arXiv subjects

Mikhail Kulyabin

Publications and source records attributed to Mikhail Kulyabin.

11 recordsLinked to original sources

arXiv2026

Light-Adapted Electroretinogram and Oscillatory Potentials (LEOPs) Dataset for Autism Spectrum Disorder and Typically Developing Individuals

The LEOPs (Light-ERG-Oscillatory Potentials) dataset provides light-adapted (LA) electroretinogram (ERG) and Oscillatory Potentials (OPs) waveforms for typically developing Control, Autism Spectrum Disorder (ASD) and ASD + Attention Deficit Hyperactivity Disorder (ADHD) childhood and adolescent populations. The ERGs were recorded in the Right And Left eyes with skin electrodes using the handheld RETeval device at two sites in Australia and the United Kingdom. The LEOPs dataset includes 5309 single flash ERG and 4434 OPs waveforms as well as images selected from each participant showing the position of the skin electrode. The LEOPs dataset is constructed from recordings using a 9 step randomized flash series from $-0.37$ to $1.20$~$Td.s$, a 2 step at 113 and 446 $Td.s$ flash strengths (2500 Control, 1730 ASD and 451 ASD + ADHD samples), as well as the $85$~$Td.s$ (Light Adapted 3 $cd.s.m^{-2}$ (LA3)) equivalent International Society of Clinical Electrophysiology of Vision (ISCEV) Standard flash with 435 Control, 176 ASD and 37 ASD + ADHD waveform samples. Code for the stimulus is provided along with participant demographics, date and time of testing, and where available diagnostic scores for the ASD and ASD + ADHD groups, alongside iris color, electrode position with image files and time domain values for the ERG and summed values for the OPs. The repository contains excel file, exported JSON files on the patient level that are more suitable for machine learning tasks, images of electrode position for each recording and the protocol files for use with the RETeval.

physics.med-ph↗

arXiv2026

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.

cs.AI↗

arXiv2026

Tables or Sankey Diagrams? Investigating User Interaction with Different Representations of Simulation Parameters

Understanding complex parameter dependencies is critical for effective configuration and maintenance of software systems across diverse domains - from Computer-Aided Engineering (CAE) to cloud infrastructure and database management. However, legacy tabular interfaces create a major bottleneck: engineers cannot easily comprehend how parameters relate across the system, leading to inefficient workflows, costly configuration errors, and reduced system trust - a fundamental program comprehension challenge in configuration-intensive software. This research evaluates whether interactive Sankey diagrams can improve comprehension of parameter dependencies compared to traditional spreadsheet interfaces. We employed a heuristic evaluation using the PURE method with three expert evaluators (UX design, simulation, and software development specialists) to compare a Sankey-based prototype to traditional tabular representations for core engineering tasks. Our key contribution demonstrates that flow-based parameter visualizations significantly reduce cognitive load (51% lower PURE scores) and interaction complexity (56% fewer steps) compared to traditional tables, while making parameter dependencies immediately visible rather than requiring mental reconstruction. By explicitly visualizing parameter relationships, Sankey diagrams address a core software visualization challenge: helping users comprehend complex system configurations without requiring deep tool-specific knowledge. While demonstrated through CAE software, this research contributes to program comprehension and software visualization by showing that dependency-aware visualizations can significantly improve understanding of configuration-intensive systems. The findings have implications for any software domain where comprehending complex parameter relationships is essential for effective system use and maintenance.

cs.HC↗

arXiv2025

User eXperience Perception Insights Dataset (UXPID): Synthetic User Feedback from Public Industrial Forums

Customer feedback in industrial forums offers rich but underexplored insights into real-world product experience. Yet systematic analysis remains challenging due to unstructured, domain-specific content and the scarcity of high-quality labeled datasets. This paper presents the User eXperience Perception Insights Dataset (UXPID), a collection of 7130 synthesized and anonymized user feedback branches extracted from a public industrial automation forum. Each JSON record contains multi-post comments enriched with metadata and annotated by a large language model (LLM) for UX insights, user expectations, severity ratings, sentiment, and topic classifications. UXPID is designed to facilitate research in user requirements, user experience (UX) analysis, and AI-driven feedback processing, particularly where privacy and licensing restrictions limit access to real-world data. It supports the training and evaluation of transformer-based models for tasks such as issue detection, sentiment analysis, and requirements extraction in technical forums, providing a valuable resource for advancing NLP methods within industrial product support and software engineering domains.

cs.CL↗

arXiv2025

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.

cs.HC↗

arXiv2024

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.

eess.IV↗

arXiv2024

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 2000 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.

eess.IV↗

arXiv2024

Generating synthetic light-adapted electroretinogram waveforms using Artificial Intelligence to improve classification of retinal conditions in under-represented populations

Visual electrophysiology is often used clinically to determine functional changes associated with retinal or neurological conditions. The full-field flash electroretinogram (ERG) assesses the global contribution of the outer and inner retinal layers initiated by the rods and cone pathways depending on the state of retinal adaptation. Within clinical centers reference normative data are used to compare with clinical cases that may be rare or underpowered within a specific demographic. To bolster either reference or case datasets the application of synthetic ERG waveforms may offer benefits to disease classification and case-control studies. In this study and as a proof of concept, artificial intelligence (AI) to generate synthetic signals using Generative Adversarial Networks is deployed to up-scale male participants within an ISCEV reference dataset containing 68 participants, with waveforms from the right and left eye. Random Forest Classifiers further improved classification for sex within the group from a balanced accuracy of 0.72 to 0.83 with the added synthetic male waveforms. This is the first study to demonstrate the generation of synthetic ERG waveforms to improve machine learning classification modelling with electroretinogram waveforms.

q-bio.NC↗

arXiv2024

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.

eess.IV↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.CL↗