Objectives: Despite the recent adoption of large language models (LLMs) for biomedical information extraction, challenges in prompt engineering and algorithms persist, with no dedicated software available. To address this, we developed LLM-IE: a Python package for building complete information extraction pipelines. Our key innovation is an interactive LLM agent to support schema definition and prompt design. Materials and Methods: The LLM-IE supports named entity recognition, entity attribute extraction, and relation extraction tasks. We benchmarked on the i2b2 datasets and conducted a system evaluation. Results: The sentence-based prompting algorithm resulted in the best performance while requiring a longer inference time. System evaluation provided intuitive visualization. Discussion: LLM-IE was designed from practical NLP experience in healthcare and has been adopted in internal projects. It should hold great value to the biomedical NLP community. Conclusion: We developed a Python package, LLM-IE, that provides building blocks for robust information extraction pipeline construction.

This thesis investigates how natural language understanding and generation with transformer models can benefit from grounding the models with knowledge representations. Currently, the most prevailing paradigm for training language models is through pre-training on abundant raw text data and fine-tuning on downstream tasks. Although language models continue to advance, especially the recent trend of Large Language Models (LLMs) such as ChatGPT, there seem to be limits to what can be achieved with text data alone and it is desirable to study the impact of applying and integrating rich forms of knowledge representation to improve model performance. The most widely used form of knowledge for language modelling is structured knowledge in the form of triples consisting of entities and their relationships, often in English. This thesis explores beyond this conventional approach and aims to address several key questions: Can knowledge of entities extend its benefits beyond entity-centric tasks such as entity linking? How can we faithfully and effectively extract such structured knowledge from raw text, especially noisy web text? How do other types of knowledge, beyond structured knowledge, contribute to improving NLP tasks?