BioNLP@ACL

Publications

2023

Hao Li, Yu-Ping Wu, Viktor Schlegel, Riza Batista-Navarro, Thanh-Tung Nguyen, Abhinav Ramesh Kashyap, Xiao-Jun Zeng, Daniel Beck, Stefan Winkler, Goran Nenadic
Team: PULSAR at ProbSum 2023: PULSAR: Pre-training with Extracted Healthcare Terms for Summarising Patients' Problems and Data Augmentation with Black-box Large Language Models. BioNLP@ACL (2023)
Skyler Zou, Xiang Dai, Grant Brinkworth, Pennie Taylor, Sarvnaz Karimi
Can Social Media Inform Dietary Approaches for Health Management? A Dataset and Benchmark for Low-Carb Diet. BioNLP@ACL (2023)
Mong Yuan Sim, Xiang Dai, Maciej Rybinski, Sarvnaz Karimi
CSIRO Data61 Team at BioLaySumm Task 1: Lay Summarisation of Biomedical Research Articles Using Generative Models. BioNLP@ACL (2023)
Vera Pavlova, Mohammed Makhlouf
BIOptimus: Pre-training an Optimal Biomedical Language Model with Curriculum Learning for Named Entity Recognition. BioNLP@ACL (2023)
David Kartchner, Selvi Ramalingam, Irfan Al-Hussaini, Olivia Kronick, Cassie S. Mitchell
Zero-Shot Information Extraction for Clinical Meta-Analysis using Large Language Models. BioNLP@ACL (2023)
Aaron Nicolson, Jason Dowling, Bevan Koopman
e-Health CSIRO at RadSum23: Adapting a Chest X-Ray Report Generator to Multimodal Radiology Report Summarisation. BioNLP@ACL (2023)
Domenic Rosati
GRASUM at BioLaySumm Task 1: Background Knowledge Grounding for Readable, Relevant, and Factual Biomedical Lay Summaries. BioNLP@ACL (2023)
Simon Suster, Timothy Baldwin, Karin Verspoor
Promoting Fairness in Classification of Quality of Medical Evidence. BioNLP@ACL (2023)
Masaki Asada, Makoto Miwa
BioNART: A Biomedical Non-AutoRegressive Transformer for Natural Language Generation. BioNLP@ACL (2023)
Koshi Yamada, Makoto Miwa, Yutaka Sasaki
Biomedical Relation Extraction with Entity Type Markers and Relation-specific Question Answering. BioNLP@ACL (2023)
A. s. Poornash, Atharva Deshmukh, Archit Sharma, Sriparna Saha
APTSumm at BioLaySumm Task 1: Biomedical Breakdown, Improving Readability by Relevancy Based Selection. BioNLP@ACL (2023)
Tianlin Zhang, Kailai Yang, Sophia Ananiadou
Sentiment-guided Transformer with Severity-aware Contrastive Learning for Depression Detection on Social Media. BioNLP@ACL (2023)
Mariia Chizhikova, Manuel Carlos Díaz-Galiano, Luis Alfonso Ureña López, María Teresa Martín-Valdivia
SINAI at RadSum23: Radiology Report Summarization Based on Domain-Specific Sequence-To-Sequence Transformer Model. BioNLP@ACL (2023)
Sanjeev Kumar Karn, Rikhiya Ghosh, Kusuma P, Oladimeji Farri
shs-nlp at RadSum23: Domain-Adaptive Pre-training of Instruction-tuned LLMs for Radiology Report Impression Generation. BioNLP@ACL (2023)
Mariana L. Neves, Ines Schadock, Beryl Eusemann, Gilbert Schönfelder, Bettina Bert, Daniel Butzke
Is the ranking of PubMed similar articles good enough? An evaluation of text similarity methods for three datasets. BioNLP@ACL (2023)
Prateek Chhikara, Ujjwal Pasupulety, John Marshall, Dhiraj Chaurasia, Shweta Kumari
Privacy Aware Question-Answering System for Online Mental Health Risk Assessment. BioNLP@ACL (2023)
Cagla Colak, Lknur Karadeniz
ISIKSumm at BioLaySumm Task 1: BART-based Summarization System Enhanced with Bio-Entity Labels. BioNLP@ACL (2023)
Jiarun Cao, Niels Peek, Andrew G. Renehan, Sophia Ananiadou
Gaussian Distributed Prototypical Network for Few-shot Genomic Variant Detection. BioNLP@ACL (2023)
Sanghwan Kim, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, Ryo Sakamoto, Fabio Rinaldi, Michael Krauthammer
Boosting Radiology Report Generation by Infusing Comparison Prior. BioNLP@ACL (2023)
Oisn Turbitt, Robert Bevan, Mouhamad Aboshokor
MDC at BioLaySumm Task 1: Evaluating GPT Models for Biomedical Lay Summarization. BioNLP@ACL (2023)
Tomas Goldsack, Zheheng Luo, Qianqian Xie, Carolina Scarton, Matthew Shardlow, Sophia Ananiadou, Chenghua Lin
BioLaySumm 2023 Shared Task: Lay Summarisation of Biomedical Research Articles. BioNLP@ACL (2023)
Ken Yano, Makoto Miwa, Sophia Ananiadou
DISTANT: Distantly Supervised Entity Span Detection and Classification. BioNLP@ACL (2023)
Shreya Chandrasekhar, Chieh-Yang Huang, Ting-Hao K. Huang
Good Data, Large Data, or No Data? Comparing Three Approaches in Developing Research Aspect Classifiers for Biomedical Papers. BioNLP@ACL (2023)
Yanjun Gao, Dmitriy Dligach, Timothy Miller, Majid Afshar
Overview of the Problem List Summarization (ProbSum) 2023 Shared Task on Summarizing Patients' Active Diagnoses and Problems from Electronic Health Record Progress Notes. BioNLP@ACL (2023)
Frontmatter. BioNLP@ACL (2023)
Irfan Al-Hussaini, Austin Wu, Cassie S. Mitchell
Pathology Dynamics at BioLaySumm: the trade-off between Readability, Relevance, and Factuality in Lay Summarization. BioNLP@ACL (2023)
Laura Zanella, Yannick Toussaint
How Much do Knowledge Graphs Impact Transformer Models for Extracting Biomedical Events? BioNLP@ACL (2023)
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, BioNLP@ACL 2023, Toronto, Canada, 13 July 2023. BioNLP@ACL (2023)
Ming Liu, Dan Zhang, Weicong Tan, He Zhang
DeakinNLP at ProbSum 2023: Clinical Progress Note Summarization with Rules and Language ModelsClinical Progress Note Summarization with Rules and Languague Models. BioNLP@ACL (2023)
Gangwoo Kim, Hajung Kim, Lei Ji, Seongsu Bae, Chanhwi Kim, Mujeen Sung, Hyunjae Kim, Kun Yan, Eric Chang, Jaewoo Kang
KU-DMIS-MSRA at RadSum23: Pre-trained Vision-Language Model for Radiology Report Summarization. BioNLP@ACL (2023)
Takuma Matsubara, Makoto Miwa, Yutaka Sasaki
Distantly Supervised Document-Level Biomedical Relation Extraction with Neighborhood Knowledge Graphs. BioNLP@ACL (2023)
Chao-Yi Chen, Jen-Hao Yang, Lung-Hao Lee
NCUEE-NLP at BioLaySumm Task 2: Readability-Controlled Summarization of Biomedical Articles Using the PRIMERA Models. BioNLP@ACL (2023)
Potsawee Manakul, Yassir Fathullah, Adian Liusie, Vyas Raina, Vatsal Raina, Mark J. F. Gales
CUED at ProbSum 2023: Hierarchical Ensemble of Summarization Models. BioNLP@ACL (2023)
Vinayak Arannil, Tomal Deb, Atanu Roy
ADEQA: A Question Answer based approach for joint ADE-Suspect Extraction using Sequence-To-Sequence Transformers. BioNLP@ACL (2023)
Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Patrick R. Johnstone, Shinjae Yoo, Francis J. Alexander
Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges. BioNLP@ACL (2023)
Ghadeer Mobasher, Wolfgang Mller, Olga Krebs, Michael Gertz
WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning. BioNLP@ACL (2023)
Mourad Sarrouti, Carson Tao, Yoann Mamy Randriamihaja
Exploring Drug Switching in Patients: A Deep Learning-based Approach to Extract Drug Changes and Reasons from Social Media. BioNLP@ACL (2023)
Jinge Wu, Daqian Shi, Abul Hasan, Honghan Wu
KnowLab at RadSum23: comparing pre-trained language models in radiology report summarization. BioNLP@ACL (2023)
Bernal Jimenez Gutierrez, Huan Sun, Yu Su
Biomedical Language Models are Robust to Sub-optimal Tokenization. BioNLP@ACL (2023)
Yu-Hsuan Wu, Ying-Jia Lin, Hung-Yu Kao
IKM_Lab at BioLaySumm Task 1: Longformer-based Prompt Tuning for Biomedical Lay Summary Generation. BioNLP@ACL (2023)
Harsh Verma, Sabine Bergler, Narjesossadat Tahaei
Comparing and combining some popular NER approaches on Biomedical tasks. BioNLP@ACL (2023)
Nesrine Bannour, Bastien Rance, Xavier Tannier, Aurélie Névéol
Event-independent temporal positioning: application to French clinical text. BioNLP@ACL (2023)
Sudipta Singha Roy, Robert E. Mercer
Extracting Drug-Drug and Protein-Protein Interactions from Text using a Continuous Update of Tree-Transformers. BioNLP@ACL (2023)
Hongyi Yuan, Keming Lu, Zheng Yuan
Exploring Partial Knowledge Base Inference in Biomedical Entity Linking. BioNLP@ACL (2023)
Niklas Kammer, Florian Borchert, Silvia Winkler, Gerard de Melo, Matthieu-P. Schapranow
Resolving Elliptical Compounds in German Medical Text. BioNLP@ACL (2023)
Chenhan Yuan, Qianqian Xie, Sophia Ananiadou
Zero-shot Temporal Relation Extraction with ChatGPT. BioNLP@ACL (2023)
Oumaima El Khettari, Solen Quiniou, Samuel Chaffron
Building a Corpus for Biomedical Relation Extraction of Species Mentions. BioNLP@ACL (2023)
Ryan Whetten, Casey Kennington
Evaluating and Improving Automatic Speech Recognition using Severity. BioNLP@ACL (2023)
Tongnian Wang, Xingmeng Zhao, Anthony Rios
UTSA-NLP at RadSum23: Multi-modal Retrieval-Based Chest X-Ray Report Summarization. BioNLP@ACL (2023)
Vicent Ahuir Esteve, Encarna Segarra, Lluís F. Hurtado
ELiRF-VRAIN at BioNLP Task 1B: Radiology Report Summarization. BioNLP@ACL (2023)