Katja Ovchinnikova

computer scientist and climate activist

I work on computational analysis of mass spectrometry and marine science data at the European Molecular Biology Laboratory, Heidelberg, Germany. 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.

Current projects

METASPACE

Computational metabolite annotation of imaging mass spectrometry data. I work on applying natural language processing and computer vision algorithms to metabolite data.

project website
Coral health

Statistical analysis of the lesion distribution to describe coral disease and computer vision analysis of the imagery of coral colonies. In collaboration with UH Hilo Hawaii.

coral data
Scallop detection

Automatic detection of scallops in sea bottom imagery. In collaboration with University of St. Andrews.

Past projects

XPERIENCE

Xperience implements, adapts, and extends a complete robot system for automating introspective, predictive, and interactive understanding of actions and dynamic situations. I worked on a dialog system, planning, and domain-specific knowledge extraction from corpora.

project website
Photo ID of manta rays

Development of an algorithm and a desktop application for automatic identification of manta ray images. In collaboration with Hawaii Association for Marine Education & Research.

manta ray data
Photo ID of blue whales

Prototype project on developing of 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.


Heider-Simmel Interactive Theater

Interpretation and narrativization of simple two-dimensional videos in terms of goals, plans, beliefs, and emotions. I worked on application of probabilistic abduction to scene recognition.

project website
Metaphor Interpretation for Cultural Schemas

Detection of linguistic metaphors in English, Spanish, Russian, and Farsi texts, and mapping of them to conceptual metaphors. I supervised a group responsible for development of an abduction-based metaphor interpretation pipeline and corpus-based knowledge extraction.

github repo
Grammar Formalisms and Parsing

Online course for teaching grammar formalisms and parsing. I developed the MoMo graphical tool for visualizing formal grammars.

course materials

Adaptive Ontologies on extreme Markup Structures

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.

project website
Distributional Idiosyncrasies

Study of 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.

project website
Machine Reading

Acquisition of knowledge by machine reading. I worked on turning lexical-semantic databases like WordNet and FrameNet into machine-readable FOL axioms applicable for reasoning.

Scientific publications

Books

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

Journal articles

K. Ovchinnikova, V. Kovalev, L. Stuart and T. Alexandrov (2020). OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images. In: BMC Bioinformatics 21, 129. https://doi.org/10.1186/s12859-020-3425-x

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. In: the 4th issue of the International Journal of Interoperability in Business Information Systems (IBIS) on Information Modeling and Ontologies. [PDF]

Preprints

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]

Other

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 activism

Homeward Bound

Leadership program for women in STEMM focusing on climate change. I'm an alumna of the 4th cohort.

website
Climathon

Hackathon focusing on climate change. I'm the main organizer of the first Climathon in Heidelberg.

website
Climate change and action

Interactive workshop on climate science, politics, and action. I designed the materials and ran the workshops together with Jan-Marcus Nasse.

workshop materials

Selected media


My videos and writing

Symposium at sea in Antartica
Climate change and action lecture
Science for our planet and communities: interviews

Press about me

EMBLetc. magazine about my Homeward Bound journey
read article
Energy News Network about our Antarctica voyage
read article
Interview for "Women in science" book
download e-book
Interview for EMBLetc. magazine
read article

Contact

email: katja@ovchinnikova.me

blog: katja-hb.home.blog

twitter: @Katja_HB4