Katja Ovchinnikova

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I currently work on computational analysis of mass spectrometry data as well as on coral health at the European Molecular Biology Laboratory, Heidelberg. I'm also part of Homeward Bound, a leadership program for women in STEMM focusing on climate change. For more details, please check my blog and twitter @Katja_HB4.

Research interests

  • human and automated reasoning
  • computational analysis in molecular biology
  • computational analysis in ecology and marine science
  • language and vision
  • computational natural language understanding
  • computational analysis of mass media



METASPACE. This project is on computational metabolite annotation of imaging mass spectrometry data. In this project, I work on applying natural language processing and computer vision algorithm to metabolite data.

Coral Health. This project is on analysing coral disease based on statistical analysis of the lesion distribution as well as on computer vision analysis of the coral colonies. In collaboration with UH Hilo Hawaii.

Scallop detection. This project is on detecting scallops in sea bottom imagery. In collaboration with University of St. Andrews.


XPERIENCE: Robots Bootstrapped through Learning from Experience. The goal of the project was to extend state‐of‐the‐art enactive systems by using structural bootstrapping to generate new knowledge. Xperience implements, adapts, and extends a complete robot system for automating introspective, predictive, and interactive understanding of actions and dynamic situations. In this project, I worked on a dialog system, planning, and domain-specific knowledge extraction from corpora.

Photo Identification of Manta Ray Images. This project is on developing an algorithm and a desktop application for automatic identification of manta ray images. In collaboration with Mark Deakos from Hawaii Association for Marine Education & Research.

Mediator: Computational Analysis of Mass Media. This was a pilot study project on computational analysis of mass media. Our long-term goals were to develop tools for 1) tracking distribution of media content, i.e. looking for information sources, citations, and modifications, 2) finding contradicting and supporting evidence for news statements, 3) detecting media bias, 4) detecting manufactured spread of opinions.

Photo Identification of Whales. This project is on developing a web service for uploading and annotating photographs of whales, matching new images against the accumulated whale catalogue, acquiring statistics about whale migration paths and population distributions. The main algorithm for automatic matching of whale images can be found in this repository.

Heider-Simmel Interactive Theater (USC/ISI, USA). This project was on interpretation and narrativization of simple two-dimensional videos in terms of goals, plans, beliefs, and emotions. In this project, I worked on application of probabilistic abduction to scene recognition.

Metaphor Interpretation for Cultural Schemas (USC/ISI, USA). This project is on detecting linguistic metaphors in English, Spanish, Russian, and Farsi texts, and mapping them to conceptual metaphors. I supervised a group (6 people) responsible for development of an abduction-based metaphor interpretation pipeline [Code] and corpus-based knowledge extraction.

Machine Reading (USC/ISI, USA). This project is on acquiring knowledge by machine reading. I worked on turning lexical-semantic databases like WordNet and FrameNet into machine-readable FOL axioms applicable for reasoning.

Adaptive Ontologies on extreme Markup Structures (University of Tübingen, Germany). This project is on automatic extraction of ontological knowledge from text and updating existing knowledge bases. I developed algorithms for non-monotonic ontology updates including automatic resolution of ontological inconsistencies.

Distributional Idiosyncrasies (SFB 441 at the University of Tübingen, Germany). This project is on studying how syntactic, semantic, and selectional properties constraint lexical elements in their contexts of use. I worked on developing a similarity measure for comparing grammatical structures and on implementing a web service for psycholinguistic experiments.

Grammar Formalisms and Parsing (Department of Linguistics, University of Tübingen, Germany). This project is on developing an online course for teaching grammar formalisms and parsing. I developed the MoMo graphical tool for visualizing formal grammars (MoMo can be found here).


       Ovchinnikova, E. (2012). Integration of World Knowledge for Natural Language Understanding, Atlantis Press, Springer.

Journal articles

K. Ovchinnikova, A. Rakhlin, L. Stuart, S. Nikolenko and T. Alexandrov (2020). ColocML: Machine learning quantifies co-localization between mass spectrometry images. In: Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa085

M. Wächter, E. Ovchinnikova, V. Wittenbeck, P. Kaiser, S. Szedmak, W. Mustafa, D. Kraft, N. Krüger, J. Piater and T. Asfour (2018). Integrating Multi-Purpose Natural Language Understanding, Robot's Memory, and Symbolic Planning for Task Execution in Humanoid Robots. In: Robotics and Autonomous Systems, Vol. 99, pp. 148-165. [Link]

Aksoy, E., E. Ovchinnikova, A. Orhan, Y. Yang and T. Asfour (2017). Unsupervised Linking of Visual Features to Textual Descriptions in Long Manipulation Activities. In: IEEE Robotics and Automation Letters, Vol. 2, No. 3, pp. 1397-1404. [Link]

Burns, J., T. Alexandrov, E. Ovchinnikova, R. D. Gates and M. Takabayashi (2016). Investigating the spatial distribution of Growth Anomalies affecting Montipora capitata corals in a 3-dimensional framework. In: Journal of Invertebrate Pathology, 140:51-57. [Link]

Burns, J., T. Alexandrov, E. Ovchinnikova, R. D. Gates and M. Takabayashi (2016). Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques. In: Data Brief, 9:460-462. [Link]

Palmer, A., E. Ovchinnikova, M. Thune, R. Lavigne, B. Guevel, A. Dyatlov, O. Vitek, C. Pineau, M. Boren and T. Alexandrov (2015). Using collective expert judgements to evaluate quality measures of mass spectrometry images. In: Bioinformatics (special issue ISMB/ECCB'15), 31(12):375-384. [Link]

Zock, M., Wandmacher, T. and Ovchinnikova, E. (2010) Are vector-based approaches a feasible solution to the "tip-of-the-tongue" problem? In eLexicography in the 21st century: New challenges, new applications, vol. 7, pp. 355-365.

Ovchinnikova, E. and Kühnberger, K.-U. (2007). Automatic Ontology Extension: Resolving Inconsistencies, GLDV-Journal for Computational Linguistics and Language Technology 22(2):19-33.[PDF]

Ovchinnikova, E. and Richter, F. (2007): Morph Moulder: Graphical Software for Teaching and Visualizing Logic for HPSG and Description Logics. In Logic Journal of IGPL 15(4):333-345. [Link]

Ovchinnikova, E., Wandmacher, T. and Kühnberger, K.-U. (2007): Solving Terminological Inconsistency Problems in Ontology Design. To appear in: the 4th issue of the International Journal of Interoperability in Business Information Systems (IBIS) on Information Modeling and Ontologies. [PDF]


K. Ovchinnikova, V. Kovalev, L. Stuart and T. Alexandrov (2019). Recognizing off-sample mass spectrometry images with machine and deep learning. [BioRxiv 518977 preprint]

T. Alexandrov, K. Ovchnnikova, A. Palmer, V. Kovalev, A. Tarasov, L. Stuart, R. Nigmetzianov, D. Fay and Key METASPACE Contributors (2019). METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease. Submitted to Nature Biotechnology. [BioRxiv 539478 preprint]

Book chapters

Inoue, N., E. Ovchinnikova, K. Inui and J. R. Hobbs (2014). Weighted Abduction for Discourse Processing Based on Integer Linear Programming. In Sukthankar, G., Goldman, R. P., Geib, S., Pynadath, D. V., Hung, H. B. (eds.) : Plan, Activity, and Intent Recognition, pp. 33-55. [Link]

Ovchinnikova, E., N. Montazeri, T. Alexandrov, J. R. Hobbs, M. C. McCord and R. Mulkar-Mehta (2014). Abductive Reasoning with a Large Knowledge Base for Discourse Processing. In Hunt, H., Bos, J. and Pulman, S. (eds.) : Computing Meaning, vol. 47, pp. 107-127. [PDF]

Wandmacher, T., Ovchinnikova, E., Mönnich, U., Michaelis, J. and Kühnberger, K.-U. (2011). Adaptation of Ontological Knowledge from Structured Textual Data. In Mehler, A., Kühnberger, K.-U., Lobin, H., Lüngen, H., Storrer, A. and Witt, A. (eds.): Modeling, Learning, and Processing of Text Technological Data Structures, pp. 129-153, Springer. [Link]

Refereed proceedings

Ovchinnikova, E., M. Wächter, V. Wittenbeck, and T. Asfour (2015). Multi-Purpose Natural Language Understanding Linked to Sensorimotor Experience in Humanoid Robots. In Proc. of Humaniods'15, 365--372. [PDF]

Ovchinnikova, E., R. Israel, S. Wertheim, V. Zaytsev, V. Montazeri, and J. R. Hobbs (2014). Abductive Inference for Interpretation of Metaphors. In Proc. of ACL 2014 Workshop on Metaphor in NLP. Baltimore, 33--41. [PDF]

Ovchinnikova, E., A. Gordon, and J. R. Hobbs (2013). Abduction for Discourse Interpretation: A Probabilistic Framework. In Proceedings of the Joint Symposium on Semantic Processing, 42--50. [PDF]

Inoue, N., E. Ovchinnikova, K. Inui, and J. R. Hobbs (2012). Coreference Resolution with ILP-based Weighted Abduction. In Proceedings of COLING 2012, pp.1291-1308. [PDF]

Peñas, A. and Ovchinnikova, E. (2012). Unsupervised Acquisition of Axioms to Paraphrase Noun Compounds and Genitives. In Proceedings of the International Conference on Intelligent Text Processing and Computational Linguistics (CICLing), Part I, LNCS 7181, pp. 388-401, Springer. [Link]

Ovchinnikova, E., N. Montazeri, T. Alexandrov, J. R. Hobbs, M. C. McCord and R. Mulkar-Mehta (2011). Abductive Reasoning with a Large Knowledge Base for Discourse Processing. In Proceedings the 9th International Conference on Computational Semantics (IWCS'11), pp. 225-234. [Link]

Ovchinnikova, E., L. Vieu, A. Oltramari, S. Borgo and T. Alexandrov (2010). Data-Driven and Ontological Analysis of FrameNet for Natural Language Reasoning. In Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC'10), Valletta, Malta. [PDF]

Ovchinnikova, E., Alexandrov, T. and Wandmacher, T. (2009). Automatic acquisition of the argument-predicate relations from a frame-annotated corpus. In Proceedings of Conf. on Empirical Methods in Natural Language Processing (EMNLP), pp. 1388-1397. [PDF]

Wandmacher, T., Ovchinnikova, E. and Alexandrov, T. (2008). Does Latent Semantic Analysis reflect Human Associations? In Proceedings of the Lexical Semantics workshop at ESSLLI'08, Hamburg, Germany.[PDF]

Wandmacher, T., Ovchinnikova, E., Krumnack, U. and Dittmann, H. (2007). Extraction, evaluation and integration of lexical-semantic relations for the automated construction of a lexical ontology. In Proceedings of the AOW'07 Workshop.[PDF]

Krumnack, U., Ovchinnikova, E. and Wandmacher, T. (2007). LexO: Constructing a lexical ontology from heterogenous resources. In Proceedings of the OntoLex 2007 Workshop.

Kühnberger, K.-U., Wandmacher T., Schwering, A., Ovchinnikova, E., Krumnack, U., Gust, H. & Geibel, P. (2007): I-Cog: A Computational Framework for Integrated Cognition of Higher Cognitive Abilities, in Proceedings of 6th Mexican International Conference on Artificial Intelligence (MICAI 2007), LNAI 4827, pp. 203-214, Springer.

Kühnberger, K.-U., Wandmacher, T., Ovchinnikova, E., Krumnack, U., Gust, H. & Geibel, P. (2007): Modeling Human-Level Intelligence by Integrated Cognition in a Hybrid Architecture, in P. Hitzler, T. Roth-Berghofer, S. Rudolph: Foundations of Artificial Intelligence (FAInt-07), Workshop at KI 2007, CEUR-WS, vol. 277, pp. 1-15.

Mönnich, U., Michaelis, J., Ovchinnikova, E., Wandmacher, T. & Kühnberger, K.-U. (2007). Information Extraction from Annotation Graphs Serving for the Adaptation of Ontologies - Position Paper. In Proceedings of the Workshop "Learning from Non-Vectorial Data" (LNVD 2007) held in conjunction with KI 2007, Osnabrück.

Ovchinnikova, E. and Kühnberger, K.-U. (2007). Automatic Ontology Extension: Resolving Inconsistencies - Extended Abstract -. In: Proceedings "Ontologies and Text Technology: Approaches to Extract Semantic Knowledge from Syntactic Information", PICS, vol. 2007-1, pp. 93-98.

Azarova, I., Ivanov, V., Ovchinnikova, E. and Sinopalnikova, A. (2006): RussNet as a Semantic Component of the Text Analyser for Russian. In: Third International WordNet Conference (GWC'06). Jeju Island, Korea, January 22-26 2006: Proceedings. Brno: Masaryk University. pp. 19-27. [PDF]

Azarova, I., Ivanov V. and Ovchinnikova, E.(2006): Inheritance of the Valency Frames in RussNet Thesaurus for the Automatic Text Analysis. In: Computer linguistics and intellectual technologies. Proc. of the international conference Dialog'2006 (in Russian). [PDF]

Ovchinnikova, E. and Richter, F. (2006): Morph Moulder: Graphical Software for Teaching and Visualizing RSRL and Description Logics. In: Proc. of the Second International Congress on Tools for Teaching Logic (SICTTL). pp. 143-147. [PDF]

Azarova, I. and Ovchinnikova, E. (2006): Semantic Interpretation of the Noun Phrases in Russian Corpora. In Proc. of the International ConferenceCorpus Linguistics - 2006 (in Russian). [PDF]

Ovchinnikova, E. and Kühnberger, K.-U. (2006). Adaptive ALE-TBox for Extending Terminological Knowledge. In A. Sattar & B. H. Kang (eds.): AI 2006, Proceedings of the 19th ACS Australian Joint Conference on Artificial Intelligence, LNAI 4304 (Lecture Notes in Artificial Intelligence), Springer, pp. 1111-1115. [PDF]

Ovchinnikova, E. and Kühnberger, K.-U. (2006). Aspects of Automatic Ontology Extension: Adapting and Regeneralizing Dynamic Updates, in M. Orgun (Hrsg.): Advances in Ontologies. Proceedings of the Australasian Ontology Workshop (AOW 2006), Conferences in Research and Practice in Information Technology, vol. 72, pp. 52-60. [PDF]

Azarova, I., Ivanov, V. and Ovchinnikova, E. (2005): Semantic Structure of the Proposition in the Procedure Extracting Facts from Russian Texts. In: Koboseva, Nariniani, Selegea (eds): Computer linguistics and intellectual technologies. Proceedings of the international conference Dialog'2005 (in Russian). pp. 6-11.

Richter, F., Ovchinnikova, E., Trawinski, B. and Meurers, D. (2002): Interactive Graphical Software for Teaching the Formal Foundations of Head-Driven Phrase Structure Grammar. In: Gerhard Jäger, Paola Monachesi, Gerald Penn, and Shuly Wintner (eds): Proceedings of Formal Grammar 2002. pp. 137-148. [PDF]


Ovchinnikova, E., Zaytsev, V., Wertheim, S., Israel, R. (2014). Generating Conceptual Metaphors from Proposition Stores. arXiv preprint arXiv:1409.7619. [PDF]

Gordon, A., Hobbs, J., Ovchinnikova, K., Roemmele, M., and Morency, L. (2013) Abduction of mental states with a formal theory of commonsense psychology. Abstract. Workshop on Mental model ascription by language-enabled intelligent agents, July 31, 2013, Berlin, Germany. [PDF]

Climate science and action workshop materials [Link]

Colocalization for molecular images [Code]

Background recognition for molecular images [Code]

Media analysis tools [Code] [Web interface]

Inference-based natural language understanding pipeline for English, Spanish, Russian, and Farsi [Code]

Proposition store generator [Code] [Data]

SIFT-based algorithm for idenfication of whale images [Code]

Morph Moulder graphical software for visualizing formal grammars [Software]

Tutorial on Natural Language Understanding with World Knowledge and Inference (KR 2014, Summer of Logic, Vienna) [Slides]