Academic article
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Kim, Hyeongji; Choi, Changkyu; Kampffmeyer, Michael Christian
et al. (2025). ProxyDR: Deep Hyperspherical Metric Learning with Distance Ratio-Based Formulation. (external link)
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Pala, Ahmet; Oleynik, Anna; Malde, Ketil
et al. (2024). Self-supervised feature learning for acoustic data analysis. (external link)
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Canovi, Noemi; Ellis, Benjamin A.; Sørdalen, Tonje Knutsen
et al. (2024). Trajectory-based fish event classification through pre-training with diffusion models. (external link)
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Kim, Hyeongji; Parviainen, Pekka; Malde, Ketil
(2023). Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary. (external link)
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Olsen, Ørjan Langøy; Sørdalen, Tonje Knutsen; Goodwin, Morten
et al. (2023). A contrastive learning approach for individual re-identification in a wild fish population. (external link)
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Moen, Endre; Vabø, Rune; Smolinski, Szymon
et al. (2023). Age interpretation of cod otoliths using deep learning. (external link)
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Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil
(2023). Annotating otoliths with a deep generative model. (external link)
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Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan
et al. (2023). Machine learning in marine ecology: an overview of techniques and applications. (external link)
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Wyngaard, Grace; Skern-Mauritzen, Rasmus; Malde, Ketil
et al. (2022). The salmon louse genome may be much larger than sequencing suggests. (external link)
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Politikos, Dimitris V.; Sykiniotis, Nikolaos; Petasis, Georgios
et al. (2022). DeepOtolith v1.0: An Open-Source AI Platform for Automating Fish Age Reading from Otolith or Scale Images. (external link)
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Skern-Mauritzen, Rasmus; Malde, Ketil; Eichner, Christiane
et al. (2021). The salmon louse genome: Copepod features and parasitic adaptations. (external link)
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Allken, Vaneeda; Rosen, Shale Pettit; Handegard, Nils Olav
et al. (2021). A real-world dataset and data simulation algorithm for automated fish species identification. (external link)
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Allken, Vaneeda; Rosen, Shale Pettit; Handegard, Nils Olav
et al. (2021). A deep learning-based method to identify and count pelagic and mesopelagic fishes from trawl camera images. (external link)
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Vabø, Rune; Moen, Endre; Smolinski, Szymon
et al. (2021). Automatic interpretation of salmon scales using deep learning. (external link)
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Dalvin, Sussie; Skaftnesmo, Kai Ove; Malde, Ketil
et al. (2020). Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis. . (external link)
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Malde, Ketil; Handegard, Nils Olav; Eikvil, Line
et al. (2020). Machine intelligence and the data-driven future of marine science. (external link)
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Brautaset, Olav; Waldeland, Anders Ueland; Johnsen, Espen
et al. (2020). Acoustic classification in multifrequency echosounder data using deep convolutional neural networks. (external link)
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Jansson, Eeva; Besnier, Francois; Malde, Ketil
et al. (2020). Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. (external link)
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Boitsov, Stepan; Grøsvik, Bjørn Einar; Nesje, Guri
et al. (2019). Levels and temporal trends of persistent organic pollutants (POPs) in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) from the southern Barents Sea. (external link)
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Fields, David M.; Handegard, Nils Olav; Dalen, John
et al. (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. (external link)
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Myers, Savannah Carolyn; Thorsen, Anders; Smolinski, Szymon
et al. (2019). An efficient protocol and data set for automated otolith image analysis. (external link)
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Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale
et al. (2018). Fish species identification using a convolutional neural network trained on synthetic data. (external link)
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Moen, Endre; Handegard, Nils Olav; Allken, Vaneeda
et al. (2018). Automatic interpretation of otoliths using deep learning. (external link)
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Jørgensen, Katarina Mariann; Solberg, Monica Favnebøe; Besnier, Francois
et al. (2018). Judging a salmon by its spots: Environmental variation is the primary determinant of spot patterns in Salmo salar. (external link)
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Malde, Ketil; Seliussen, Bjørghild Breistein; Sanchez, Maria Quintela
et al. (2017). Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. (external link)
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Eichner, Christiane; Dalvin, Sussie Trine; Skern-Mauritzen, Rasmus
et al. (2015). Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction. (external link)
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Besnier, Francois; Kent, Matthew Peter; Skern-Mauritzen, Rasmus
et al. (2014). Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis. (external link)
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Malde, Ketil
(2014). Simulating a population genomics data set using FlowSim. (external link)
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Edvardsen, Rolf; Dalvin, Sussie Trine; Furmanek, Tomasz
et al. (2014). Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues. (external link)
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Malde, Ketil
(2014). Estimating the information value of polymorphic sites using pooled sequences. (external link)
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Skern-Mauritzen, Rasmus; Malde, Ketil; Besnier, Francois
et al. (2013). How does sequence variability affect de novo assembly quality?. (external link)
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Balzer, Susanne; Malde, Ketil; Grohme, Markus A.
et al. (2013). Filtering duplicate reads from 454 pyrosequencing data. (external link)
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Malde, Ketil; Furmanek, Tomasz
(2013). Increasing Sequence Search Sensitivity with Transitive Alignments. (external link)
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Kleppe, Lene; Edvardsen, Rolf; Kuhl, H
et al. (2012). Maternal 3 ' UTRs: from egg to onset of zygotic transcription in Atlantic cod. (external link)
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Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel
et al. (2011). The genome sequence of Atlantic cod reveals a unique immune system. (external link)
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Edvardsen, Rolf; Malde, Ketil; Mittelholzer, Christian
et al. (2011). EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua). (external link)
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Sagstad, Anita; Grotmol, Sindre; Kryvi, Harald
et al. (2011). Identification of vimentin- and elastin-like transcripts specifically expressed in developing notochord of Atlantic salmon (Salmo salar L.). (external link)
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Balzer, Susanne; Malde, Ketil; Jonassen, Inge
(2011). Systematic exploration of error sources in pyrosequencing flowgram data. (external link)
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Malde, Marian Kjellevold; Bugel, S; Kristensen, M.
et al. (2010). Calcium from salmon and cod bone is well absorbed in young healthy men: a double-blinded randomised crossover design. (external link)
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Balzer, Susanne; Malde, Ketil; Lanzén, Anders
et al. (2010). Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. (external link)
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Patel, Sonal; Malde, Kjetil; Lanzén, Anders
et al. (2009). Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation. (external link)
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Malde, Ketil
(2008). The effect of sequence quality on sequence alignment. (external link)
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Malde, Ketil; Jonassen, Inge
(2008). Repeats and EST analysis for new organisms. (external link)
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Malde, Ketil; Schneeberger, Korbinian; Coward, Eivind
et al. (2006). RBR: library-less repeat detection for ESTs. (external link)
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Malde, Ketil; Giegerich, Robert
(2006). Calculating PSSM probabilities with lazy dynamic programming. (external link)
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Malde, Ketil; Coward, Eivind; Jonassen, Inge
(2005). A graph based algorithm for generating EST consensus sequences. (external link)
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Schneeberger, Korbinian; Malde, Ketil; Coward, Eivind
et al. (2005). Masking repeats while clustering ESTs. (external link)
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Malde, Ketil; Coward, Eivind; Jonassen, Inge
(2003). Fast Sequence Clustering Using a Suffix Array Algorithm. (external link)
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Malde, Ketil; Coward, Eivind; Jonasen, Inge
(2003). A Fast Algorithm for EST Clustering using Suffix Arrays. (external link)
Academic lecture
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Pala, Ahmet; Handegaard, Nils Olav; Alendal, Guttorm
et al. (2024). Deep Learning for Fisheries Acoustics . (external link)
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Handegard, Nils Olav; Bildøy, Leif; Brautaset, Olav
et al. (2024). Fisheries acoustics and deep learning. (external link)
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Sørdalen, Tonje Knutsen; Malde, Ketil; Halvorsen, Kim Aleksander Tallaksen
(2024). Decoding female mimicry in a fish using deep learning. (external link)
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Handegard, Nils Olav; Bildøy, Leif; Brautaset, Olav
et al. (2024). Analysing large amounts of echosounder data using cloud based data access combined with deep learning models
. (external link)
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Eliassen, Inge Kristian; Malde, Ketil
(2024). Processing of large datasets using python and Korona
. (external link)
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Pala, Ahmet; Oleynik, Anna; Malde, Ketil
et al. (2024). Unraveling Acoustic Signal Patterns in Fisheries Through DINO-Based Self-Supervised Learning. (external link)
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Pala, Ahmet; Oleynik, Anna; Malde, Ketil
et al. (2024). Annotation-Free Feature Learning for Improved Acoustic Target Classification. (external link)
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Malde, Ketil; Parviainen, Pekka; Kim, Hyeongji
(2023). Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary. (external link)
-
Handegard, Nils Olav; Bildøy, Leif; Brautaset, Olav
et al. (2023). A story about data extraction and deep learning applied to fishery acoustic data. (external link)
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Holager, Knut T. A.; Handegard, Nils Olav; Malde, Ketil
(2022). Selecting maximally informative frequency subsets for acoustic surveys. (external link)
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Politikos, Dimitris V.; Sykiniotis, Nikolaos; Petasis, Georgios
et al. (2022). An online otolith age reader using deep neural networks: Perspectives and challenges. (external link)
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Allken, Vaneeda; Sørdalen, Tonje Knutsen; Beyan, Cigdem
et al. (2022). A deep learning approach for individual re-identification (re-ID) of fish in the wild. (external link)
-
Moen, Endre; Vabø, Rune; Denechaud, Come
et al. (2022). Exploring imaging protocols and neural network architectures for automated otolith analysis. (external link)
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Allken, Vaneeda; Klevjer, Thor Aleksander; Løvall, Kristoffer
et al. (2022). Using deep learning models to count and identify fish species from in-trawl images. (external link)
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Rosen, Shale Pettit; Garcia Seoane, Eva; Underwood, Melanie
et al. (2021). Combined trawl-mounted optic and acoustic methods to study the mesopelagic ecosystem. (external link)
-
Salberg, Arnt Børre; Eikvil, Line; Malde, Ketil
et al. (2019). The COGMAR project. (external link)
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Handegard, Nils Olav; Allken, Vaneeda; Malde, Ketil
(2018). Drowning in data: Can deep learning approaches be the solution?. (external link)
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Malde, Ketil
(2013). Identifying diagnostic SNPs in the presence of sequencing errors. (external link)
-
Malde, Ketil
(2013). Can Software Transactional Memory make concurrent programs simple and safe?. (external link)
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Edvardsen, Rolf; Mæhle, Stig; Furmanek, Tomasz
et al. (2012). Transcriptomic analysis of the salmon louse. (external link)
-
Skern-Mauritzen, Rasmus; Malde, Ketil; Furmanek, Tomasz
et al. (2012). The Salmon Louse Genome Project. (external link)
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Wargelius, Anna ; Edvardsen, Rolf; Haugen, Trine
et al. (2012). Attempts to induce sterility in Atlantic salmon by morfolino and zink finger techniques. (external link)
-
Kleppe, Lene; Edvardsen, Rolf; Kuhl, Heiner
et al. (2011). Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod. (external link)
-
Malde, Ketil; O'Sullivan, Bryan
(2009). Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell. (external link)
-
Malde, Ketil; Coward, Eivind; Jonasen, Inge
(2002). A Fast Algorithm for EST Clustering using Suffix Trees. (external link)
Poster
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Kim, Hyeongji; Choi, Changkyu; Kampffmeyer, Michael Christian
et al. (2024). ProxyDR: Deep Hyperspherical Metric Learning with Distance Ratio-Based Formulation. (external link)
-
Kim, Hyeongji; Choi, Changkyu; Kampffmeyer, Michael Christian
et al. (2024). ProxyDR: Deep Hyperspherical Metric Learning with Distance Ratio-Based Formulation. (external link)
-
Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil
(2023). Escaping the black box: explicit annotation of otolith growth rings with deep learning. (external link)
-
Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil
(2023). Annotating Otoliths with a Deep Generative Model. (external link)
-
Vabø, Rune; Moen, Endre; Kim, Hyeongji
et al. (2020). Automatic interpretation of salmon scales using deep learning. (external link)
-
Godiksen, Jane Aanestad; Geffen, Audrey J.; Folkvord, Arild
et al. (2019). Otoliths as life history indicators. (external link)
-
Handegard, Nils Olav; Malde, Ketil; Tenningen, Maria
et al. (2017). Automatisk klassifisering av svømming i not
. (external link)
-
Malde, Ketil
(2013). A data storage strategy for generic, heterogenous scientific data. (external link)
Doctoral dissertation
Masters thesis
Lecture
Report
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Handegard, Nils Olav; Andersen, Lars Nonboe; Brautaset, Olav
et al. (2021). Fisheries acoustics and Acoustic Target Classification - Report from the COGMAR/CRIMAC workshop on machine learning methods in fisheries acoustics. (external link)
-
Guidi, Lionel; Fernandez Guerra, A.; Canchaya, C
et al. (2020). Big Data in Marine Science. (external link)
-
Malde, Ketil
(2019). WORKING GROUP ON MACHINE LEARNING
IN MARINE SCIENCE (WGMLEARN). (external link)
-
Malde, Ketil; Handegard, Nils Olav; Hammersland, Hege
et al. (2019). Machine learning to improve marine science for the sustainability of living ocean resources: Report from the 2019 Norway - U.S. Workshop. (external link)
-
Malde, Ketil; Syed, Shaheen
(2018). Report of the Workshop on Machine Learning in Marine Science (WKMLEARN). (external link)
Article in business/trade/industry journal
Short communication
See a complete overview of publications in Cristin.