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Ketil Malde

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Researcher
Telephone: 98691834
Department: Økosystemakustikk

Publications

Academic articles

2023

Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary

Hyeongji Kim, Pekka Parviainen, Ketil Malde
Proceedings of the Northern Lights Deep Learning Workshop
2023

A contrastive learning approach for individual re-identification in a wild fish population

Ørjan Langøy Olsen, Tonje Knutsen Sørdalen, Morten Goodwin, Ketil Malde, Kristian Muri Knausgård, Kim Aleksander Tallaksen Halvorsen
Proceedings of the Northern Lights Deep Learning Workshop 4
2023

Age interpretation of cod otoliths using deep learning

Endre Moen, Rune Vabø, Szymon Smolinski, Côme Denechaud, Nils Olav Handegard, Ketil Malde
Ecological Informatics
2023

Annotating otoliths with a deep generative model

Troels Arnfred Bojesen, Côme Denechaud, Ketil Malde
ICES Journal of Marine Science
2023

Machine learning in marine ecology: an overview of techniques and applications

Peter Rubbens, Stephanie Brodie, Tristan Cordier, Diogo Desto Barcellos, Paul DeVos, Jose A Fernandes-Salvador, Jennifer Fincham, Alessandra Gomes, Nils Olav Handegard, Kerry L. Howell, Cédric Jamet, Kyrre Heldal Kartveit, Hassan Moustahfid, Clea Parcerisas, Dimitris V. Politikos, Raphaëlle Sauzède, Maria Sokolova, Laura Uusitalo, Laure Van den Bulcke, Aloysius van Helmond, Jordan T. Watson, Heather Welch, Oscar Beltran-Perez, Samuel Chaffron, David S. Greenberg, Bernhard Kühn, Rainer Kiko, Madiop Lo, Rubens M. Lopes, Klas Ove Möller, William Michaels, Ahmet Pala, Jean-Baptiste Romagnan, Pia Schuchert, Vahid Seydi, Sebastian Villasante, Ketil Malde, Jean-Olivier Irisson
ICES Journal of Marine Science 80 p. 1829-1853
2023

Machine learning in marine ecology: an overview of techniques and applications

Peter Rubbens, Stephanie Brodie, Tristan Cordier, Diogo Desto Barcellos, Paul DeVos, Jose A Fernandes-Salvador, Jennifer Fincham, Alessandra Gomes, Nils Olav Handegard, Kerry L. Howell, Cédric Jamet, Kyrre Heldal Kartveit, Hassan Moustahfid, Clea Parcerisas, Dimitris V. Politikos, Raphaëlle Sauzède, Maria Sokolova, Laura Uusitalo, Laure Van den Bulcke, Aloysius van Helmond, Jordan T. Watson, Heather Welch, Oscar Beltran-Perez, Samuel Chaffron, David S. Greenberg, Bernhard Kühn, Rainer Kiko, Madiop Lo, Rubens M. Lopes, Klas Ove Möller, William Michaels, Ahmed Pala, Jean-Baptiste Romagnan, Pia Schuchert, Vahid Seydi, Sebastian Villasante, Ketil Malde, Jean-Olivier Irisson
ICES Journal of Marine Science 80 p. 1829-1853
2022

The salmon louse genome may be much larger than sequencing suggests

Grace Wyngaard, Rasmus Skern-Mauritzen, Ketil Malde, Rachel Prendergast, Stefano Peruzzi
Scientific Reports 12 p. 1-14
2022

DeepOtolith v1.0: An Open-Source AI Platform for Automating Fish Age Reading from Otolith or Scale Images

Dimitris V. Politikos, Nikolaos Sykiniotis, Georgios Petasis, Pavlos Dedousis, Alba Ordonez, Rune Vabø, Aikaterini Anastasopoulou, Endre Moen, Chryssi Mytilineou, Arnt-Børre Salberg, Archontia Chatzispyrou, Ketil Malde
Fishes 7
2021

A real-world dataset and data simulation algorithm for automated fish species identification

Vaneeda Allken, Shale Pettit Rosen, Nils Olav Handegard, Ketil Malde
Geoscience Data Journal
2021

Automatic interpretation of salmon scales using deep learning

Rune Vabø, Endre Moen, Szymon Smolinski, Åse Husebø, Nils Olav Handegard, Ketil Malde
Ecological Informatics 63
2021

A deep learning-based method to identify and count pelagic and mesopelagic fishes from trawl camera images

Vaneeda Allken, Shale Pettit Rosen, Nils Olav Handegard, Ketil Malde
ICES Journal of Marine Science 78 p. 3780-3792
2021

The salmon louse genome: Copepod features and parasitic adaptations

Rasmus Skern-Mauritzen, Ketil Malde, Christiane Eichner, Michael Dondrup, Tomasz Furmanek, Francois Besnier, Anna Zofia Komisarczuk, Michael Nuhn, Sussie Dalvin, Rolf Brudvik Edvardsen, Sven Klages, Bruno Huettel, Kurt Stueber, Sindre Grotmol, Egil Erlingsson Karlsbakk, Paul Kersey, Jong S Leong, Kevin Alan Glover, Richard Reinhardt, Sigbjørn Lien, Inge Jonassen, Ben F Koop, Frank Nilsen
Genomics 113 p. 3666-3680
2020

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Eeva Jansson, Francois Besnier, Ketil Malde, Carl André, Geir Dahle, Kevin Glover
BMC Genetics 21 p. 1-15
2020

Acoustic classification in multifrequency echosounder data using deep convolutional neural networks

Olav Brautaset, Anders Ueland Waldeland, Espen Johnsen, Ketil Malde, Line Eikvil, Arnt-Børre Salberg, Nils Olav Handegard
ICES Journal of Marine Science 77 p. 1391-1400
2020

Machine intelligence and the data-driven future of marine science

Ketil Malde, Nils Olav Handegard, Line Eikvil, Arnt Børre Salberg
ICES Journal of Marine Science
2020

Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis.

Sussie Dalvin, Kai Ove Skaftnesmo, Ketil Malde, Kevin Glover, Jong S Leong, Ben F. Koop, Rolf Brudvik Edvardsen, Nina Sandlund
Marine Genomics 49
2019

An efficient protocol and data set for automated otolith image analysis

Savannah Carolyn Myers, Anders Thorsen, Szymon Smolinski, Jane Aanestad Godiksen, Ketil Malde, Nils Olav Handegard
Geoscience Data Journal p. 1-9
2019

Airgun blasts used in marine seismic surveys have limited effects on mortality, and no sublethal effects on behaviour or gene expression, in the copepod Calanus finmarchicus

David M. Fields, Nils Olav Handegard, John Dalen, Christiane Eichner, Ketil Malde, Ørjan Karlsen, Anne Berit Skiftesvik, Caroline Durif, Howard Browman
ICES Journal of Marine Science 76 p. 2033-2044
2019

Machine intelligence and the data-driven future of marine science

Ketil Malde, Nils Olav Handegard, Line Eikvil, Arnt-Børre Salberg.
ICES Journal of Marine Science
2019

Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis.

Sussie Dalvin, Kai Ove Skaftnesmo, Ketil Malde, Kevin Alan Glover, Jong Leong, Ben Koop, Rolf Brudvik Edvardsen, Nina Sandlund.
Marine Genomics In Press
2019

\emph{Airgun blasts used in marine seismic surveys have a minor effect on survival at distances less than 10 m and no sub-lethal effects on behaviour or gene expression in the copepod Calanus finmarchicus}

David M Fields, Nils Olav Handegard, John Dalen, Christiane Eichner, Ketil Malde, Ørjan Karlsen, Anne Berit Skiftesvik, Caroline M. F. Durif, Howard I Browman.
ICES Journal of Marine Science In press
2019

Levels and temporal trends of persistent organic pollutants (POPs) in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) from the southern Barents Sea

Stepan Boitsov, Bjørn Einar Grøsvik, Guri Nesje, Ketil Malde, Jarle Klungsøyr
Environmental Research 172 p. 89-97
2018

Automatic interpretation of otoliths using deep learning

Endre Moen, Nils Olav Handegard, Vaneeda Allken, Ole Thomas Albert, Alf Harbitz, Ketil Malde
PLOS ONE 13 p. 1-14
2018

Fish species identification using a convolutional neural network trained on synthetic data

Vaneeda Allken, Nils Olav Handegard, Shale Rosen, Tiffanie Schreyeck, Thomas Mahiout, Ketil Malde
ICES Journal of Marine Science 76 p. 342-349
2018

Judging a salmon by its spots: Environmental variation is the primary determinant of spot patterns in Salmo salar

Katarina Mariann Jørgensen, Monica Favnebøe Solberg, Francois Besnier, Anders Thorsen, Per Gunnar Fjelldal, Øystein Skaala, Ketil Malde, Kevin Glover
BMC Ecology 18:14 p. 1-13
2017

Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species

Ketil Malde, Bjørghild Breistein Seliussen, Maria Quintela Sanchez, Geir Dahle, Francois Besnier, Hans J. Skaug, Nils Inge Øien, Hiroko Kato Solvang, Tore Haug, Rasmus Skern-Mauritzen, Naohisa Kanda, Luis A. Pastene, Inge Jonassen, Kevin Glover
BMC Genomics 18:76 p. 1-11
2015

Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction

Christiane Eichner, Sussie Trine Dalvin, Rasmus Skern-Mauritzen, Ketil Malde, Heidi Kongshaug, Frank Nilsen
BMC Genomics 16:81
2014

Estimating the information value of polymorphic sites using pooled sequences

Malde, Ketil
BMC Genomics 15
2014

Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis

Francois Besnier, Matthew Peter Kent, Rasmus Skern-Mauritzen, Sigbjørn Lien, Ketil Malde, Rolf Edvardsen, Simon Taylor, Lina Ljungfeldt, Frank Nilsen, Kevin Glover
BMC Genomics
2014

Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues

Rolf Edvardsen, Sussie Trine Dalvin, Tomasz Furmanek, Ketil Malde, Stig Mæhle, Bjørn Olav Kvamme, Rasmus Skern-Mauritzen
Marine Genomics 18 p. 39-44
2014

Simulating a population genomics data set using FlowSim

Malde, Ketil
BMC Research Notes 7:68
2013

How does sequence variability affect de novo assembly quality?

Rasmus Skern-Mauritzen, Ketil Malde, Francois Besnier, Frank Nilsen, Inge Jonassen, Richard Reinhardt, Ben F. Koop, Sussie Trine Dalvin, Stig Mæhle, Heidi Kongshaug, Kevin Glover
Journal of Natural History 47 p. 901-910
2013

Increasing Sequence Search Sensitivity with Transitive Alignments

Ketil Malde, Tomasz Furmanek
PLOS ONE 8
2013

Filtering duplicate reads from 454 pyrosequencing data

Susanne Balzer, Ketil Malde, Markus A. Grohme, Inge Jonassen
Bioinformatics 29 p. 830-836
2012

Maternal 3 ' UTRs: from egg to onset of zygotic transcription in Atlantic cod

Lene Kleppe, Rolf Edvardsen, H Kuhl, Ketil Malde, Tomasz Furmanek, O Drivenes, R Reinhardt, Geir Lasse Taranger, Anna Wargelius
BMC Genomics 13
2011

The genome sequence of Atlantic cod reveals a unique immune system

Bastiaan Star, Alexander Johan Nederbragt, Sissel Jentoft, Unni Grimholt, Martin Malmstrøm, Tone Fredsvik Gregers, Trine Ballestad Rounge, Jonas Paulsen, Monica Hongrø Solbakken, Animesh Sharma, Ola Frang Wetten, Anders Lanzén, Roger Winer, James Knight, Jan-Hinnerk Vogel, Bronwen Aken, Øivind Andersen, Karin Lagesen, Ave Tooming-Klunderud, Rolf Edvardsen, G. Tina Kirubakaran, Mari Espelund, Chirag Nepal, A. Christopher Previti, Bård Ove Karlsen, Truls Moum, Morten Skage, Paul Ragnar Berg, Tor Gjøen, Heiner Kuhl, Jim Thorsen, Ketil Malde, Richard Reinhardt, Lei Du, Steinar Daae Johansen, Steve Searle, Sigbjørn Lien, Frank Nilsen, Inge Jonassen, Stig W Omholt, Nils Christian Stenseth, Kjetill Sigurd Jakobsen
Nature 477 p. 207-210
2011

Systematic exploration of error sources in pyrosequencing flowgram data

Susanne Balzer, Ketil Malde, Inge Jonassen
Bioinformatics 27 p. I304-I309
2011

EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua)

Rolf Edvardsen, Ketil Malde, Christian Mittelholzer, Geir Lasse Taranger, Frank Nilsen
Comparative Biochemistry and Physiology - Part D:Genomics and Proteomics 6 p. 23-30
2011

Flower: extracting information from pyrosequencing data

Malde, Ketil
Bioinformatics 27 p. 1041-1042
2011

Identification of vimentin- and elastin-like transcripts specifically expressed in developing notochord of Atlantic salmon (Salmo salar L.)

Anita Sagstad, Sindre Grotmol, Harald Kryvi, Christel Krossøy, Geir Kåre Totland, Ketil Malde, Shou Wang, Tom Johnny Hansen, Anna Sofie Troedsson Wargelius
Cell and Tissue Research 346 p. 191-202
2010

Calcium from salmon and cod bone is well absorbed in young healthy men: a double-blinded randomised crossover design

Marian Kjellevold Malde, S Bugel, M. Kristensen, Ketil Malde, Ingvild Eide Graff, Jan I Pedersen
Nutrition & Metabolism 7
2010

Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim

Susanne Balzer, Ketil Malde, Anders Lanzén, Animesh Sharma, Inge Jonassen
Bioinformatics 26 p. i420-i425
2009

Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation

Sonal Patel, Kjetil Malde, Anders Lanzén, Rolf Hetlelid Olsen, Audun H. Nerland
Fish and Shellfish Immunology 27 p. 729-738
2008

The effect of sequence quality on sequence alignment

Malde, Ketil
Bioinformatics 24 p. 897-900
2008

Repeats and EST analysis for new organisms

Ketil Malde, Inge Jonassen
BMC Genomics 9
2006

Calculating PSSM probabilities with lazy dynamic programming

Ketil Malde, Robert Giegerich
Journal of functional programming 16 p. 75-81
2006

RBR: library-less repeat detection for ESTs

Ketil Malde, Korbinian Schneeberger, Eivind Coward, Inge Jonassen
Bioinformatics 22 p. 2232-2236
2005

A graph based algorithm for generating EST consensus sequences

Ketil Malde, Eivind Coward, Inge Jonassen
Bioinformatics 21 p. 1371-1375
2005

Masking repeats while clustering ESTs

Korbinian Schneeberger, Ketil Malde, Eivind Coward, Inge Jonassen
Nucleic Acids Research (NAR) 33 p. 2176-2180
2003

Fast Sequence Clustering Using a Suffix Array Algorithm

Ketil Malde, Eivind Coward, Inge Jonassen
Bioinformatics 19 p. 1221-1226
2003

A Fast Algorithm for EST Clustering using Suffix Arrays

Ketil Malde, Eivind Coward, Inge Jonasen
Bioinformatics

Scientific lectures

2024

Annotation-Free Feature Learning for Improved Acoustic Target Classification

Ahmet Pala, Anna Oleynik, Ketil Malde, Nils Olav Handegard
2024

Unraveling Acoustic Signal Patterns in Fisheries Through DINO-Based Self-Supervised Learning

Ahmet Pala, Anna Oleynik, Ketil Malde, Nils Olav Handegard
2023

Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary

Ketil Malde, Pekka Parviainen, Hyeongji Kim
2023

A story about data extraction and deep learning applied to fishery acoustic data

Nils Olav Handegard, Leif Bildøy, Olav Brautaset, Tomasz Furmanek, Arne Johannes Holmin, Ingrid Utseth, Sindre Vatnehol, Ketil Malde
2022

Artificial Intelligence methods for fisheries management

Malde, Ketil
2022

An online otolith age reader using deep neural networks: Perspectives and challenges

Dimitris V. Politikos, Nikolaos Sykiniotis, Georgios Petasis, Pavlos Dedousis, Alba Ordonez, Rune Vabø, Aikaterini Anastasopoulou, Endre Moen, Chryssi Mytilineou, Arnt-Børre Salberg, Archontia Chatzispyrou, Ketil Malde
2022

Using deep learning models to count and identify fish species from in-trawl images

Vaneeda Allken, Thor Aleksander Klevjer, Kristoffer Løvall, Ketil Malde, Shale Pettit Rosen, Eugenie Heliana Taraneh Westergerling, Nils Olav Handegard
2022

Exploring imaging protocols and neural network architectures for automated otolith analysis

Endre Moen, Rune Vabø, Come Denechaud, Szymon Smolinski, Ketil Malde
2022

Selecting maximally informative frequency subsets for acoustic surveys

Knut T. A. Holager, Nils Olav Handegard, Ketil Malde
2022

A deep learning approach for individual re-identification (re-ID) of fish in the wild

Vaneeda Allken, Tonje Knutsen Sørdalen, Cigdem Beyan, Ketil Malde, Howard Browman, Kim Aleksander Tallaksen Halvorsen
2021

Combined trawl-mounted optic and acoustic methods to study the mesopelagic ecosystem

Shale Pettit Rosen, Eva Garcia Seoane, Melanie Underwood, Thor Aleksander Klevjer, Gavin John Macaulay, Mette Dalgaard Agersted, Webjørn Raunsgård Melle, Nils Olav Handegard, Ketil Malde, Vaneeda Allken
2019

Using a CNN trained on synthetic data for fish species identification

Vaneeda Allken, Nils Olav Handegard, Shale Rosen, Ketil Malde
2019

Using a CNN trained on synthetic data for fish species identification

Vaneeda Allken, Nils Olav Handegard, Shale Rosen, Ketil Malde
2019

The COGMAR project

Arnt Børre Salberg, Line Eikvil, Ketil Malde, Nils Olav Handegard
2018

Drowning in data: Can deep learning approaches be the solution?

Nils Olav Handegard, Vaneeda Allken, Ketil Malde
2016

Big Data og Big Analysis - hvordan drikke fra brannslangen

Malde, Ketil
2015

Insitute of Marine Research - a research and advisory institute

Malde, Ketil
2013

Identifying diagnostic SNPs in the presence of sequencing errors

Malde, Ketil
2013

Can Software Transactional Memory make concurrent programs simple and safe?

Malde, Ketil
2012

Attempts to induce sterility in Atlantic salmon by morfolino and zink finger techniques

Anna Wargelius, Rolf Edvardsen, Trine Haugen, Ståle Ellingsen, Eva Andersson, Ketil Malde, Ørjan Karlsen, Per Gunnar Fjelldal, Geir Lasse Taranger, Øyvind Drivenes
2012

Transcriptomic analysis of the salmon louse

Rolf Edvardsen, Stig Mæhle, Tomasz Furmanek, Ketil Malde, Bjørn Olav Kvamme, Sussie Trine Dalvin, Rasmus Skern-Mauritzen
2012

The Salmon Louse Genome Project

Rasmus Skern-Mauritzen, Ketil Malde, Tomasz Furmanek, Richard Reinhardt, Ben F Koop, Frank Nilsen
2011

Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod

Lene Kleppe, Rolf Edvardsen, Heiner Kuhl, Ketil Malde, Tomasz Furmanek, Øyvind Drivenes, Richard Reinhardt, Geir Lasse Taranger, Anna Wargelius
2009

Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell

Ketil Malde, Bryan O'Sullivan
2002

A Fast Algorithm for EST Clustering using Suffix Trees

Ketil Malde, Eivind Coward, Inge Jonasen

Poster

2023

Escaping the black box: explicit annotation of otolith growth rings with deep learning

Troels Arnfred Bojesen, Côme Denechaud, Ketil Malde
2023

Annotating Otoliths with a Deep Generative Model

Troels Arnfred Bojesen, Côme Denechaud, Ketil Malde
2020

Automatic interpretation of salmon scales using deep learning

Rune Vabø, Endre Moen, Hyeongji Kim, Nils Olav Handegard, Ketil Malde
2019

Otoliths as life history indicators

Jane Aanestad Godiksen, Audrey J. Geffen, Arild Folkvord, Jon-Ivar Westgaard, Torild Johansen, Ole Thomas Albert, Arved Staby, Alf Harbitz, Aril Slotte, Ketil Malde, Christian Irgens, Olav Sigurd Kjesbu
2017

Automatisk klassifisering av svømming i not

Nils Olav Handegard, Ketil Malde, Maria Tenningen, Hector Pena
2013

A data storage strategy for generic, heterogenous scientific data

Malde, Ketil

Reports and dissertations

2023

On the Significance of Distance in Machine Learning

Hyeongji Kim, Ketil Malde, Pekka Parviainen
2023

Object Tracking Approach for Catch Estimation on Trawl Surveys

Peter Løkhammer Liessem, Ketil Malde, Vaneeda Allken
2022

Selecting Maximally Informative Frequency Subsets for Acoustic Surveys

Ketil Malde, Nils Olav Handegard, Knut T. A. Holager
2021

Fisheries acoustics and Acoustic Target Classification - Report from the COGMAR/CRIMAC workshop on machine learning methods in fisheries acoustics

Nils Olav Handegard, Lars Nonboe Andersen, Olav Brautaset, Changkyu Choi, Inge Kristian Eliassen, Yngve Heggelund, Arne Johan Hestnes, Ketil Malde, Håkon Osland, Alba Ordonez, Ruben Patel, Geir Pedersen, Ibrahim Umar, Tom Van Engeland, Sindre Vatnehol
2020

Big Data in Marine Science

Lionel Guidi, A. Fernandez Guerra, C Canchaya, Ed Curry, F. Foglini, J.-O. Irisson, Ketil Malde, C. T. Marshall, M. Obst, R. P. Ribeiro, Jerry Tjiputra, D. C. E. Bakker
2019

WORKING GROUP ON MACHINE LEARNING IN MARINE SCIENCE (WGMLEARN)

Malde, Ketil
2019

Machine learning to improve marine science for the sustainability of living ocean resources: Report from the 2019 Norway - U.S. Workshop

Ketil Malde, Nils Olav Handegard, Hege Hammersland, William Michaels
2018

Report of the Workshop on Machine Learning in Marine Science (WKMLEARN)

Ketil Malde, Shaheen Syed
2005

Algorithms for the Analysis of Expressed Sequence Tags

Malde, Ketil
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