Anastasia Krithara

Anastasia Krithara
National Center for Scientific Research Demokritos | ncsr · Insititute of Informatics and Telecommunications

Post-doctoral researcher

About

65
Publications
9,685
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,009
Citations
Citations since 2017
41 Research Items
863 Citations
2017201820192020202120222023050100150
2017201820192020202120222023050100150
2017201820192020202120222023050100150
2017201820192020202120222023050100150
Introduction
I am a research associate in Insititute of Informatics and Telecommunications (IIT) of NCSR "Demokritos", where I am involved in national and international projects.
Additional affiliations
October 2008 - July 2020
National Center for Scientific Research Demokritos
Position
  • PostDoc Position
April 2005 - April 2008
Xerox Corporation
Position
  • Researcher
Education
April 2005 - June 2008
Polytech Paris-UPMC
Field of study
  • Computer Science
September 2003 - September 2004
University of Bristol
Field of study
  • Computer Science
September 1999 - June 2003
Athens University of Economics and Business
Field of study
  • Computer Science

Publications

Publications (65)
Preprint
Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors, representing topics of interest for the biomedical community. Several related but distinct biomedical concepts are often grouped together in a single coarse-grained descriptor and are treated as a single topic for semantic indexing. This study proposes a ne...
Preprint
The BioASQ question answering (QA) benchmark dataset contains questions in English, along with golden standard (reference) answers and related material. The dataset has been designed to reflect real information needs of biomedical experts and is therefore more realistic and challenging than most existing datasets. Furthermore, unlike most previous...
Preprint
This paper presents an overview of the tenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2022. BioASQ is an ongoing series of challenges that promotes advances in the domain of large-scale biomedical semantic indexing and question answering. In this edition, the challenge was composed of...
Article
In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug-drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the...
Conference Paper
Full-text available
There is a pressing need for advanced semantic annotation technologies of medical content, in particular medical publications, clinical trials and clinical records. Search engines and information retrieval systems require semantic annotation and indexing systems to support more advanced user search queries. Considering the relevance of disease conc...
Chapter
This paper presents an overview of the tenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2022. BioASQ is an ongoing series of challenges that promotes advances in the domain of large-scale biomedical semantic indexing and question answering. In this edition, the challenge was composed of...
Preprint
Full-text available
In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug-drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the...
Article
Full-text available
The development of the CRISPR-Cas9 technology has provided a simple yet powerful system for genome editing. Current gRNA design tools serve as an important platform for the efficient application of the CRISPR systems. However, most of the existing tools are black-box models that suffer from limitations, such as variable performance and unclear mech...
Preprint
Full-text available
The development of the CRISPR-Cas9 technology has provided a simple yet powerful system for targeted genome editing. Compared with previous gene-editing tools, the CRISPR-Cas9 system identifies target sites by the complementarity between the guide RNA (gRNA) and the DNA sequence, which is less expensive and time-consuming, as well as more precise a...
Chapter
The tenth version of the BioASQ Challenge will be held as an evaluation Lab within CLEF2022. The motivation driving BioASQ is the continuous advancement of approaches and tools to meet the need for efficient and precise access to the ever-increasing biomedical knowledge. In this direction, a series of annual challenges are organized, in the fields...
Article
Full-text available
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become a successful and promising technology for gene-editing. To facilitate its effective application, various computational tools have been developed. These tools can assist researchers in the guide RNA (gRNA) design process by pred...
Article
Full-text available
The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary widely used in biomedical knowledge systems, particularly for semantic indexing of scientific literature. As the MeSH hierarchy evolves through annual version updates, some new descriptors are introduced that were not previously available. This paper explores the conceptual pr...
Chapter
Advancing the state-of-the-art in large-scale biomedical semantic indexing and question answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks where different teams develop systems that are evaluated on the same benchmark datasets that represent the real information needs of experts in the biomedical domain. This pap...
Preprint
Full-text available
Advancing the state-of-the-art in large-scale biomedical semantic indexing and question answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks where different teams develop systems that are evaluated on the same benchmark datasets that represent the real information needs of experts in the biomedical domain. This pap...
Preprint
Full-text available
In this paper, we present an overview of the eighth edition of the BioASQ challenge, which ran as a lab in the Conference and Labs of the Evaluation Forum (CLEF) 2020. BioASQ is a series of challenges aiming at the promotion of systems and methodologies for large-scale biomedical semantic indexing and question answering. To this end, shared tasks a...
Preprint
In this document, we report an analysis of the Public MeSH Note field of the new descriptors introduced in the MeSH thesaurus between 2006 and 2020. The aim of this analysis was to extract information about the previous status of these new descriptors as Supplementary Concept Records. The Public MeSH Note field contains information in semi-structur...
Chapter
This paper describes the ninth edition of the BioASQ Challenge, which will run as an evaluation Lab in the context of CLEF2021. The aim of BioASQ is the promotion of systems and methods for highly precise biomedical information access. This is done through the organization of a series of challenges (shared tasks) on large-scale biomedical semantic...
Preprint
Full-text available
The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary widely used in biomedical knowledge systems, particularly for semantic indexing of scientific literature. As the MeSH hierarchy evolves through annual version updates, some new descriptors are introduced that were not previously available. This paper explores the conceptual pr...
Chapter
Knowledge Graphs provide insights from data extracted in various domains. In this paper, we present an approach discovering probable drug-to-drug interactions, through the generation of a Knowledge Graph from disease-specific literature. The Graph is generated using natural language processing and semantic indexing of biomedical publications and op...
Article
In this work, we propose a method for the automated refinement of subject annotations in biomedical literature at the level of concepts. Semantic indexing and search of biomedical articles in MEDLINE/PubMed are based on semantic subject annotations with MeSH descriptors that may correspond to several related but distinct biomedical concepts. Such s...
Chapter
In this paper, we present an overview of the eighth edition of the BioASQ challenge, which ran as a lab in the Conference and Labs of the Evaluation Forum (CLEF) 2020. BioASQ is a series of challenges aiming at the promotion of systems and methodologies for large-scale biomedical semantic indexing and question answering. To this end, shared tasks a...
Preprint
Full-text available
The results of the seventh edition of the BioASQ challenge are presented in this paper. The aim of the BioASQ challenge is the promotion of systems and methodologies through the organization of a challenge on the tasks of large-scale biomedical semantic indexing and question answering. In total, 30 teams with more than 100 systems participated in t...
Preprint
In this work, we propose a method for the automated refinement of subject annotations in biomedical literature at the level of concepts. Semantic indexing and search of biomedical articles in MEDLINE/PubMed are based on semantic subject annotations with MeSH descriptors that may correspond to several related but distinct biomedical concepts. Such s...
Chapter
This paper describes the eighth edition of the BioASQ Challenge, which will run as an evaluation Lab in the context of CLEF2020. The aim of BioASQ is the promotion of systems and methods for highly precise biomedical information access. This is done through the organization of a series of challenges (shared tasks) on large-scale biomedical semantic...
Chapter
Full-text available
The results of the seventh edition of the BioASQ challenge are presented in this paper. The aim of the BioASQ challenge is the promotion of systems and methodologies through the organization of a challenge on the tasks of large-scale biomedical semantic indexing and question answering. In total, 30 teams with more than 100 systems participated in t...
Preprint
Full-text available
Biomedical researchers working on a specific disease need up-to-date and unified access to knowledge relevant to the disease of their interest. Knowledge is continuously accumulated in scientific literature and other resources such as biomedical ontologies. Identifying the specific information needed is a challenging task and computational tools ca...
Article
Full-text available
In this work, we study the task of predicting the closing price of the following day of a stock, based on technical analysis, news articles and public opinions. The intuition of this study lies in the fact that technical analysis contains information about the event, but not the cause of the change, while data like news articles and public opinions...
Article
Full-text available
Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these...
Article
Full-text available
Artificial Intelligence has been an active research field in Greece for over forty years, and there are more than thirty AI groups throughout the country covering almost all subareas of AI. One milestone for AI research in Greece was in 1988, when the Hellenic Artificial Intelligence Society (EETN) was founded as a non-profit, scientific organizati...
Article
Full-text available
We survey the AI research carried out in Greece recently. We concentrate on the case of linked geospatial data, an area with significant practical importance, very interesting research results, and implemented systems developed by a Greek research team. Copyright © 2018, Association for the Advancement of Artificial Intelligence. All rights reserve...
Conference Paper
The past years have seen a growing amount of research on question answering (QA) over Semantic Web data, shaping an interaction paradigm that allows end users to profit from the expressive power of Semantic Web standards while, at the same time, hiding their complexity behind an intuitive and easy-to-use interface. On the other hand, the growing am...
Article
The workshop on Medical Information Retrieval took place at SIGIR 2016 in Pisa, Italy on July 21. The workshop programme included seven oral presentations of refereed papers, four posters and an invited keynote presentation. This allowed time for lively discussions among the 27 participants. These made clear the significant and diverse challenges i...
Article
Full-text available
Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these...
Chapter
BioASQ is a series of challenges that aims to assess the performance of information systems in supporting two tasks that are central to the biomedical question answering process: (a) the indexing of large volumes of unlabelled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generatio...
Conference Paper
Full-text available
In this report, we summarize the outcome of the "Evaluation-as-a-Service" workshop that was held on the 5th and 6th March 2015 in Sierre, Switzerland. The objective of the meeting was to bring together initiatives that use cloud infrastructures, virtual machines, APIs (Application Programming Interface) and related projects that provide evaluation...
Conference Paper
Full-text available
Modern online social networks, such as Twitter and Instagram, are nowadays important sources for publishing information and content around breaking news stories and incidents related to public safety, ranging from natural disasters and aeroplane accidents to terrorist attacks and industrial accidents. A crucial issue regarding such information and...
Article
Full-text available
This article provides an overview of the first BIOASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BIOASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-u...
Article
In the past years social media services received content contributions from millions of users, making them a fruitful source for data analysis. In this paper we present a novel approach for mining Twitter data in order to extract factual information concerning trending events. Our approach is based on relation extraction between named entities, suc...
Conference Paper
Most common methods for inquiring genomic sequence composition, are based on the bag-of-words approach and thus largely ignore the original sequence structure or the relative positioning of its constituent oligonucleotides. We here present a novel methodology that takes into account both word representation and relative positioning at various lengt...
Conference Paper
In this work, we consider a transfer learning approach based on K-means for splice site recognition. We use different representations for the sequences, based on n-gram graphs. In addition, a novel representation based on the secondary structure of the sequences is proposed. We evaluate our approach on genomic sequence data from model organisms of...
Conference Paper
Full-text available
A new transfer learning method is presented in this paper, addressing a particularly hard transfer learning problem: the case where the target domain shares only a subset of its classes with the source domain and only unlabeled data are provided for the target domain. This is a situation that occurs frequently in real-world applications, such as th...
Conference Paper
Full-text available
News and social media are emerging as a dominant source of information for numerous applications. However, their vast unstructured content present challenges to efficient extraction of such information. In this paper, we present the SYNC3 system that aims to intelligently structure content from both traditional news media and the blogosphere. To ac...
Article
In this paper, we address the problem of learning aspect models with partially labeled data for the task of document categorization. The motivation of this work is to take advantage of the amount of available unlabeled data together with the set of labeled examples to learn latent models whose structure and underlying hypotheses take more accuratel...
Conference Paper
Full-text available
Ontology learning is the process of acquiring (constructing or integrating) an ontology (semi-) automatically. Being a knowledge acquisition task, it is a complex activity, which becomes even more complex in the context of the BOEMIE project, due to the management of multimedia resources and the multi-modal semantic interpretation that they require...
Conference Paper
Full-text available
In this paper, we address the problem of learning aspect models with partially labeled examples. We propose a method which benefits from both semi-supervised and active learning frameworks. In particular, we combine a semi-supervised extension of the PLSA algorithm [11] with two active learning techniques. We perform experiments over four different...
Article
Full-text available
In this paper we describe a semi-automated approach for ontology learning. Exploiting an ontology-based multimodal information extraction system, the ontology learning subsystem accumulates documents that are insufficiently analysed and through clustering proposes new concepts, relations and interpretation rules to be added to the ontology.
Conference Paper
Full-text available
This paper investigates a new extension of the Probabilistic Latent Semantic Analysis (PLSA) model [6] for text classification where the training set is partially labeled. The proposed approach iteratively labels the unlabeled documents and estimates the probabilities of its labeling errors. These probabilities are then taken into account in the es...

Network

Cited By

Projects

Projects (4)
Project
The goal of Project IASIS is to seize the opportunity provided by a wave of data heading our way and turn this into actionable information that would match the right treatment with the right type of patient. A current challenge is that there are large, heterogeneous sets of data ranging from different sources, which if combined would enable the best decisions to be made, allowing for diagnosis and treatment to be personalised to each individual. IASIS is testing this approach in two disease areas – lung cancer and Alzheimer’s disease – but with the longer-term ambition that this approach will be more widely applicable to other disease areas.
Project
Project
[taken from www.bioasq.org] BioASQ organizes challenges on biomedical semantic indexing and question answering (QA). The challenges include tasks relevant to hierarchical text classification, machine learning, information retrieval, QA from texts and structured data, multi-document summarization and many other areas. Monetary and other prizes are awarded to the best performing systems. The project, a large collaborative effort, has received funding from the FP7, and is coordinated by researchers from the NCSR "Demokritos". Currently, it's at its 5th year. The project has a panel of biomedical experts. My role is the formulation of biomedical questions & answers relevant to my field of interest that will serve as input for the participating systems, and the evaluation of the systems' responses.