Glasgow AI4BioMed Lab

Publications

Recent and selected publications from the lab.

2026

  1. Xi Zhang, Zaiqiao Meng, Jake Lever, Edmond S. L. Ho. CCD: Mitigating Hallucinations in Radiology MLLMs via Clinical Contrastive Decoding. Findings of ACL 2026.

2025

  1. Xinhao Yi, Jake Lever, Kevin Bryson, Zaiqiao Meng. Can We Edit LLMs for Long-Tail Biomedical Knowledge?. Findings of EMNLP 2025.
  2. Xi Zhang, Zaiqiao Meng, Jake Lever, Edmond S. L. Ho. Libra: Leveraging Temporal Images for Biomedical Radiology Analysis. Findings of ACL 2025.
  3. Javier Sanz-Cruzado, Jake Lever. Accelerating Cross-Encoders in Biomedical Entity Linking. BioNLP at ACL 2025.
  4. Lars E. Schimmelpfennig, Kriti Bhattarai, Inez Y. Oh, Jake Lever, Obi L. Griffith, Malachi Griffith, Albert M. Lai, Zachary B. Abrams. CeRTS: Certainty Retrieval Token Search in Large Language Model Clinical Information Extraction. Journal of Biomedical Informatics.

2024

  1. Zhaohan Meng, Zaiqiao Meng, Iadh Ounis. FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction. AI4Science@ICML 2024.
  2. Zhaohan Meng, Siwei Liu, Shangsong Liang, Bhautesh Jani, Zaiqiao Meng. Heterogeneous biomedical entity representation learning for gene-disease association prediction. Briefings in Bioinformatics.
  3. Xinhao Yi, Siwei Liu, Yu Wu, Douglas McCloskey, Zaiqiao Meng. BPP: a platform for automatic biochemical pathway prediction. Briefings in Bioinformatics.
  4. Erlend Frayling, Jake Lever, Graham McDonald. Zero-shot and Few-shot Generation Strategies for Artificial Clinical Records. arXiv preprint.
  5. Xi Zhang, Zaiqiao Meng, Jake Lever, Edmond S.L. Ho. Visual Instruction-tuned Adaptation for Radiology Report Generation. BioNLP at ACL 2024.
  6. Erlend Frayling, Jake Lever, Graham McDonald. UoG Siephers at "Discharge Me!": Exploring Ways to Generate Synthetic Patient Notes From Multi-Part Electronic Health Records. BioNLP at ACL 2024.
  7. Giacomo Frisoni, Alessio Cocchieri, Alex Presepi, Gianluca Moro, Zaiqiao Meng. To generate or to retrieve? On the effectiveness of artificial contexts for medical open-domain question answering. ACL 2024.
  8. Jinyuan Fang, Zaiqiao Meng, Craig Macdonald. TRACE the Evidence: Constructing Knowledge-Grounded Reasoning Chains for Retrieval-Augmented Generation. arXiv preprint.
  9. Jinyuan Fang, Zaiqiao Meng, Craig Macdonald. REANO: Optimising Retrieval-Augmented Reader Models through Knowledge Graph Generation. ACL 2024.
  10. Jiahang Cao, Jinyuan Fang, Zaiqiao Meng, Shangsong Liang. Knowledge Graph Embedding: A Survey from the Perspective of Representation Spaces. ACM Computing Surveys 2024.
  11. Zihao Fu, Meiru Zhang, Zaiqiao Meng, Yannan Shen, David Buckeridge, Nigel Collier. BAND: Biomedical Alert News Dataset. AAAI 2024.

2023

  1. Kilannin Krysiak, Jake Lever, et al. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Research.
  2. Daniel N. Sosa, Rogier Hintzen, Betty Xiong, Alex de Giorgio, Julien Fauqueur, Mark Davies, Jake Lever, Russ B. Altman. Associating biological context with protein-protein interactions through text mining at PubMed scale. Journal of Biomedical Informatics.
  3. Jinyuan Fang, Xiaobin Wang, Zaiqiao Meng, Pengjun Xie, Fei Huang, Yong Jiang. MANNER: A Variational Memory-Augmented Model for Cross Domain Few-Shot Named Entity Recognition. ACL 2023.
  4. Zihao Fu, Yixuan Su, Zaiqiao Meng, Nigel Collier. Biomedical Named Entity Recognition via Dictionary-based Synonym Generalization. EMNLP 2023.

2022 and Before

  1. Zaiqiao Meng, et al. BioCaster in 2021: automatic disease outbreaks detection from global news media. Bioinformatics.
  2. Zaiqiao Meng, Fangyu Liu, Ehsan Shareghi, Yixuan Su, Charlotte Collins, Nigel Collier. Rewire-then-Probe. ACL 2022.
  3. Zaiqiao Meng, Fangyu Liu, Thomas Hikaru Clark, Ehsan Shareghi, Nigel Collier. Mixture-of-Partitions: Infusing Large Biomedical Knowledge Graphs into BERT. EMNLP 2021.
  4. Fangyu Liu, Ehsan Shareghi, Zaiqiao Meng, Marco Basaldella, Nigel Collier. Self-alignment Pre-training for Biomedical Entity Representations. NAACL 2021.
  5. Jake Lever, Russ B. Altman. Analyzing the vast coronavirus literature with CoronaCentral. PNAS 2021.
  6. Jake Lever, Russ B. Altman, Jin-Dong Kim. Extending TextAE for annotation of non-contiguous entities. Genomics and Informatics.