- E-mailketil.malde@uib.no
- Visitor AddressHIB - Thormøhlens gate 555006 Bergen
- Postal AddressPostboks 78035020 Bergen
Academic article
- (2023). Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary. Proceedings of the Northern Lights Deep Learning Workshop. 8 pages.
- (2023). Machine learning in marine ecology: an overview of techniques and applications. ICES Journal of Marine Science. 1829-1853.
- (2023). Annotating otoliths with a deep generative model. ICES Journal of Marine Science. 55-65.
- (2023). Age interpretation of cod otoliths using deep learning. Ecological Informatics. 11 pages.
- (2023). A contrastive learning approach for individual re-identification in a wild fish population. Proceedings of the Northern Lights Deep Learning Workshop. 8 pages.
- (2022). The salmon louse genome may be much larger than sequencing suggests. Scientific Reports. 1-14.
- (2022). DeepOtolith v1.0: An Open-Source AI Platform for Automating Fish Age Reading from Otolith or Scale Images. Fishes. 11 pages.
- (2021). The salmon louse genome: Copepod features and parasitic adaptations. Genomics. 3666-3680.
- (2021). Automatic interpretation of salmon scales using deep learning. Ecological Informatics. 10 pages.
- (2021). A real-world dataset and data simulation algorithm for automated fish species identification. Geoscience Data Journal.
- (2021). A deep learning-based method to identify and count pelagic and mesopelagic fishes from trawl camera images. ICES Journal of Marine Science. 3780-3792.
- (2020). Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis. . Marine Genomics. 4 pages.
- (2020). Machine intelligence and the data-driven future of marine science. ICES Journal of Marine Science. 12 pages.
- (2020). Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genetics. 1-15.
- (2020). Acoustic classification in multifrequency echosounder data using deep convolutional neural networks. ICES Journal of Marine Science. 1391-1400.
- (2019). Levels and temporal trends of persistent organic pollutants (POPs) in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) from the southern Barents Sea. Environmental Research. 89-97.
- (2019). An efficient protocol and data set for automated otolith image analysis. Geoscience Data Journal. 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. ICES Journal of Marine Science. 2033-2044.
- (2018). Judging a salmon by its spots: Environmental variation is the primary determinant of spot patterns in Salmo salar. BMC Ecology. 1-13.
- (2018). Fish species identification using a convolutional neural network trained on synthetic data. ICES Journal of Marine Science. 342-349.
- (2018). Automatic interpretation of otoliths using deep learning. PLOS ONE. 1-14.
- (2017). Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics. 1-11.
- (2015). Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction. BMC Genomics. 22 pages.
- (2014). Simulating a population genomics data set using FlowSim. BMC Research Notes.
- (2014). Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis. BMC Genomics. 18 pages.
- (2014). Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues. Marine Genomics. 39-44.
- (2014). Estimating the information value of polymorphic sites using pooled sequences. BMC Genomics. 11 pages.
- (2013). Increasing Sequence Search Sensitivity with Transitive Alignments. PLOS ONE. 7 pages.
- (2013). How does sequence variability affect de novo assembly quality? Journal of Natural History. 901-910.
- (2013). Filtering duplicate reads from 454 pyrosequencing data. Bioinformatics. 830-836.
- (2012). Maternal 3 ' UTRs: from egg to onset of zygotic transcription in Atlantic cod. BMC Genomics. 14 pages.
- (2011). The genome sequence of Atlantic cod reveals a unique immune system. Nature. 207-210.
- (2011). Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics. I304-I309.
- (2011). Identification of vimentin- and elastin-like transcripts specifically expressed in developing notochord of Atlantic salmon (Salmo salar L.). Cell and Tissue Research. 191-202.
- (2011). EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua). Comparative Biochemistry and Physiology - Part D:Genomics and Proteomics. 23-30.
- (2010). Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics. i420-i425.
- (2010). Calcium from salmon and cod bone is well absorbed in young healthy men: a double-blinded randomised crossover design. Nutrition & Metabolism. 9 pages.
- (2009). Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation. Fish and Shellfish Immunology. 729-738.
- (2008). The effect of sequence quality on sequence alignment. Bioinformatics. 897-900.
- (2008). Repeats and EST analysis for new organisms. BMC Genomics. 7 pages.
- (2006). RBR: library-less repeat detection for ESTs. Bioinformatics. 2232-2236.
- (2006). Calculating PSSM probabilities with lazy dynamic programming. Journal of functional programming. 75-81.
- (2005). Masking repeats while clustering ESTs. Nucleic Acids Research (NAR). 2176-2180.
- (2005). A graph based algorithm for generating EST consensus sequences. Bioinformatics. 1371-1375.
- (2003). Fast Sequence Clustering Using a Suffix Array Algorithm. Bioinformatics. 1221-1226.
- (2003). A Fast Algorithm for EST Clustering using Suffix Arrays. Bioinformatics.
Report
- (2021). Fisheries acoustics and Acoustic Target Classification - Report from the COGMAR/CRIMAC workshop on machine learning methods in fisheries acoustics. 2021 - 25. 2021 - 25. .
- (2020). Big Data in Marine Science. 6. 6. .
- (2019). WORKING GROUP ON MACHINE LEARNING IN MARINE SCIENCE (WGMLEARN). .
- (2019). Machine learning to improve marine science for the sustainability of living ocean resources: Report from the 2019 Norway - U.S. Workshop. .
- (2018). Report of the Workshop on Machine Learning in Marine Science (WKMLEARN). .
Lecture
- (2022). Artificial Intelligence methods for fisheries management.
- (2019). Using a CNN trained on synthetic data for fish species identification.
- (2019). Using a CNN trained on synthetic data for fish species identification.
- (2016). Big Data og Big Analysis - hvordan drikke fra brannslangen.
- (2015). Insitute of Marine Research - a research and advisory institute.
Academic lecture
- (2024). Unraveling Acoustic Signal Patterns in Fisheries Through DINO-Based Self-Supervised Learning.
- (2023). Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary.
- (2023). A story about data extraction and deep learning applied to fishery acoustic data.
- (2022). Using deep learning models to count and identify fish species from in-trawl images.
- (2022). Selecting maximally informative frequency subsets for acoustic surveys.
- (2022). Exploring imaging protocols and neural network architectures for automated otolith analysis.
- (2022). An online otolith age reader using deep neural networks: Perspectives and challenges.
- (2022). A deep learning approach for individual re-identification (re-ID) of fish in the wild.
- (2021). Combined trawl-mounted optic and acoustic methods to study the mesopelagic ecosystem.
- (2019). The COGMAR project.
- (2018). Drowning in data: Can deep learning approaches be the solution?
- (2013). Identifying diagnostic SNPs in the presence of sequencing errors.
- (2013). Can Software Transactional Memory make concurrent programs simple and safe?
- (2012). Transcriptomic analysis of the salmon louse.
- (2012). The Salmon Louse Genome Project.
- (2012). Attempts to induce sterility in Atlantic salmon by morfolino and zink finger techniques.
- (2011). Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod.
- (2009). Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell.
- (2002). A Fast Algorithm for EST Clustering using Suffix Trees.
Short communication
- (2011). Flower: extracting information from pyrosequencing data. Bioinformatics. 1041-1042.
Masters thesis
- (2023). Object Tracking Approach for Catch Estimation on Trawl Surveys.
- (2022). Selecting Maximally Informative Frequency Subsets for Acoustic Surveys.
Doctoral dissertation
- (2023). On the Significance of Distance in Machine Learning.
- (2005). Algorithms for the Analysis of Expressed Sequence Tags.
Poster
- (2023). Escaping the black box: explicit annotation of otolith growth rings with deep learning.
- (2023). Annotating Otoliths with a Deep Generative Model.
- (2020). Automatic interpretation of salmon scales using deep learning.
- (2019). Otoliths as life history indicators.
- (2017). Automatisk klassifisering av svømming i not .
- (2013). A data storage strategy for generic, heterogenous scientific data.
Article in business/trade/industry journal
- (2021). Machine Learning + Marine Science: Critical Role of Partnerships in Norway. Journal of Ocean Technology. 1-9.
More information in national current research information system (CRIStin)
Fields of competence