Publications

Also on Google Scholar, DBLP. ResearchGate, and ORCID.

Journal Conference / Workshop Preprint / Other
2026
Containing the Reproducibility Gap: Automated Repository-Level Containerization for Scholarly Jupyter Notebooks
Sheeba Samuel, Daniel Mietchen, Hemanta Lo, Martin Gaedke
arXiv preprint, 2026
Preprint
Learning to be Reproducible: Custom Loss Design for Robust Neural Networks
Waqas Ahmed, Sheeba Samuel, Kevin Coakley, Birgitta Koenig-Ries, Odd Erik Gundersen
arXiv preprint, 2026
Preprint Bibtex
2025
Multi-LLM Information Retrieval Pipeline for Extracting Deep Learning Methodologies in Biodiversity Research
Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel
PeerJ Computer Science, 2025
Paper Bibtex
Evaluating the Method Reproducibility of Deep Learning Models in the Biodiversity Domain
Waqas Ahmed, Vamsi Krishna Kommineni, Birgitta König-Ries, Jitendra Gaikwad, Luiz M. R. Gadelha Jr., Sheeba Samuel
PeerJ Computer Science, 2025
Paper Bibtex
FAIRJupyter4AI: A Corpus of Computational Notebooks for AI
Daniel Mietchen, Sheeba Samuel
Research Ideas and Outcomes, 2025
Paper
ShEx2SPARQL: Translating Shape Expressions into SPARQL Queries
Christoph Göpfert, Sheeba Samuel, Martin Gaedke
25th International Conference on Web Engineering (ICWE), 2025
Paper Preprint
ResearchFlow: An End-User Development Approach to Research Data Management Workflow Composition
Jan Haas, Martin Gaedke, Sheeba Samuel, Jeffrey Kelling
25th International Conference on Web Engineering (ICWE), 2025
Paper Preprint
Facilitating RDF Querying in Research Data Management through ShEx-Based SPARQL Query Construction
Christoph Göpfert, Sheeba Samuel, Martin Gaedke
2nd International Workshop on Natural Scientific Language Processing and Research Knowledge Graphs (NSLP 2025), co-located with ESWC 2025
Paper
Analyzing the Reproducibility of Research-Related Jupyter Notebooks at Scale
Daniel Mietchen, Sheeba Samuel
Software Engineering 2025
Paper Bibtex
2024
Computational Reproducibility of Jupyter Notebooks from Biomedical Publications
Sheeba Samuel, Daniel Mietchen
GigaScience, 13, giad113, 2024
Paper
FAIR Jupyter: A Knowledge Graph Approach to Semantic Sharing and Granular Exploration of a Computational Notebook Reproducibility Dataset
Sheeba Samuel, Daniel Mietchen
Transactions on Graph Data and Knowledge (TGDK), 2(2), 4:1–4:24, 2024
Paper Bibtex
Integrating Domain Knowledge for Enhanced Concept Model Explainability in Plant Disease Classification
Jihen Amara, Sheeba Samuel, Birgitta König-Ries
21st European Semantic Web Conference (ESWC), In-Use Track, 2024
Paper Bibtex
Facilitating End-User Development of Websites with Micro-Frontends
Jan-Ingo Haas, Sheeba Samuel, Martin Gaedke
26th International Conference on Information Integration and Web Intelligence (iiWAS), 2024
PaperBibtex
A Method for Integrating Heterogeneous Data into a Knowledge Graph
Christoph Göpfert, Sheeba Samuel, Martin Gaedke
26th International Conference on Information Integration and Web Intelligence (iiWAS), 2024
PaperBibtex
Reducing Run-to-Run Variability in Neural Networks: A Comparative Study of Weight Optimization Methods
Waqas Ahmed, Birgitta König-Ries, Sheeba Samuel
5th International Workshop on Reproducible Research in Pattern Recognition (RRPR), 2024
PaperBibtex
Towards the Automation of Knowledge Graph Construction Using Large Language Models
Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel
NLP4KGC Workshop at SEMANTiCS 2024
Paper
From Human Experts to Machines: An LLM Supported Approach to Ontology and Knowledge Graph Construction
Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel
arXiv preprint, 2024
Preprint
Explainability of Deep Learning-Based Plant Disease Classifiers Through Automated Concept Identification
Jihen Amara, Birgitta König-Ries, Sheeba Samuel
arXiv preprint, 2024
Preprint
Enhancing Explainability in Multimodal Large Language Models Using Ontological Context
Jihen Amara, Birgitta König-Ries, Sheeba Samuel
arXiv preprint, 2024
Preprint
Harnessing Multiple LLMs for Information Retrieval: A Case Study on Deep Learning Methodologies in Biodiversity Publications
Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel
arXiv preprint, 2024
Preprint
Data Provenance for Reproducible Research
Sheeba Samuel
Dagstuhl Seminar 23372 – Human-Centered Approaches for Provenance in Automated Data Science, 2024
Paper
2023
Concept Explainability for Plant Diseases Classification
Jihen Amara, Birgitta König-Ries, Sheeba Samuel
18th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications (VISAPP), 2023
Paper Preprint Bibtex
MLProvLab: Provenance Management for Data Science Notebooks
Dominik Kerzel, Birgitta König-Ries, Sheeba Samuel
DE4DS Workshop at BTW 2023
Paper Bibtex
MLProvCodeGen: A Tool for Provenance Data Input and Capture of Customizable Machine Learning Scripts
Tarek Al Mustafa, Birgitta König-Ries, Sheeba Samuel
BTW 2023 Student Program
Paper Bibtex
The Role of Ontology Matching in Ontology Network Development
Sheeba Samuel, Birgitta König-Ries, Alsayed Algergawy
18th International Workshop on Ontology Matching (OM), co-located with ISWC 2023
Paper
Reproducible Domain-Specific Knowledge Graphs in the Life Sciences: A Systematic Literature Review
Samira Babalou, Sheeba Samuel, Birgitta König-Ries
arXiv preprint, 2023
Preprint
How Reproducible are the Results Gained with the Help of Deep Learning Methods in Biodiversity Research?
Waqas Ahmed, Vamsi Krishna Kommineni, Birgitta König-Ries, Sheeba Samuel
Biodiversity Information Science and Standards (BISS), TDWG 2023
Abstract
2022
End-to-End Provenance Representation for the Understandability and Reproducibility of Scientific Experiments using a Semantic Approach
Sheeba Samuel, Birgitta König-Ries
Journal of Biomedical Semantics, 13(1):1, 2022
Paper Bibtex
A Collaborative Semantic-Based Provenance Management Platform for Reproducibility
Sheeba Samuel, Birgitta König-Ries
PeerJ Computer Science, 8:e921, 2022
Paper Bibtex
BiodivNERE: Gold Standard Corpora for Named Entity Recognition and Relation Extraction in the Biodiversity Domain
Nora Abdelmageed, Felicitas Löffler, Leila Feddoul, Alsayed Algergawy, Sheeba Samuel, Jitendra Gaikwad, Anahita Kazem, Birgitta König-Ries
Biodiversity Data Journal, 10:e89481, 2022
Paper Bibtex
[RE] Nondeterminism and Instability in Neural Network Optimization
Waqas Ahmed, Sheeba Samuel
ReScience Journal — ML Reproducibility Challenge 2021 (Fall Edition), 2022
Paper Bibtex
Toward a Framework for Integrative, FAIR, and Reproducible Management of Data on the Dynamic Balance of Microbial Communities
Luiz Gadelha, Martin Hohmuth, Mahnoor Zulfiqar, David Schöne, Sheeba Samuel, Maria Sorokina, Christoph Steinbeck, Birgitta König-Ries
IEEE 18th International Conference on e-Science (eScience), 2022
Paper Preprint Bibtex
2021
Understanding Experiments and Research Practices for Reproducibility: An Exploratory Study
Sheeba Samuel, Birgitta König-Ries
PeerJ, 9:e11140, 2021
Paper Bibtex
Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles
Sheeba Samuel, Frank Löffler, Birgitta König-Ries
Provenance and Annotation of Data and Processes — IPAW 2020 + IPAW 2021
Paper Bibtex
ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks
Sheeba Samuel, Birgitta König-Ries
Provenance and Annotation of Data and Processes — IPAW 2020 + IPAW 2021
Paper Bibtex
Towards Tracking Provenance from Machine Learning Notebooks
Dominik Kerzel, Sheeba Samuel, Birgitta König-Ries
13th International Conference on Knowledge Discovery and Information Retrieval (KDIR), 2021
Paper Bibtex
Capturing and Semantically Describing Provenance to Tell the Story of R Scripts
Maria Luiza Mondelli, Sheeba Samuel, Birgitta König-Ries, Luiz M. R. Gadelha Jr.
ReWords Workshop at IEEE 17th e-Science, 2021
Paper Bibtex
BiodivOnto: Towards a Core Ontology for Biodiversity
Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel, Birgitta König-Ries
18th Extended Semantic Web Conference (ESWC), Poster Track, 2021
Paper Bibtex
Towards an Ontology Network for the Reproducibility of Scientific Studies
Sheeba Samuel, Alsayed Algergawy, Birgitta König-Ries
8th International Workshop on Ontologies and Conceptual Modeling (OntoCom), co-located with FOIS 2021
Paper Slides Bibtex
A Data-driven Approach for Core Biodiversity Ontology Development
Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel, Birgitta König-Ries
3rd International Workshop on Semantics for Biodiversity (S4BioDiv), co-located with ICBO, 2021
Paper Bibtex
2020
A Virtual "Werkstatt" for Digitization in the Sciences
Sheeba Samuel, Maha Shadaydeh, Sebastian Böcker, Bernd Brügmann, Solveig Franziska Bucher, Volker Deckert, Joachim Denzler, Peter Dittrich, Ferdinand von Eggeling, Daniel Güllmar, Orlando Guntinas-Lichius, Birgitta König-Ries, Frank Löffler, Lutz Maicher, Manja Marz, Mirco Migliavacca, Jürgen R. Reichenbach, Markus Reichstein, Christine Römermann, Andrea Wittig
Research Ideas and Outcomes, 6:e54106, 2020
Paper
ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks
Sheeba Samuel, Birgitta König-Ries
ProvenanceWeek 2020
Paper Slides Bibtex
Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles
Sheeba Samuel, Frank Löffler, Birgitta König-Ries
ProvenanceWeek 2020
Paper Slides Bibtex
2019
A Provenance-based Semantic Approach to Support Understandability, Reproducibility, and Reuse of Scientific Experiments
Sheeba Samuel
PhD Dissertation, Friedrich Schiller University Jena, Germany, 2019
Thesis Defense Slides Bibtex
2018
The Story of an Experiment: A Provenance-based Semantic Approach towards Research Reproducibility
Sheeba Samuel, Kathrin Groeneveld, Frank Taubert, Daniel Walther, Tom Kache, Teresa Langenstück, Birgitta König-Ries, H. Martin Bücker, Christoph Biskup
11th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS), 2018
Paper Preprint Slides Bibtex
ProvBook: Provenance-based Semantic Enrichment of Interactive Notebooks for Reproducibility
Sheeba Samuel, Birgitta König-Ries
17th International Semantic Web Conference (ISWC), Demo Track, 2018
Paper Demo Bibtex
Combining P-Plan and the REPRODUCE-ME Ontology to Achieve Semantic Enrichment of Scientific Experiments using Interactive Notebooks
Sheeba Samuel, Birgitta König-Ries
15th Extended Semantic Web Conference (ESWC), Poster Track, 2018
Paper Bibtex
2017
Towards Reproducibility of Microscopy Experiments
Sheeba Samuel, Frank Taubert, Daniel Walther, Birgitta König-Ries, H. Martin Bücker
D-Lib Magazine, 23(1/2), 2017
Paper Bibtex
REPRODUCE-ME: Ontology-based Data Access for Reproducibility of Microscopy Experiments
Sheeba Samuel, Birgitta König-Ries
14th Extended Semantic Web Conference (ESWC), Poster Track, 2017
Paper Bibtex
Integrative Data Management for Reproducibility of Microscopy Experiments
Sheeba Samuel
14th Extended Semantic Web Conference (ESWC), PhD Symposium, 2017
Paper Bibtex
2012
Hadoop Compatible Framework for Discovering Network Topology and Detecting Hardware Failures
Ventrapragada Anusha, Sheeba Samuel, Varsha Raja Vidya, Shwetha Muralidharan, Shrisha Rao
3rd International Conference on Services in Emerging Markets (ICSEM), IEEE, 2012
Paper Bibtex