217 citations · 272 across the 13 of their papers we have counts for
13 papers
Use as Directed? A Comparison of Software Tools Intended to Check Rigor and Transparency of Published Work
Peter Eckmann, Adrian Barnett, Alexandra Bannach-Brown +17
The causes of the reproducibility crisis include lack of standardization and transparency in scientific reporting. Checklists such as ARRIVE and CONSORT seek to improve transparenc…
Multi-label Sequential Sentence Classification via Large Language Model
Mengfei Lan, Lecheng Zheng, Shufan Ming +1
Sequential sentence classification (SSC) in scientific publications is crucial for supporting downstream tasks such as fine-grained information retrieval and extractive summarizati…
DiMB-RE: Mining the Scientific Literature for Diet-Microbiome Associations
Gibong Hong, Veronica Hindle, Nadine M. Veasley +2
Objective: To develop a corpus annotated for diet-microbiome associations from the biomedical literature and train natural language processing (NLP) models to identify these associ…
BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine
Mingchen Li, Halil Kilicoglu, Hua Xu +1
Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues suc…
Examining the Causal Effect of First Names on Language Models: The Case of Social Commonsense Reasoning
Sullam Jeoung, Jana Diesner, Halil Kilicoglu
As language models continue to be integrated into applications of personal and societal relevance, ensuring these models' trustworthiness is crucial, particularly with respect to p…
Complementary and Integrative Health Lexicon (CIHLex) and Entity Recognition in the Literature
Huixue Zhou, Robin Austin, Sheng-Chieh Lu +5
Objective: Our study aimed to construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to better represent the often underrepresented physical and psycho…
Commonsense-Aware Prompting for Controllable Empathetic Dialogue Generation
Yiren Liu, Halil Kilicoglu
Improving the emotional awareness of pre-trained language models is an emerging important problem for dialogue generation tasks. Although prior studies have introduced methods to i…
Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions
Sanya B. Taneja, Tiffany J. Callahan, Mary F. Paine +4
Pharmacokinetic natural product-drug interactions (NPDIs) occur when botanical natural products are co-consumed with pharmaceutical drugs. Understanding mechanisms of NPDIs is key…
Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature
Dalton Schutte, Jake Vasilakes, Anu Bompelli +7
OBJECTIVE: Leverage existing biomedical NLP tools and DS domain terminology to produce a novel and comprehensive knowledge graph containing dietary supplement (DS) information for…
UIUC_BioNLP at SemEval-2021 Task 11: A Cascade of Neural Models for Structuring Scholarly NLP Contributions
Haoyang Liu, M. Janina Sarol, Halil Kilicoglu
We propose a cascade of neural models that performs sentence classification, phrase recognition, and triple extraction to automatically structure the scholarly contributions of NLP…
Drug Repurposing for COVID-19 via Knowledge Graph Completion
Rui Zhang, Dimitar Hristovski, Dalton Schutte +3
Objective: To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. Methods: We propose a novel, integrative…
Attention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
Preventable adverse events as a result of medical errors present a growing concern in the healthcare system. As drug-drug interactions (DDIs) may lead to preventable adverse events…
A Multi-Task Learning Framework for Extracting Drugs and Their Interactions from Drug Labels
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
Preventable adverse drug reactions as a result of medical errors present a growing concern in modern medicine. As drug-drug interactions (DDIs) may cause adverse reactions, being a…