Anastasia Krithara, PhD

Selected publications

11.A. Sakor, S. Jozashoori, E. Niazmand, A. Rivas, K. Bougiatiotis, F. Aisopos, E. Iglesias, P. D. Rohde, T. Padiya, A. Krithara, G. Paliouras, M.-E. Vidal, Knowledge4COVID-19: A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments' toxicities, In Journal of Web Semantics, Elsevier BV, volume 75, (Pages: 100760), 2023. (Publisher's online version)
10.V. Konstantakos, A. Nentidis, A. Krithara, G. Paliouras, CRISPR-Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning, In Nucleic Acids Research, Oxford University Press (OUP), volume 50, (Pages: 3616–3637), 2022. (Publisher's online version)
9.V. Konstantakos, A. Nentidis, A. Krithara, G. Paliouras, CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions, In Nucleic Acids Research, Oxford University Press (OUP), 2022. (Publisher's online version)
8. K. Bougiatiotis, F. Aisopos, A. Nentidis, A. Krithara and G. Paliouras. "Drug-Drug Interaction Prediction on a Biomedical Literature Knowledge Graph". International Conference on Artificial Intelligence in Medicine (AIME 2020).
7. A. Nentidis, A. Krithara, G. Tsoumakas, G. Paliouras. "Beyond MeSH: Fine-Grained Semantic Indexing of Biomedical Literature Based on Weak Supervision". Information Processing and Management journal, Volume 57, Issue 5, September 2020
6. A. Nentidis, K. Bougiatiotis, A. Krithara, G. Paliouras. "iASiS Open Data Graph: Automated Semantic Integration of Disease-Specific Knowledge". IEEE 33rd International Symposium on Computer Based Medical Systems (CBMS) 2020.
5. A. Hanbury, H. Müller, K. Balog, T. Brodt, G. V Cormack, I. Eggel, T. Gollub, F. Hopfgartner, J. Kalpathy-Cramer, N. Kando, A. Krithara, J. Lin, S. Mercer, M. Potthast,"Evaluation-as-a-Service: Overview and outlook", ACM Journal of Data and Information Quality, 10 (4). 15. ISSN 1936-1955 (2018). (Pdf)
4. G. Tsatsaronis, G. Balikas, P. Malakasiotis, I. Partalas, M. Zschunke, M.R. Alvers, D. Weissenborn, A. Krithara, S. Petridis, D. Polychronopoulos, Y. Almirantis, J. Pavlopoulos, N. Baskiotis, P. Gallinari, T. Artieres, A. Ngonga, N. Heino, E. Gaussier, L. Barrio-Alvers, M. Schroeder, I. Androutsopoulos and G. Paliouras, An overview of the BIOASQ large- scale biomedical semantic indexing and question answering competition, BMC Bioinformatics, v. 16, n. 138 (2015). (Publisher's online version) (pdf preprint)
3. A. Krithara, G. Paliouras. TL-PLSA: Transfer Learning between Domains with Different Classes. IEEE International Conference on Data Mining series (ICDM), Dallas, Texas, December 2013. ( Publisher's online version)
2. A. Krithara, M. Amini, C. Goutte and J.M. Renders. Learning Aspect Models with Partially Labeled Data. Pattern Recognition Letters -Elsevier. (2011). ( Publisher's online version)
1. G. Petasis, V. Karkaletsis, G.Paliouras, A. Krithara and I. Zavitsanos. Ontology Population and Enrichment: State of the art. Book chapter in Knowledge-Driven Mulitmedia Informaton Extraction and Ontology Evolution". Lecture Notes in Computer Science, Springer. (2011). ( Publisher's online version)

Projects

smartHEALTH

European Digital Innovation Hub on Precision Medicine and Innovative E-health Services.

P4LUCAT

Personalized medicine for lung cancer treatment: using Big Data-driven approaches for decision support

BioASQ

A challenge on large-scale biomedical semantic indexing and question answering

Courses

2017-today: Teaching "Machine learning" at the MSc in "Data Science" . NCSR "Demokritos -University of Peloponnese.
2017-2019: Teaching "Natural language analytics" at the MSc in "Data Science" . NCSR "Demokritos -University of Peloponnese.
2015-2018: Teaching "Biomedical databases and information extraction" at the MSc in "Information Technologies in Medicine and Biology" . University of Athens.
2011-2012: Teaching "Machine Learning and Data Mining" and "Data visualization" at the Study abroad program. UTA-NCSR "Demokritos"- Aegean University - Marine Conservation, Research Institute “Archipelagos”.
2009: Teaching assistant, "Information Extraction from Text" at “Technoglossia”. Interdisciplinary Interuniversity Postgraduate Course in Language Technologies. UΟA-NTUA-ILSP –NCSR “Demokritos”.

Supervising BSc/MSc theses

2008- today: Supervising several BSc/MSc students as well as interships in Machine learning, Information extraction, Natural language processing, Bioinformatics.

Lab's MSc, BSc theses

Lab's Interships

Lab's Suggested Topics

Other activities

2012- today: Co-organizing the BioASQ challenges and workshops.

2019: Co-organized the AthNLP (Athens Natural Language Processing Summer School), in NCSR "Demokritos".

2017: Co-organized the 7th Open Challenge on Question Answering over Linked Data (QALD-7)., ESWC, Portoroz, Slovenia, May 2017.

2016-2017: Co-organized the ISWC Workshop on Benchmarking Linked Data (BLINK).

2016: Co-organized the Workshop on Medical Information Retrieval (MedIR), SIGIR 2016 Pisa, Italy,July 2016.

2015: Co-organized the CLEF QA Track: CLEF Question Answering Track. CLEF, Toulouse, France, September, 2015.

2014: Co-organized the IRSS14: International Research-centered Summer School in “Cognitive Systems and Interactive Robotics, Data and Content Analysis”, in NCSR "Demokritos", Greece, 3rd-30th July 2014.

2013: Co-organized the IRSS13: International Research-centered Summer School in "Cognitive Systems and Interactive Robotics, Social Media, Digital Preservation", in NCSR "Demokritos", Greece, 4th-31th July 2013.

2012: Co-organized the Tutorial:"Bootstrapping ontology evolution: a generic approach relying on ontology-based information extraction", LREC2012, Instabul, May 2015.

Curriculum Vitae

Studies

PhD in artificial intelligence, Pierre et Marie Curie (Paris VI) University, Paris, France, 2008

Thesis: Semi-supervised and active learning for text classification. Supervisors: Prof. Patrick Gallinari, Dr. Jean-Michel Renders, Prof. Massih-Reza Amini.

In collaboration with Xerox Research Center Europe (now NAVER LABS Europe).

PhD scholarship (Conventions Industrielles de Formation par la REcherche - CIFRE GRANT) of the French center of research and technology (ANRT – Association Nationale de la Recherche et de la Technologie).

MSc in Advanced computer science (Machine Learning and Data Mining), Bristol University, Department of informatics, Bristol, UK, 2004

Thesis: Semantic classification. Supervisors: Dr. Steve Cayzer, Prof. Peter Flach.

In collaboration with HP labs, Bristol.

BSc in informatics, Department of Informatics, Athens University of Economics and Business, Athens, Greece, 2003

Working Experience

2008 – today: Postdoctoral researcher, Institute of Informatics and Telecommunications, National Center for Scientific Research (NCSR) “Demokritos”

Research and Development in the context of the EU and national projects.

2009-2012: External consultant (part time), “BYTE COMPUTER ABEE” company.

Project bids and management.

2005 – 2008: Researcher, Xerox Research Center Europe (XRCE), Grenoble, France.

Research and development in the following areas: Machine learning, information extraction, document classification.

2004 (6 months): Internship (research student), HP research labs, Bristol, UK.

Research and development: Machine learning, semantic web, document classification.

Short CV

Dr Anastasia Krithara has been a post-doctoral researcher in the Institute of Informatics and Telecommunications at NCSR "Demokritos" since 2008. She is a member of the Software and Knowledge Engineering Laboratory (SKEL), and the head of the Biomedical and Health Informatics Team (BioHIT). Before, she was a research engineer in Xerox Research Centre Europe, in Grenoble, France, where she carried out research in the area of machine learning. She holds a BSc in Computer Science from Athens University of Economics and Business, an MSc in Machine Learning and Data Mining from University of Bristol and a PhD in Machine Learning from Pierre and Marie Curie University (Paris VI). Her research interests include Machine Learning, Information Retrieval, Bioinformatics, Knowledge Engineering and Natural Language Processing. She is program committee member of several international conferences and workshops and her work has been published in international journals, conferences and books. She is involved in many European and national research projects and she has the technical coordinator role in some of them. In particular, she was the depute coordinator of the FP7 project BioASQ and the technical coordinator of the H2020 project iASiS. She has supervised more than 25 student theses and internships the last 10 years. She is teaching postgraduate courses and she has co-organised the International Research-centered Summer Schools (IRSS-2013 and IRSS-2014), the Athens Natural Language Processing Summer Schools (AthNLP 2019), as well as the BioASQ challenges and workshops (2012- today). She has served as a member of the board (2017-2018) the general secretary (2019-2020) of the Hellenic Artificial Intelligence Society (EETN).

Dr. Anastasia Krithara