How to Build AI Agents by Augmenting LLMs with Codified Human Expert Domain Knowledge? A Software Engineering Framework

Critical domain knowledge typically resides with few experts, creating organizational bottlenecks in scalability and decision-making. Non-experts struggle to create effective visualizations, leading to suboptimal insights and diverting expert time. This paper investigates how to capture and embed human domain knowledge into AI agent systems through an industrial case study. We propose a software engineering framework to capture human domain knowledge for engineering AI agents in simulation data visualization by augmenting a Large Language Model (LLM) with a request classifier, Retrieval-Augmented Generation (RAG) system for code generation, codified expert rules, and visualization design principles unified in an agent demonstrating autonomous, reactive, proactive, and social behavior. Evaluation across five scenarios spanning multiple engineering domains with 12 evaluators demonstrates 206% improvement in output quality, with our agent achieving expert-level ratings in all cases versus baseline's poor performance, while maintaining superior code quality with lower variance. Our contributions are: an automated agent-based system for visualization generation and a validated framework for systematically capturing human domain knowledge and codifying tacit expert knowledge into AI agents, demonstrating that non-experts can achieve expert-level outcomes in specialized domains.

AI for Better UX in Computer-Aided Engineering: Is Academia Catching Up with Industry Demands? A Multivocal Literature Review

Computer-Aided Engineering (CAE) enables simulation experts to optimize complex models, but faces challenges in user experience (UX) that limit efficiency and accessibility. While artificial intelligence (AI) has demonstrated potential to enhance CAE processes, research integrating these fields with a focus on UX remains fragmented. This paper presents a multivocal literature review (MLR) examining how AI enhances UX in CAE software across both academic research and industry implementations. Our analysis reveals significant gaps between academic explorations and industry applications, with companies actively implementing LLMs, adaptive UIs, and recommender systems while academic research focuses primarily on technical capabilities without UX validation. Key findings demonstrate opportunities in AI-powered guidance, adaptive interfaces, and workflow automation that remain underexplored in current research. By mapping the intersection of these domains, this study provides a foundation for future work to address the identified research gaps and advance the integration of AI to improve CAE user experience.

Automated Segmentation and Analysis of Cone Photoreceptors in Multimodal Adaptive Optics Imaging

Accurate detection and segmentation of cone cells in the retina are essential for diagnosing and managing retinal diseases. In this study, we used advanced imaging techniques, including confocal and non-confocal split detector images from adaptive optics scanning light ophthalmoscopy (AOSLO), to analyze photoreceptors for improved accuracy. Precise segmentation is crucial for understanding each cone cell's shape, area, and distribution. It helps to estimate the surrounding areas occupied by rods, which allows the calculation of the density of cone photoreceptors in the area of interest. In turn, density is critical for evaluating overall retinal health and functionality. We explored two U-Net-based segmentation models: StarDist for confocal and Cellpose for calculated modalities. Analyzing cone cells in images from two modalities and achieving consistent results demonstrates the study's reliability and potential for clinical application.

Generalist Segmentation Algorithm for Photoreceptors Analysis in Adaptive Optics Imaging

Analyzing the cone photoreceptor pattern in images obtained from the living human retina using quantitative methods can be crucial for the early detection and management of various eye conditions. Confocal adaptive optics scanning light ophthalmoscope (AOSLO) imaging enables visualization of the cones from reflections of waveguiding cone photoreceptors. While there have been significant improvements in automated algorithms for segmenting cones in confocal AOSLO images, the process of labelling data remains labor-intensive and manual. This paper introduces a method based on deep learning (DL) for detecting and segmenting cones in AOSLO images. The models were trained on a semi-automatically labelled dataset of 20 AOSLO batches of images of 18 participants for 0$^{\circ}$, 1$^{\circ}$, and 2$^{\circ}$ from the foveal center. F1 scores were 0.968, 0.958, and 0.954 for 0$^{\circ}$, 1$^{\circ}$, and 2$^{\circ}$, respectively, which is better than previously reported DL approaches. Our method minimizes the need for labelled data by only necessitating a fraction of labelled cones, which is especially beneficial in the field of ophthalmology, where labelled data can often be limited.

Synthetic Electroretinogram Signal Generation Using Conditional Generative Adversarial Network for Enhancing Classification of Autism Spectrum Disorder

The electroretinogram (ERG) is a clinical test that records the retina's electrical response to light. The ERG is a promising way to study different neurodevelopmental and neurodegenerative disorders, including autism spectrum disorder (ASD) - a neurodevelopmental condition that impacts language, communication, and reciprocal social interactions. However, in heterogeneous populations, such as ASD, where the ability to collect large datasets is limited, the application of artificial intelligence (AI) is complicated. Synthetic ERG signals generated from real ERG recordings carry similar information as natural ERGs and, therefore, could be used as an extension for natural data to increase datasets so that AI applications can be fully utilized. As proof of principle, this study presents a Generative Adversarial Network capable of generating synthetic ERG signals of children with ASD and typically developing control individuals. We applied a Time Series Transformer and Visual Transformer with Continuous Wavelet Transform to enhance classification results on the extended synthetic signals dataset. This approach may support classification models in related psychiatric conditions where the ERG may help classify disorders.

SNOBERT: A Benchmark for clinical notes entity linking in the SNOMED CT clinical terminology

The extraction and analysis of insights from medical data, primarily stored in free-text formats by healthcare workers, presents significant challenges due to its unstructured nature. Medical coding, a crucial process in healthcare, remains minimally automated due to the complexity of medical ontologies and restricted access to medical texts for training Natural Language Processing models. In this paper, we proposed a method, "SNOBERT," of linking text spans in clinical notes to specific concepts in the SNOMED CT using BERT-based models. The method consists of two stages: candidate selection and candidate matching. The models were trained on one of the largest publicly available dataset of labeled clinical notes. SNOBERT outperforms other classical methods based on deep learning, as confirmed by the results of a challenge in which it was applied.

OCTDL: Optical Coherence Tomography Dataset for Image-Based Deep Learning Methods

Optical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 1600 high-resolution OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.