Objectives: Our objective is to create an end-to-end system called AutoRD, which automates extracting information from clinical text about rare diseases. We have conducted various tests to evaluate the performance of AutoRD and highlighted its strengths and limitations in this paper. Materials and Methods: Our system, AutoRD, is a software pipeline involving data preprocessing, entity extraction, relation extraction, entity calibration, and knowledge graph construction. We implement this using large language models and medical knowledge graphs developed from open-source medical ontologies. We quantitatively evaluate our system on entity extraction, relation extraction, and the performance of knowledge graph construction. Results: AutoRD achieves an overall F1 score of 47.3%, a 14.4% improvement compared to the base LLM. In detail, AutoRD achieves an overall entity extraction F1 score of 56.1% (rare_disease: 83.5%, disease: 35.8%, symptom_and_sign: 46.1%, anaphor: 67.5%) and an overall relation extraction F1 score of 38.6% (produces: 34.7%, increases_risk_of: 12.4%, is_a: 37.4%, is_acronym: 44.1%, is_synonym: 16.3%, anaphora: 57.5%). Our qualitative experiment also demonstrates that the performance in constructing the knowledge graph is commendable. Discussion: AutoRD demonstrates the potential of LLM applications in rare disease detection. This improvement is attributed to several design, including the integration of ontologies-enhanced LLMs. Conclusion: AutoRD is an automated end-to-end system for extracting rare disease information from text to build knowledge graphs. It uses ontologies-enhanced LLMs for a robust medical knowledge base. The superior performance of AutoRD is validated by experimental evaluations, demonstrating the potential of LLMs in healthcare.

We propose a novel approach to the statistical analysis of stochastic simulation models and, especially, agent-based models (ABMs). Our main goal is to provide fully automated, model-independent and tool-supported techniques and algorithms to inspect simulations and perform counterfactual analysis. Our approach: (i) is easy-to-use by the modeller, (ii) improves reproducibility of results, (iii) optimizes running time given the modeller's machine, (iv) automatically chooses the number of required simulations and simulation steps to reach user-specified statistical confidence, and (v) automates a variety of statistical tests. In particular, our techniques are designed to distinguish the transient dynamics of the model from its steady-state behaviour (if any), estimate properties in both 'phases', and provide indications on the (non-)ergodic nature of the simulated processes - which, in turn, allows one to gauge the reliability of a steady-state analysis. Estimates are equipped with statistical guarantees, allowing for robust comparisons across computational experiments. To demonstrate the effectiveness of our approach, we apply it to two models from the literature: a large-scale macro-financial ABM and a small scale prediction market model. Compared to prior analyses of these models, we obtain new insights and we are able to identify and fix some erroneous conclusions.