Computational & Data Science Preprint Repository

  • 2025

    • G Aletras, M Bachlitzanaki, M Stratinaki, E Lamprogiannakis, S Panagoutsos, K Kantartzi, T Georgopoulou, I Petrakis, E Foukarakis, Y Pantazis, M Hamilos, K Stylianou (2025) Unraveling Acute Cardiorenal Syndrome: Predictors and Consequences in Acute Heart Failure, Journal of Clinical Medicine 14 (7), 2270.
    • G Aletras, M Bachlitzanaki, M Stratinaki, I Petrakis, T Georgopoulou, Y Pantazis, E Foukarakis, M Hamilos, K Stylianou (2025) The Role of Chloride in Cardiorenal Syndrome: A Practical Review, Journal of Clinical Medicine 14 (15), 5230, https://doi.org/10.3390/jcm14155230
    • G Arampatzis, S Katsarakis, C Makridakis (2025) A generative modeling/Physics-Informed Neural Network approach to random differential equations, arXiv preprint arXiv:2507.01687
    • A Castellani, Z Papadovasilakis, G Papoutsoglou, M Cole, B Bautsch, T Rodemann, I Tsamardinos, A Harden (2025) Predicting and Explaining Traffic Crash Severity Through Crash Feature Selection, arXiv preprint arXiv:2508.11504
    • YC Cheng, H Gu, TO McDonald, W Wu, S Tripathi, C Guarducci, D Russo, DL Abravanel, M Bailey, Y Wang, Y Zhang, Y Pantazis, H Levine, R Jeselsohn, MA Katsoulakis, F Michor (2025) PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses, bioRxiv, 2025.06. 27.662030, (pdf)
    • A Doxa, C Adam, N Nagkoulis, AD Mazaris, S Katsanevakis (2025) prior3D: An R package for three-dimensional conservation prioritization, Ecological Modelling 499, 110919.
    • K Ellrott, CK Wong, C Yau, MAA Castro, JA Lee, BJ Karlberg, JK Grewal, V Lagani, B Tercan, V Friedl, T Hinoue, V Uzunangelov, L Westlake, X Loinaz, I Felau, PI Wang, A Kemal, SJ Caesar-Johnson, I Shmulevich, AJ Lazar, I Tsamardinos,... (2025) Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets, Cancer Cell (pdf file)
    • E Georgoulis, MA Zervou, Y Pantazis (2025) Transfer Learning on Protein Language Models Improves Antimicrobial Peptide Classification, https://doi.org/10.21203/rs.3.rs-5768912/v1
    • A Gerontopoulos, S Gidaris, N Komodakis (2025) Multi-Token Prediction Needs Registers, arXiv preprint arXiv:2505.10518
    • S Giakoumi, AJ Richardson, A Doxa, S Moro, M Andrello, JO Hanson, V Hermoso, T Mazor, J McGowan, H Kujala, E Law, JG Álvarez-Romero, RA Magris, E Gissi, N Arafeh-Dalmau, A Metaxas, EA Virtanen, NC Ban, RM Runya, DC Dunn, S Fraschetti, I Galparsoro, RJ Smith, F Bastardie, V Stelzenmüller, HP Possingham, S Katsanevakis (2025) Advances in systematic conservation planning to meet global biodiversity goals, Trends in Ecology & Evolution 40 (4), 395-410.
    • N Gkorgkolis, N Kougioulis, MX Wang, B Caglayan, A Tonon, D Simionato, I Tsamardinos (2025) Temporal Causal-based Simulation for Realistic Time-series Generation, arXiv preprint arXiv:2506.02084
    • G Grekas, K Koumatos, C Makridakis, A Vikelis (2025) Convergence of Discontinuous Galerkin Methods for Quasiconvex and Relaxed Variational Problems, arXiv preprint arXiv:2501.11944
    • G Grekas, K Koumatos, C Makridakis, A Vikelis (2025) A class of discontinuous Galerkin methods for nonlinear variational problems, Mathematics of Computation 94 (355), 2221-2250, (preprint)
    • G Grekas, CG Makridakis, T Pryer (2025) PINN-DG: Residual neural network methods trained with Finite Elements, arXiv preprint arXiv:2507.03521
    • G Grekas, CG Makridakis (2025) Deep Ritz - Finite element methods: Neural network methods trained with finite elements, Computer Methods in Applied Mechanics and Engineering, Vol. 437, 117798, https://doi.org/10.1016/j.cma.2025.117798
    • JK Grewal, AG Robertson, K Ellrott, CK Wong, JA Lee, C Yau, B Tercan, M Castro, CC Benz, TA Knijnenburg, VS Chagas, VH Apolonio, V Friedl, JM Stuart, V Uzunangelov, JB Andersen, AD Cherniack, GF Gao, G Getz, SH Hoyt, W Roh, L Westlake, S Jones, SJ Caesar-Johnson, JA Demchok, I Felau, A Kemal, R Tarnuzzer, Z Wang, L Yang, JC Zenklusen, R Akbani, BM Broom, Z Ju, A Schultz, AI Ojesina, KA Hoadley, A Lal, D Ramazzotti, C Wang, AJ Lazar, LR Roberts, TK Kim, I Shmulevich, P Charonyktakis, V Lagani, I Tsamardinos, E Drill, R Shen, ML Ferguson, KE Chiotti, BJ Karlberg, E Lowenstein, A Struck, PT Spellman, T Hinoue, PW Laird (2025) Protocol for obtaining cancer type and subtype predictions using subSCOPE, STAR protocols 6 (2), 103705, https://doi.org/10.1016/j.xpro.2025.103705
    • E Karypidis, I Kakogeorgiou, S Gidaris, N Komodakis (2025) Advancing Semantic Future Prediction through Multimodal Visual Sequence Transformers, Proceedings of the Computer Vision and Pattern Recognition Conference, 3793-3803.
    • K Konsta, A Doxa, S Katsanevakis, AD Mazaris (2025) Projected marine heatwaves over the Mediterranean Sea and the network of marine protected areas: a three-dimensional assessment, Climatic Change 178 (2), 1-20.
    • T Kouzelis, I Kakogeorgiou, S Gidaris, N Komodakis (2025) EQ-VAE: Equivariance Regularized Latent Space for Improved Generative Image Modeling, arXiv preprint arXiv:2502.09509
    • T Kouzelis, E Karypidis, I Kakogeorgiou, S Gidaris, N Komodakis (2025) Boosting Generative Image Modeling via Joint Image-Feature Synthesis, arXiv preprint arXiv:2504.16064
    • S LaPlante, E Perković, S Triantafillou (2025) Data-Driven Adjustment for Multiple Treatments, arXiv preprint arXiv:2503.08971
    • K Lelova, GF Cooper, S Triantafillou (2025) Testing Identifiability and Transportability with Observational and Experimental Data, arXiv preprint arXiv:2505.12801
    • C. Makridakis, A. Pim, T. Pryer, N. Rekatsinas (2025) Deep Uzawa for Kinetic Transport with Lagrange-Enforced Boundaries, arXiv preprint arXiv:2507.19907
    • N Myrtakis, I Tsamardinos, V Christophides (2025) A Comparative Analysis of Influence Signals for Data Debugging, arXiv preprint arXiv:2506.11584
    • N Myrtakis, I Tsamardinos, V Christophides (2025) Data Glitches Discovery using Influence-based Model Explanations, Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and and Data Mining V.1, pp. 1068-1079. https://doi.org/10.1145/3690624.3709285
    • N Myrtakis, I Tsamardinos, V Christophides (2025) Data Glitches Discovery using Influence-based Model Explanations, Greeks in AI Symposium 2025 (pdf)
    • M Panagopoulou, M Papadaki, M Karaglani, T Theodosiou, K Michaelidou, S Baritaki, I Tsamardinos, S Kakolyris, S Agelaki, E Chatzaki (2025), Νovel methylation biomarkers in liquid biopsy and classifying biosignatures for the clinical management of Breast Cancer, https://doi.org/10.21203/rs.3.rs-6697291/v1
    • C Papadaki, M Mortoglou, AE Boukouris, K Gourlia, M Markaki, E Lagoudaki, A Koutsopoulos, I Tsamardinos, D Mavroudis, S Agelaki (2025) MicroRNA Expression Analysis and Biological Pathways in Chemoresistant Non-Small Cell Lung Cancer, Cancers 17 (15), 2504.
    • G Paterakis, A Castellani, G Papoutsoglou, T Rodemann, I Tsamardinos (2025) A Comprehensive Perspective on Explainable AI across the Machine Learning Workflow, arXiv preprint arXiv:2508.11529
    • B Psomas, D Christopoulos, E Baltzi, I Kakogeorgiou, T Aravanis, N Komodakis, K Karantzalos, Y Avrithis, G Tolias (2025) Attention, Please! Revisiting Attentive Probing for Masked Image Modeling, arXiv preprint arXiv:2506.10178
    • C Sarafoglou, A Kofidis, M de Boer, M Mylonakis, K Mavrakis, G Zacharakis, Y Pantazis, G Gouridis (2025) NEXT-FRET: A solution-based smFRET platform to resolve folding intermediates under native conditions, bioRxiv, 2025.07. 30.666321, (pdf)
    • FA Shah, VB Talisa, CCH Chang, S Triantafyllou, L Tang, FB Mayr, ... (2025) Heterogeneity in the effect of early goal-directed therapy for septic shock: A secondary analysis of two multicenter international trials, Critical Care Medicine 53 (1), e4-e14.
    • D Shopkhoev, A Ali, M Zhussip, V Malykh, S Lefkimmiatis, N Komodakis, S Zagoruyko (2025) ReplaceMe: Network Simplification via Layer Pruning and Linear Transformations, arXiv preprint arXiv:2505.02819
    • O Simantiraki, M Markaki, Y Pantazis (2025) Dynamic Speech Generation to Enhance Intelligibility in Noisy Environments, ICASSP 2025-2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Hyderabad, India, 2025, pp. 1-5, doi: 10.1109/ICASSP49660.2025.10887886
    • Q Spinat, B Audelan, X Jiang, B Caba, A Benichoux, D Ioannidou, O Teboul, N Komodakis, W Huijbers, R Gabr, A Gafson, C Eliott, D Arnold, N Paragios, S Belachew (2025) Deep learning detection of acute and sub-acute lesion activity from single-timepoint conventional brain MRI in multiple sclerosis, Medical Image Analysis, 103619.
    • B Tercan, V Apolonio, V Chagas, C Wong, J Lee, C Yau, C Benz, J Stuart, B Karlberg, K Ellrott, J Grewal, S Jones, T Knijnenberg, M Castro, V Friedl, V Uzunangelov, R Beroukhim, A Cherniack, G Gao, G Getz, S Hoyt, X Loinaz, W Roh, C Stewart, L Westlake, AG Robertson, S Caesar-Johnson, J Demchok, I Felau, A Kemal, R Tarnuzzer, P Wang, Z Wang, L Yang, J Zenklusen, R Akbani, B Broom, Z Ju, A Schultz, A Ojesina, K Hoadley, A Lal, D Ramazzotti, C Wang, A Lazar, L Roberts, TK Kim, I Shmulevich, P Charonyktakis, V Lagani, I Tsamardinos, ... (2025) Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods, STAR protocols 6 (2), 103681.

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