage issue. We evaluate our model on five benchmarks for sentiment, topic, and relation classifications. The results show that our model outperforms state-of-the-art weakly-supervised and semi-supervised methods consistently, and achieves comparable performance with fully-supervised methods even without any labeled data. Our code can be found at https://github.com/weakrules/Denoise-multi-weak-sources.