Domain-Grounded Tool Orchestration for LLM-Guided Scientific Analysis
Jeff LeeSebastien JourdainCory QuammenPatrick O'LearyBerk Geveci
Sep 2026
Human-computer Interaction
Abstract
Scientific analysis workflows encode deep domain knowledge through sequences of tightly coupled operations where correctness depends on tool selection, execution order, and parameterization. A CFD engineer investigating flow separation must extract wall shear stress, identify zero-crossings in skin friction, and confirm with boundary-layer profiles: a chain that requires both domain expertise and proficiency with visualization tools. Current approaches to LLM-assisted scientific visualization generate scripts that encode this knowledge implicitly, and often incorrectly, producing code that executes but yields wrong results. We present an architecture that separates intent interpretation (LLM) from execution (deterministic domain tools) from explanation (LLM), connected by the Model Context Protocol (MCP) and grounded by domain ontologies that constrain planning to valid analysis chains. We instantiate the architecture in two domains on the same ParaView server infrastructure: computational fluid dynamics post-processing and topological data analysis via the Topology ToolKit (TTK). Adding the second domain required only an ontology and tool wrappers around existing filters, with no change to the architecture, protocol, or deployment. By construction the design removes whole classes of failure that affect script generation (such as API hallucination and missing pipeline stages) and narrows the strategic errors that remain. An ablation across both domains locates the ontology's empirical effect: it does not change which tools the planner selects, which is already reliable, but corrects how the model interprets results, raising interpretation accuracy from 0.41 to 0.91, and only when the relevant fact is retrieved in scoped rather than bulk form. ParaView's client-server model carries analysis to production-scale datasets through a thin browser client.
Agile - denoting "the quality of being agile, readiness for motion, nimbleness, activity, dexterity in motion" - software development methods are attempting to offer an answer to the eager business community asking for lighter weight along with faster and nimbler software development processes. This is especially the case with the rapidly growing and volatile Internet software industry as well as for the emerging mobile application environment. The new agile methods have evoked substantial amount of literature and debates. However, academic research on the subject is still scarce, as most of existing publications are written by practitioners or consultants. The aim of this publication is to begin filling this gap by systematically reviewing the existing literature on agile software development methodologies. This publication has three purposes. First, it proposes a definition and a classification of agile software development approaches. Second, it analyses ten software development methods that can be characterized as being "agile" against the defined criterion. Third, it compares these methods and highlights their similarities and differences. Based on this analysis, future research needs are identified and discussed.
P. Abrahamsson, O. Salo, Jussi Ronkainen et al.· arXiv.org· 728 citations· ⚡54
Context: Software startups are newly created companies with no operating history and fast in producing cutting-edge technologies. These companies develop software under highly uncertain conditions, tackling fast-growing markets under severe lack of resources. Therefore, software startups present a unique combination of characteristics which pose several challenges to software development activities. Objective: This study aims to structure and analyze the literature on software development in startup companies, determining thereby the potential for technology transfer and identifying software development work practices reported by practitioners and researchers. Method: We conducted a systematic mapping study, developing a classification schema, ranking the selected primary studies according their rigor and relevance, and analyzing reported software development work practices in startups. Results: A total of 43 primary studies were identified and mapped, synthesizing the available evidence on software development in startups. Only 16 studies are entirely dedicated to software development in startups, of which 10 result in a weak contribution (advice and implications (6); lesson learned (3); tool (1)). Nineteen studies focus on managerial and organizational factors. Moreover, only 9 studies exhibit high scientific rigor and relevance. From the reviewed primary studies, 213 software engineering work practices were extracted, categorized and analyzed. Conclusion: This mapping study provides the first systematic exploration of the state-of-art on software startup research. The existing body of knowledge is limited to a few high quality studies. Furthermore, the results indicate that software engineering work practices are chosen opportunistically, adapted and configured to provide value under the constrains imposed by the startup context.
Nicolò Paternoster, Carmine Giardino, M. Unterkalmsteiner et al.· Information and Software Tec...· 394 citations· ⚡54
A new method, called CW-Net, translates the reasoning process of an autonomous vehicle’s AI system into understandable concepts that explain its behavior.
