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  • 1.
    Andersson, Olov
    et al.
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    Sidén, Per
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Dahlin, Johan
    Kotte Consulting AB.
    Doherty, Patrick
    Linköping University, Department of Computer and Information Science, Artificial Intelligence and Integrated Computer Systems. Linköping University, Faculty of Science & Engineering.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences. Stockholm University, Stockholm, Sweden.
    Real-Time Robotic Search using Structural Spatial Point Processes2019Conference paper (Refereed)
  • 2.
    Dahlin, Johan
    et al.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Schön, Thomas Bo
    Department of Information Technology, Uppsala University.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences.
    Approximate inference in state space models with intractable likelihoods using Gaussian process optimisation2014Report (Other academic)
    Abstract [en]

    We propose a novel method for MAP parameter inference in nonlinear state space models with intractable likelihoods. The method is based on a combination of Gaussian process optimisation (GPO), sequential Monte Carlo (SMC) and approximate Bayesian computations (ABC). SMC and ABC are used to approximate the intractable likelihood by using the similarity between simulated realisations from the model and the data obtained from the system. The GPO algorithm is used for the MAP parameter estimation given noisy estimates of the log-likelihood. The proposed parameter inference method is evaluated in three problems using both synthetic and real-world data. The results are promising, indicating that the proposed algorithm converges fast and with reasonable accuracy compared with existing methods.

  • 3.
    Eklund, Anders
    et al.
    Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA, USA.
    Dufort, Paul
    Department of Medical Imaging, University of Toronto, Toronto, ON, Canada.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences.
    LaConte, Stephen
    Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, VA, USA/School of Biomedical Engineering and Sciences, Virginia Tech-Wake Forest University, Blacksburg, VA, USA.
    BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs2014In: Frontiers in Neuroinformatics, ISSN 1662-5196, E-ISSN 1662-5196, Vol. 8, no 24Article in journal (Refereed)
    Abstract [en]

    Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful graphics processing units (GPUs) to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further, dramatic speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github (https://github.com/wanderine/BROCCOLI/).

  • 4.
    Eklund, Anders
    et al.
    Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, USA.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences.
    LaConte, Stephen
    Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, USA; School of Biomedical Engineering & Sciences, Virginia Tech-Wake Forest University, Blacksburg, USA.
    Harnessing graphics processing units for improved neuroimaging statistics2013In: Cognitive, Affective, & Behavioral Neuroscience, ISSN 1530-7026, E-ISSN 1531-135X, Vol. 13, no 3, p. 587-597Article in journal (Refereed)
    Abstract [en]

    Simple models and algorithms based on restrictive assumptions are often used in the field of neuroimaging for studies involving functional magnetic resonance imaging, voxel based morphometry, and diffusion tensor imaging. Nonparametric statistical methods or flexible Bayesian models can be applied rather easily to yield more trustworthy results. The spatial normalization step required for multisubject studies can also be improved by taking advantage of more robust algorithms for image registration. A common drawback of algorithms based on weaker assumptions, however, is the increase in computational complexity. In this short overview, we will therefore present some examples of how inexpensive PC graphics hardware, normally used for demanding computer games, can be used to enable practical use of more realistic models and accurate algorithms, such that the outcome of neuroimaging studies really can be trusted.

  • 5.
    Giordani, Paolo
    et al.
    Sveriges Riksbank, Sweden.
    Jacobson, Tor
    Sveriges Riksbank, Sweden.
    von Schedvin, Erik
    Sveriges Riksbank, Sweden.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences.
    Taking the Twists into Account: Predicting Firm Bankruptcy Risk with Splines of Financial Ratios2014In: Journal of financial and quantitative analysis, ISSN 0022-1090, E-ISSN 1756-6916, Vol. 49, no 4, p. 1071-1099Article in journal (Refereed)
    Abstract [en]

    We demonstrate improvements in predictive power when introducing spline functions to take account of highly nonlinear relationships between firm failure and leverage, earnings, and liquidity in a logistic bankruptcy model. Our results show that modeling excessive nonlinearities yields substantially improved bankruptcy predictions, on the order of 70%-90%, compared with a standard logistic model. The spline model provides several important and surprising insights into nonmonotonic bankruptcy relationships. We find that low-leveraged as well as highly profitable firms are riskier than those given by a standard model, possibly a manifestation of credit rationing and excess cash-flow volatility.

  • 6.
    Gu, Xuan
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Sidén, Per
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.
    Wegmann, Bertil
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.
    Eklund, Anders
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Bayesian Diffusion Tensor Estimation with Spatial Priors2017In: CAIP 2017: Computer Analysis of Images and Patterns, 2017, Vol. 10424, p. 372-383Conference paper (Refereed)
    Abstract [en]

    Spatial regularization is a technique that exploits the dependence between nearby regions to locally pool data, with the effect of reducing noise and implicitly smoothing the data. Most of the currently proposed methods are focused on minimizing a cost function, during which the regularization parameter must be tuned in order to find the optimal solution. We propose a fast Markov chain Monte Carlo (MCMC) method for diffusion tensor estimation, for both 2D and 3D priors data. The regularization parameter is jointly with the tensor using MCMC. We compare FA (fractional anisotropy) maps for various b-values using three diffusion tensor estimation methods: least-squares and MCMC with and without spatial priors. Coefficient of variation (CV) is calculated to measure the uncertainty of the FA maps calculated from the MCMC samples, and our results show that the MCMC algorithm with spatial priors provides a denoising effect and reduces the uncertainty of the MCMC samples.

  • 7.
    Li, Feng
    et al.
    Stockholm University, Sweden .
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences.
    Efficient Bayesian Multivariate Surface Regression2013In: Scandinavian Journal of Statistics, ISSN 0303-6898, E-ISSN 1467-9469, Vol. 40, no 4, p. 706-723Article in journal (Refereed)
    Abstract [en]

    Methods for choosing a fixed set of knot locations in additive spline models are fairly well established in the statistical literature. The curse of dimensionality makes it nontrivial to extend these methods to nonadditive surface models, especially when there are more than a couple of covariates. We propose a multivariate Gaussian surface regression model that combines both additive splines and interactive splines, and a highly efficient Markov chain Monte Carlo algorithm that updates all the knot locations jointly. We use shrinkage prior to avoid overfitting with different estimated shrinkage factors for the additive and surface part of the model, and also different shrinkage parameters for the different response variables. Simulated data and an application to firm leverage data show that the approach is computationally efficient, and that allowing for freely estimated knot locations can offer a substantial improvement in out-of-sample predictive performance.

  • 8.
    Maghazeh, Arian
    et al.
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Bordoloi, Unmesh D.
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Science & Engineering.
    Eles, Petru
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Peng, Zebo
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Perception-aware power management for mobile games via dynamic resolution scaling2015In: 2015 IEEE/ACM INTERNATIONAL CONFERENCE ON COMPUTER-AIDED DESIGN (ICCAD), IEEE , 2015, p. 613-620Conference paper (Refereed)
    Abstract [en]

    Modern mobile devices provide ultra-high resolutions in their display panels. This imposes ever increasing workload on the GPU leading to high power consumption and shortened battery life. In this paper, we first show that resolution scaling leads to significant power savings. Second, we propose a perception-aware adaptive scheme that sets the resolution during game play. We exploit the fact that game players are often willing to trade quality for longer battery life. Our scheme uses decision theory, where the predicted user perception is combined with a novel asymmetric loss function that encodes users' alterations in their willingness to save power.

  • 9.
    Magnusson, Måns
    et al.
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences. Aalto University, Espoo, Finland.
    Jonsson, Leif
    Ericsson AB, Stockholm, Sweden.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences. Stockholm University, Stockholm, Sweden.
    DOLDA: a regularized supervised topic model for high-dimensional multi-class regression2019In: Computational statistics (Zeitschrift), ISSN 0943-4062, E-ISSN 1613-9658Article in journal (Refereed)
    Abstract [en]

    Generating user interpretable multi-class predictions in data-rich environments with many classes and explanatory covariates is a daunting task. We introduce Diagonal Orthant Latent Dirichlet Allocation (DOLDA), a supervised topic model for multi-class classification that can handle many classes as well as many covariates. To handle many classes we use the recently proposed Diagonal Orthant probit model (Johndrow et al., in: Proceedings of the sixteenth international conference on artificial intelligence and statistics, 2013) together with an efficient Horseshoe prior for variable selection/shrinkage (Carvalho et al. in Biometrika 97:465–480, 2010). We propose a computationally efficient parallel Gibbs sampler for the new model. An important advantage of DOLDA is that learned topics are directly connected to individual classes without the need for a reference class. We evaluate the model’s predictive accuracy and scalability, and demonstrate DOLDA’s advantage in interpreting the generated predictions.

  • 10.
    Magnusson, Måns
    et al.
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.
    Jonsson, Leif
    Linköping University, Department of Computer and Information Science. Linköping University, Faculty of Science & Engineering.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.
    Broman, David
    School of Information and Communication Technology, Royal Institute of Technology KTH, Stockholm, Sweden.
    Sparse Partially Collapsed MCMC for Parallel Inference in Topic Models2018In: Journal of Computational And Graphical Statistics, ISSN 1061-8600, E-ISSN 1537-2715, Vol. 27, no 2, p. 449-463Article in journal (Refereed)
    Abstract [en]

    Topic models, and more specifically the class of Latent Dirichlet Allocation (LDA), are widely used for probabilistic modeling of text. MCMC sampling from the posterior distribution is typically performed using a collapsed Gibbs sampler. We propose a parallel sparse partially collapsed Gibbs sampler and compare its speed and efficiency to state-of-the-art samplers for topic models on five well-known text corpora of differing sizes and properties. In particular, we propose and compare two different strategies for sampling the parameter block with latent topic indicators. The experiments show that the increase in statistical inefficiency from only partial collapsing is smaller than commonly assumed, and can be more than compensated by the speedup from parallelization and sparsity on larger corpora. We also prove that the partially collapsed samplers scale well with the size of the corpus. The proposed algorithm is fast, efficient, exact, and can be used in more modeling situations than the ordinary collapsed sampler.

  • 11.
    Nott, David J.
    et al.
    National University of Singapore.
    Tan, Siew Li
    National University of Singapore.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, The Institute of Technology.
    Kohn, Robert
    University of New South Wales, Sydney, Australia.
    Regression density estimation with variational methods and stochastic approximation2012In: Journal of Computational And Graphical Statistics, ISSN 1061-8600, E-ISSN 1537-2715, Vol. 21, no 3, p. 797-820Article in journal (Refereed)
    Abstract [en]

    Regression density estimation is the problem of flexibly estimating a response distribution as a function of covariates. An important approach to regression density estimation uses finite mixture models and our article considers flexible mixtures of heteroscedastic regression (MHR) models where the response distribution is a normal mixture, with the component means, variances and mixture weights all varying as a function of covariates. Our article develops fast variational approximation methods for inference. Our motivation is that alternative computationally intensive MCMC methods for fitting mixture models are difficult to apply when it is desired to fit models repeatedly in exploratory analysis and model choice. Our article makes three contributions. First, a variational approximation for MHR models is described where the variational lower bound is in closed form. Second, the basic approximation can be improved by using stochastic approximation methods to perturb the initial solution to attain higher accuracy. Third, the advantages of our approach for model choice and evaluation compared to MCMC based approaches are illustrated. These advantages are particularly compelling for time series data where repeated refitting for one step ahead prediction in model choice and diagnostics and in rolling window computations is very common. Supplemental materials for the article are available online.

  • 12.
    Quiroz, Matias
    et al.
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Science & Engineering. Research Division, Sveriges Riksbank, Stockholm, Sweden.
    Tran, Minh-Ngoc
    Discipline of Business Analytics, University of Sydney, Camperdown NSW, Australia.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering.
    Kohn, Robert
    Australian School of Business, University of New South Wales, Sydney NSW, Australia.
    Speeding up MCMC by Delayed Acceptance and Data Subsampling2018In: Journal of Computational And Graphical Statistics, ISSN 1061-8600, E-ISSN 1537-2715, Vol. 27, no 1, p. 12-22Article in journal (Refereed)
    Abstract [en]

    The complexity of the Metropolis–Hastings (MH) algorithm arises from the requirement of a likelihood evaluation for the full dataset in each iteration. One solution has been proposed to speed up the algorithm by a delayed acceptance approach where the acceptance decision proceeds in two stages. In the first stage, an estimate of the likelihood based on a random subsample determines if it is likely that the draw will be accepted and, if so, the second stage uses the full data likelihood to decide upon final acceptance. Evaluating the full data likelihood is thus avoided for draws that are unlikely to be accepted. We propose a more precise likelihood estimator that incorporates auxiliary information about the full data likelihood while only operating on a sparse set of the data. We prove that the resulting delayed acceptance MH is more efficient. The caveat of this approach is that the full dataset needs to be evaluated in the second stage. We therefore propose to substitute this evaluation by an estimate and construct a state-dependent approximation thereof to use in the first stage. This results in an algorithm that (i) can use a smaller subsample m by leveraging on recent advances in Pseudo-Marginal MH (PMMH) and (ii) is provably within O(m^-2) of the true posterior.

  • 13.
    Ukhov, Ivan
    et al.
    Linköping University, Department of Computer and Information Science, ESLAB - Embedded Systems Laboratory. Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, Faculty of Arts and Sciences.
    Eles, Petru
    Linköping University, Department of Computer and Information Science, ESLAB - Embedded Systems Laboratory. Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    Peng, Zebo
    Linköping University, Department of Computer and Information Science, ESLAB - Embedded Systems Laboratory. Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, The Institute of Technology.
    Statistical Analysis of Process Variation Based on Indirect Measurements for Electronic System Design2014In: 2014 19TH ASIA AND SOUTH PACIFIC DESIGN AUTOMATION CONFERENCE (ASP-DAC), New York: IEEE conference proceedings, 2014, p. 436-442Conference paper (Refereed)
    Abstract [en]

    We present a framework for the analysis of process variation across semiconductor wafers. The framework is capable of quantifying the primary parameters affected by process variation, e.g., the effective channel length, which is in contrast with the former techniques wherein only secondary parameters were considered, e.g., the leakage current. Instead of taking direct measurements of the quantity of interest, we employ Bayesian inference to draw conclusions based on indirect observations, e.g., on temperature. The proposed approach has low costs since no deployment of expensive test structures might be needed or only a small subset of the test equipments already deployed for other purposes might need to be activated. The experimental results present an assessment of our framework for a wide range of configurations.

  • 14.
    Villani, Mattias
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, The Institute of Technology. Linköping University, Faculty of Arts and Sciences. Linköping University, Faculty of Science & Engineering.
    Fractional Bayesian lag length inference in multivariate autoregressive processes2001In: Journal of Time Series Analysis, ISSN 0143-9782, E-ISSN 1467-9892, Vol. 22, no 1, p. 67-86Article in journal (Refereed)
    Abstract [en]

    The posterior distribution of the number of lags in a multivariate autoregression is derived under an improper prior for the model parameters. The fractional Bayes approach is used to handle the indeterminacy in the model selection caused by the improper prior. An asymptotic equivalence between the fractional approach and the Schwarz Bayesian Criterion (SBC) is proved. Several priors and three loss functions are entertained in a simulation study which focuses on the choice of lag length. The fractional Bayes approach performs very well compared to the three most widely used information criteria, and it seems to be reasonably robust to changes in the prior distribution for the lag length, especially under the zero-one loss.

  • 15.
    Villani, Mattias
    et al.
    Linköping University, Department of Computer and Information Science, Statistics. Linköping University, The Institute of Technology.
    Kohn, Robert
    University of New South Wales, Sydney, Australia.
    Nott, David J.
    National University of Singapore.
    Generalized Smooth Finite Mixtures2012In: Journal of Econometrics, ISSN 0304-4076, E-ISSN 1872-6895, Vol. 171, no 2, p. 121-133Article in journal (Refereed)
    Abstract [en]

    We propose a general class of models and a unified Bayesian inference methodology for flexibly estimating the density of a response variable conditional on a possibly high-dimensional set of covariates. Our model is a finite mixture of component models with covariate-dependent mixing weights. The component densities can belong to any parametric family, with each model parameter being a deterministic function of covariates through a link function. Our MCMC methodology allows for Bayesian variable selection among the covariates in the mixture components and in the mixing weights. The model's parameterization and variable selection prior are chosen to prevent overtting. We use simulated and real datasets to illustrate the methodology

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