Geir Kjetil Sandve

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 30

Top Topics

Hopfield Networks

Exact And Approximate

Machine Learning

Top Venues

Briefings Bioinform.

Publications

Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Tatiana Belova, Marieke L. Kuijjer
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. CoRR (2024)
Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff
Linguistics-based formalization of the antibody language as a basis for antibody language models. Nat. Comput. Sci. 4 (6) (2024)
Milena Pavlovic, Ghadi S. Al Hajj, Chakravarthi Kanduri, Johan Pensar, Mollie Wood, Ludvig Magne Sollid, Victor Greiff, Geir Kjetil Sandve
Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. Nat. Mac. Intell. 6 (1) (2024)
Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Geir Kjetil Sandve, Victor Greiff, Dag Trygve Truslew Haug
Linguistically inspired roadmap for building biologically reliable protein language models. Nat. Mac. Intell. 5 (5) (2023)
Ping-Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinform. 39 (10) (2023)
Shiva Dahal-Koirala, Gabriel Balaban, Ralf Stefan Neumann, Lonneke Scheffer, Knut Erik Aslaksen Lundin, Victor Greiff, Ludvig Magne Sollid, Shuo-Wang Qiao, Geir Kjetil Sandve
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings Bioinform. 23 (2) (2022)
Torbjørn Rognes, Lonneke Scheffer, Victor Greiff, Geir Kjetil Sandve
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinform. 38 (17) (2022)
Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff
ImmunoLingo: Linguistics-based formalization of the antibody language. CoRR (2022)
Geir Kjetil Sandve, Victor Greiff
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking. Bioinform. 38 (21) (2022)
Milena Pavlovic, Ghadi S. Al Hajj, Johan Pensar, Mollie Wood, Ludvig M. Sollid, Victor Greiff, Geir Kjetil Sandve
Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics. CoRR (2022)
Philippe A. Robert, Rahmad Akbar, Robert Frank, Milena Pavlovic, Michael Widrich, Igor Snapkov, Andrei Slabodkin, Maria Chernigovskaya, Lonneke Scheffer, Eva Smorodina, Puneet Rawat, Brij Bhushan Mehta, Mai Ha Vu, Ingvild Frøberg Mathisen, Aurél Prósz, Krzysztof Abram, Alex Olar, Enkelejda Miho, Dag Trygve Truslew Haug, Fridtjof Lund-Johansen, Sepp Hochreiter, Ingrid Hobæk Haff, Günter Klambauer, Geir Kjetil Sandve, Victor Greiff
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. Nat. Comput. Sci. 2 (12) (2022)
Ghadi S. Al Hajj, Johan Pensar, Geir Kjetil Sandve
DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation. CoRR (2022)
Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Victor Greiff, Geir Kjetil Sandve, Dag Trygve Truslew Haug
Advancing protein language models with linguistics: a roadmap for improved interpretability. CoRR (2022)
Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve
Ten simple rules for quick and dirty scientific programming. PLoS Comput. Biol. 17 (3) (2021)
Milena Pavlovic, Lonneke Scheffer, Keshav Motwani, Chakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, Knut Waagan, Fabian L. M. Bernal, Alexandre Almeida Costa, Brian Corrie, Rahmad Akbar, Ghadi S. Al Hajj, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank, Ivar Grytten, Sveinung Gundersen, Ingrid Hobæk Haff, Eivind Hovig, Ping-Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini, Thomas Minotto, Johan Pensar, Knut D. Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig M. Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff, Geir Kjetil Sandve
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat. Mach. Intell. 3 (11) (2021)
Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Kristine Glad, Geir Kjetil Sandve
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings Bioinform. 21 (5) (2020)
Michael Widrich, Bernhard Schäfl, Milena Pavlovic, Hubert Ramsauer, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer
Modern Hopfield Networks and Attention for Immune Repertoire Classification. NeurIPS (2020)
Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlovic, Igor Snapkov, Geir Kjetil Sandve, Sai T. Reddy, Victor Greiff
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Bioinform. 36 (11) (2020)
Hubert Ramsauer, Bernhard Schäfl, Johannes Lehner, Philipp Seidl, Michael Widrich, Lukas Gruber, Markus Holzleitner, Milena Pavlovic, Geir Kjetil Sandve, Victor Greiff, David P. Kreil, Michael Kopp, Günter Klambauer, Johannes Brandstetter, Sepp Hochreiter
Hopfield Networks is All You Need. CoRR (2020)
Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinform. 21 (1) (2020)
Michael Widrich, Bernhard Schäfl, Hubert Ramsauer, Milena Pavlovic, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer
Modern Hopfield Networks and Attention for Immune Repertoire Classification. CoRR (2020)
Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput. Biol. 15 (2) (2019)
Chakravarthi Kanduri, Christoph Bock, Sveinung Gundersen, Eivind Hovig, Geir Kjetil Sandve
Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinform. 35 (9) (2019)
Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve
Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. BMC Bioinform. 19 (1) (2018)
Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander V. Favorov, Ryan M. Layer, Andrey A. Mironov, Aaron R. Quinlan, Nathan C. Sheffield, Gosia Trynka, Geir Kjetil Sandve
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Knut D. Rand, Ivar Grytten, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve
Coordinates and intervals in graph-based reference genomes. BMC Bioinform. 18 (1) (2017)
Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes, Alexander Johan Nederbragt
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinform. 18 (1) (2017)
Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve
The rainfall plot: its motivation, characteristics and pitfalls. BMC Bioinform. 18 (1) (2017)
Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Cech, Geir Kjetil Sandve
Galaxy Portal: interacting with the galaxy platform through mobile devices. Bioinform. 32 (11) (2016)
Antonio Mora, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland
In the loop: promoter-enhancer interactions and bioinformatics. Briefings Bioinform. 17 (6) (2016)
Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinform. 30 (11) (2014)
Doug James, Nancy Wilkins-Diehr, Victoria Stodden, Dirk Colbry, Carlos Rosales, Mark R. Fahey, Justin Shi, Rafael Ferreira da Silva, Kyo Lee, Ralph Roskies, Laurence Loewe, Susan Lindsey, Rob Kooper, Lorena A. Barba, David H. Bailey, Jonathan M. Borwein, Óscar Corcho, Ewa Deelman, Michael C. Dietze, Benjamin Gilbert, Jan Harkes, Seth Keele, Praveen Kumar, Jong Lee, Erika Linke, Richard Marciano, Luigi Marini, Chris Mattmann, Dave Mattson, Kenton McHenry, Robert T. McLay, Sheila Miguez, Barbara S. Minsker, María S. Pérez-Hernández, Dan Ryan, Mats Rynge, Idafen Santana-Pérez, Mahadev Satyanarayanan, Gloriana St. Clair, Keith Webster, Eivind Hovig, Daniel S. Katz, Sophie Kay, Geir Kjetil Sandve, David Skinner, Gabrielle Allen, John Cazes, Kym Won Cho, Jim Fonseca, Lorraine J. Hwang, Lars Koesterke, Pragnesh Patel, Line Pouchard, Edward Seidel, Isuru Suriarachchi
Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE. CoRR (2014)
Geir Kjetil Sandve, Sveinung Gundersen, Morten Johansen, Ingrid Kristine Glad, Krishanthi Gunathasan, Lars Holden, Marit Holden, Knut Liestøl, Ståle Nygård, Vegard Nygaard, Jonas Paulsen, Halfdan Rydbeck, Kai Trengereid, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Matús Kalas, Tonje Lien, Morten Rye, Arnoldo Frigessi, Eivind Hovig
The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig
Ten Simple Rules for Reproducible Computational Research. PLoS Comput. Biol. 9 (10) (2013)
Sveinung Gundersen, Matús Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve
Identifying elemental genomic track types and representing them uniformly. BMC Bioinform. 12 (2011)
Geir Kjetil Sandve, Egil Ferkingstad, Ståle Nygård
Sequential Monte Carlo multiple testing. Bioinform. 27 (23) (2011)
Kjetil Klepper, Geir Kjetil Sandve, Osman Abul, Jostein Johansen, Finn Drabløs
Assessment of composite motif discovery methods. BMC Bioinform. 9 (2008)
Geir Kjetil Sandve, Osman Abul, Finn Drabløs
Compo: composite motif discovery using discrete models. BMC Bioinform. 9 (2008)
Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Selen Uguroglu, Eric P. Xing
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. RECOMB (2008)
Geir Kjetil Sandve, Osman Abul, Vegard Walseng, Finn Drabløs
Improved benchmarks for computational motif discovery. BMC Bioinform. 8 (2007)
Osman Abul, Geir Kjetil Sandve, Finn Drabløs
False Discovery Rates in Identifying Functional DNA Motifs. BIBE (2007)
Geir Kjetil Sandve, Magnar Nedland, Øyvind Bø Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabløs
Accelerating Motif Discovery: Motif Matching on Parallel Hardware. WABI (2006)
Geir Kjetil Sandve, Finn Drabløs
Generalized Composite Motif Discovery. KES (3) (2005)