Multi-Task LLM with LoRA Fine-Tuning for Automated Cancer Staging and Biomarker Extraction

Pathology reports serve as the definitive record for breast cancer staging, yet their unstructured format impedes large-scale data curation. While Large Language Models (LLMs) offer semantic reasoning, their deployment is often limited by high computational costs and hallucination risks. This study introduces a parameter-efficient, multi-task framework for automating the extraction of Tumor-Node-Metastasis (TNM) staging, histologic grade, and biomarkers. We fine-tune a Llama-3-8B-Instruct encoder using Low-Rank Adaptation (LoRA) on a curated, expert-verified dataset of 10,677 reports. Unlike generative approaches, our architecture utilizes parallel classification heads to enforce consistent schema adherence. Experimental results demonstrate that the model achieves a Macro F1 score of 0.976, successfully resolving complex contextual ambiguities and heterogeneous reporting formats that challenge traditional extraction methods including rule-based natural language processing (NLP) pipelines, zero-shot LLMs, and single-task LLM baselines. The proposed adapter-efficient, multi-task architecture enables reliable, scalable pathology-derived cancer staging and biomarker profiling, with the potential to enhance clinical decision support and accelerate data-driven oncology research.

Automating Bibliometric Analysis with Sentence Transformers and Retrieval-Augmented Generation (RAG): A Pilot Study in Semantic and Contextual Search for Customized Literature Characterization for High-Impact Urban Research

Bibliometric analysis is essential for understanding research trends, scope, and impact in urban science, especially in high-impact journals, such Nature Portfolios. However, traditional methods, relying on keyword searches and basic NLP techniques, often fail to uncover valuable insights not explicitly stated in article titles or keywords. These approaches are unable to perform semantic searches and contextual understanding, limiting their effectiveness in classifying topics and characterizing studies. In this paper, we address these limitations by leveraging Generative AI models, specifically transformers and Retrieval-Augmented Generation (RAG), to automate and enhance bibliometric analysis. We developed a technical workflow that integrates a vector database, Sentence Transformers, a Gaussian Mixture Model (GMM), Retrieval Agent, and Large Language Models (LLMs) to enable contextual search, topic ranking, and characterization of research using customized prompt templates. A pilot study analyzing 223 urban science-related articles published in Nature Communications over the past decade highlights the effectiveness of our approach in generating insightful summary statistics on the quality, scope, and characteristics of papers in high-impact journals. This study introduces a new paradigm for enhancing bibliometric analysis and knowledge retrieval in urban research, positioning an AI agent as a powerful tool for advancing research evaluation and understanding.

Towards Next-Generation Urban Decision Support Systems through AI-Powered Generation of Scientific Ontology using Large Language Models -- A Case in Optimizing Intermodal Freight Transportation

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. Yet, addressing complex urban and environmental management problems normally requires in-depth domain science and informatics expertise. This expertise is essential for deriving data and simulation-driven for informed decision support. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs). By adopting ChatGPT API as the reasoning core, we outline an integrated workflow that encompasses natural language processing, methontology-based prompt tuning, and transformers. This workflow automates the creation of scenario-based ontology using existing research articles and technical manuals of urban datasets and simulations. The outcomes of our methodology are knowledge graphs in widely adopted ontology languages (e.g., OWL, RDF, SPARQL). These facilitate the development of urban decision support systems by enhancing the data and metadata modeling, the integration of complex datasets, the coupling of multi-domain simulation models, and the formulation of decision-making metrics and workflow. The feasibility of our methodology is evaluated through a comparative analysis that juxtaposes our AI-generated ontology with the well-known Pizza Ontology employed in tutorials for popular ontology software (e.g., prot\'eg\'e). We close with a real-world case study of optimizing the complex urban system of multi-modal freight transportation by generating anthologies of various domain data and simulations to support informed decision-making.