Publications
Journals Conferences and Announcements Other Theses
Journals
- S.-C. Fragkouli, P. Nousi, N. Passalis, P. Iosif, N. Stergioulas, and A. Tefas, “Deep residual error and bag-of-tricks learning for gravitational wave surrogate modeling,” Applied Soft Computing, p. 110746, 2023, doi: https://doi.org/10.1016/j.asoc.2023.110746.
Deep learning methods have been employed in gravitational-wave astronomy to accelerate the construction of surrogate waveforms for the inspiral of spin-aligned black hole binaries, among other applications. We face the challenge of modeling the residual error of an artificial neural network that models the coefficients of the surrogate waveform expansion (especially those of the phase of the waveform) which we demonstrate has sufficient structure to be learnable by a second network. Adding this second network, we were able to reduce the maximum mismatch for waveforms in a validation set by 13.4 times. We also explored several other ideas for improving the accuracy of the surrogate model, such as the exploitation of similarities between waveforms, the augmentation of the training set, the dissection of the input space, using dedicated networks per output coefficient and output augmentation. In several cases, small improvements can be observed, but the most significant improvement still comes from the addition of a second network that models the residual error. Since the residual error for more general surrogate waveform models (when e.g., eccentricity is included) may also have a specific structure, one can expect our method to be applicable to cases where the gain in accuracy could lead to significant gains in computational time.
- L. Zaragoza-Infante, V. Junet, N. Pechlivanis, S.-C. Fragkouli, S. Amprachamian, T. Koletsa, A. Chatzidimitriou, M. Papaioannou, K. Stamatopoulos, A. Agathangelidis, and F. Psomopoulos, “IgIDivA: immunoglobulin intraclonal diversification analysis,” Briefings in Bioinformatics, Aug. 2022, doi: 10.1093/bib/bbac349.
Intraclonal diversification (ID) within the immunoglobulin (IG) genes expressed by B cell clones arises due to ongoing somatic hypermutation (SHM) in a context of continuous interactions with antigen(s). Defining the nature and order of appearance of SHMs in the IG genes can assist in improved understanding of the ID process, shedding light into the ontogeny and evolution of B cell clones in health and disease. Such endeavor is empowered thanks to the introduction of high-throughput sequencing in the study of IG gene repertoires. However, few existing tools allow the identification, quantification and characterization of SHMs related to ID, all of which have limitations in their analysis, highlighting the need for developing a purpose-built tool for the comprehensive analysis of the ID process. In this work, we present the immunoglobulin intraclonal diversification analysis (IgIDivA) tool, a novel methodology for the in-depth qualitative and quantitative analysis of the ID process from high-throughput sequencing data. IgIDivA identifies and characterizes SHMs that occur within the variable domain of the rearranged IG genes and studies in detail the connections between identified SHMs, establishing mutational pathways. Moreover, it combines established and new graph-based metrics for the objective determination of ID level, combined with statistical analysis for the comparison of ID level features for different groups of samples. Of importance, IgIDivA also provides detailed visualizations of ID through the generation of purpose-built graph networks. Beyond the method design, IgIDivA has been also implemented as an R Shiny web application. IgIDivA is freely available at https://bio.tools/igidiva
- P. Nousi, S.-C. Fragkouli, N. Passalis, P. Iosif, T. Apostolatos, G. Pappas, N. Stergioulas, and A. Tefas, “Autoencoder-driven spiral representation learning for gravitational wave surrogate modelling,” Neurocomputing, vol. 491, pp. 67–77, 2022, doi: https://doi.org/10.1016/j.neucom.2022.03.052.
Recently, artificial neural networks have been gaining momentum in the field of gravitational wave astronomy, for example in surrogate modelling of computationally expensive waveform models for binary black hole inspiral and merger. Surrogate modelling yields fast and accurate approximations of gravitational waves and neural networks have been used in the final step of interpolating the coefficients of the surrogate model for arbitrary waveforms outside the training sample. We investigate the existence of underlying structures in the empirical interpolation coefficients using autoencoders. We demonstrate that when the coefficient space is compressed to only two dimensions, a spiral structure appears, wherein the spiral angle is linearly related to the mass ratio. Based on this finding, we design a spiral module with learnable parameters, that is used as the first layer in a neural network, which learns to map the input space to the coefficients. The spiral module is evaluated on multiple neural network architectures and consistently achieves better speed-accuracy trade-off than baseline models. A thorough experimental study is conducted and the final result is a surrogate model which can evaluate millions of input parameters in a single forward pass in under 1 ms on a desktop GPU, while the mismatch between the corresponding generated waveforms and the ground-truth waveforms is better than the compared baseline methods. We anticipate the existence of analogous underlying structures and corresponding computational gains also in the case of spinning black hole binaries.
Conferences and Announcements
- S.-C. Fragkouli, N. Pechlivanis, A. Orfanou, A. Anastasiadou, A. Agathangelidis, and F. Psomopoulos, “Synth4bench: a framework for generating synthetic genomics data for the evaluation of somatic variant calling algorithms, 17th Conference of Hellenic Society for Computational Biology and Bioinformatics (HSCBB),” Oct. 2023, doi: 10.5281/zenodo.8432060.
- S.-C. Fragkouli, N. Pechlivanis, A. Agathangelidis, and F. Psomopoulos, “Synthetic Genomics Data Generation and Evaluation for the Use Case of Benchmarking Somatic Variant Calling Algorithms, 31st Conference in Intelligent Systems For Molecular Biology and the 22nd European Conference On Computational Biology (ISΜB-ECCB23) ,” Jul. 2023, doi: 10.7490/f1000research.1119575.1.
- G. Gavriilidis, S.-C. Fragkouli, E. Theodosiou, V. Vasileiou, S. Keisaris, and F. Psomopoulos, “SCell-wise fluxomics of Chronic Lymphocytic Leukemia single-cell data reveal novel metabolic adaptations to Ibrutinib therapy, 31st Conference in Intelligent Systems For Molecular Biology and the 22nd European Conference On Computational Biology (ISΜB-ECCB23) ,” Jul. 2023.
- S.-C. Fragkouli, A. Agathangelidis, and F. Psomopoulos, “Shedding Light on Somatic Variant Calling, 16th Conference of the Hellenic Society for Computational Biology and Bioinformatics HSCBB22,” Oct. 2022, doi: 10.13140/RG.2.2.12701.18402.
Other
- S.-C. Fragkouli, N. Pechlivanis, A. Anastasiadou, G. Karakatsoulis, A. Orfanou, P. Kollia, A. Agathangelidis, and F. E. Psomopoulos, “Synth4bench: a framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.” 2024, doi: 10.1101/2024.03.07.582313.
- S.-C. Fragkouli, A. Agathangelidis, and F. E. Psomopoulos, “10 Synthetic Genomics Datasets.” Feb. 2024, doi: 10.5281/zenodo.10683211.
- F. Adriano, E. Parkinson, D. Bianchini, F. Psomopoulos, M. Varadi, M. Andrabi, S.-C. Fragkouli, and U. Vadadokhau, “RDMkit, Your Domain, Machine Learning.” 2024, [Online]. Available at: https://rdmkit.elixir-europe.org/machine_learning.
- S.-C. Fragkouli, A. Agathangelidis, and F. E. Psomopoulos, “TP53 synthetic genomics data for benchmarking variant callers.” Jun. 2023, doi: 10.5281/zenodo.8095898.
- S.-C. Fragkouli, “DOME ANNOTATION: THE CROWDSOURCING EFFORT,” ELIXIR DOME Strategic Implementation Study Kickoff meeting. Apr. 2023, doi: 10.5281/zenodo.10688490.
- “Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing.” 2022, doi: https://doi.org/10.18129/B9.bioc.lineagespot.
- S.-C. Fragkouli, P. Nousi, N. Passalis, P. Iosif, N. Stergioulas, and A. Tefas, “Deep Residual Error and Bag-of-Tricks Learning for Gravitational Wave Surrogate Modeling.” arXiv, 2022, doi: 10.48550/ARXIV.2203.08434.
- S.-C. Fragkouli, P. Nousi, N. Passalis, P. Iosif, N. Stergioulas, and A. Tefas, “Deep Residual Error and Bag-of-Tricks Learning for Gravitational Wave Surrogate Modeling,” G2net WG1(Machine Learning for Gravitational Wave Astronomy) meeting. Apr. 2022.
- S.-C. Fragkouli, “Deep Residual Error and Bag-of-Tricks Learning for Gravitational Wave Surrogate Μodeling,” LIGO-Virgo-Kagra Collaboration Waveform WG meeting. Feb. 2022, doi: 10.5281/zenodo.10688323.
Theses
- S.-C. Fragkouli, “Deep Learning Applications on Gravitational Waves.” Informatics Department, Aristotle University of Thessaloniki, 2021.
- S.-C. Fragkouli, “Study of the merging of a neutron star with a black hole and the role of the equation of state.” Physics Department, Aristotle University of Thessaloniki, 2017, [Online]. Available at: http://ikee.lib.auth.gr/record/294627/files/thesis.pdf.