10,166 research outputs found
Multivariate type G Mat\'ern stochastic partial differential equation random fields
For many applications with multivariate data, random field models capturing
departures from Gaussianity within realisations are appropriate. For this
reason, we formulate a new class of multivariate non-Gaussian models based on
systems of stochastic partial differential equations with additive type G noise
whose marginal covariance functions are of Mat\'ern type. We consider four
increasingly flexible constructions of the noise, where the first two are
similar to existing copula-based models. In contrast to these, the latter two
constructions can model non-Gaussian spatial data without replicates.
Computationally efficient methods for likelihood-based parameter estimation and
probabilistic prediction are proposed, and the flexibility of the suggested
models is illustrated by numerical examples and two statistical applications
A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models
Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks
Structural Properties, Order-Disorder Phenomena and Phase Stability of Orotic Acid Crystal Forms
Orotic acid (OTA) is reported to exist in the anhydrous (AH), monohydrate (Hy1) and dimethylsulfoxide monosolvate (SDMSO) forms. In this study we investigate the (de)hydration/desolvation behavior, aiming at an understanding of the elusive structural features of anhydrous OTA by a combination of experimental and computational techniques, namely, thermal analytical methods, gravimetric moisture (de)sorption studies, water activity measurements, X-ray powder diffraction, spectroscopy (vibrational, solid-state NMR), crystal energy landscape and chemical shift calculations. The Hy1 is a highly stable hydrate, which dissociates above 135°C and loses only a small part of the water when stored over desiccants (25°C) for more than one year. In Hy1, orotic acid and water molecules are linked by strong hydrogen bonds in nearly perfectly planar arranged stacked layers. The layers are spaced by 3.1 Å and not linked via hydrogen-bonds. Upon dehydration the X-ray powder diffraction and solid-state NMR peaks become broader indicating some disorder in the anhydrous form. The Hy1 stacking reflection (122) is maintained, suggesting that the OTA molecules are still arranged in stacked layers in the dehydration product. Desolvation of SDMSO, a non-layer structure, results in the same AH phase as observed upon dehydrating Hy1. Depending on the desolvation conditions different levels of order-disorder of layers present in anhydrous OTA are observed, which is also suggested by the computed low energy crystal structures. These structures provide models for stacking faults as intergrowth of different layers is possible. The variability in anhydrate crystals is of practical concern as it affects the moisture dependent stability of AH with respect to hydration
The Scaled-Charge Additive Force Field for Amino Acid Based Ionic Liquids
Abstract. Ionic liquids (ILs) constitute an emerging field of research. New
ILs are continuously introduced involving more and more organic and inorganic
ions. Amino acid based ILs (AAILs) represent a specific interest due to their
evolutional connection to proteins. We report a new non- polarizable force
field (FF) for the eight AAILs comprising 1-ethyl-3-methylimidazolium cation
and amino acid anions. The anions were obtained via deprotonation of carboxyl
group. Specific cation-anion non-covalent interactions have been taken into
account by computing electrostatic potential for ion pairs, in contrast to
isolated ions. The van der Waals interactions have been transferred from the
CHARMM36 FF with minor modifications. Therefore, compatibility between our
parameters and CHARMM36 parameters is preserved. Our FF can be easily
implemented using a variety of popular molecular dynamics programs. It will
find broad applications in computational investigation of ILs
Multi-Particle Collision Dynamics -- a Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids
In this review, we describe and analyze a mesoscale simulation method for
fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now
called multi-particle collision dynamics (MPC) or stochastic rotation dynamics
(SRD). The method consists of alternating streaming and collision steps in an
ensemble of point particles. The multi-particle collisions are performed by
grouping particles in collision cells, and mass, momentum, and energy are
locally conserved. This simulation technique captures both full hydrodynamic
interactions and thermal fluctuations. The first part of the review begins with
a description of several widely used MPC algorithms and then discusses
important features of the original SRD algorithm and frequently used
variations. Two complementary approaches for deriving the hydrodynamic
equations and evaluating the transport coefficients are reviewed. It is then
shown how MPC algorithms can be generalized to model non-ideal fluids, and
binary mixtures with a consolute point. The importance of angular-momentum
conservation for systems like phase-separated liquids with different
viscosities is discussed. The second part of the review describes a number of
recent applications of MPC algorithms to study colloid and polymer dynamics,
the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of
viscoelastic fluids
Semantic Information G Theory and Logical Bayesian Inference for Machine Learning
An important problem with machine learning is that when label number n\u3e2, it is very difficult to construct and optimize a group of learning functions, and we wish that optimized learning functions are still useful when prior distribution P(x) (where x is an instance) is changed. To resolve this problem, the semantic information G theory, Logical Bayesian Inference (LBI), and a group of Channel Matching (CM) algorithms together form a systematic solution. MultilabelMultilabel A semantic channel in the G theory consists of a group of truth functions or membership functions. In comparison with likelihood functions, Bayesian posteriors, and Logistic functions used by popular methods, membership functions can be more conveniently used as learning functions without the above problem. In Logical Bayesian Inference (LBI), every label’s learning is independent. For Multilabel learning, we can directly obtain a group of optimized membership functions from a big enough sample with labels, without preparing different samples for different labels. A group of Channel Matching (CM) algorithms are developed for machine learning. For the Maximum Mutual Information (MMI) classification of three classes with Gaussian distributions on a two-dimensional feature space, 2-3 iterations can make mutual information between three classes and three labels surpass 99% of the MMI for most initial partitions. For mixture models, the Expectation-Maxmization (EM) algorithm is improved and becomes the CM-EM algorithm, which can outperform the EM algorithm when mixture ratios are imbalanced, or local convergence exists. The CM iteration algorithm needs to combine neural networks for MMI classifications on high-dimensional feature spaces. LBI needs further studies for the unification of statistics and logic
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