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Corander, J., Remes, U., Holopainen, I. & Koski, T. (2026). Likelihood-free Inference with Jensen–Shannon Divergence for Simulator-based Models with Categorical Output. Sankhya A
Open this publication in new window or tab >>Likelihood-free Inference with Jensen–Shannon Divergence for Simulator-based Models with Categorical Output
2026 (English)In: Sankhya A, ISSN 0976-836XArticle in journal (Refereed) Epub ahead of print
Abstract [en]

Likelihood-free inference for simulator-based statistical models has recently attracted an interest, both in the machine learning and statistics. The primary focus of has been to approximate the posterior distribution of model parameters, either by various types of Monte Carlo sampling algorithms or deep neural network -based surrogate models. Frequentist inference for simulator-based models has been given much less attention to date, despite that it would be particularly amenable to applications, where implicit asymptotic approximation of the likelihood is expected to be accurate and can leverage computationally efficient strategies. Here we derive a set of results to enable estimation, hypothesis testing and construction of confidence intervals for model parameters using asymptotic properties of the Jensen–Shannon divergence. Such asymptotic approximation offers a rapid alternative to more computation-intensive approaches and can be attractive for diverse applications of simulator-based models.

Place, publisher, year, edition, pages
Springer Nature, 2026
Keywords
Bayesian optimization, Bernstein polynomials, Moments of multinomials, Shannon entropy, Sufficiency, Voronovskaya’s asymptotic formula, ϕ-divergence, χ2-divergence
National Category
Probability Theory and Statistics Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-377339 (URN)10.1007/s13171-026-00434-z (DOI)001686803600001 ()2-s2.0-105029739251 (Scopus ID)
Note

QC 20260226

Available from: 2026-02-26 Created: 2026-02-26 Last updated: 2026-02-26Bibliographically approved
Favero, M., Hult, H. & Koski, T. (2021). A dual process for the coupled Wright-Fisher diffusion. Journal of Mathematical Biology, 82(1-2), Article ID 6.
Open this publication in new window or tab >>A dual process for the coupled Wright-Fisher diffusion
2021 (English)In: Journal of Mathematical Biology, ISSN 0303-6812, E-ISSN 1432-1416, Vol. 82, no 1-2, article id 6Article in journal (Refereed) Published
Abstract [en]

The coupled Wright-Fisher diffusion is a multi-dimensional Wright-Fisher diffusion for multi-locus and multi-allelic genetic frequencies, expressed as the strong solution to a system of stochastic differential equations that are coupled in the drift, where the pairwise interaction among loci is modelled by an inter-locus selection. In this paper, an ancestral process, which is dual to the coupled Wright-Fisher diffusion, is derived. The dual process corresponds to the block counting process of coupled ancestral selection graphs, one for each locus. Jumps of the dual process arise from coalescence, mutation, single-branching, which occur at one locus at the time, and double-branching, which occur simultaneously at two loci. The coalescence and mutation rates have the typical structure of the transition rates of the Kingman coalescent process. The single-branching rate not only contains the one-locus selection parameters in a form that generalises the rates of an ancestral selection graph, but it also contains the two-locus selection parameters to include the effect of the pairwise interaction on the single loci. The double-branching rate reflects the particular structure of pairwise selection interactions of the coupled Wright-Fisher diffusion. Moreover, in the special case of two loci, two alleles, with selection and parent independent mutation, the stationary density for the coupled Wright-Fisher diffusion and the transition rates of the dual process are obtained in an explicit form.

Place, publisher, year, edition, pages
Springer Nature, 2021
Keywords
Wright-Fisher diffusion, Markov processes, Duality, Population genetics, Ancestral graphs
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:kth:diva-289942 (URN)10.1007/s00285-021-01555-9 (DOI)000610064300001 ()33483865 (PubMedID)2-s2.0-85099808509 (Scopus ID)
Note

QC 20210211

Available from: 2021-02-11 Created: 2021-02-11 Last updated: 2022-06-25Bibliographically approved
Garcia-Pareja, C., Hult, H. & Koski, T. (2021). EXACT SIMULATION OF COUPLED WRIGHT-FISHER DIFFUSIONS. Advances in Applied Probability, 53(4), 923-950
Open this publication in new window or tab >>EXACT SIMULATION OF COUPLED WRIGHT-FISHER DIFFUSIONS
2021 (English)In: Advances in Applied Probability, ISSN 0001-8678, E-ISSN 1475-6064, Vol. 53, no 4, p. 923-950Article in journal (Refereed) Published
Abstract [en]

In this paper an exact rejection algorithm for simulating paths of the coupled Wright- Fisher diffusion is introduced. The coupled Wright-Fisher diffusion is a family of multivariate Wright-Fisher diffusions that have drifts depending on each other through a coupling term and that find applications in the study of networks of interacting genes. The proposed rejection algorithm uses independent neutral Wright-Fisher diffusions as candidate proposals, which are only needed at a finite number of points. Once a candidate is accepted, the remainder of the path can be recovered by sampling from neutral multivariate Wright-Fisher bridges, for which an exact sampling strategy is also provided. Finally, the algorithm's complexity is derived and its performance demonstrated in a simulation study.

Place, publisher, year, edition, pages
Cambridge University Press (CUP), 2021
Keywords
Exact simulation, rejection algorithm, multivariate diffusions, population genetics, coupled Wright-Fisher model, epistasis
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:kth:diva-306756 (URN)10.1017/apr.2021.9 (DOI)000729990600001 ()2-s2.0-85120611250 (Scopus ID)
Note

QC 20211230

Available from: 2021-12-30 Created: 2021-12-30 Last updated: 2022-12-19Bibliographically approved
Armerin, F., Hallgren, J. & Koski, T. (2019). Forecasting Ranking in Harness Racing Using Probabilities Induced by Expected Positions. Applied Artificial Intelligence, 33(2), 171-189
Open this publication in new window or tab >>Forecasting Ranking in Harness Racing Using Probabilities Induced by Expected Positions
2019 (English)In: Applied Artificial Intelligence, ISSN 0883-9514, E-ISSN 1087-6545, Vol. 33, no 2, p. 171-189Article in journal (Refereed) Published
Abstract [en]

Ranked events are pivotal in many important AI-applications such as Question Answering and recommendations systems. This paper studies ranked events in the setting of harness racing. For each horse there exists a probability distribution over its possible rankings. In the paper, it is shown that a set of expected positions (and more generally, higher moments) for the horses induces this probability distribution. The main contribution of the paper is a method, which extracts this induced probability distribution from a set of expected positions. An algorithm is proposed where the extraction of the induced distribution is given by the estimated expectations. MATLAB code is provided for the methodology. This approach gives freedom to model the horses in many different ways without the restrictions imposed by for instance logistic regression. To illustrate this point, we employ a neural network and ordinary ridge regression. The method is applied to predicting the distribution of the finishing positions for horses in harness racing. It outperforms both multinomial logistic regression and the market odds. The ease of use combined with fine results from the suggested approach constitutes a relevant addition to the increasingly important field of ranked events.

Place, publisher, year, edition, pages
TAYLOR & FRANCIS INC, 2019
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:kth:diva-245167 (URN)10.1080/08839514.2018.1536105 (DOI)000458323800005 ()2-s2.0-85055740089 (Scopus ID)
Note

QC 20190307

Available from: 2019-03-07 Created: 2019-03-07 Last updated: 2022-06-26Bibliographically approved
Koski, T., Jung, B. & Hognas, G. (2018). EXIT TIMES FOR ARMA PROCESSES. Advances in Applied Probability, 50(A), 191-195
Open this publication in new window or tab >>EXIT TIMES FOR ARMA PROCESSES
2018 (English)In: Advances in Applied Probability, ISSN 0001-8678, E-ISSN 1475-6064, Vol. 50, no A, p. 191-195Article in journal (Refereed) Published
Abstract [en]

We study the asymptotic behaviour of the expected exit time from an interval for the ARMA process, when the noise level approaches 0.

Place, publisher, year, edition, pages
APPLIED PROBABILITY TRUST, 2018
Keywords
ARMA model, autoregressive, exit time, first passage time, stationary distribution
National Category
Mathematics
Identifiers
urn:nbn:se:kth:diva-244143 (URN)10.1017/apr.2018.79 (DOI)000457454600017 ()2-s2.0-85060992178 (Scopus ID)
Note

QC 20190218

Available from: 2019-02-18 Created: 2019-02-18 Last updated: 2022-06-26Bibliographically approved
Geilhufe, M., Olsthoorn, B., Ferella, A. D., Koski, T., Kahlhoefer, F., Conrad, J. & Balatsky, A. V. (2018). Materials Informatics for Dark Matter Detection. Physica Status Solidi. Rapid Research Letters, 12(11), Article ID 1800293.
Open this publication in new window or tab >>Materials Informatics for Dark Matter Detection
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2018 (English)In: Physica Status Solidi. Rapid Research Letters, ISSN 1862-6254, E-ISSN 1862-6270, Vol. 12, no 11, article id 1800293Article in journal (Refereed) Published
Abstract [en]

Dark Matter particles are commonly assumed to be weakly interacting massive particles (WIMPs) with a mass in the GeV to TeV range. However, recent interest has shifted toward lighter WIMPs, which are more difficult to probe experimentally. A detection of sub-GeV WIMPs will require the use of small gap materials in sensors. Using recent estimates of the WIMP mass, we identify the relevant target space toward small gap materials (100 to 10 meV). Dirac Materials, a class of small- or zero-gap materials, emerge as natural candidates for sensors for Dark Matter detection. We propose the use of informatics tools to rapidly assay materials band structures to search for small gap semiconductors and semimetals, rather than focusing on a few preselected compounds. As a specific example of the proposed strategy, we use the organic materials database () to identify organic candidates for sensors: the narrow band gap semiconductors BNQ-TTF and DEBTTT with gaps of 40 and 38 meV, and the Dirac-line semimetal (BEDT-TTF)center dot Br which exhibits a tiny gap of approximate to 50 meV when spin-orbit coupling is included. We outline a novel and powerful approach to search for dark matter detection sensor materials by means of a rapid assay of materials using informatics tools.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2018
Keywords
BEDT-TTF, dark matter detection, Dirac materials, materials informatics, organic materials database
National Category
Materials Engineering
Identifiers
urn:nbn:se:kth:diva-239810 (URN)10.1002/pssr.201800293 (DOI)000450130300008 ()2-s2.0-85053502622 (Scopus ID)
Note

QC 20190107

Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2023-02-26Bibliographically approved
Corander, J., Diekmann, O. & Koski, T. (2016). A tribute to Mats Gyllenberg, on the occasion of his 60th birthday. Journal of Mathematical Biology, 72(4), 793-795
Open this publication in new window or tab >>A tribute to Mats Gyllenberg, on the occasion of his 60th birthday
2016 (English)In: Journal of Mathematical Biology, ISSN 0303-6812, E-ISSN 1432-1416, Vol. 72, no 4, p. 793-795Article in journal (Refereed) Published
National Category
Mathematics
Identifiers
urn:nbn:se:kth:diva-183611 (URN)10.1007/s00285-016-0965-9 (DOI)000370269200001 ()26815046 (PubMedID)2-s2.0-84958113835 (Scopus ID)
Note

QC 20160319

Available from: 2016-03-19 Created: 2016-03-18 Last updated: 2022-06-23Bibliographically approved
Nyman, H., Pensar, J., Koski, T. & Corander, J. (2016). Context-specific independence in graphical log-linear models. Computational statistics (Zeitschrift), 31(4), 1493-1512
Open this publication in new window or tab >>Context-specific independence in graphical log-linear models
2016 (English)In: Computational statistics (Zeitschrift), ISSN 0943-4062, E-ISSN 1613-9658, Vol. 31, no 4, p. 1493-1512Article in journal (Refereed) Published
Abstract [en]

Log-linear models are the popular workhorses of analyzing contingency tables. A log-linear parameterization of an interaction model can be more expressive than a direct parameterization based on probabilities, leading to a powerful way of defining restrictions derived from marginal, conditional and context-specific independence. However, parameter estimation is often simpler under a direct parameterization, provided that the model enjoys certain decomposability properties. Here we introduce a cyclical projection algorithm for obtaining maximum likelihood estimates of log-linear parameters under an arbitrary context-specific graphical log-linear model, which needs not satisfy criteria of decomposability. We illustrate that lifting the restriction of decomposability makes the models more expressive, such that additional context-specific independencies embedded in real data can be identified. It is also shown how a context-specific graphical model can correspond to a non-hierarchical log-linear parameterization with a concise interpretation. This observation can pave way to further development of non-hierarchical log-linear models, which have been largely neglected due to their believed lack of interpretability.

Place, publisher, year, edition, pages
Springer, 2016
Keywords
Graphical model, Context-specific interaction model, Log-linear model, Parameter estimation
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:kth:diva-196063 (URN)10.1007/s00180-015-0606-6 (DOI)000385201700013 ()2-s2.0-84990182255 (Scopus ID)
Note

QC 20161117

Available from: 2016-11-17 Created: 2016-11-11 Last updated: 2024-03-18Bibliographically approved
Cui, Y., Sirén, J., Koski, T. & Corander, J. (2016). Simultaneous Predictive Gaussian Classifiers. Journal of Classification, 1-30
Open this publication in new window or tab >>Simultaneous Predictive Gaussian Classifiers
2016 (English)In: Journal of Classification, ISSN 0176-4268, E-ISSN 1432-1343, p. 1-30Article in journal (Refereed) Published
Abstract [en]

Gaussian distribution has for several decades been ubiquitous in the theory and practice of statistical classification. Despite the early proposals motivating the use of predictive inference to design a classifier, this approach has gained relatively little attention apart from certain specific applications, such as speech recognition where its optimality has been widely acknowledged. Here we examine statistical properties of different inductive classification rules under a generic Gaussian model and demonstrate the optimality of considering simultaneous classification of multiple samples under an attractive loss function. It is shown that the simpler independent classification of samples leads asymptotically to the same optimal rule as the simultaneous classifier when the amount of training data increases, if the dimensionality of the feature space is bounded in an appropriate manner. Numerical investigations suggest that the simultaneous predictive classifier can lead to higher classification accuracy than the independent rule in the low-dimensional case, whereas the simultaneous approach suffers more from noise when the dimensionality increases.

Place, publisher, year, edition, pages
Springer-Verlag New York, 2016
Keywords
Bayesian modeling, Discriminant analysis, Inductive learning, Predictive inference, Probabilistic classification
National Category
Probability Theory and Statistics
Identifiers
urn:nbn:se:kth:diva-188231 (URN)10.1007/s00357-016-9197-3 (DOI)000376508200005 ()2-s2.0-84959159530 (Scopus ID)
Note

QC 20160613

Available from: 2016-06-13 Created: 2016-06-09 Last updated: 2024-03-18Bibliographically approved
Koski, T., Sandström, E. & Sandström, U. (2016). Towards field-adjusted production: Estimating research productivity from a zero-truncated distribution. Journal of Informetrics, 10(4), 1143-1152
Open this publication in new window or tab >>Towards field-adjusted production: Estimating research productivity from a zero-truncated distribution
2016 (English)In: Journal of Informetrics, ISSN 1751-1577, E-ISSN 1875-5879, Vol. 10, no 4, p. 1143-1152Article in journal (Refereed) Published
Abstract [en]

Measures of research productivity (e.g. peer reviewed papers per researcher) is a fundamental part of bibliometric studies, but is often restricted by the properties of the data available. This paper addresses that fundamental issue and presents a detailed method for estimation of productivity (peer reviewed papers per researcher) based on data available in bibliographic databases (e.g. Web of Science and Scopus). The method can, for example, be used to estimate average productivity in different fields, and such field reference values can be used to produce field adjusted production values. Being able to produce such field adjusted production values could dramatically increase the relevance of bibliometric rankings and other bibliometric performance indicators. The results indicate that the estimations are reasonably stable given a sufficiently large data set.

Place, publisher, year, edition, pages
Elsevier, 2016
Keywords
Research productivity, Waring distribution, Field adjusted production, Size-dependent indicators
National Category
Information Studies Other Social Sciences
Research subject
Industrial Engineering and Management
Identifiers
urn:nbn:se:kth:diva-197085 (URN)10.1016/j.joi.2016.09.002 (DOI)000389548900019 ()2-s2.0-84992025500 (Scopus ID)
Funder
Riksbankens Jubileumsfond, P12-1302:1
Note

QC 20170109

Available from: 2016-11-29 Created: 2016-11-29 Last updated: 2022-06-27Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1489-8512

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