Yusuf Abdulle

Publications

Under Review

  1. Abdulle, Y., Dinu, V., Wu, J., Kim, Y., Budhdeo, S., Yao, Z., Tomlinson, C., Al-Chalabi, A., Wu, H., Dobson, R., & Iacoangeli, A. (2026). Symptom-based phenotype discovery in motor neuron disease using natural language processing of electronic health records. medRxiv.

  2. Jiang, A., Hu, J., Abdulle, Y., Pain, O., & Iacoangeli, A. (2026). An integrated knowledge graph and network medicine pipeline for drug repurposing: Benchmarking across human diseases and application to amyotrophic lateral sclerosis. bioRxiv.

  3. Abdulle, Y., Wu, J. (joint first), Budhdeo, S., Kim, Y., Shen, J., Sun, E., Ali, W., Dai, C., Scordis, P., Patra, A., Al Khleifat, A., Al-Chalabi, A., Iacoangeli, A., Zhang, H., Taylor, P., Wild, S., Ibrahim, Z., Dobson, R., & Wu, H. (2025). Characteristics and early diagnosis of motor neuron disease (MND) in 67 million individuals in England: A comparative study on phenotyping models derived by AI, knowledge graphs and the MND Association. medRxiv.

  4. Vasu, R., Dong, H., Abdulle, Y., Harrison, J., & Wu, H. (2025). A large language model based framework for dementia related hypothesis generation.

Journal Papers

  1. Spears, S. D. J., Abdulle, Y., Lester, T., Torii, R., Kalaskar, D. M., & Sharma, N. (2024). Understanding neck collar preferences and user experiences in motor neuron disease: A survey-based study. Disability and Health Journal, 101585.

  2. Spears, S. D. J., Abdulle, Y., Korovilas, D., Torii, R., Kalaskar, D. M., & Sharma, N. (2023). Neck collar assessment for people living with motor neuron disease: Are current outcome measures suitable?. Interactive Journal of Medical Research, 12, e43274.

  3. Budhdeo, S., Zhang, J., Abdulle, Y., Agapow, P. M., McKechnie, D. G. J., Archer, M., Shah, V., Forte, E., Noori, A., Zitnik, M., Ashrafian, H., & Sharma, N. (2025). Scoping review of knowledge graph applications in biomedical and healthcare sciences. Wellcome Open Research, 10, 66.

Conference Papers

  1. Kim, Y., Abdulle, Y., & Wu, H. (2025). BioHopR: A benchmark for multi-hop, multi-answer reasoning in biomedical domain. In Findings of the Association for Computational Linguistics: ACL 2025 (pp. 12894–12908). Association for Computational Linguistics.

  2. Kim, Y., Wu, J., Abdulle, Y., & Wu, H. (2024). MedExQA: Medical question answering benchmark with multiple explanations. In Proceedings of the 23rd Workshop on Biomedical Natural Language Processing (pp. 167–181). Association for Computational Linguistics.

  3. Kim, Y., Wu, J., Abdulle, Y., Gao, Y., & Wu, H. (2024). Enhancing human-computer interaction in chest X-ray analysis using vision and language model with eye gaze patterns. In Medical Image Computing and Computer Assisted Intervention – MICCAI 2024 (pp. 184–194). Springer.

  4. Kim, Y., Wu, J., Abdulle, Y., Gao, Y., & Wu, H. (2024). Human-in-the-loop chest X-ray diagnosis: Enhancing large multimodal models with eye fixation inputs. In Trustworthy Artificial Intelligence for Healthcare (TAI4H 2024) (pp. 66–80). Springer.

  5. Groves, E., Wang, M., Abdulle, Y., Kunz, H., Hoelscher-Obermaier, J., Wu, R., & Wu, H. (2024). Benchmarking and analyzing in-context learning, fine-tuning and supervised learning for biomedical knowledge curation: A focused study on chemical entities of biological interest. In VLDB 2024 Workshop: LLM+KG.

  6. Budhdeo, S., Abdulle, Y., Sharma, N., & Cosco, T. (2023). Meta-analysis of cerebrospinal fluid immune markers in frontotemporal dementia patients compared to healthy controls. European Journal of Neurology.

  7. Budhdeo, S., Abdulle, Y., Kaczmarczyk, I., & Sharma, N. (2023). Using a PET atlas to probe neurotransmitter-disease associations in mild cognitive impairment and Alzheimer’s disease. European Journal of Neurology.