Dr. Sheeba Samuel

Personal Website
ORCiD 0000-0002-7981-8504
Heinz Nixdorf Chair for Distributed Information Systems
Sheeba Samuel, Dr
Postdoctoral Researcher
sheeba.samuel
JenTower
Leutragraben 1
07743 Jena

Research Area 

My research area includes:

  • Reproducible Research
  • Data provenance
  • Scientific Data Management and processing
  • Semantic Web
  • Machine Learning

Projects 

Current 

  • A virtual “Werkstatt” for digitization in the sciences
  • Semantic Annotations for Building a Reproducible and Interoperable Solution for End-to-End Machine Learning Pipelines
  • ThurAI (Thuringian Artifical Intelligence) 

Completed 

  • Project Z2 of CRC ReceptorLight: Integrative Data Management and Processing

Professional Activities 

Conferences and Journals

Invited Speaker Talks

  • Invited Speaker Talk on “Reproducible Research: Responding to 6W and 1H Questions of Data Provenance” in the HEIBRiDS Lecture Series at Einstein Center Digital Future, Berlin, Germany, 5th January 2022. [Slides]
  • Invited Speaker Talk on “Provenance and Reproducibility: a look into Jupyter Notebooks” in Thuringian RDM-Days 2021 “Data documentation: A love note to the future!” [Slides]
  • Invited Speaker Talk on “The Story of an Open Science Experiment” in Open Science Days at Max Planck Society, Berlin, 2021.
  • Invited Speaker Talk on “Contributions to Open Science for Reproducible Research” in QPTData Open Science Workshop at FIZ Karlsruhe, 2020. [Slides]
  • Speaker Talk at JupyterCon 2020

Work (Material)

Reproducibility work website:  https://w3id.org/reproduceme/research

Personal website: https://sheeba-samuel.github.io/

Curriculum Vitae

Past Positions:

  • Member of Technical Staff II – Aruba, a Hewlett Packard Enterprise Company (July 2013-December 2015)
  • Graduate Technical Intern – Aruba, a Hewlett Packard Enterprise Company (January 2013-June 2013)

Education:

  • PhD, Computer Science, Friedrich Schiller University Jena, Germany (2016-2019)
  • Master of Technology (M Tech), Information Technology, International Institute of Information Technology, Bangalore, India (2011-2013)
  • Bachelor of Technology (B Tech), Computer Science and Engineering, Cochin University of Science and Technology (CUSAT), India (2007-2011)

Grants

  • ProChance 2017 Grant, Friedrich Schiller University Jena
    Promotion of the scientific interaction of young female researchers.
  • IMPULSE project 2020 de, Friedrich Schiller University Jena
    Support Programme for early and advanced postdocs to apply for own third-party funds. Funding code: IP 2020-10
  • Start-up funding from MSCJ for the project “Integrating Knowledge Graphs for DL Interpretability”
  • Freistaats Thüringen funding for the research project ‘Explainability and Reproducibility for AI’
2022 Expand entry
  • 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
    6.1.2022
2021 Expand entry
  • Towards Tracking Provenance from Machine Learning Notebooks
    Dominik Kerzel, Sheeba Samuel, Birgitta König-Ries
    13th International Conference on Knowledge Discovery and Information Retrieval (KDIR)
    25.10.2021
  • 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, co-located with 17th IEEE e-Science 2021 27.9.2021
  • A Data-driven Approach for Core Biodiversity Ontology Development.
    Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel, Birgitta König-Ries
    Third International Workshop on Semantics for Biodiversity, co-located with ICBO, 2021 15.9.2021
  • Towards an Ontology Network for the reproducibility of scientific studies
    Sheeba Samuel, Alsayed Algergawy, Birgitta König-Ries
    JOWO Workshops 2021 13.9.2021
  • ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks
    Sheeba Samuel and Birgitta König-Ries
    Provenance Week 2021
    Provenance and Annotation of Data and Processes - 8th and 9th International Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021, Virtual Event, July 19-22, 2021 19.7.2021
  • Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles.
    Sheeba Samuel, Frank Löffler, Birgitta König-Rie
    Provenance Week 2021
    Provenance and Annotation of Data and Processes - 8th and 9th International Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021, Virtual Event, July 19-22, 2021 19.7.2021
  • BiodivOnto: Towards a Core Ontology for Biodiversity
    Nora Abdelmageed, Alsayed Algergawy, Sheeba Samuel and Birgitta Koenig-Ries
    The Semantic Web: ESWC 2021 Satellite Events: poster and demo
    4.6.2021
  • Understanding experiments and research practices for reproducibility: an exploratory study
    Sheeba Samuel, Birgitta König-Ries
    PeerJ 21.4.2021
2020 Expand entry
  • ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks
    Sheeba Samuel and Birgitta König-Ries
    Provenance Week 2020
    Charlotte, North Carolina, USA 22.6.2020
  • Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles
    Sheeba Samuel, Frank Löffler and Birgitta König-Ries
    Provenance Week 2020
    Charlotte, North Carolina, USA 22.6.2020
  • 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
    11.5.2020
2019 Expand entry
  • A Provenance-based Semantic Approach to Support Understandability, Reproducibility, and Reuse of Scientific Experiments
    Sheeba Samuel
    Friedrich Schiller University Jena 20.12.2019
2018 Expand entry
  • 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 and Christoph Biskup
    11th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2018)
    Antwerp, Belgium 5.12.2018
  • ProvBook: Provenance-based Semantic Enrichment of Interactive Notebooks for Reproducibility
    Sheeba Samuel and Birgitta König-Ries
    The 17th International Semantic Web Conference (ISWC) Demo Track 2018
    Monterey, California, USA 10.10.2018
  • Combining P-Plan and the REPRODUCE-ME Ontology to Achieve Semantic Enrichment of Scientific Experiments using Interactive Notebooks
    Sheeba Samuel and Birgitta König-Ries
    15th Extended Semantic Web Conference (ESWC) Posters & Demo 2018
    Crete, Greece 6.6.2018
2017 Expand entry
  • Integrative Data Management for Reproducibility of Microscopy Experiments
    Sheeba Samuel
    14th Extended Semantic Web Conference (ESWC) 2017
    Portoroz, Slovenia 28.5.2017
  • REPRODUCE-ME: Ontology-based Data Access for Reproducibility of Microscopy Experiments
    Sheeba Samuel, Birgitta König-Ries
    14th Extended Semantic Web Conference (ESWC) 2017
    Portoroz, Slovenia 28.5.2017
2016 Expand entry
  • Towards Reproducibility of Microscopy Experiments
    Sheeba Samuel, Frank Taubert, Daniel Walther, Birgitta König-Ries and H. Martin Bücker
    First International Workshop on Reproducible Open Science, 2016 co-located with TPDL
    Hannover, Germany 9.9.2016

Talks 

  • Reproducible Research: Responding to 6W and 1H Questions of Data Provenance
    The HEIBRiDS Lecture Series
    Helmholtz Einstein International Berlin Research School in Data Science (HEIBRiDS) 5.1.2022
  • The Story of an Open Science Experiment
    Max Planck Digital Library (MPDL) Open Science Days 2021
    Max Planck Digital Library (MPDL), Berlin, Germany 20.10.2021
  • Towards an Ontology Network for the reproducibility of scientific studies
    8th International Workshop on Ontologies and Conceptual Modeling, co-located with FOIS, 2021
    Online 13.9.2021
  • Provenance and Reproducibility: A Look into Jupyter Notebooks
    Thuringian RDM Days 2021 'Data documentation: A love note to the future!'
    Germany 22.6.2021
  • ProvBook: Capturing and Visualizing Provenance in Jupyter Notebooks for Reproducibility
    JupyterCon 2020
    JupyterCon 2020 13.10.2020
  • Analyzing the use and reproducibility of Jupyter Notebooks using ReproduceMeGit
    JupyterCon 2020
    JupyterCon 2020 13.10.2020
  • ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks
    Provenance Week 2020
    Virtual Provenance Week 2020 22.6.2020
  • Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles
    Virtual Provenance Week
    Provenance Week 2020 22.6.2020
  • Contributions to Open Science for Reproducible Research
    QPTData Open Science Workshop
    FIZ Karlsruhe 23.1.2020
  • A Provenance-based Semantic Approach to Support Understandability, Reproducibility, and Reuse of Scientific Experiments
    PhD Dissertation Defense
    Friedrich Schiller University Jena 20.12.2019
  • The Story of an Experiment: A Provenance-based Semantic Approach towards Research Reproducibility
    11th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2018)
    Antwerp, Belgium 4.12.2018
  • Provenance-based Semantic Approach for the Reproducibility of Scientific Experiments
    ICEI2018 - The 10th International Conference on Ecological Informatics
    Jena, Germany 27.9.2018
  • Integrative Data Management for Reproducibility of Microscopy Experiments
    14th Extended Semantic Web Conference (ESWC) 2017 PhD Symposium
    Portoroz, Slovenia 29.5.2017
  • Towards Reproducibility of Microscopy Experiments
    First International Workshop on Reproducible Open Science (RepScience 2016)
    Hannover, Germany 9.9.2016

Teaching 

Supervised Theses 

  • Reproducibility of Machine Learning Experiments given the provenance data
    Tarek Al Mustafa - Bachelor
    Friedrich-Schiller-Universität Jena
    17.5.2021
  • Tracking Provenance in Machine Learning Scripts
    Dominik Kerzel - Bachelor
    Friedrich-Schiller-Universität Jena
    1.4.2021

Lectures  

  • WiSe 2019/ 2020 - Semantic Web Technologies
  • WiSe 2018/ 2019 - Semantic Web Technologies
  • SoSe 2018 - Management of Scientific Data
  • WiSe 2017/ 18 - Semantic Technologies for Science