Funding and support: The Generative AI Challenge is funded by grants from the Future Health Research and Innovation Fund (FHRIF), Grant ID IC2023-GAIA/11. Conflict of interest statement: The authors declare no conflicts of interest. Abstract This exploratory pilot study investigated the potential of combining a domain-specific model, BERN2, with large language models (LLMs) to enhance automated disease phenotyping from research survey data. Motivated by the need for efficient and accurate methods to harmonize the growing volume of survey data with standardized disease ontologies, we employed BERN2, a biomedical named entity recognition and normalization model, to extract disease information from the ORIGINS birth cohort survey data. After rigorously evaluating BERN2's performance against a manually curated ground truth dataset, we integrated various LLMs using prompt engineering, Retrieval-Augmented Generation (RAG), and Instructional Fine-Tuning (IFT) to refine the model's outputs. BERN2 demonstrated high performance in extracting and normalizing disease mentions, and the integration of LLMs, particularly with Few Shot Inference and RAG orchestration, further improved accuracy. This approach, especially when incorporating structured examples, logical reasoning prompts, and detailed context, offers a promising avenue for developing tools to enable efficient cohort profiling and data harmonization across large, heterogeneous research datasets. Introduction The increasing availability of research survey data from cohort studies and clinical trials offers unprecedented opportunities to advance biomedical research and improve healthcare (1).

In order to assist the drug discovery/development process, pharmaceutical companies often apply biomedical NER and linking techniques over internal and public corpora. Decades of study of the field of BioNLP has produced a plethora of algorithms, systems and datasets. However, our experience has been that no single open source system meets all the requirements of a modern pharmaceutical company. In this work, we describe these requirements according to our experience of the industry, and present Kazu, a highly extensible, scalable open source framework designed to support BioNLP for the pharmaceutical sector. Kazu is a built around a computationally efficient version of the BERN2 NER model (TinyBERN2), and subsequently wraps several other BioNLP technologies into one coherent system. KAZU framework is open-sourced: https://github.com/AstraZeneca/KAZU

In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.