Hopfield networks is all you need H Ramsauer, B Schäfl, J Lehner, P Seidl, M Widrich, T Adler, L Gruber, ... arXiv preprint arXiv:2008.02217, 2020 | 593 | 2020 |
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding R Akbar, PA Robert, M Pavlović, JR Jeliazkov, I Snapkov, A Slabodkin, ... Cell Reports 34 (11), 2021 | 188 | 2021 |
Modern hopfield networks and attention for immune repertoire classification M Widrich, B Schäfl, M Pavlović, H Ramsauer, L Gruber, M Holzleitner, ... Advances in neural information processing systems 33, 18832-18845, 2020 | 150 | 2020 |
In silico proof of principle of machine learning-based antibody design at unconstrained scale R Akbar, PA Robert, CR Weber, M Widrich, R Frank, M Pavlović, ... MAbs 14 (1), 2031482, 2022 | 111 | 2022 |
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires AJ Brown, I Snapkov, R Akbar, M Pavlović, E Miho, GK Sandve, V Greiff Molecular Systems Design & Engineering 4 (4), 701-736, 2019 | 76 | 2019 |
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires M Pavlović, L Scheffer, K Motwani, C Kanduri, R Kompova, N Vazov, ... Nature Machine Intelligence 3, 936–944, 2021 | 74 | 2021 |
Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction PA Robert, R Akbar, R Frank, M Pavlović, M Widrich, I Snapkov, ... Nature Computational Science 2 (12), 845-865, 2022 | 72* | 2022 |
immuneSIM: tunable multi-feature simulation of B-and T-cell receptor repertoires for immunoinformatics benchmarking CR Weber, R Akbar, A Yermanos, M Pavlović, I Snapkov, GK Sandve, ... Bioinformatics 36 (11), 3594-3596, 2020 | 72 | 2020 |
The future of blood testing is the immunome RA Arnaout, ETL Prak, N Schwab, F Rubelt, ... Frontiers in Immunology 12, 626793, 2021 | 35 | 2021 |
Individualized VDJ recombination predisposes the available Ig sequence space A Slabodkin, M Chernigovskaya, I Mikocziova, R Akbar, L Scheffer, ... Genome Research 31 (12), 2209-2224, 2021 | 34 | 2021 |
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification C Kanduri, M Pavlović, L Scheffer, K Motwani, M Chernigovskaya, V Greiff, ... GigaScience 11, giac046, 2022 | 29 | 2022 |
T cell receptor repertoire as a potential diagnostic marker for celiac disease Y Yao, A Zia, RS Neumann, M Pavlovic, G Balaban, KEA Lundin, ... Clinical Immunology 222, 108621, 2021 | 18 | 2021 |
Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics M Pavlović, GS Al Hajj, C Kanduri, J Pensar, ME Wood, LM Sollid, V Greiff, ... Nature Machine Intelligence 6 (1), 15-24, 2024 | 13* | 2024 |
Artificial intelligence-driven prediction of COVID-19-related hospitalization and death: a systematic review S Shakibfar, F Nyberg, H Li, J Zhao, HME Nordeng, GKF Sandve, ... Frontiers in Public Health 11, 1183725, 2023 | 13 | 2023 |
Hopfield networks is all you need. CoRR abs/2008.02217 (2020) H Ramsauer, B Schäfl, J Lehner, P Seidl, M Widrich, L Gruber, ... | 13 | 2008 |
BioNumPy: array programming for biology KD Rand, I Grytten, M Pavlović, C Kanduri, GK Sandve Nature Methods, 1-2, 2024 | 5* | 2024 |
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning M Chernigovskaya, M Pavlović, C Kanduri, S Gielis, PA Robert, L Scheffer, ... Nucleic Acids Research 53 (3), gkaf025, 2025 | 4 | 2025 |
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods C Kanduri, L Scheffer, M Pavlović, KD Rand, M Chernigovskaya, ... GigaScience 12, giad074, 2023 | 3 | 2023 |
Using causal modeling to analyze generalization of biomarkers in high-dimensional domains: a case study of adaptive immune repertoires M Pavlovic, GS Al Hajj, V Greiff, J Pensar, GK Sandve ICML 2022: Workshop on Spurious Correlations, Invariance and Stability, 2022 | 2 | 2022 |
Revealing the hidden sequence distribution of epitope-specific TCR repertoires and its influence on machine learning model performance S Gielis, M Chernigovskaya, M Pavlovic, V Van Deuren, R Vandoren, ... bioRxiv, 2024.10. 21.619364, 2024 | 1 | 2024 |