4 papers
A PubMed-Scale Dataset of Structured Biomedical Abstracts
Chia-Hsuan Chang, Haerin Song, Brian Ondov +1
Structured abstracts are important for biomedical literature processing, by facilitating information retrieval, text mining, and knowledge synthesis. However, a vast portion of abs…
IRIS: time-structured manifold projections
Brian Ondov, Chia-Hsuan Chang, Weipeng Zhou +6
High-dimensional biomedical data, such as cell-by-gene matrices, are increasingly generated temporally. However, Manifold Learning algorithms, like t-SNE and UMAP, cannot incorpora…
MedViz: An Agent-based, Visual-guided Research Assistant for Navigating Biomedical Literature
Huan He, Xueqing Peng, Yutong Xie +6
Biomedical researchers face increasing challenges in navigating millions of publications in diverse domains. Traditional search engines typically return articles as ranked text lis…
ctELM: Decoding and Manipulating Embeddings of Clinical Trials with Embedding Language Models
Brian Ondov, Chia-Hsuan Chang, Yujia Zhou +2
Text embeddings have become an essential part of a variety of language applications. However, methods for interpreting, exploring and reversing embedding spaces are limited, reduci…