6 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…
Lessons from the TREC Plain Language Adaptation of Biomedical Abstracts (PLABA) track
Brian Ondov, William Xia, Kush Attal +3
Objective: Recent advances in language models have shown potential to adapt professional-facing biomedical literature to plain language, making it accessible to patients and caregi…
JEBS: A Fine-grained Biomedical Lexical Simplification Task
William Xia, Ishita Unde, Brian Ondov +1
Online medical literature has made health information more available than ever, however, the barrier of complex medical jargon prevents the general public from understanding it. Th…