Fagområder:

• bioinformatikk
• funksjonelle språk
• maskinlæring/deep learning

Jeg har også en stilling som forsker ved Havforskningsinstituttet i gruppen for populasjonsgenetikk.

Vitenskapelig foredrag

• Pala, Ahmet; Handegaard, Nils Olav; Alendal, Guttorm et al. (2024). Deep Learning for Fisheries Acoustics . (ekstern lenke)
• Pala, Ahmet; Oleynik, Anna; Malde, Ketil et al. (2024). Annotation-Free Feature Learning for Improved Acoustic Target Classification. (ekstern lenke)
• Pala, Ahmet; Oleynik, Anna; Malde, Ketil et al. (2024). Unraveling Acoustic Signal Patterns in Fisheries Through DINO-Based Self-Supervised Learning. (ekstern lenke)
• Malde, Ketil; Parviainen, Pekka; Kim, Hyeongji (2023). Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary. (ekstern lenke)
• Handegard, Nils Olav; Bildøy, Leif; Brautaset, Olav et al. (2023). A story about data extraction and deep learning applied to fishery acoustic data. (ekstern lenke)
• 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. (ekstern lenke)
• Holager, Knut T. A.; Handegard, Nils Olav; Malde, Ketil (2022). Selecting maximally informative frequency subsets for acoustic surveys. (ekstern lenke)
• Moen, Endre; Vabø, Rune; Denechaud, Come et al. (2022). Exploring imaging protocols and neural network architectures for automated otolith analysis. (ekstern lenke)
• Politikos, Dimitris V.; Sykiniotis, Nikolaos; Petasis, Georgios et al. (2022). An online otolith age reader using deep neural networks: Perspectives and challenges. (ekstern lenke)
• Allken, Vaneeda; Klevjer, Thor Aleksander; Løvall, Kristoffer et al. (2022). Using deep learning models to count and identify fish species from in-trawl images. (ekstern lenke)
• Rosen, Shale Pettit; Garcia Seoane, Eva; Underwood, Melanie et al. (2021). Combined trawl-mounted optic and acoustic methods to study the mesopelagic ecosystem. (ekstern lenke)
• Salberg, Arnt Børre; Eikvil, Line; Malde, Ketil et al. (2019). The COGMAR project. (ekstern lenke)
• Handegard, Nils Olav; Allken, Vaneeda; Malde, Ketil (2018). Drowning in data: Can deep learning approaches be the solution?. (ekstern lenke)
• Malde, Ketil (2013). Identifying diagnostic SNPs in the presence of sequencing errors. (ekstern lenke)
• Malde, Ketil (2013). Can Software Transactional Memory make concurrent programs simple and safe?. (ekstern lenke)
• Edvardsen, Rolf; Mæhle, Stig; Furmanek, Tomasz et al. (2012). Transcriptomic analysis of the salmon louse. (ekstern lenke)
• Skern-Mauritzen, Rasmus; Malde, Ketil; Furmanek, Tomasz et al. (2012). The Salmon Louse Genome Project. (ekstern lenke)
• Wargelius, Anna ; Edvardsen, Rolf; Haugen, Trine et al. (2012). Attempts to induce sterility in Atlantic salmon by morfolino and zink finger techniques. (ekstern lenke)
• Kleppe, Lene; Edvardsen, Rolf; Kuhl, Heiner et al. (2011). Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod. (ekstern lenke)
• Malde, Ketil; O'Sullivan, Bryan (2009). Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell. (ekstern lenke)
• Malde, Ketil; Coward, Eivind; Jonasen, Inge (2002). A Fast Algorithm for EST Clustering using Suffix Trees. (ekstern lenke)

Vitenskapelig artikkel

• Canovi, Noemi; Ellis, Benjamin A.; Sørdalen, Tonje Knutsen et al. (2024). Trajectory-based fish event classification through pre-training with diffusion models. (ekstern lenke)
• Kim, Hyeongji; Choi, Changkyu; Kampffmeyer, Michael Christian et al. (2024). ProxyDR: Deep Hyperspherical Metric Learning with Distance Ratio-Based Formulation. (ekstern lenke)
• Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil (2023). Annotating otoliths with a deep generative model. (ekstern lenke)
• Moen, Endre; Vabø, Rune; Smolinski, Szymon et al. (2023). Age interpretation of cod otoliths using deep learning. (ekstern lenke)
• Kim, Hyeongji; Parviainen, Pekka; Malde, Ketil (2023). Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary. (ekstern lenke)
• Olsen, Ørjan Langøy; Sørdalen, Tonje Knutsen; Goodwin, Morten et al. (2023). A contrastive learning approach for individual re-identification in a wild fish population. (ekstern lenke)
• Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan et al. (2023). Machine learning in marine ecology: an overview of techniques and applications. (ekstern lenke)
• Wyngaard, Grace; Skern-Mauritzen, Rasmus; Malde, Ketil et al. (2022). The salmon louse genome may be much larger than sequencing suggests. (ekstern lenke)
• 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. (ekstern lenke)
• Skern-Mauritzen, Rasmus; Malde, Ketil; Eichner, Christiane et al. (2021). The salmon louse genome: Copepod features and parasitic adaptations. (ekstern lenke)
• Vabø, Rune; Moen, Endre; Smolinski, Szymon et al. (2021). Automatic interpretation of salmon scales using deep learning. (ekstern lenke)
• 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. (ekstern lenke)
• Allken, Vaneeda; Rosen, Shale Pettit; Handegard, Nils Olav et al. (2021). A real-world dataset and data simulation algorithm for automated fish species identification. (ekstern lenke)
• Brautaset, Olav; Waldeland, Anders Ueland; Johnsen, Espen et al. (2020). Acoustic classification in multifrequency echosounder data using deep convolutional neural networks. (ekstern lenke)
• Jansson, Eeva; Besnier, Francois; Malde, Ketil et al. (2020). Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. (ekstern lenke)
• Malde, Ketil; Handegard, Nils Olav; Eikvil, Line et al. (2020). Machine intelligence and the data-driven future of marine science. (ekstern lenke)
• Dalvin, Sussie; Skaftnesmo, Kai Ove; Malde, Ketil et al. (2020). Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis. . (ekstern lenke)
• Myers, Savannah Carolyn; Thorsen, Anders; Smolinski, Szymon et al. (2019). An efficient protocol and data set for automated otolith image analysis. (ekstern lenke)
• 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. (ekstern lenke)
• 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. (ekstern lenke)
• 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. (ekstern lenke)
• Moen, Endre; Handegard, Nils Olav; Allken, Vaneeda et al. (2018). Automatic interpretation of otoliths using deep learning. (ekstern lenke)
• Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale et al. (2018). Fish species identification using a convolutional neural network trained on synthetic data. (ekstern lenke)
• 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. (ekstern lenke)
• 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. (ekstern lenke)
• Malde, Ketil (2014). Simulating a population genomics data set using FlowSim. (ekstern lenke)
• Edvardsen, Rolf; Dalvin, Sussie Trine; Furmanek, Tomasz et al. (2014). Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues. (ekstern lenke)
• 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. (ekstern lenke)
• Malde, Ketil (2014). Estimating the information value of polymorphic sites using pooled sequences. (ekstern lenke)
• Skern-Mauritzen, Rasmus; Malde, Ketil; Besnier, Francois et al. (2013). How does sequence variability affect de novo assembly quality?. (ekstern lenke)
• Balzer, Susanne; Malde, Ketil; Grohme, Markus A. et al. (2013). Filtering duplicate reads from 454 pyrosequencing data. (ekstern lenke)
• Malde, Ketil; Furmanek, Tomasz (2013). Increasing Sequence Search Sensitivity with Transitive Alignments. (ekstern lenke)
• Kleppe, Lene; Edvardsen, Rolf; Kuhl, H et al. (2012). Maternal 3 ' UTRs: from egg to onset of zygotic transcription in Atlantic cod. (ekstern lenke)
• 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.). (ekstern lenke)
• 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). (ekstern lenke)
• Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel et al. (2011). The genome sequence of Atlantic cod reveals a unique immune system. (ekstern lenke)
• Balzer, Susanne; Malde, Ketil; Jonassen, Inge (2011). Systematic exploration of error sources in pyrosequencing flowgram data. (ekstern lenke)
• 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. (ekstern lenke)
• Balzer, Susanne; Malde, Ketil; Lanzén, Anders et al. (2010). Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. (ekstern lenke)
• 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. (ekstern lenke)
• Malde, Ketil (2008). The effect of sequence quality on sequence alignment. (ekstern lenke)
• Malde, Ketil; Jonassen, Inge (2008). Repeats and EST analysis for new organisms. (ekstern lenke)
• Malde, Ketil; Schneeberger, Korbinian; Coward, Eivind et al. (2006). RBR: library-less repeat detection for ESTs. (ekstern lenke)
• Malde, Ketil; Giegerich, Robert (2006). Calculating PSSM probabilities with lazy dynamic programming. (ekstern lenke)
• Schneeberger, Korbinian; Malde, Ketil; Coward, Eivind et al. (2005). Masking repeats while clustering ESTs. (ekstern lenke)
• Malde, Ketil; Coward, Eivind; Jonassen, Inge (2005). A graph based algorithm for generating EST consensus sequences. (ekstern lenke)
• Malde, Ketil; Coward, Eivind; Jonassen, Inge (2003). Fast Sequence Clustering Using a Suffix Array Algorithm. (ekstern lenke)
• Malde, Ketil; Coward, Eivind; Jonasen, Inge (2003). A Fast Algorithm for EST Clustering using Suffix Arrays. (ekstern lenke)

Poster

• Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil (2023). Annotating Otoliths with a Deep Generative Model. (ekstern lenke)
• Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil (2023). Escaping the black box: explicit annotation of otolith growth rings with deep learning. (ekstern lenke)
• Vabø, Rune; Moen, Endre; Kim, Hyeongji et al. (2020). Automatic interpretation of salmon scales using deep learning. (ekstern lenke)
• Godiksen, Jane Aanestad; Geffen, Audrey J.; Folkvord, Arild et al. (2019). Otoliths as life history indicators. (ekstern lenke)
• Handegard, Nils Olav; Malde, Ketil; Tenningen, Maria et al. (2017). Automatisk klassifisering av svømming i not . (ekstern lenke)
• Malde, Ketil (2013). A data storage strategy for generic, heterogenous scientific data. (ekstern lenke)

Doktorgradsavhandling

• Kim, Hyeongji; Malde, Ketil; Parviainen, Pekka (2023). On the Significance of Distance in Machine Learning. (ekstern lenke)
• Malde, Ketil (2005). Algorithms for the Analysis of Expressed Sequence Tags. (ekstern lenke)

Mastergradsoppgave

• Liessem, Peter Løkhammer; Malde, Ketil; Allken, Vaneeda (2023). Object Tracking Approach for Catch Estimation on Trawl Surveys. (ekstern lenke)
• Malde, Ketil; Handegard, Nils Olav; Holager, Knut T. A. (2022). Selecting Maximally Informative Frequency Subsets for Acoustic Surveys. (ekstern lenke)

Faglig foredrag

• Malde, Ketil (2022). Artificial Intelligence methods for fisheries management. (ekstern lenke)
• Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale et al. (2019). Using a CNN trained on synthetic data for fish species identification. (ekstern lenke)
• Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale et al. (2019). Using a CNN trained on synthetic data for fish species identification. (ekstern lenke)
• Malde, Ketil (2016). Big Data og Big Analysis - hvordan drikke fra brannslangen. (ekstern lenke)
• Malde, Ketil (2015). Insitute of Marine Research - a research and advisory institute. (ekstern lenke)

Rapport

• 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. (ekstern lenke)
• Guidi, Lionel; Fernandez Guerra, A.; Canchaya, C et al. (2020). Big Data in Marine Science. (ekstern lenke)
• 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. (ekstern lenke)
• Malde, Ketil (2019). WORKING GROUP ON MACHINE LEARNING IN MARINE SCIENCE (WGMLEARN). (ekstern lenke)
• Malde, Ketil; Syed, Shaheen (2018). Report of the Workshop on Machine Learning in Marine Science (WKMLEARN). (ekstern lenke)

Fagartikkel

• Handegard, Nils Olav; Eikvil, Line; Jenssen, Robert et al. (2021). Machine Learning + Marine Science: Critical Role of Partnerships in Norway. (ekstern lenke)

Short communication

• Malde, Ketil (2011). Flower: extracting information from pyrosequencing data. (ekstern lenke)

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