22 papers · ranked by Valyu relevance
J.D. Karslake, E.D. Donarski, S.A. Shelby, L.M. Demey + 3 more
Single-molecule fluorescence microscopy probes nanoscale, subcellular biology in real time. Existing methods for analyzing single-particle tracking data provide dynamical information, but can suffer from supervisory biases and high uncertainties. Here, we introduce a new approach to analyzing single-molecule…
Nils Lid Hjort
The intersection set of Bayesian and nonparametric statistics was almost empty until about 1973, but now is growing at a healthy rate. This chapter, for the {\it Highly Structured Stochastic Systems} book (Oxford University Press, 2003) gives an overview of various theoretical and applied research themes inside this…
Nils Lid Hjort, Chris Holmes, Peter Mueller, Stephen G. Walker
This extended preface [to the Book `Bayesian Nonparametrics', Cambridge University Press, 2010, by NL Hjort, CC Holmes, P Mueller, SG Walker] is meant to explain why you are right to be curious about Bayesian nonparametrics -- why you may actually need it and how you can manage to understand it and use it. The preface…
Zoubin Ghahramani
Modelling is fundamental to many fields of science and engineering. A model can be thought of as a representation of possible data one could predict from a system. The probabilistic approach to modelling uses probability theory to express all aspects of uncertainty in the model. The probabilistic approach is synonymous…
Nils Lid Hjort
This invited paper proposes and discusses several Bayesian attempts at nonparametric and semiparametric density estimation. The main categories of these ideas are as follows: 1) Build a nonparametric prior around a given parametric model. We look at cases where the nonparametric part of the construction is a Dirichlet…
Ricky Sexton, Mohamadreza Fazel, Maxwell Schweiger, Steve Pressé + 1 more
Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid-protein binding kinetics has remained challenging due to considerable noise and low…
Richard A. Chechile, Daniel H. Barch Jr.
Nonparametric (or distribution-free) statistics have been widely used in psychological research because behavioral data can be messy and inconsistent with the Gaussian model for measurement error. Distribution-free procedures only use categorical or rank information, so they avoid the problems of outliers and…
Antonio R. Linero, Joseph Antonelli
Spurred on by recent successes in causal inference competitions, Bayesian nonparametric (and high-dimensional) methods have recently seen increased attention in the causal inference literature. In this paper, we present a comprehensive overview of Bayesian nonparametric applications to causal inference. Our aims are to…
Vinayak Rao, Lizhen Lin, David B. Dunson
The Stiefel manifold Vp,d is the space of all d × p orthonormal matrices, with the d−1 hypersphere and the space of all orthogonal matrices constituting special cases. In modeling data lying on the Stiefel manifold, parametric distributions such as the matrix Langevin distribution are often used; however, model…
Max Hinne, David Leeftink, Marcel A. J. van Gerven, Luca Ambrogioni + 1 more
'Lalit Chandra Saikia'] Quasi-experimental research designs, such as regression discontinuity and interrupted time series, allow for causal inference in the absence of a randomized controlled trial, at the cost of additional assumptions. In this paper, we provide a framework for discontinuity-based designs using…
Julia A. Palacios, John Wakeley, Sohini Ramachandran
Sophisticated inferential tools coupled with the coalescent model have recently emerged for estimating past population sizes from genomic data. Accurate methods are available for data from a single locus or from independent loci. Recent methods that model recombination require small sample sizes, make constraining…
Luca Ambrogioni, Patrick W. J. Ebel, Max Hinne, Umut Güçlü + 2 more
Estimating causal connectivity between spiking neurons from measured spike sequences is one of the main challenges of systems neuroscience. In this paper we introduce two nonparametric Bayesian methods for spike-membrane and spikespike causal connectivity based on Gaussian process regression. For spike-spike…
Manuel Mendoza, Alberto Contreras-Cristán, Eduardo Gutiérrez-Peña, Jacinto Martín
'Jacinto Martín'] Statistical methods to produce inferences based on samples from finite populations have been available for at least 70 years. Topics such as Survey Sampling and Sampling Theory have become part of the mainstream of the statistical methodology. A wide variety of sampling schemes as well as estimators…
Kazuhiro Yamaguchi, Yanlong Liu, Gongjun Xu
This study extends the loss function-based parameter estimation method for diagnostic classification models proposed by Ma, de la Torre, et al. (2023, Psychometrika) to consider prior knowledge and uncertainty of sampling. To this end, we integrate the loss function-based estimation method with the generalized Bayesian…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? This type of solution degeneracy often exists in physics-based simulations and wet-lab experiments, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and…
Mitra Kharabati, Morteza Amini, Mohammad Arashi
Count data with overdispersion and high-dimensional predictors pose significant challenges in modern applications. While negative binomial regression offers a flexible modeling framework, existing Bayesian approaches rely on computationally expensive MCMC methods that become impractical in high-dimensional settings.…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Qingyang Zhang, Xuan Shi
Gaussian Bayesian networks have become a widely used framework to estimate directed associations between joint Gaussian variables, where the network structure encodes decomposition of multivariate normal density into local terms. However, the resulting estimates can be inaccurate when normality assumption is moderately…
Yifan Wu, Aron Walsh, Alex Ganose
What is the minimum number of experiments, or calculations, required to find an optimal solution? Relevant chemical problems range from identifying a compound with target functionality within a given phase space to controlling materials synthesis and device fabrication conditions. A common feature in this application…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…
Robert Arbon, Yanchen Zhu, Antonia S. J. S. Mey
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or…