Sophia Tsoka

39 papers A* 1B 1Journal 32Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Stitch in Time: Learning Procedural Workflow via Self-Supervised Plackett-Luce Ranking.
CoRR
Chengan Che, Chao Wang, Xinyue Chen, Sophia Tsoka, Luis C. García-Peraza-Herrera
2025 J jnl
Back to the Feature: Explaining Video Classifiers with Video Counterfactual Explanations.
CoRR
Chao Wang, Chengan Che, Xinyue Chen, Sophia Tsoka, Luis C. García-Peraza-Herrera
2025 A* conf
Enhancing Generalized Few-Shot Semantic Segmentation via Effective Knowledge Transfer.
AAAI
Xinyue Chen, Miaojing Shi, Zijian Zhou, Lianghua He, Sophia Tsoka
2025 J jnl
Interpretable optimisation-based approach for hyper-box classification.
Mach. Learn.
Georgios I. Liapis, Sophia Tsoka, Lazaros G. Papageorgiou
2025 J jnl
Subset-Contrastive Multi-Omics Network Embedding.
CoRR
Pedro Henrique da Costa Avelar, Min Wu, Sophia Tsoka
2025 J jnl
Surg-3M: A Dataset and Foundation Model for Perception in Surgical Settings.
CoRR
Chengan Che, Chao Wang, Tom Vercauteren, Sophia Tsoka, Luis C. García-Peraza-Herrera
2024 J jnl
CLigOpt: controllable ligand design through target-specific optimization.
Bioinform.
Yutong Li, Pedro Henrique da Costa Avelar, Xinyue Chen, Li Zhang, Min Wu, Sophia Tsoka
2024 J jnl
Enhancing Generalized Few-Shot Semantic Segmentation via Effective Knowledge Transfer.
CoRR
Xinyue Chen, Miaojing Shi, Zijian Zhou, Lianghua He, Sophia Tsoka
2024 J jnl
Optimisation-based modelling for explainable lead discovery in malaria.
Artif. Intell. Medicine
Yutong Li, Jonathan Cardoso-Silva, John M. Kelly, Michael J. Delves, Nicholas Furnham, Lazaros G. Papageorgiou, Sophia Tsoka
2024 — conf
Pathway Activity Autoencoders for Enhanced Omics Analysis and Clinical Interpretability.
BIBM
Pedro Henrique da Costa Avelar, Le Ou-Yang, Min Wu, Sophia Tsoka
2023 J jnl
Drug repurposing and prediction of multiple interaction types via graph embedding.
BMC Bioinform.
E. Amiri Souri, A. Chenoweth, S. N. Karagiannis, Sophia Tsoka
2023 J jnl
Incorporating Prior Knowledge in Deep Learning Models via Pathway Activity Autoencoders.
CoRR
Pedro Henrique da Costa Avelar, Min Wu, Sophia Tsoka
2022 — conf
A Matrix Factorization-Based Drug-Virus Link Prediction Method for SARS-CoV-2 Drug Prioritization.
LOD (1)
Yutong Li, Xiaorui Xu, Sophia Tsoka
2022 J jnl
Multi-Omic Data Integration and Feature Selection for Survival-based Patient Stratification via Supervised Concrete Autoencoders.
CoRR
Pedro Henrique da Costa Avelar, Roman Laddach, Sophia Karagiannis, Min Wu, Sophia Tsoka
2022 — conf
Multi-omic Data Integration and Feature Selection for Survival-Based Patient Stratification via Supervised Concrete Autoencoders.
LOD (2)
Pedro Henrique da Costa Avelar, Roman Laddach, Sophia Karagiannis, Min Wu, Sophia Tsoka
2022 J jnl
Novel drug-target interactions via link prediction and network embedding.
BMC Bioinform.
E. Amiri Souri, Roman Laddach, S. N. Karagiannis, Lazaros G. Papageorgiou, Sophia Tsoka
2020 — conf
Identification of Important Biological Pathways for Ischemic Stroke Prediction through a Mathematical Programming Optimisation Model-DIGS.
ICBBT
Yongnan Chen, Konstantinos Theofilatos, Lazaros G. Papageorgiou, Sophia Tsoka
2019 J jnl
Network-based piecewise linear regression for QSAR modelling.
J. Comput. Aided Mol. Des.
Jonathan Cardoso-Silva, Lazaros G. Papageorgiou, Sophia Tsoka
2018 J jnl
Reactome Pengine: a web-logic API to the Homo sapiens reactome.
Bioinform.
Samuel R. Neaves, Sophia Tsoka, Louise A. C. Millard
2017 J jnl
A regression tree approach using mathematical programming.
Expert Syst. Appl.
Lingjian Yang, Songsong Liu, Sophia Tsoka, Lazaros G. Papageorgiou
2016 J jnl
Community Structure Detection for Directed Networks through Modularity Optimisation.
Algorithms
Lingjian Yang, Jonathan Cardoso-Silva, Lazaros G. Papageorgiou, Sophia Tsoka
2016 J jnl
Mathematical programming for piecewise linear regression analysis.
Expert Syst. Appl.
Lingjian Yang, Songsong Liu, Sophia Tsoka, Lazaros G. Papageorgiou
2016 J jnl
Organizational principles of the Reactome human BioPAX model using graph theory methods.
J. Complex Networks
Aristotelis Kittas, Laura Bennett, Henning Hermjakob, Sophia Tsoka
2015 J jnl
CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.
BMC Syst. Biol.
Aristotelis Kittas, Amélie Barozet, Jekaterina Sereshti, Niels Grabe, Sophia Tsoka
2015 J jnl
Link Prediction Methods and Their Accuracy for Different Social Networks and Network Metrics.
Sci. Program.
Fei Gao, Katarzyna Musial, Colin Cooper, Sophia Tsoka
2015 J jnl
Sample re-weighting hyper box classifier for multi-class data classification.
Comput. Ind. Eng.
Lingjian Yang, Songsong Liu, Sophia Tsoka, Lazaros G. Papageorgiou
2015 B conf
Using ILP to Identify Pathway Activation Patterns in Systems Biology.
ILP
Samuel R. Neaves, Louise A. C. Millard, Sophia Tsoka
2014 J jnl
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework.
BMC Bioinform.
Lingjian Yang, Chrysanthi Ainali, Sophia Tsoka, Lazaros G. Papageorgiou
2012 J jnl
Detection of Disjoint and Overlapping Modules in Weighted Complex Networks.
Adv. Complex Syst.
Laura Bennett, Songsong Liu, Lazaros G. Papageorgiou, Sophia Tsoka
2012 — conf
Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum.
CMSB
Laura Bennett, Artem Lysenko, Lazaros G. Papageorgiou, Martin Urban, Kim E. Hammond-Kosack, Christopher J. Rawlings, Mansoor A. S. Saqi, Sophia Tsoka
2010 J jnl
A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin.
PLoS Comput. Biol.
Najl V. Valeyev, Christian Hundhausen, Yoshinori Umezawa, Nikolai V. Kotov, Gareth Williams, Alex Clop, Crysanthi Ainali, Christos A. Ouzounis, Sophia Tsoka, Frank O. Nestle
2010 J jnl
Module detection in complex networks using integer optimisation.
Algorithms Mol. Biol.
Gang Xu, Laura Bennett, Lazaros G. Papageorgiou, Sophia Tsoka
2010 J jnl
Promoter Complexity and Tissue-Specific Expression of Stress Response Components in
PLoS Comput. Biol.
Chrysa Pantzartzi, Elena Drosopoulou, Minas Yiangou, Ignat Drozdov, Sophia Tsoka, Christos A. Ouzounis, Zacharias G. Scouras
2009 J jnl
Stratification of co-evolving genomic groups using ranked phylogenetic profiles.
BMC Bioinform.
Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, Christos A. Ouzounis
2007 J jnl
Computational methodologies for genome evolution and functional association.
Comput. Chem. Eng.
Sophia Tsoka
2005 J jnl
CoGenT++: an extensive and extensible data environment for computational genomics.
Bioinform.
Leon Goldovsky, Paul J. Janssen, Dag G. Ahrén, Benjamin Audit, Ildefonso Cases, Nikos Darzentas, Anton J. Enright, Núria López-Bigas, José M. Peregrín-Alvarez, Mike Smith, Sophia Tsoka, Victor Kunin, Christos A. Ouzounis
2003 J jnl
Evaluation of annotation strategies using an entire genome sequence.
Bioinform.
Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vasilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David M. A. Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis
2002 J jnl
Modeling the percolation of annotation errors in a database of protein sequences.
Bioinform.
Walter R. Gilks, Benjamin Audit, Daniela De Angelis, Sophia Tsoka, Christos A. Ouzounis
2000 J jnl
CAST: an iterative algorithm for the complexity analysis of sequence tracts.
Bioinform.
Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis