lnu.sePublications
Change search
Link to record
Permanent link

Direct link
Alternative names
Publications (10 of 41) Show all publications
Sachenkova, O., Andreasson, M., Tan, D. & Lincke, A. (2026). Agentic RAG for Maritime AIoT: Natural Language Access to Structured Data. Sensors, 26(4), Article ID 1227.
Open this publication in new window or tab >>Agentic RAG for Maritime AIoT: Natural Language Access to Structured Data
2026 (English)In: Sensors, E-ISSN 1424-8220, Vol. 26, no 4, article id 1227Article in journal (Refereed) Published
Abstract [en]

Maritime operations are increasingly reliant on sensor data to drive efficiency and enhance decision-making. However, despite rapid advances in large language models, including expanded context windows and stronger generative capabilities, critical industrial settings still require secure, role-constrained access to enterprise data and explicit limitation of model context. Retrieval-Augmented Generation (RAG) remains essential to enforce data minimization, preserve privacy, support verifiability, and meet regulatory obligations by retrieving only permissioned, provenance-tracked slices of information at query time. However, current RAG solutions lack robust validation protocols for numerical accuracy for high-stakes industrial applications. This paper introduces Lighthouse Bot, a novel Agentic RAG system specifically designed to provide natural-language access to complex maritime sensor data, including time-series and relational sensor data. The system addresses a critical need for verifiable autonomous data analysis within the Artificial Intelligence of Things (AIoT) domain, which we explore through a case study on optimizing ferry operations. We present a detailed architecture that integrates a Large Language Model with a specialized database and coding agents to transform natural language into executable tasks, enabling core AIoT capabilities such as generating Python code for time-series analysis, executing complex SQL queries on relational sensor databases, and automating workflows, while keeping sensitive data outside the prompt and ensuring auditable, policy-aligned tool use. To evaluate performance, we designed a test suite of 24 questions with ground-truth answers, categorized by query complexity (simple, moderate, complex) and data interaction type (retrieval, aggregation, analysis). Our results show robust, controlled data access with high factual fidelity: the proprietary Claude 3.7 achieved close to 90% overall factual correctness, while the open-source Qwen 72B achieved 66% overall and 99% on simple retrieval and aggregation queries. These findings underscore the need for a secure limited-context RAG in maritime AIoT and the potential for cost-effective automation of routine exploratory analyses.

Place, publisher, year, edition, pages
MDPI, 2026
Keywords
iot, genai, llms, rag, sensor data, maritime industry
National Category
Computer Sciences
Identifiers
urn:nbn:se:lnu:diva-145422 (URN)10.3390/s26041227 (DOI)001701316400001 ()41755167 (PubMedID)2-s2.0-105031354950 (Scopus ID)
Available from: 2026-03-09 Created: 2026-03-09 Last updated: 2026-04-16Bibliographically approved
Ji, M., Song, Y., Roth, J., Dashti, A., Lazo, J., Lincke, A., . . . Lagali, N. (2026). Deep learning-based segmentation and density estimation of corneal nerves and dendritic cells from In Vivo confocal microscopy images. Scientific Reports, 16(1), Article ID 1620.
Open this publication in new window or tab >>Deep learning-based segmentation and density estimation of corneal nerves and dendritic cells from In Vivo confocal microscopy images
Show others...
2026 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 16, no 1, article id 1620Article in journal (Refereed) Published
Abstract [en]

The purpose of this study was to compare manual assessment of corneal nerve fiber length (CNFL) and dendritic cell (DC) density with an automated assessment method utilizing deep learning segmentation to perform rule-based density estimation. Corneal images were acquired using in vivo confocal microscopy (IVCM) from 100 participants with persistent ocular symptoms after mild COVID-19 (Group 1) and 30 controls without symptoms (Group 2). In total, 1,300 IVCM images were selected and manually annotated for CNFL, and 1,300 for DCs (with dendrites and without dendrites), using FIJI tools. The between-method difference in mean CNFL density was 0.2  (95% CI: [0.09, 0.23]) for Group 1 and −0.2  (95% CI: [−0.34, −0.10]) for Group 2. For Group 1, the mean difference for DCs with dendrites was −1.1  (95% CI: [−1.78, −0.39]), and for DCs without dendrites it was −3.1  (95% CI: [−5.1, −1.0]). For Group 2, the mean difference for DCs with dendrites was −1.0  (95% CI: [−1.79, −0.27]), and for DCs without dendrites it was 0.3  (95% CI: [−1.93, 2.60]). Both manual and automated methods showed significant between-group differences for CNFL (p=0.012 and p=0.034, respectively) and DC densities (p=0.005 and p=0.010). The automated approach performed comparably to manual assessment, supporting its potential for reliable, scalable analysis of CNFL and DC in IVCM images.

Place, publisher, year, edition, pages
Springer Nature, 2026
Keywords
deep learning, confocal microscopy, cornea, nerve fibers, dendritic cells, segmentation, density, Covid-19
National Category
Medical Imaging
Identifiers
urn:nbn:se:lnu:diva-144064 (URN)10.1038/s41598-025-34412-6 (DOI)001662910900001 ()41530230 (PubMedID)2-s2.0-105027348233 (Scopus ID)
Funder
Linnaeus University
Available from: 2026-01-16 Created: 2026-01-16 Last updated: 2026-04-16Bibliographically approved
Backåberg, S., Elmgren Frykberg, G., Eriksson Östh, K., Löwe, W., Fagerström, C., Niklasson, J. & Lincke, A. (2026). Developing an AI-Trained Movement Screening Tool, Based on Skeleton Avatar Technique, to Evaluate and Promote Sustainable Physical Functioning in Daily Life. In: Mauro Giacomini; Jaime Delgado; Theodoros N. Arvanitis; Elisavet Andrikopoulou; Arriel Benis; Gabriella Balestra; Riccardo Bellazzi; Parisis Gallos; Roberto Gatta; Daniele Roberto Giacobbe; Noemi Giordano; Maria Hägglund; Lars Lindsköld; Lenka Lhotska; Sara Marceglia; Enea Parimbelli; Lucia Sacchi; Paolo Soda; Lăcrămioara Stoicu-Tivadar; Pierangelo Veltri; Patrizia Vizza (Ed.), Opening the Personal Gate between Technology and Health Care: Proceedings of MIE 2026. Paper presented at 36th Medical Informatics Europe Conference (MIE 2026), Genoa, Italy, May 25-28, 2026 (pp. 108-112). IOS Press, 336
Open this publication in new window or tab >>Developing an AI-Trained Movement Screening Tool, Based on Skeleton Avatar Technique, to Evaluate and Promote Sustainable Physical Functioning in Daily Life
Show others...
2026 (English)In: Opening the Personal Gate between Technology and Health Care: Proceedings of MIE 2026 / [ed] Mauro Giacomini; Jaime Delgado; Theodoros N. Arvanitis; Elisavet Andrikopoulou; Arriel Benis; Gabriella Balestra; Riccardo Bellazzi; Parisis Gallos; Roberto Gatta; Daniele Roberto Giacobbe; Noemi Giordano; Maria Hägglund; Lars Lindsköld; Lenka Lhotska; Sara Marceglia; Enea Parimbelli; Lucia Sacchi; Paolo Soda; Lăcrămioara Stoicu-Tivadar; Pierangelo Veltri; Patrizia Vizza, IOS Press, 2026, Vol. 336, p. 108-112Conference paper, Published paper (Refereed)
Abstract [en]

Maintaining mobility is vital for older adults. However, standardized functional tests often overlook crucial qualitative aspects, and expert assessments (EA) are costly and lack standardization. This project aims to develop an AI-based movement screening tool (SAT-Movement Analysis) utilizing the low-cost Skeleton Avatar Technique (SAT) and standardized Observational Movement Analysis (OMA) to detect deviations in daily movement. The initial phase automated expert assessments to establish a reliable foundation for machine learning. Five participants (ages 35–57) performed Sit-To-Stand, Stand-To-Sit, and One-Leg Stance, assessed by three physiotherapists using a modified IRAF protocol. Results demonstrated correspondence between automatically aggregated expert scores and consensus scores across all aggregation levels (Pearson’s r = 0.90–0.97, ICC = 0.91–0.98, = 0.78–1.00). These findings motivate continued development of an AI-trained screening tool providing accurate movement quality feedback based on 2D smartphone video, supporting early detection and personalized intervention.

Place, publisher, year, edition, pages
IOS Press, 2026
Series
Studies in Health Technology and Informatics, ISSN 0926-9630, E-ISSN 1879-8365
Keywords
machine learning, movement analysis, physical functioning, skeleton avatar technique
National Category
Physiotherapy
Research subject
Health and Caring Sciences
Identifiers
urn:nbn:se:lnu:diva-146653 (URN)10.3233/SHTI260118 (DOI)42174795 (PubMedID)2-s2.0-105039958005 (Scopus ID)9781643686615 (ISBN)
Conference
36th Medical Informatics Europe Conference (MIE 2026), Genoa, Italy, May 25-28, 2026
Available from: 2026-05-28 Created: 2026-05-28 Last updated: 2026-06-03Bibliographically approved
Kopacheva, E., Lincke, A., Björneld, O. & Hammar, T. (2025). Detecting Adverse Drug Events in Clinical Notes Using Large Language Models. In: Elisavet Andrikopoulou;Parisis Gallos;Theodoros N. Arvanitis;Rosalynn Austin;Arriel Benis;Ronald Cornet;Panagiotis Chatzistergos;Alexander Dejaco;Linda Dusseljee-Peute;Alaa Mohasseb;Pantelis Natsiavas;Haythem Nakkas;Philip Scott (Ed.), Intelligent Health Systems – From Technology to Data and Knowledge: (pp. 892-893). IOS Press
Open this publication in new window or tab >>Detecting Adverse Drug Events in Clinical Notes Using Large Language Models
2025 (English)In: Intelligent Health Systems – From Technology to Data and Knowledge / [ed] Elisavet Andrikopoulou;Parisis Gallos;Theodoros N. Arvanitis;Rosalynn Austin;Arriel Benis;Ronald Cornet;Panagiotis Chatzistergos;Alexander Dejaco;Linda Dusseljee-Peute;Alaa Mohasseb;Pantelis Natsiavas;Haythem Nakkas;Philip Scott, IOS Press, 2025, p. 892-893Chapter in book (Refereed)
Abstract [en]

Monitoring adverse drug events (ADEs) is critical for pharmacovigilance and patient safety. However, identifying ADEs remains challenging, as suspected or confirmed side effects are often documented solely in the unstructured text of electronic health records (EHRs). Manually reviewing clinical notes to detect ADEs is labor-intensive and time-consuming, highlighting the need for automated methods capable of analyzing and extracting ADE-related information from clinical documentation. In this short communication, we describe our ongoing research on fine-tuning and evaluating a large language model (LLM) for the detection of ADEs in clinical notes. Preliminary descriptive result of this study indicates that ADEs are poorly documented in discharge notes, with less than 15% explicitly linking ADEs to specific drugs, which highlights the need for improved reporting practices.

Place, publisher, year, edition, pages
IOS Press, 2025
Series
Studies in Health Technology and Informatics, ISSN 0926-9630, E-ISSN 1879-8365 ; 327
Keywords
Adverse drug event, discharge notes, medical named entities, large language model
National Category
Computer and Information Sciences Social and Clinical Pharmacy Medical Informatics
Research subject
Health and Caring Sciences, Health Informatics; Computer and Information Sciences Computer Science
Identifiers
urn:nbn:se:lnu:diva-138602 (URN)10.3233/SHTI250495 (DOI)40380603 (PubMedID)2-s2.0-105005816662 (Scopus ID)9781643685960 (ISBN)
Available from: 2025-05-21 Created: 2025-05-21 Last updated: 2026-04-16Bibliographically approved
Nordqvist, O., Björneld, O., Bergman, P., Wettermark, B., Lincke, A., Andersson, M. L. & Hammar, T. (2025). Drug-Induced QT Prolongation: Associations Between Risk Classifications in a Swedish Clinical Decision Support System and Clinical Outcomes. Clinical Pharmacology and Therapeutics, 119(2), 503-513
Open this publication in new window or tab >>Drug-Induced QT Prolongation: Associations Between Risk Classifications in a Swedish Clinical Decision Support System and Clinical Outcomes
Show others...
2025 (English)In: Clinical Pharmacology and Therapeutics, ISSN 0009-9236, E-ISSN 1532-6535, Vol. 119, no 2, p. 503-513Article in journal (Refereed) Published
Abstract [en]

Potential adverse drug events can be signaled in Clinical Decision Support Systems (CDSSs). This study validated a Swedish CDSS (Janusmed Risk Profile) by investigating associations between calculated risk classifications of drugs with QT-prolonging potential and registered related clinical outcomes. Subjects living in Kalmar County, Sweden, between 2011 and 2020 exposed to risk drugs (risk level I: somewhat increased risk, II: moderate increased risk, III: significant increased risk) were extracted from regional electronic health records and matched to controls (risk level 0: no known increased risk) by age, sex, and index date. Ventricular arrhythmia (VA), Torsade de Pointes, cardiac arrest and death were outcomes followed for one year. Logistic regression analysis was performed adjusted for age, sex, number of drugs, days in hospital and previous diagnosis. Among the 188,453 subjects, a higher proportion of those classified by the CDSS as having a risk of QT prolongation experienced VA compared to controls (risk level I = 0.26%, II = 0.34%, III = 0.71% vs risk level 0 = 0.17%). When adjusting for other risk factors, the association decreased, but risk level III remained significant with OR 2.1 (95% CI 1.6-2.9) compared to controls. Similar results were seen for the other outcomes. Although there was an association between CDSS risk classifications and clinical outcomes, only a few subjects are affected, and other factors, such as previous diagnosis, play an important role. The need for multifactorial CDSS algorithms is thus crucial to better guide prescribers in finding high-risk patients.

Place, publisher, year, edition, pages
John Wiley & Sons, 2025
National Category
Cardiology and Cardiovascular Disease
Identifiers
urn:nbn:se:lnu:diva-143003 (URN)10.1002/cpt.70121 (DOI)001609911300001 ()41208201 (PubMedID)2-s2.0-105021300285 (Scopus ID)
Available from: 2025-12-16 Created: 2025-12-16 Last updated: 2026-04-16Bibliographically approved
Kopacheva, E., Henriksson, A., Dalianis, H., Hammar, T. & Lincke, A. (2025). Fine-tuning Clinical Language Models to Identify Adverse Drug Events in Clinical Text: Machine Learning Approach. JMIR Formative Research, 9, Article ID e71949.
Open this publication in new window or tab >>Fine-tuning Clinical Language Models to Identify Adverse Drug Events in Clinical Text: Machine Learning Approach
Show others...
2025 (English)In: JMIR Formative Research, E-ISSN 2561-326X, Vol. 9, article id e71949Article in journal (Refereed) Published
Abstract [en]

Background:  Medications are essential for health care but can cause adverse drug events (ADEs), which are harmful and sometimes fatal. Detecting ADEs is a challenging task because they are often not documented in the structured data of electronic health records (EHRs) . There is a need for automatically extracting ADE-related information from clinical notes, as manual review is labor-intensive and time-consuming.

Objectives: This study aims to fine-tune the pre-trained clinical language model, SweDeClin-BERT, for medical named entity recognition (NER) and relation extraction (RE) tasks, and to implement an integrated NER-RE approach to more effectively identify ADEs in clinical notes from clinical units in Sweden. The performance of this approach is compared to our previous machine learning method, which utilized conditional random fields (CRFs) and Random Forest (RF).

Data Sources: A subset of clinical notes from the Stockholm EPR (Electronic Patient Record) Corpus, dated 2009-2010, containing suspected ADEs based on ICD-10 codes in the A.1/A.2 categories was randomly sampled. These notes were annotated by a physician with ADE-related entities and relations following the ADE annotation guidelines.

Methods: We fine-tuned the SweDeClin-BERT model for the NER and RE tasks and implemented an integrated NER-RE pipeline to extract entities and relationships from clinical notes. The models were evaluated using 395 clinical notes from clinical units in Sweden. The NER-RE pipeline was then applied to classify the clinical notes as containing or not containing ADEs. Additionally, we conducted an error analysis to better understand the model’s behavior and to identify potential areas for improvement.

Results: In total 62% of notes contained an explicit description of an ADE, indicating that an ADE-related ICD-10 code alone does not ensure detailed event documentation. The fine-tuned SweDeClin-BERT model achieved an F1-score of 0.845 for NER and 0.81 for RE task, outperforming the baseline models (CRFs for NER and Random Forests for RE). In particular, the RE task showed a 53% improvement in macro-average F1-score compared to the baseline. The integrated NER-RE pipeline achieved an overall F1-score of 0.81.

Conclusions: Utilizing a domain-specific language model like SweDeClin-BERT for detecting ADEs in clinical notes demonstrates improved classification performance (0.77 in strict and 0.81 in relaxed mode) compared to conventional machine learning models like CRFs and RF. The proposed fine-tuned ADE model requires further refinement and evaluation on annotated clinical notes from another hospital to evaluate the model’s generalizability. In addition, the annotation guidelines should be revised, as there is an overlap of words between the Finding and Disorder entity categories, which were not consistently distinguished by the annotators. Furthermore, future work should address the handling of compound words and split entities to better capture context in the Swedish language.  

Place, publisher, year, edition, pages
JMIR Publications, 2025
Keywords
electronical health records; adverse drug events; domain-specific language models; BERT; SweDeClin-BERT
National Category
Natural Language Processing Artificial Intelligence
Research subject
Computer Science, Software Technology
Identifiers
urn:nbn:se:lnu:diva-141495 (URN)10.2196/71949 (DOI)001589663200029 ()40934508 (PubMedID)2-s2.0-105015483860 (Scopus ID)
Projects
NLMED seed project funding by DISA
Available from: 2025-09-10 Created: 2025-09-10 Last updated: 2026-04-16Bibliographically approved
Yan, S., Meichen, J., Roth, J., Lincke, A., Macedo, A. F., Löwe, W. & Neil, L. (2025). Ivcmassist: decision support system for detection of acanthamoeba keratitis cysts in vivo confocal microscopy images. In: : . Paper presented at 4th International Symposium on Digital Transformation.
Open this publication in new window or tab >>Ivcmassist: decision support system for detection of acanthamoeba keratitis cysts in vivo confocal microscopy images
Show others...
2025 (English)Conference paper, Oral presentation only (Refereed)
Abstract [en]

Acanthamoeba are ubiquitous microorganisms found in the air, soil, tap and drinking water, swimming pools, and in both saltwater and freshwater environments [1].They can cause corneal infections that lead to Acanthamoeba keratitis (AK), which is serious medical condition accompanied by intense eye pain, sensitivity to light, and severely impaired vision. AK is commonly associated with contact lens use, particularly in developed countries, where up to 90% of cases are linked to contact lens wear [2]. Timely identification and diagnosis of AK are critical to preventing vision loss. Corneal culture is the gold standard for diagnosing AK, but its low sensitivity and slow turnaround can delay treatment and worsen infection [3]. A complementary method uses non-invasive clinical imaging such as in-vivo confocal microscopy (IVCM) [4,5]. Despite several advantages such as high-resolution imaging, rapid diagnosis, and the ability to monitor disease progression, IVCM has limitations, including the large volume of images generated and the needs for identifying informative/useful images and experienced interpretation. While previous approaches have primarily focused on building models to detect AK in pre- selected images, our decision support system [6], IVCMAssist, automates the entire diagnostic workflow—from processing raw IVCM images and removing artifacts, to sorting images by corneal layer, to identifying informative images, and to detecting AK signs such as cysts in informative images. It enhances the AK diagnosis process by reducing the time spent on image sorting and pre-selection of informative images (non-overlapped images with detected AK cysts), while enabling experienced observers to correct model errors through a human-in-the-loop AI approach.

Keywords
Acanthamoeba keratitis, deep learning, image processing, confocal microscopy, cysts
National Category
Artificial Intelligence Ophthalmology
Identifiers
urn:nbn:se:lnu:diva-141530 (URN)
Conference
4th International Symposium on Digital Transformation
Available from: 2025-09-12 Created: 2025-09-12 Last updated: 2026-04-16Bibliographically approved
Hammar, T., Nilsson, D., Björneld, O., Sving, C. & Lincke, A. (2025). Machine Learning to Improve Decision Support for Preventing Adverse Drug Events. In: Elisavet Andrikopoulou, Parisis Gallos, Theodoros N. Arvanitis, Rosalynn Austin, Arriel Benis, Ronald Cornet, Panagiotis Chatzistergos, Alexander Dejaco, Linda Dusseljee-Peute, Alaa Mohasseb, Pantelis Natsiavas, Haythem Nakkas, Philip Scott (Ed.), Intelligent Health Systems – From Technology to Data and Knowledge: (pp. 245-246). IOS Press
Open this publication in new window or tab >>Machine Learning to Improve Decision Support for Preventing Adverse Drug Events
Show others...
2025 (English)In: Intelligent Health Systems – From Technology to Data and Knowledge / [ed] Elisavet Andrikopoulou, Parisis Gallos, Theodoros N. Arvanitis, Rosalynn Austin, Arriel Benis, Ronald Cornet, Panagiotis Chatzistergos, Alexander Dejaco, Linda Dusseljee-Peute, Alaa Mohasseb, Pantelis Natsiavas, Haythem Nakkas, Philip Scott, IOS Press, 2025, p. 245-246Chapter in book (Refereed)
Abstract [en]

One approach to preventing adverse drug events (ADEs), such as harmful drug interactions, is the implementation of clinical decision support systems (CDSS). In an ongoing project, we are investigating the accuracy of the rule-based CDSS currently utilized in Swedish healthcare for predicting ADEs and exploring whether machine learning (ML) can improve these predictions. By analyzing real-world healthcare data from a Swedish region spanning a 10-year period, we show that ML has potential to improve ADE predictions compared to existing rule-based CDSS.

Place, publisher, year, edition, pages
IOS Press, 2025
Series
Studies in Health Technology and Informatics, ISSN 0926-9630, E-ISSN 1879-8365 ; 327
Keywords
Clinical decision support system, adverse drug event, medications, machine-learning, artificial intelligence, health data
National Category
Computer and Information Sciences Social and Clinical Pharmacy Medical Informatics
Research subject
Health and Caring Sciences, Health Informatics
Identifiers
urn:nbn:se:lnu:diva-138601 (URN)10.3233/shti250320 (DOI)2-s2.0-105005816991 (Scopus ID)9781643685960 (ISBN)
Available from: 2025-05-21 Created: 2025-05-21 Last updated: 2026-04-16Bibliographically approved
Hanscam, E., Lincke, A., Mohammed, A. T., van Oeveren, D. & Witcher, R. (2024). Digital Excavations: Text Mining Approaches for a Better Archaeology. In: : . Paper presented at 3rd International Symposium on Digital Transformation, Växjö, Sweden, 11-12 September, 2024.
Open this publication in new window or tab >>Digital Excavations: Text Mining Approaches for a Better Archaeology
Show others...
2024 (English)Conference paper, Oral presentation only (Refereed)
National Category
Educational Sciences
Research subject
Pedagogics and Educational Sciences
Identifiers
urn:nbn:se:lnu:diva-135827 (URN)
Conference
3rd International Symposium on Digital Transformation, Växjö, Sweden, 11-12 September, 2024
Available from: 2025-02-04 Created: 2025-02-04 Last updated: 2025-09-23Bibliographically approved
Hanscam, E., Hanscam, R., Lincke, A., Milrad, M., Mohammed, A. T., van Overeem, D. & Witcher, R. (2024). Exploring Antiquity Geographic Regions.
Open this publication in new window or tab >>Exploring Antiquity Geographic Regions
Show others...
2024 (Swedish)Other (Other academic)
Abstract [sv]

What constitutes 'world archaeology'?

Visualize the subject of archaeological publications by geographic region location over time.

Antiquity Journal was founded as a journal of world archaeology in 1927, continuously publishing peer-reviewed research through to the present day. This tool takes the place names listed in Antiquity abstracts from 1927 to 2015, attributes them to a geographic region, and allows the user to view and manipulate the resulting graph. Below, users may also generate visualizations of specific time periods for individual regions.

National Category
Archaeology
Research subject
Humanities, Archaeology
Identifiers
urn:nbn:se:lnu:diva-137976 (URN)
Available from: 2025-04-09 Created: 2025-04-09 Last updated: 2025-09-23Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9062-1609

Search in DiVA

Show all publications