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Archives: August 2017

Projects

Current

CAUSALPATH
Cancer-Biomarkers in HUNT

Previous

STATegra
Epilogeas – Aristeia II

people

Our team
Ioannis Tsamardinos

Associate Professor,
Department of Computer Science,
University of Crete

Vincenzo Lagani

Postgraduate research fellow,
Department of Computer Science,
University of Crete, Hellas

Maria Markaki

Postgraduate research fellow,
Department of Computer Science,
University of Crete, Hellas

Giorgos Papoutsoglou

Postgraduate research fellow,
Department of Computer Science,
University of Crete, Hellas

Michail Tsagris

Postgraduate research fellow,
Department of Computer Science,
University of Crete, Hellas

Yannis Pantazis

Postgraduate research fellow,
Department of Computer Science,
University of Crete, Hellas

Kleanthi Lakiotaki

Postgraduate research fellow,
Department of Computer Science,
University of Crete, Hellas

Georgios Borboudakis

Ph.D. student,
Department of Computer Science,
University of Crete, Hellas

Elissavet Greasidou

Graduate student,
Department of Computer Science,
University of Crete, Hellas

Mina Xenou

Graduate student,
Department of Computer Science,
University of Crete, Hellas

Christos Tselas

Graduate student,
Department of Computer Science,
University of Crete, Hellas

Glykeria Fragkioudaki

Administrative Assistant
Department of Computer Science,
University of Crete, Hellas

Konstantinos Tsirlis

Postgraduate Student, Interdepartmental Graduate Program in the Brain and Mind Sciences, University of Crete

Kleio-Maria Verrou

Graduate student,
Department of Computer Science,
University of Crete, Hellas

Zacharias Papadovasilakis

Post – graduate student Medical School, University of Crete

Marios Dimitriadis

Undergaduate student, Department of Computer Science, University of Crete, Hellas

Iordanis Xanthopoulos

Undergaduate student, Department of Computer Science, University of Crete, Hellas

Former members

publications

2018


Michail Tsagris, Giorgos Borboudakis, Vincenzo Lagani, Ioannis Tsamardinos. Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, (2018).
@article{tsagris(2018)constraint,
  title={Constraint-based causal discovery with mixed data},
  author={Tsagris, Michail and Borboudakis, Giorgos and Lagani, Vincenzo and Tsamardinos, Ioannis},
  journal={International Journal of Data Science and Analytics},
  year={(2018)}
}

Maria Markaki, Ioannis Tsamardinos, Arnulf Langhammer, Vincenzo Lagani, Kristian Hveem, Oluf Dimitri Røe. A Validated Clinical Risk Prediction Model for Lung Cancer in Smokers of All Ages and Exposure Types: A HUNT Study. EBioMedicine, (2018).
@article{markaki(2018)validated,
  title={A Validated Clinical Risk Prediction Model for Lung Cancer in Smokers of All Ages and Exposure Types: A HUNT Study},
  author={Markaki, Maria and Tsamardinos, Ioannis and Langhammer, Arnulf and Lagani, Vincenzo and Hveem, Kristian and Røe, Oluf Dimitri},
  journal={EBioMedicine},
  year={(2018)}
}

Marios Adamou, Grigoris Antoniou, Elissavet Greassidou, Vincenzo Lagani, Paulos Charonyktakis, Ioannis Tsamardinos. Towards Automatic Risk Assessment to Support Suicide Prevention. Accepted to Crisis: The Journal of Crisis Intervention and Suicide Prevention, (2018).
@article{adamou(2018)towards,
  title={Towards Automatic Risk Assessment to Support Suicide Prevention},
  author={Adamou, Marios and Antoniou, Grigoris and Greassidou, Elissavet and Lagani, Vincenzo and Charonyktakis, Paulos and Tsamardinos, Ioannis},
  journal={Accepted to Crisis: The Journal of Crisis Intervention and Suicide Prevention},
  year={(2018)}
}

Marios Adamou, Grigoris Antoniou, Elissavet Greassidou, Vincenzo Lagani, Paulos Charonyktakis, Ioannis Tsamardinos. Mining Free-Text Medical Notes for Suicide Risk Assessment. , (2018).
@article{adamou(2018)mining,
  title={Mining Free-Text Medical Notes for Suicide Risk Assessment},
  author={Adamou, Marios and Antoniou, Grigoris and Greassidou, Elissavet and Lagani, Vincenzo and Charonyktakis, Paulos and Tsamardinos, Ioannis},
  journal={},
  year={(2018)}
}

Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Georgios Georgakopoulos, Ioannis Tsamardinos. BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. Database, (2018).
@article{lakiotaki(2018)biodataome,
  title={BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology},
  author={Lakiotaki, Kleanthi and Vorniotakis, Nikolaos and Tsagris, Michail and Georgakopoulos, Georgios and Tsamardinos, Ioannis},
  journal={Database},
  year={(2018)}
}

Michail Tsagris, Vincenzo Lagani, Ioannis Tsamardinos. Feature selection for high-dimensional temporal data. BMC Bioinformatics, (2018).
@article{tsagris(2018)feature,
  title={Feature selection for high-dimensional temporal data},
  author={Tsagris, Michail and Lagani, Vincenzo and Tsamardinos, Ioannis},
  journal={BMC Bioinformatics},
  year={(2018)}
}

2017


Ioannis Tsamardinos, Elissavet Greasidou, Michalis Tsagris, Giorgos Borboudakis. Bootstrapping the Out-of-sample Predictions for Efficient and Accurate Cross-Validation. , (2017).
@article{tsamardinos(2017)bootstrapping,
  title={Bootstrapping the Out-of-sample Predictions for Efficient and Accurate Cross-Validation},
  author={Tsamardinos, Ioannis and Greasidou, Elissavet and Tsagris, Michalis and Borboudakis, Giorgos},
  journal={},
  year={(2017)}
}

Sofia Triantafillou, Vincenzo Lagani, Christina Heinze-Deml, Angelika Schmidt, Jesper Tegner, Ioannis Tsamardinos. Predicting Causal Relationships from Biological Data: Applying Automated Casual Discovery on Mass Cytometry Data of Human Immune Cells. Scientific Reports. 2017, (2017).
@article{triantafillou(2017)predicting,
  title={Predicting Causal Relationships from Biological Data: Applying Automated Casual Discovery on Mass Cytometry Data of Human Immune Cells},
  author={Triantafillou, Sofia and Lagani, Vincenzo and Heinze-Deml, Christina and Schmidt, Angelika and Tegner, Jesper and Tsamardinos, Ioannis},
  journal={Scientific Reports. 2017},
  year={(2017)}
}

Vincenzo Lagani, Giorgos Athineou, Alessio Farcomeni, Michail Tsagris, Ioannis Tsamardinos. Feature Selection with the R Package MXM: Discovering Multiple, Statistically-Equivalent, Predictive Feature Subsets. Journal of Statistical Software, (2017).
@article{lagani(2017)feature,
  title={Feature Selection with the R Package MXM: Discovering Multiple, Statistically-Equivalent, Predictive Feature Subsets},
  author={Lagani, Vincenzo and Athineou, Giorgos and Farcomeni, Alessio and Tsagris, Michail and Tsamardinos, Ioannis},
  journal={Journal of Statistical Software},
  year={(2017)}
}

Michail Tsagris, Giorgos Borboudakis, Vincenzo Lagani, Ioannis Tsamardinos. Constraint-based Causal Discovery with Mixed Data. , (2017).
@article{tsagris(2017)constraint,
  title={Constraint-based Causal Discovery with Mixed Data},
  author={Tsagris, Michail and Borboudakis, Giorgos and Lagani, Vincenzo and Tsamardinos, Ioannis},
  journal={},
  year={(2017)}
}

Konstantinos Tsirlis, Vincenzo Lagani, Sofia Triantafillou, Ioannis Tsamardinos. On Scoring Maximal Ancestral Graphs with the Max-Min Hill Climbing Algorithm. , (2017).
@article{tsirlis(2017)scoring,
  title={On Scoring Maximal Ancestral Graphs with the Max-Min Hill Climbing Algorithm},
  author={Tsirlis, Konstantinos and Lagani, Vincenzo and Triantafillou, Sofia and Tsamardinos, Ioannis},
  journal={},
  year={(2017)}
}

Georgia Orfanoudaki, Maria Markaki, Katerina Chatzi, Ioannis Tsamardinos, Anastassios Economou. MatureP: prediction of secreted proteins with exclusive information from their mature regions. Scientific Reports, (2017).
@article{orfanoudaki(2017)maturep,
  title={MatureP: prediction of secreted proteins with exclusive information from their mature regions},
  author={Orfanoudaki, Georgia and Markaki, Maria and Chatzi, Katerina and Tsamardinos, Ioannis and Economou, Anastassios},
  journal={Scientific Reports},
  year={(2017)}
}

Georgios Papoutsoglou, Giorgos Athineou, Vincenzo Lagani, Iordanis Xanthopoulos, Angelika Schmidt, Szabolcs Éliás, Jesper Tegnér, Ioannis Tsamardinos. SCENERY: a web application for (causal) network reconstruction from cytometry data. Nucleic Acids Research, (2017).
@article{papoutsoglou(2017)scenery,
  title={SCENERY: a web application for (causal) network reconstruction from cytometry data},
  author={Papoutsoglou, Georgios and Athineou, Giorgos and Lagani, Vincenzo and Xanthopoulos, Iordanis and Schmidt, Angelika and Éliás, Szabolcs and Tegnér, Jesper and Tsamardinos, Ioannis},
  journal={Nucleic Acids Research},
  year={(2017)}
}

Kyros Siomos, E Papadaki, Ioannis Tsamardinos, K Kerkentzes, M Koygioylis, CM Trakatelli. Prothrombotic and Endothelial Inflammatory Markers in Greek Patients with Type 2 Diabetes Compared to Non-Diabetics. Endocrinology & Metabolic Syndrome, (2017).
@article{siomos(2017)prothrombotic,
  title={Prothrombotic and Endothelial Inflammatory Markers in Greek Patients with Type 2 Diabetes Compared to Non-Diabetics},
  author={Siomos, Kyros and Papadaki, E and Tsamardinos, Ioannis and Kerkentzes, K and Koygioylis, M and Trakatelli, CM},
  journal={Endocrinology \& Metabolic Syndrome},
  year={(2017)}
}

2016


Jermaine Goveia, Andreas Pircher, Lena-Christin Conradi, Joanna Kalucka, Vincenzo Lagani, Mieke Dewerchin, Guy Eelen, Ralph J DeBerardinis, Ian D Wilson, Peter Carmeliet. Meta-analysis of clinical metabolic profiling studies in cancer: challenges and opportunities. EMBO Molecular Medicine, (2016).
@article{goveia(2016)meta,
  title={Meta-analysis of clinical metabolic profiling studies in cancer: challenges and opportunities},
  author={Goveia, Jermaine and Pircher, Andreas and Conradi, Lena-Christin and Kalucka, Joanna and Lagani, Vincenzo and Dewerchin, Mieke and Eelen, Guy and DeBerardinis, Ralph J and Wilson, Ian D and Carmeliet, Peter},
  journal={EMBO Molecular Medicine},
  year={(2016)}
}

Giorgos Borboudakis, Ioannis Tsamardinos. Towards Robust and Versatile Causal Discovery forBusiness Applications. , (2016).
@article{borboudakis(2016)towards,
  title={Towards Robust and Versatile Causal Discovery forBusiness Applications},
  author={Borboudakis, Giorgos and Tsamardinos, Ioannis},
  journal={},
  year={(2016)}
}

Paulos Charonyktakis, Maria Plakia, Ioannis Tsamardinos, Maria Papadopouli. On user-centric modular QoE prediction for voip based on machine-learning algorithms. IEEE Transactions on Mobile Computing, (2016).
@article{charonyktakis(2016)user,
  title={On user-centric modular QoE prediction for voip based on machine-learning algorithms},
  author={Charonyktakis, Paulos and Plakia, Maria and Tsamardinos, Ioannis and Papadopouli, Maria},
  journal={IEEE Transactions on Mobile Computing},
  year={(2016)}
}

Sofia Triantafillou, Ioannis Tsamardinos. Score based vs constraint based causal learning in the presence of confounders. , (2016).
@article{triantafillou(2016)score,
  title={Score based vs constraint based causal learning in the presence of confounders},
  author={Triantafillou, Sofia and Tsamardinos, Ioannis},
  journal={},
  year={(2016)}
}

Anna Roumpelaki, Giorgos Borboudakis, Sofia Triantafillou, Ioannis Tsamardinos. Marginal causal consistency in constraint-based causal learning. , (2016).
@article{roumpelaki(2016)marginal,
  title={Marginal causal consistency in constraint-based causal learning},
  author={Roumpelaki, Anna and Borboudakis, Giorgos and Triantafillou, Sofia and Tsamardinos, Ioannis},
  journal={},
  year={(2016)}
}

N Karathanasis, I Tsamardinos, V Lagani. omicsNPC: applying the NonParametric Combination methodology to the integrative analysis of heterogeneous omics data. PloS one, (2016).
@article{karathanasis(2016)omicsnpc,
  title={omicsNPC: applying the NonParametric Combination methodology to the integrative analysis of heterogeneous omics data},
  author={Karathanasis, N and Tsamardinos, I and Lagani, V},
  journal={PloS one},
  year={(2016)}
}

Read more

About Us

Mens Ex Machina, Mind from the Machine or "Ο από Μηχανής Νους" paraphrases the latin expression Deus Ex Machina, God from the Machine. The name was suggested by Lucy Sofiadou, Prof. Tsamardinos' wife.

We are a research group, founded in October 2006, led by Associate Professor Ioannis Tsamardinos, interested in Artificial Intelligence, Machine Learning, and Biomedical Informatics and affiliated with the Computer Science Department of University of Crete. The group’s aims are to progress science and disseminate knowledge via educational activities and computer tools. Our group is involved in

Research:

Theoretical, algorithmic, and applied research in all of the above areas; we are also involved in interdisciplinary collaborations with biologists, physicians and practitioners from other fields.

Education:

Educational activities, such as teaching university courses, tutorials, summers schools, as well as supervising undergraduate dissertations, masters projects, and Ph.D. theses.

Systems and Software:

Implementation of tools, systems, and code libraries to aid the dissemination of the research results.Funding is provided from through the University of Crete, often originating from European and International research grants.

Current research activities include but not limited to the following:

  • Causal discovery methods and the induction of causal models from observational studies. Specifically, we have recently introduced the problem of Integrative Causal Analysis (INCA).
  • Feature selection (a.k.a. variable selection) for classification and regression.
  • Induction of graphical models, such as Bayesian Networks from data.
  • Analysis of biomedical data and applications of AI and Machine Learning methods to induce new biomedical knowledge.
  • Activity recognition in Ambient Intelligent environments.

Ioannis Tsamardinos
Associate Professor, Department of Computer Science, University of Crete