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2 results on '"Pasen, Martin"'

1. Merging of neural networks

Author

Pašen, Martin and Boža, Vladimír

Subjects
Computer Science - Machine Learning
Abstract

We propose a simple scheme for merging two neural networks trained with different starting initialization into a single one with the same size as the original ones. We do this by carefully selecting channels from each input network. Our procedure might be used as a finalization step after one tries multiple starting seeds to avoid an unlucky one. We also show that training two networks and merging them leads to better performance than training a single network for an extended period of time. Availability: https://github.com/fmfi-compbio/neural-network-merging

Published
2022

2. PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes

Author

Cormican, John A., Medfai, Lobna, Wawrzyniuk, Magdalena, Pasen, Martin, Afrache, Hassnae, Fourny, Constance, Khan, Sahil, Gneiße, Pascal, Soh, Wai Tuck, Timelli, Arianna, Nolfi, Emanuele, Pannekoek, Yvonne, Cope, Andrew, Urlaub, Henning, Sijts, Alice J.A. M., Mishto, Michele, and Liepe, Juliane

Abstract

Here, we develop PEPSeek, a web-server based software to allow higher performance in the identification of pathogen-derived epitope candidates detected via mass spectrometry in MHC class I immunopeptidomes. We apply it to human and mouse cell lines infected with either SARS-CoV-2, Listeria monocytogenesor Chlamydia trachomatis, thereby identifying a large number of novel antigens and epitopes that we prove to be recognized by CD8+T cells. In infected cells, we identified antigenic peptide features that suggested how processing and presentation of pathogenic antigens differ between pathogens. The quantitative tools of PEPSeek also helped to define how C. trachomatisinfection cycle could impact on the antigenic landscape of the host human cell system, likely reflecting metabolic changes occurred in the infected cells.

Published
2025
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