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The Program at a Glance
Who: Two Universities,one Research Center and one Medical Center  
Where: Heraklion and Chania,Crete  
When: Applications extended to August 31, 2020 (NEW!), lectures to start September 28, 2020 
How: A distance learning program (afternoon hours) plus an 15-day Intensive Lab training requiring physical presence  
Duration/Credits: 15 Months (90 ECTS) or 24 Months (120 ECTS)  

1st TRIMESTER  20/9-20/11 Introductory Module

2nd TRIMESTER 26/11-12/2 Biofabrication, Molecular Diagnostics and Therapy Module

3rd TRIMESTER 26/2-16/4 Bio-Medical Imaging Module

4th TRIMESTER 01/05-20/06 Medical Information Systems Module


4th TRIMESTER 01/05-20/06 Medical Information Systems Module

ΒΜΕ 16 - Artificial Intelligence and Medical Decision Support Systems

          M. Lagoudakis TUC , G. Chalkiadakis

BME 17 - Bio-Informatics

P. Pavlidis, I. Lagouvardos

εναλλακτικά: G. Potamias, A. Kanterakis

ΒΜΕ 18 - Medical Informatics and eHealth

V. Sakkalis, S. Sfakianakis

ΒΜΕ 19 - Medical Robotics and VR

P. Trahanias

BME 20 - Big Data Analhytics in Medicine and Health Care

M. Garofalakis,D. Plexousakis, H. Kondilakis

ΒΜΕ 16 - Artificial Intelligence and Medical Decision Support Systems

MICHAIL LAGOUDAKIS

Michail G. Lagoudakis is currently an associate professor with the School of Electrical and Computer Engineering (ECE) at the Technical University of Crete (TUC), Greece since September 2005. Prior to this appointment, he held a post-doctoral fellow position at the Georgia Institute of Technology, USA, from 2003 to 2005, and a visiting researcher position at the Shannon Laboratory of AT&T Labs during the summer of 2000. He received his Doctoral degree in Computer Science with distinction from Duke University, USA in 2003, a Master's degree in Computer Science from the University of Louisiana, Lafayette, USA in 1998, and a Diploma in Computer Engineering and Informatics from the University of Patras, Greece in 1995. His research interests are mainly in Machine Learning and Robotics with extensive research experience and expertise in the area of Decision Making under Uncertainty and Reinforcement Learning. He teaches undergraduate (Theory of Computation, Structured Programming, Artificial Intelligence, Autonomous Agents) and graduate (Machine Learning, Probabilistic Robotics) at TUC and has supervised 1 doctoral, 4 master’s and 68 diploma theses. Soon after his arrival at TUC, he founded Team "Kouretes", which conducts research in autonomous robotics. His published research work includes 5 book chapters, 9 journal and 46 conference articles and has been cited more than 3900 times by other researchers (Google Scholar h-index: 24).

More details on Michail and his research can be found at: http://www.intelligence.tuc.gr/~lagoudakis/index_gr.html


 

Georgios CHALKIADAKIS

Georgios Chalkiadakis is an associate Professor joined the faculty of the School of Electrical and Computer Engineering at the Technical University of Crete in March 2011. His research interests lie mainly in the area of Multiagent Systems (MAS); and more specifically on decision making under uncertainty and machine learning in MAS environments, coalition formation and cooperation in MAS, and cooperative game theory. He is a co-author of the graduate level textbook “Computational Aspects of Cooperative Game Theory” (Morgan and Claypool, 2011), while his PhD Dissertation (University of Toronto, 2007), was a candidate for the IFAAMAS Victor Lesser Distinguished Dissertation Award. He has also co-authored 3 book chapters in scientific collections, and more than 60 research papers in journals and conferences in his areas of expertise (several of which have received awards or award nominations). He has served in the Editorial Board of the Journal of Artificial Intelligence Research (JAIR). Since 2018 he is the Deputy Chair of the European Association for Multi-Agent Systems (EURAMAS), while between 2015 and 2019 he served as the General Secretary of the Hellenic Artificial Intelligence Society (EETN).

More details on Georgios and his research can be found at: http://www.intelligence.tuc.gr/~gehalk


 

ΒΜΕ17: Bio-Informatics Instructors: P. Pavlidis, Ilias Lagkouvardos

Pavlos Pavlidis

Dr. Pavlos Pavlidis is a Research Associate of the Computational BioMedicine Laboratory (CBML) at the Institute of Computer Science (ICS), FORTH. He holds a Diploma (M.Sc. Equivalent) degree in Agricultural Biotechnology, an M.Sc. in Plant Molecular Biology and Biotechnology. He received his Ph.D. degree in 2011 (summa cum laude) from the University of Munich, Germany under the supervision of Prof. Wolfgang Stephan. From 2011 to 2013 he worked in the group of Prof. Alexandros Stamatakis in Heidelberg on high performance population genetics as a postdoctoral fellow. In 2013, he returned in Greece as a postdoctoral fellow and from 2014 to 2016 he was a Marie-Curie postdoctoral fellow. Since April 2016 he has joined the CBML at ICS as a Researcher C. His expertise and research lies on the computational and theoretical population genetics and evolutionary biology. He is also interested in Bioinformatics on genomics data. He is teaching in the Bioinformatics Graduate program of the Medical School of UoC and Bioinformatics related courses in the Biology and Computer Science departments of UoC.

Current research areas and interests include:

  • Detection of selective sweeps from whole genome data
  • Species delimitation
  • Genome evolution and statistical physics
  • Evolution of Gene Regulatory Networks
  • Co-evolution
  • Chromatin structure and evolution
  • Complex demographic models of natural populations and selection detection approaches
  • Metagenomics
  • Microbial population genetics
  • Spatial population simulations

https://projects.ics.forth.gr/cbml/index_main.php?l=g&c=723


 

Dr. Ilias Lagkouvardos

Ilias Lagkouvardos is a microbial ecologist and data integration enthusiast who utilizes bioinformatic methods and tools to address questions related to microbial diversity and ecology in various environments. The primary focus of his research group is the elucidation of the role of distinct microbial compositions in human health and disease by means of sequencing of the versatile 16S rRNA gene.  In addition, we explore microbial genomics and metagenomics sequences for insights into the functionality and dynamics of complex microbial communities.Through integration of thousands of microbial profiles, we investigate the sequence supported global diversity and the occurrence of still undescribed microbial species in different environments. Additional insights are gained over the intrinsic forces guiding the assembly of those communities that will help us effectively and in a personalized manner modulate human microbiome towards a healthier composition.For better understanding of the developing stages of our microbiome and the ways we can control it for better health, we apply machine learning algorithms that will allow us to predict the future course of a microbial community by looking at different timepoints, starting from birth towards adulthood. One basic line of research in the Lagkouvardos group is to utilize state-of-the-art methods and tools to build specialized analytical pipelines and thereby develop user-friendly bioinformatic solutions for public use. One example of such novel bioinformatic tool is the IMNGS platform (www.imngs.org), a web database that automatically retrieves all publicly available 16S rRNA gene amplicon sequences and processes them in a uniform and organized way. The group also released Rhea, a set of R scripts for the analysis of microbial profiles (lagkouvardos.github.io/Rhea/). Courses disseminating expert knowledge on sequence analysis and demonstrating the usability of these tools are organized regularly.

https://www.researchgate.net/profile/Ilias_Lagkouvardos

https://www.ziel.tum.de/arbeitsgruppen/fg-microbial-bioinformatics/


 

ΒΜΕ 18 - Medical Informatics and eHealth Instructors: Vangelis Sakkalis, Stelios Sfakianakis

Vangelis Sakkalis

Dr. Vangelis Sakkalis holds a Principal Researcher position in the Institute of Computer Science – Foundation for Research and Technology (ICS - FORTH). He is the Head of the Computational Neuroscience group and the Head of Multiscale Cancer Modelling group at the Computational Biomedicine Laboratory. He received his PhD in Electronic and Computer Engineering after completing his Master's degree at Imperial College of Science, Technology and Medicine, UK. He has been a member of the board of Directors at FORTH and was elected president of the board of researchers at FORTH. He holds a Visiting Professor appointment at the University of Crete, School of Medicine. His background falls in Biomedical Engineering and His research interests include biosignal and image analysis, visualization, classification algorithms and biostatistics applied in computational medicine, cognitive neuroscience and biomedical informatics. He has long experience as the coordinator and PI of EU and national projects. He has published more than 150 papers in scientific archival journals, proceedings of international conferences & workshops and scientific newsletters, related to his fields of expertise. He is highly interested in translating academic research to innovative growth. He has given numerous invited lectures worldwide and his research has been funded by numerous funding agencies and companies.

His research interests include:

  • Computational Neuroscience – Brain Computer Interfaces
    • Biosignal Analysis (EEG, MEG, ECG, PPG)
    • Time frequency & nonlinear synchronization analysis
    • Functional Connectivity analysis & Source localization techniques
    • Network Visualization and Characterization
  • Biomedical Informatics
    • Architectures based on standards and protocols for the efficient integration and management of biomedical information
  • Computational Oncology
    • “In silico” tumor growth modeling
    • Precision Medicine
    • Modern optical tomography, characterization, molecular and medical imaging techniques
  • Ambient Intelligence and Smart Environments

www.sakkalis.com  


 

Stelios Sfakianakis

Dr. Stelios Sfakianakis received his BSc and MSc diplomas from the Department of Informatics and Telecommunications of the University of Athens and his Ph.D. from the School of Electrical and Computer Engineering of the Technical University of Crete. Since 2000 he has been with the Computational BioMedicine Laboratory of FORTH, working on integrating systems in the field of biomedicine, semantic interoperability, and building tools and services for intelligent data analysis. He has participated as work packages leader in numerous European research projects, focusing on the development of innovative ICT solutions to support large-scale transcription research on cancer, the discovery of biological cancer markers, transcription medicine, and the design and implementation of computational infrastructures for the integration of data and services. His research interests include biomedical computing, web-based cloud-based software architectures, and data mining and analysis with modern computing tools. He has published more than 60 articles in international journals and conference proceedings related to his areas of expertise.

Current research areas and interests include:

  • Biomedical Informatics
  • Biomedical information systems
  • Semantic Web
  • Information Modeling & Data Integration
  • Service oriented architectures and technologies
  • Machine Learning

 

ΒΜΕ 19 - Medical Robotics and VR Main Instructor: Panos Trahanias

 

Panos Trahanias

Panos Trahanias is a Professor with the Department of Computer Science, University of Crete. He is also affiliated with the Institute of Computer Science, FORTH, where he Heads the Computational Vision and Robotics Laboratory (CVRL). He received his Ph.D. in Computer Science from the National Technical University of Athens, Greece, in 1988. From 1985 to 1989 he served as a Research Assistant at the Institute of Informatics & Telecommunications, National Center for Scientific Research "Demokritos", Athens, Greece, and from 1990 to 1991 he worked at the same Institute as a Postdoctoral Research Associate. From 1991 to 1993 he was with the Department of Electrical & Computer Engineering, University of Toronto, Toronto, Canada, as a Postdoctoral Research Associate. He has participated in many R & D programs in image processing and analysis at the University of Toronto and has been a consultant to SPAR Aerospace Ltd., Toronto, in a program regarding the analysis of Infrared images. Since 1993, he is with the University of Crete and ICS-FORTH. He has held the position of Director of Graduate Studies at the Department of Computer Science, University of Crete. At CVRL he has participated in numerous R & D projects funded by the European Commission and Greek funding agencies. His research interests are in human-robot interaction, robot navigation, brain-inspired robotic control and augmented reality applications. He has been the General Chair of Eurographics 2008 (EG’08) and the European Conference of Computer Vision 2010 (ECCV’10). He has published over 110 papers in technical journals and conference proceedings.

His research interests are in the broader areas of Computational Vision and Autonomous Robots:

  • Computational Vision
  • Articulated object tracking
  • Gesture recognition
  • Autonomous Robots
  • Autonomous Robot Navigation
  • Human-Robot Interaction
  • Biologically-inspired Robot-control Architectures

https://www.ics.forth.gr/cvrl/head-of-the-lab/7


 

BME 20 - Big Data Analhytics in Medicine and Health Care

MINOS GAROFALAKIS

Minos Garofalakis is the Director of the Information Management Systems Institute (IMSI) at the ATHENA Research and Innovation Center and a Professor of Computer Science at the Technical University of Crete, where he also directs the Software Technology and Network Applications Lab (SoftNet). He received the MSc and PhD degrees in Computer Science from the University of Wisconsin-Madison in 1994 and 1998, respectively, and worked as a Member of Technical Staff at Bell Labs, Lucent Technologies (1998-2005), as a Senior Researcher at Intel Research Berkeley (2005-2007), and as a Principal Research Scientist at Yahoo! Research (2007-2008). In parallel, he also held an Adjunct Associate Professor position at the EECS Department of the University of California, Berkeley (2006-2008).Prof. Garofalakis' research interests are in the broad areas of Big Data Analytics and Large-Scale Machine Learning. He has published over 170 scientific papers in refereed international conferences and journals in these areas, is the co-editor of a volume on Data Stream Management published by Springer in 2016, and has delivered several invited keynote talks and tutorials in major international events. Prof. Garofalakis' work has resulted in 36 US Patent filings (29 patents issued) for companies such as Lucent, Yahoo!, and AT&T; in addition, he is/has been the PI in a number of important research projects funded by the European Union. Google Scholar gives over 13.500 citations to his work, and an h-index value of 63. Prof. Garofalakis is an ACM Fellow (2018) "for contributions to data processing and analytics", an IEEE Fellow (2017) "for contributions to data streaming analytics", and a recipient of the TUC "Excellence in Research" Award (2015), a Marie-Curie International Reintegration Fellowship (2010-2014), the 2009 IEEE ICDE Best Paper Award, the Bell Labs President's Gold Award (2004), and the Bell Labs Teamwork Award (2003).

More details:  http://softnet.tuc.gr/~minos/


 

Dimitris Plexousakis

Dimitrios Plexousakis is a Professor and former Chair of the Department of Computer Science, University of Crete and a Researcher at  the Institute of Computer Science, FORTH in Greece,  head of the Information Systems Laboratory since 2012. As of 12/2009 he is the head of the University of Crete’s Data Processing Laboratory and Computing Center and since 2012 he is the head  of the Information Systems Laboratory of FORTH-ICS. He received his B.Sc. degree in Computer Science from the Department of Computer Science, University of Crete in 1988 and M.Sc. and Ph.D degrees in Computer Science from the Department of Computer Science, University of Toronto in 1990 and 1996 respectively. His research interests span the following areas: Knowledge Representation and Knowledge Base Design with emphasis on the representation and management of temporal knowledge; Distributed Database Systems and Databases on the Web with focus on the study of formal knowledge representation models and query languages for the Semantic Web; Formal reasoning systems and applications of artificial intelligence in database systems with focus on dynamic action theories and belief revision; Business process and e-service modeling over wide-area distributed information systems. He has published over 140 articles in international conferences and journals and has served on the program committees of numerous international conferences. He co-chaired the 1st International Workshop on the Semantic Web and the International Workshop on E-Services and the Semantic Web in 2000 and 2003 respectively. He was the executive chair of the 9th International Conference on Extending Database Technology (March 14-18, 2004, Heraklion, Greece) and the Program Committee co-Chair of the 3rd International Semantic Web Conference (November 7-11, 2004, Hiroshima, Japan).He has extensive experience in the scientific coordination of research projects at the national and European levels. He served as the Scientific Coordination of the FET Coordination Action "Beyond the Horizon" and as a member of the Scientific Steering Committee of the FET Coordination Action "InterLink". He participates to the S-Cube Network of Excellence on Service Science, Software and Systems. He is a member of the ACM and IEEE.

His research interests are in the broader area of Data and Knowledge Management:

  • Knowledge Representation and Reasoning
  • Formal models and query languages for the Semantic Web
  • Process and service modelling
  • Conceptual Modeling
  • Knowledge Base Management Systems
  • Knowledge Representation and Management on the Semantic Web and in Ambient Intelligence Environments
  • Web-based Information Systems
  • Peer-to-peer Data Management
  • Digital Libraries
  • Discovery and Composition of E-Services
  • Service-Oriented Architectures
  • Business Process Modeling and Analysis
  • Temporal, Active and Deductive Databases
  • Applications of Information Systems in Bioinformatics

https://www.ics.forth.gr/isl/head-of-the-lab/2


 

Haridimos Kondylakis

Haridimos Kondylakis is currently a Collaborating Researcher at Computational BioMedicine Laboratory (CBML), Institute of Computer Science, Foundation of Research & Technology-Hellas (FORTH). He holds a Ph.D and an M.Sc. in Computer Science from University of Crete. He is also a visiting lecturer at the Computer Science Department, University of Crete and at the Department of Electric and Computer Engineeringat Hellenic Mediterranean University and at Hellenic Open University, teaching lessons related to data management and semantics.

 

His interests include:

  • semantic-based, big data management topics and their application in healthcare,
  • e-Consent through semantic rules,
  • semantically-enabled medical recommendations for patient empowerment,
  • ontology summarization and evolution,
  • efficient infrastructures for collecting, partitioning, indexing, integrating and managing eHealth information and data series data,
  • personal health environments,
  • modular ontologies for healthcare and mappings to the various data sources.

In the past he has participated in more that 15 EU research projects with a total budget over 60Mie and he is currently participating in two H2020 EU (BOUNCE - WP Leader & STARS) research projects. He has more than 130 publications in international conferences, books and journals including ACM SIGMOD, VLDB, JWS, KER, EDBT, ISWC, ESWC etc. He is the lead guest editor of the special issue for PHRs at the JBI journal, the publicity chair of ISWC 2020, the organizer of the International Workshop on Semantic Web Technologies for Health Data Management, the organizational chair of ISIP 2019 conference and the special session chair of BIBE 2019. He also acts as a regular reviewer and a PC member for a number of premier journals and conferences, such as JWS, JODS, CIKM, EDBT, ISWC etc.