Katja Ovchinnikova

data scientist for climate solutions

Who I am

I am a data scientist specializing in machine learning and artificial intelligence. During my career, I have had the opportunity to work in a range of application fields: language processing, robotics, molecular biology, precision medicine, marine and environmental sciences, climate solution technology. Currently, I'm transitioning from academia to climate tech and working as an AI/ML consultant for organizations focusing on climate solutions.

I'm part of Homeward Bound, a leadership community for women in STEMM focusing on climate change, and an alumna of Terra.do Learning for Action, an educational program for climate solution professionals. For more details, please check out my blog.

What I do

Design data analysis workflows

Develop experimental design
for collecting data annotations

Prototype and evaluate AI/ML models


Consult on AI/ML
for climate solutions

Write scientific papers and blog posts

Run interactive workshops
on climate science/solutions

Current projects

Decarbonization of buildings

Data science for predicting locations for installing solar panels, heat pumps, EV chargers. AI consultant for Cquel.

Cquel website
Coral health

Computer vision analysis of the coral reef imagery. In collaboration with MEGA Lab at UH Hilo Hawaii.

Coral data
Scallop detection

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

Past projects

AI-driven precision medicine

Application of AI/ML to drug recommendation for cancer patients; at DBMR, University of Bern.

Lab website
METASPACE

AI/ML for computational metabolite annotation of imaging mass spectrometry data; at European Molecular Biology Laboratory.

Project website
Photo ID of manta rays

Automatic identification of manta rays; with Hawaii Association for Marine Education & Research.

Manta ray data

Photo ID of blue whales

Prototype project on automatic identification of blue whales.

XPERIENCE

Development of a dialog system, planning, and domain-specific knowledge extraction for a kitchen robot; at KIT, University of Karlsruhe.

Project website
Heider-Simmel Interactive Theater

Abductive reasoning for interpretation and narrativization of two-dimensional videos; at ISI Univeristy of Southern California.

Project website
Metaphor Interpretation for Cultural Schemas

Abductive reasoning for detection and interpretation of linguistic metaphors; at ISI Univeristy of Southern California.

Github repo

Machine Reading

Acquisition of knowledge by machine reading using lexical-semantic databases; at ISI Univeristy of Southern California.

Adaptive Ontologies on extreme Markup Structures

Automatic extraction of ontological knowledge from text and updating existing knowledge bases; at IKW University of Osnabrük.

Project website
Grammar Formalisms and Parsing

Development of an interactive tool visualizing formal grammars for an online course on grammar formalisms; at SfS University of Tübingen.

Course materials
Distributional Idiosyncrasies

Development of a similarity measure for comparing grammatical structures and on implementiation of a web service for psycholinguistic experiments; at SfS University of Tübingen.

Project website

Scientific publications

Books

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

Journal articles

L. Rappez, M. Stadler, S. Triana, R. Muthoni Gathungu, K. Ovchinnikova, P. Phapale, M. Heikenwalder and T. Alexandrov (2021). SpaceM reveals metabolic states of single cells. In: Nature Methods, 18, 799–805 . [Link]

K. Ovchinnikova, M. A. James, T. Mendo, M. Dawkins, J. Crall, K. Boswarva (2021). Exploring the potential to use low cost imaging and an open source convoluted neural network detector to support stock assessment of the king scallop (Pecten maximus). In: Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101233

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, 1-11. [Link]

K. Ovchinnikova, A. Rakhlin, L. Stuart, S. Nikolenko and T. Alexandrov (2020). ColocML: Machine learning quantifies co-localization between mass spectrometry images. In: Bioinformatics, 36(10), 3215-3224. [Link]

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

AntarcticaNow

Intinitative on preserving the Western Antarctic Peninsula with a Marine Protected Area. I'm part of the AntarcticaNow team.

website
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
linkedIn: katja-ovchinnikova-34980871