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The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and other parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.
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http://dx.doi.org/10.1109/TPAMI.2025.3598182 | DOI Listing |
JAMIA Open
October 2025
Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, United States.
Objectives: Unstructured data, such as procedure notes, contain valuable medical information that is frequently underutilized due to the labor-intensive nature of data extraction. This study aims to develop a generative artificial intelligence (GenAI) pipeline using an open-source Large Language Model (LLM) with built-in guardrails and a retry mechanism to extract data from unstructured right heart catheterization (RHC) notes while minimizing errors, including hallucinations.
Materials And Methods: A total of 220 RHC notes were randomly selected for pipeline development and 200 for validation from the Pulmonary Vascular Disease Registry.
IEEE Conf Artif Intell
May 2025
Potentia Analytics Inc, IL, USA.
The shift toward patient-centric healthcare requires understanding comprehensive patient journeys. Current healthcare data systems often fail to provide holistic representations, hindering coordinated care. Patient Journey Knowledge Graphs (PJKGs) solve this by integrating diverse patient information into unified, structured formats.
View Article and Find Full Text PDFLarge Language Models (LLMs), AI agents and co-scientists promise to accelerate scientific discovery across fields ranging from chemistry to biology. Bioinformatics- the analysis of DNA, RNA and protein sequences plays a crucial role in biological research and is especially amenable to AI-driven automation given its computational nature. Here, we assess the bioinformatics capabilities of three popular general-purpose LLMs on a set of tasks covering basic analytical questions that include code writing and multi-step reasoning in the domain.
View Article and Find Full Text PDFInt J Surg
September 2025
Department of Urology and Andrology Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
Objective: The performance of large language models (LLMs) in complex clinical reasoning tasks is not well established. This study compares ChatGPT (GPT-3.5, GPT-4) and DeepSeek (DeepSeek-V3, DeepSeek-R1) in the Chinese anesthesiology attending physician examination (CAAPE), aiming to set AI benchmarks in medical assessments and enhance AI-driven medical education.
View Article and Find Full Text PDFFront Robot AI
August 2025
Information Technologies Institute, The Centre for Research and Technology Hellas, Thessaloniki, Greece.
Agentic AI refers to autonomous systems that can perceive their environment, make decisions, and take actions to achieve goals with minimal or no human intervention. Recent advances in Large Language Models (LLMs) have opened new pathways to imbue robots with such "agentic" behaviors by leveraging the LLMs' vast knowledge and reasoning capabilities for planning and control. This survey provides the first comprehensive exploration of LLM-based robotic systems integration into agentic behaviors that have been validated in real-world applications.
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