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Hans Julius Skaug's picture

Hans Julius Skaug

Professor
Department of Mathematics
Google Scholar
  • E-mailhans.skaug@uib.no
  • Phone+47 55 58 48 61+47 469 45 448
  • Visitor Address
    Realfagbygget, Allegaten 41, 4 etg. sør.
    Bergen
    Room 
    4A17d
  • Postal Address
    Postboks 7803
    5020 Bergen

Biostatistics

I am interested in applications of statistics and probability to biology, especially to marine ecology. I have developed methods for line transect surveys and CKMR (close-kin mark recapture) methods in particular. Key reference: Bravington, MV, Skaug, HJ, Anderson, EC (2016). Close-kin Mark-Recapture. Statistical Science.

Computational statistics

My opinion for a long time has been that Statisticians should have Automatic Differentiation (AD) in their toolbox. My conjecture has been that a combination of AD and the Laplace approximation is a powerful platform for fitting models with continuous latent variables. Software projects in which this idea is implemented are:

Artificial intelligence (AI)

Witnessing the recent breakthroughs in the field, my research interests have turned towards AI. Techniques such as variational autoencoders and diffusion models are probabilistic in nature, and Backpropagation in Deep Learning is the same computational technique as AD, which I have been working with for 20 years.

Editorial services

co-Editor in chief of Scandinavian Journal of Statistics (2018–2021)

Teaching at UiB (last 5 years)

 

Short courses / workshops (in the past)

  • CKMR (Close-kin mark recapture) course (co-thought) Dalhousie University, Halifax, July 2019.
  • TMB (Template Model Builder) course (co-thought) at IMR Bergen, June 2019.
  • Modelling in TMB (Template Model Builder). Course (co-thought) at IMR Bergen,  June 2018.
  • An introduction to fish stock assessment in TMB (Template Model Builder). Course given Oct. 2017 in La Jolla

 

    Google scholar profile 

    From CRIStin (Current research information system in Norway):

    • Show author(s) (2023). A TMB Approach to Study Spatial Variation in Weather-Generated Claims in Insurance. SN Operations Research Forum.
    • Show author(s) (2022). The heritability of BMI varies across the range of BMI—a heritability curve analysis in a twin cohort. International Journal of Obesity. 1786-1791.
    • Show author(s) (2022). Mixed Frequency Data in a (S,s) Pricing Model.
    • Show author(s) (2022). Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population. Evolutionary Applications. 1-13.
    • Show author(s) (2021). Variation in use of Caesarean section in Norway: An application of spatio-temporal Gaussian random fields. Scandinavian Journal of Public Health. 8 pages.
    • Show author(s) (2021). The Sibling Distribution for Multivariate Life Time Data. Sankhya B, The Indian Journal of Statistics. 340-363.
    • Show author(s) (2021). Report of the NAMMCO-ICES Workshop on Seal Modelling (WKSEALS 2020). NAMMCO scientific publications.
    • Show author(s) (2021). Measurement error model for the Norwegian common minke whale (Balaenoptera acutorostrata acutorostrata) surveys 2008-2013. Journal of Cetacean Research and Management. 16 pages.
    • Show author(s) (2021). Epistemic uncertainty quantification in deep learning classification by the Delta method. Neural Networks. 164-176.
    • Show author(s) (2021). Considering sampling bias in close-kin mark–recapture abundance estimates of Atlantic salmon. Ecology and Evolution.
    • Show author(s) (2021). Consideration of measurement errors for the Norwegian common minke whale (Balaenoptera acutorostrata acutorostrata) surveys. Journal of Cetacean Research and Management. 1-16.
    • Show author(s) (2020). Heritability curves: A local measure of heritability in family models. Statistics in Medicine. 1357-1382.
    • Show author(s) (2020). Experimental design for parameter estimation in steady-state linear models of metabolic networks. Mathematical Biosciences.
    • Show author(s) (2020). Estimation and identifiability of kinetic parameters in dynamical models of biochemical reaction networks.
    • Show author(s) (2020). A comparison of Monte Carlo sampling methods for metabolic network models. PLOS ONE. 1-24.
    • Show author(s) (2019). dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA) – HIGHLIGHTS SO FAR.
    • Show author(s) (2019). dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA) – HIGHLIGHTS SO FAR.
    • Show author(s) (2019). Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance. Methods in Ecology and Evolution. 1445-1453.
    • Show author(s) (2019). Stochastic data assimilation of observations with a detection limit.
    • Show author(s) (2019). Integration by differentiation; almost a free lunch.
    • Show author(s) (2019). Efficient Computation of Hessian Matrices in TensorFlow . arXiv.org.
    • Show author(s) (2019). Editorial. Scandinavian Journal of Statistics. 1-1.
    • Show author(s) (2019). Drivers of the summer-distribution of Northeast Atlantic mackerel (Scomber scombrus) in the Nordic Seas from 2011 to 2017; a Bayesian hierarchical modelling approach. ICES Journal of Marine Science. 530-548.
    • Show author(s) (2019). Contaminant accumulation and biological responses in Atlantic cod (Gadus morhua) caged at a capped waste disposal site in Kollevåg, Western Norway. Marine Environmental Research. 39-51.
    • Show author(s) (2019). Close-Kin Mark-Recapture (CKMR).
    • Show author(s) (2019). Close-Kin Mark-Recapture (CKMR).
    • Show author(s) (2019). Close kin mark recapture in fisheries .
    • Show author(s) (2019). Bayesian flux balance analysis of metabolic pathways.
    • Show author(s) (2019). Bayesian and frequentist computation with application to data from the Medical Birth Registry of Norway.
    • Show author(s) (2018). dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA).
    • Show author(s) (2018). Model Reduction for Tracer Transport and Applications.
    • Show author(s) (2018). Mathematical methods for detection and localization of CO2 leaks.
    • Show author(s) (2018). Machine Learning in CO2 leak detection.
    • Show author(s) (2018). Experimental design for estimation of first order kinetic parameters in steady-state metabolic networks.
    • Show author(s) (2018). Ecotoxicological responses in Atlantic cod (Gadus morhua) after caging at a capped waste disposal site in Kollevåg, Western Norway .
    • Show author(s) (2018). Ecotoxicological responses in Atlantic cod (Gadus morhua) after caging at a capped waste disposal site in Kollevåg, Western Norway .
    • Show author(s) (2018). Combining Models and Machine Learning Techniques to Design Leak Detection Monitoring .
    • Show author(s) (2018). Bayesian flux balance analysis; concepts and computation.
    • Show author(s) (2017). glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. The R Journal. 378-400.
    • Show author(s) (2017). dCod 1.0: decoding the systems toxicology of Atlantic cod (Gadus morhua).
    • Show author(s) (2017). dCod 1.0 decoding the systems toxicology of Atlantic cod.
    • Show author(s) (2017). Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics. 1-11.
    • Show author(s) (2017). The parent-offspring probability when sampling age-structured populations. Theoretical Population Biology. 20-26.
    • Show author(s) (2017). TMB: a flexible framework for developing mixed model software in R.
    • Show author(s) (2017). Structural identifiability of kinetic parameters.
    • Show author(s) (2017). Structural identifiability of kinetic parameters.
    • Show author(s) (2017). PRECISION-CUT LIVER SLICES (PCLS) FOR TOXICOGENOMIC STUDIES IN ATLANTIC COD (Gadus morhua): THE dCOD 1.0 PROJECT.
    • Show author(s) (2017). On the application of improved symplectic integrators in Hamiltonian Monte Carlo. Communications in Statistics - Simulation and Computation. 500-509.
    • Show author(s) (2017). Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway.
    • Show author(s) (2017). Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway.
    • Show author(s) (2017). Mathematical modeling of regulatory interactions in the fatty acid synthesis pathway.
    • Show author(s) (2017). Bayes’ theorem as the fundament to design monitoring programs.
    • Show author(s) (2017). Assessment of machine learning methods as a tool in detecting leakages.
    • Show author(s) (2017). Assessment of Topological Data Analysis and Machine Learning Technologies as Tools for Seep Detection.
    • Show author(s) (2016). Trade-offs between accuracy and interpretability in von Bertalanffy random-effects models of growth. Ecological Applications. 1535-1552.
    • Show author(s) (2016). TMB: Automatic differentiation and laplace approximation. Journal of Statistical Software. 1-21.
    • Show author(s) (2016). Likelihood Estimation of Jump-Diffusions: Extensions from Diffusions to Jump-Diffusions, Implementation with Automatic Differentiation, and Applications.
    • Show author(s) (2016). Close-kin mark-recapture. Statistical Science. 259-274.
    • Show author(s) (2016). Bayes’ theorem as the fundament to design monitoring programs.
    • Show author(s) (2015). The importance of spatial models for estimating the strength of density dependence. Ecology. 1202-1212.
    • Show author(s) (2015). Spatial factor analysis: A new tool for estimating joint species distributions and correlations in species range. Methods in Ecology and Evolution. 627-637.
    • Show author(s) (2015). Panel data model with mixed frequency – an application to producers' pricing behaviour.
    • Show author(s) (2015). Measurement error model for the Norwegian minke whale surveys 2008-2013.
    • Show author(s) (2015). Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Science. 1297-1310.
    • Show author(s) (2015). Fitting state-space models to seal populations with scarce data. ICES Journal of Marine Science. 1462-1469.
    • Show author(s) (2015). Distance sampling with a random scale detection function. Environmental and Ecological Statistics. 725-737.
    • Show author(s) (2015). Data assimilation by use of the iterative ensemble smoother for 2D facies models. SPE Journal. 169-185.
    • Show author(s) (2015). DNA-register for vågehval: en skattekiste for studier av hvalbiologi. Fisken og Havet, Særnummer. 108-109.
    • Show author(s) (2015). Bandwidth selection in pre-smoothed particle filters. Statistics and computing. 16 pages.
    • Show author(s) (2015). Abundance estimates of common minke whales in the Northeast Atlantic base don survey data collected over the period 2008-2013.
    • Show author(s) (2014). Unødvendig med fem fangstområder for vågehval. Forskning.no.
    • Show author(s) (2014). Preliminary abundance estimates of common minke whales in the Northeast Atlantic based on survey data collected over the period 2008-2013.
    • Show author(s) (2014). Next-generation sequencing for molecular ecology: a caveat regarding pooled samples. Molecular Ecology. 502-512.
    • Show author(s) (2014). Maximum likelihood estimation of partially observed diffusion models. Journal of Econometrics. 73-80.
    • Show author(s) (2014). Investigating population genetic structure in a highly mobile marine organism: The minke whale balaenoptera acutorostrata acutorostrata in the north east atlantic. PLOS ONE.
    • Show author(s) (2014). Estimation of production rates with transient well-flow modeling and the auxiliary particle filter. SPE Journal. 172-180.
    • Show author(s) (2014). Determining individual variation in growth and its implication for life-history and population processes using the Empirical Bayes Method. PLoS Computational Biology.
    • Show author(s) (2014). Bandwidth Selection In Pre-Smoothed Particle Filters.
    • Show author(s) (2014). A flexible and automated likelihood based framework for inference in stochastic volatility models. Computational Statistics & Data Analysis. 642-654.
    • Show author(s) (2013). Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution. 501-512.
    • Show author(s) (2013). Markov-modulated nonhomogeneous poisson processes for modeling detections in surveys of marine mammal abundance. Journal of the American Statistical Association. 840-851.
    • Show author(s) (2013). Hybrids between common and Antarctic minke whales are fertile and can back-cross. BMC Genetics. 11 pages.
    • Show author(s) (2013). Estimating genotyping error rates from parent-offspring dyads. Statistics and Probability Letters. 812-819.
    • Show author(s) (2012). The Norwegian minke whale DNA register: a data base monitoring commercial harvest and trade of whale products. Fish and Fisheries. 313-332.
    • Show author(s) (2012). Numerical comparison of Ensemble Kalman Filter and Randomized maximum Likelihood.
    • Show author(s) (2012). Good ethics or political and cultural censoring in science? ICES Journal of Marine Science. 493-497.
    • Show author(s) (2012). Fitting general stochastic volatility models using Laplace accelerated sequential importance sampling. Computational Statistics & Data Analysis. 3105-3119.
    • Show author(s) (2012). Filtering with state space localized Kalman gain. Physica D : Non-linear phenomena. 1123-1135.
    • Show author(s) (2012). Data Assimilation Using the Iterative Ensemble Smoother for 2-D Categorical Models.
    • Show author(s) (2012). Comparing the adaptive Gaussian mixture filter with the ensemble Kalman filter on synthetic reservoir models. Computational Geosciences. 467-482.
    • Show author(s) (2012). Abundance estimation of long-diving animals using line transect methods. Biometrics. 504-513.
    • Show author(s) (2012). AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods and Software. 233-249.
    • Show author(s) (2011). Quantifying Monte Carlo Uncertainty in the Ensemble Kalman Filter. SPE Journal. 172-182.
    • Show author(s) (2011). Genotyping errors in a calibrated DNA register: implications for identification of individuals. BMC Genetics. 10 pages.
    • Show author(s) (2011). Bridging the ensemble Kalman filter and particle filters: the adaptive Gaussian mixture filter. Computational Geosciences. 293-305.
    • Show author(s) (2010). Simulated maximum likelihood estimation of continuous time stochastic volatility models. 25 pages.
    • Show author(s) (2010). Migration of Antarctic Minke Whales to the Arctic. PLOS ONE.
    • Show author(s) (2010). Maximum Simulated Likelihood Methods and Applications. Emerald Group Publishing Limited.
    • Show author(s) (2010). Hva kan et register over vågehvalens DNA fortelle om adferd og biologi? Ottar. 10-15.
    • Show author(s) (2010). Global occurrence trajectories of microfossils: environmental volatility and the rise and fall of individual species. Paleobiology. 224-252.
    • Show author(s) (2010). Estimating genetic architectures from artificial-selection responses: A random-effect framework. Theoretical Population Biology. 119-130.
    • Show author(s) (2010). Detecting dyads of related individuals in large collections of DNA-profiles by controlling the false discovery rate. Molecular Ecology Resources. 693-700.
    • Show author(s) (2010). Asymptotic bias of the hazard probability model under model mis-specification. Journal of Cetacean Research and Management. 249-252.
    • Show author(s) (2010). A method for defining management units based on genetically determined close relatives. ICES Journal of Marine Science. 551-558.
    • Show author(s) (2008). Genetic analyses reveal promiscuous mating in female minke whales, Balaenoptera acutorostrata. Journal of Cetacean Research and Management. 249-251.
    • Show author(s) (2008). Fitting mixed-effects models when data are left truncated. Insurance, Mathematics & Economics. 121-133.
    • Show author(s) (2008). Estimating distributions of correlated individual life-history traits from mark-recapture data.
    • Show author(s) (2008). Building and Fitting Non-Gaussian Latent Variable Models via the Moment-Generating Function. Scandinavian Journal of Statistics. 664-676.
    • Show author(s) (2007). Historical population assessment of Barents Sea harp sea's (Pagophilus groenlandicus). ICES Journal of Marine Science. 1356-1365.
    • Show author(s) (2006). On Curvature and Separability in Unconstrained Optimisation.
    • Show author(s) (2006). Markov modulated Poisson processes for clustered line transect data. Environmental and Ecological Statistics. 199-211.
    • Show author(s) (2006). DNA registers of legally obtained wildlife and derived products as means to identify illegal takes. Conservation Biology. 1284-1293.
    • Show author(s) (2006). Automatic Approximation of the Marginal Likelihood in non-Gaussian Hierarchical Models. Computational Statistics & Data Analysis. 699-709.
    • Show author(s) (2006). An integrated-likelihood method for estimating genetic differentiation between populations. Genetics. 2073-2082.
    • Show author(s) (2005). Genetic tagging of males in North Atlantic minke whales through comparison of mother and fetus DNA-profiles. Journal of Cetacean Research and Management. 113-117.
    • Show author(s) (2005). Genetic tagging of male North Atlantic minke whales through comparison of maternal and foetal DNA-profiles. Journal of Cetacean Research and Management. 113-117.
    • Show author(s) (2005). Disentangling the effects of capture efficiency and population abundance on catch data using random effects models. ICES Journal of Marine Science. 1543-1555.
    • Show author(s) (2004). Abundance of minke whales (Balaenoptera acutorostrata) in the Northeastern Atlantic. Canadian Journal of Fisheries and Aquatic Sciences. 870-886.
    • Show author(s) (2002). Automatic differentiation to facilitate maximum likelihood estimation in nonlinear random effects models. Journal of Computational And Graphical Statistics (JCGS). 458-470.
    • Show author(s) (2001). Allele-sharing methods for estimation of population size. Biometrics. 750-756.
    • Show author(s) (2000). Towards a statistical model for the uncertainty in fisheries data for stock asssessment in the Barents Sea. SAMBA/06/00. SAMBA/06/00. .
    • Show author(s) (1999). Simulated likelihood methods for complex double-platform line transect surveys. Biometrics. 678-687.
    • Show author(s) (1999). Hazard models for line transect surveys with independent observers. Biometrics. 29-36.
    • Show author(s) (1997). Do Minke Whales (Balaenoptera acutorostrara) Exhibit Particular Prey Preferences? Journal of Northwest Atlantic Fishery Science. 91-104.
    • Show author(s) (1997). Abundance of northeastern Atlantic minke whales, estimates for 1989 and 1995. Rep. int. Whal. Commn. 453-483.
    • Show author(s) (1996). Perpendicular distance line transect methods based on integrated spatial hazard probability models. Ukjent.
    • Show author(s) (1996). NAILS-96, System Design and Program Documentation. Ukjent.
    • Show author(s) (1996). NAILS-96 Specification document.
    • Show author(s) (1996). Diet and food avaliability for Northeastern Atlantic minke whales, Balaenoptera Acutorostrata. Reports of the International Whaling Commission. 371-382.
    • Show author(s) (1996). Abundance of northeastern Atlantic minke whales, estimates for 1989 and 1995. Ukjent.
    • Show author(s) (1995). Methods for simulation of stochastic vector-fields in NSPACE. STAT/18/95. STAT/18/95. .
    • Show author(s) (1994). Nonparametric tests of serial indepence.
    • Show author(s) (1994). Nonparametric functional estimation with application to hypothesis testing.
    • Show author(s) (1994). Ikkeparametriske tester for seriell uavhengighet.
    • Show author(s) (1993). The limit distribution of the Hoeffding statistic for test of serial independence. Report No.22 Jan. 1993. .
    • Show author(s) (1993). A nonparametric test of serial independence based on the empirical distribution function. Biometrika. 591-602.
    • Show author(s) (1991). Edgeworth utvikling og bootstrapping i tidsrekke analyse.

    More information in national current research information system (CRIStin)

    Fields of competence 
    Artificial Intelligence
    Biostatistics
    Machine Learning
    Statistics