arXiv subjects

Mauricio A. Álvarez

Publications and source records attributed to Mauricio A. Álvarez.

34 records · Page 2Linked to original sources

arXiv2019

Black-Box Inference for Non-Linear Latent Force Models

Latent force models are systems whereby there is a mechanistic model describing the dynamics of the system state, with some unknown forcing term that is approximated with a Gaussian process. If such dynamics are non-linear, it can be difficult to estimate the posterior state and forcing term jointly, particularly when there are system parameters that also need estimating. This paper uses black-box variational inference to jointly estimate the posterior, designing a multivariate extension to local inverse autoregressive flows as a flexible approximater of the system. We compare estimates on systems where the posterior is known, demonstrating the effectiveness of the approximation, and apply to problems with non-linear dynamics, multi-output systems and models with non-Gaussian likelihoods.

stat.ML↗

arXiv2019

Continual Multi-task Gaussian Processes

We address the problem of continual learning in multi-task Gaussian process (GP) models for handling sequential input-output observations. Our approach extends the existing prior-posterior recursion of online Bayesian inference, i.e.\ past posterior discoveries become future prior beliefs, to the infinite functional space setting of GP. For a reason of scalability, we introduce variational inference together with an sparse approximation based on inducing inputs. As a consequence, we obtain tractable continual lower-bounds where two novel Kullback-Leibler (KL) divergences intervene in a natural way. The key technical property of our method is the recursive reconstruction of conditional GP priors conditioned on the variational parameters learned so far. To achieve this goal, we introduce a novel factorization of past variational distributions, where the predictive GP equation propagates the posterior uncertainty forward. We then demonstrate that it is possible to derive GP models over many types of sequential observations, either discrete or continuous and amenable to stochastic optimization. The continual inference approach is also applicable to scenarios where potential multi-channel or heterogeneous observations might appear. Extensive experiments demonstrate that the method is fully scalable, shows a reliable performance and is robust to uncertainty error propagation over a plenty of synthetic and real-world datasets.

stat.ML↗

arXiv2019

Non-linear process convolutions for multi-output Gaussian processes

The paper introduces a non-linear version of the process convolution formalism for building covariance functions for multi-output Gaussian processes. The non-linearity is introduced via Volterra series, one series per each output. We provide closed-form expressions for the mean function and the covariance function of the approximated Gaussian process at the output of the Volterra series. The mean function and covariance function for the joint Gaussian process are derived using formulae for the product moments of Gaussian variables. We compare the performance of the non-linear model against the classical process convolution approach in one synthetic dataset and two real datasets.

stat.ML↗

arXiv2019

Heterogeneous Multi-output Gaussian Process Prediction

We present a novel extension of multi-output Gaussian processes for handling heterogeneous outputs. We assume that each output has its own likelihood function and use a vector-valued Gaussian process prior to jointly model the parameters in all likelihoods as latent functions. Our multi-output Gaussian process uses a covariance function with a linear model of coregionalisation form. Assuming conditional independence across the underlying latent functions together with an inducing variable framework, we are able to obtain tractable variational bounds amenable to stochastic variational inference. We illustrate the performance of the model on synthetic data and two real datasets: a human behavioral study and a demographic high-dimensional dataset.

stat.ML↗

arXiv2018

Sparse Gaussian Process Audio Source Separation Using Spectrum Priors in the Time-Domain

Gaussian process (GP) audio source separation is a time-domain approach that circumvents the inherent phase approximation issue of spectrogram based methods. Furthermore, through its kernel, GPs elegantly incorporate prior knowledge about the sources into the separation model. Despite these compelling advantages, the computational complexity of GP inference scales cubically with the number of audio samples. As a result, source separation GP models have been restricted to the analysis of short audio frames. We introduce an efficient application of GPs to time-domain audio source separation, without compromising performance. For this purpose, we used GP regression, together with spectral mixture kernels, and variational sparse GPs. We compared our method with LD-PSDTF (positive semi-definite tensor factorization), KL-NMF (Kullback-Leibler non-negative matrix factorization), and IS-NMF (Itakura-Saito NMF). Results show that the proposed method outperforms these techniques.

eess.AS↗

arXiv2018

Gaussian Process Latent Force Models for Learning and Stochastic Control of Physical Systems

This article is concerned with learning and stochastic control in physical systems which contain unknown input signals. These unknown signals are modeled as Gaussian processes (GP) with certain parametrized covariance structures. The resulting latent force models (LFMs) can be seen as hybrid models that contain a first-principles physical model part and a non-parametric GP model part. We briefly review the statistical inference and learning methods for this kind of models, introduce stochastic control methodology for the models, and provide new theoretical observability and controllability results for them.

eess.SY↗

arXiv2017

Switched latent force models for reverse-engineering transcriptional regulation in gene expression data

To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult task to measure experimentally TF behaviours, and the challenges to capture their quick-time dynamics, different types of models based on differential equations have been proposed. However, those approaches usually incur in costly procedures, and they present problems to describe sudden changes in TF regulators. In this paper, we present a switched dynamical latent force model for reverse-engineering transcriptional regulation in gene expression data which allows the exact inference over latent TF activities driving some observed gene expressions through a linear differential equation. To deal with discontinuities in the dynamics, we introduce an approach that switches between different TF activities and different dynamical systems. This creates a versatile representation of transcription networks that can capture discrete changes and non-linearities We evaluate our model on both simulated data and real-data (e.g. microaerobic shift in E. coli, yeast respiration), concluding that our framework allows for the fitting of the expression data while being able to infer continuous-time TF profiles.

physics.bio-ph↗

arXiv2017

Efficient Modeling of Latent Information in Supervised Learning using Gaussian Processes

Often in machine learning, data are collected as a combination of multiple conditions, e.g., the voice recordings of multiple persons, each labeled with an ID. How could we build a model that captures the latent information related to these conditions and generalize to a new one with few data? We present a new model called Latent Variable Multiple Output Gaussian Processes (LVMOGP) and that allows to jointly model multiple conditions for regression and generalize to a new condition with a few data points at test time. LVMOGP infers the posteriors of Gaussian processes together with a latent space representing the information about different conditions. We derive an efficient variational inference method for LVMOGP, of which the computational complexity is as low as sparse Gaussian processes. We show that LVMOGP significantly outperforms related Gaussian process methods on various tasks with both synthetic and real data.

stat.ML↗

arXiv2016

A Three Spatial Dimension Wave Latent Force Model for Describing Excitation Sources and Electric Potentials Produced by Deep Brain Stimulation

Deep brain stimulation (DBS) is a surgical treatment for Parkinson's Disease. Static models based on quasi-static approximation are common approaches for DBS modeling. While this simplification has been validated for bioelectric sources, its application to rapid stimulation pulses, which contain more high-frequency power, may not be appropriate, as DBS therapeutic results depend on stimulus parameters such as frequency and pulse width, which are related to time variations of the electric field. We propose an alternative hybrid approach based on probabilistic models and differential equations, by using Gaussian processes and wave equation. Our model avoids quasi-static approximation, moreover, it is able to describe dynamic behavior of DBS. Therefore, the proposed model may be used to obtain a more realistic phenomenon description. The proposed model can also solve inverse problems, i.e. to recover the corresponding source of excitation, given electric potential distribution. The electric potential produced by a time-varying source was predicted using proposed model. For static sources, the electric potential produced by different electrode configurations were modeled. Four different sources of excitation were recovered by solving the inverse problem. We compare our outcomes with the electric potential obtained by solving Poisson's equation using the Finite Element Method (FEM). Our approach is able to take into account time variations of the source and the produced field. Also, inverse problem can be addressed using the proposed model. The electric potential calculated with the proposed model is close to the potential obtained by solving Poisson's equation using FEM.

q-bio.NC↗

arXiv2016

Short-term time series prediction using Hilbert space embeddings of autoregressive processes

Linear autoregressive models serve as basic representations of discrete time stochastic processes. Different attempts have been made to provide non-linear versions of the basic autoregressive process, including different versions based on kernel methods. Motivated by the powerful framework of Hilbert space embeddings of distributions, in this paper we apply this methodology for the kernel embedding of an autoregressive process of order $p$. By doing so, we provide a non-linear version of an autoregressive process, that shows increased performance over the linear model in highly complex time series. We use the method proposed for one-step ahead forecasting of different time-series, and compare its performance against other non-linear methods.

stat.ML↗

arXiv2015

Sparse Linear Models applied to Power Quality Disturbance Classification

Power quality (PQ) analysis describes the non-pure electric signals that are usually present in electric power systems. The automatic recognition of PQ disturbances can be seen as a pattern recognition problem, in which different types of waveform distortion are differentiated based on their features. Similar to other quasi-stationary signals, PQ disturbances can be decomposed into time-frequency dependent components by using time-frequency or time-scale transforms, also known as dictionaries. These dictionaries are used in the feature extraction step in pattern recognition systems. Short-time Fourier, Wavelets and Stockwell transforms are some of the most common dictionaries used in the PQ community, aiming to achieve a better signal representation. To the best of our knowledge, previous works about PQ disturbance classification have been restricted to the use of one among several available dictionaries. Taking advantage of the theory behind sparse linear models (SLM), we introduce a sparse method for PQ representation, starting from overcomplete dictionaries. In particular, we apply Group Lasso. We employ different types of time-frequency (or time-scale) dictionaries to characterize the PQ disturbances, and evaluate their performance under different pattern recognition algorithms. We show that the SLM reduce the PQ classification complexity promoting sparse basis selection, and improving the classification accuracy.

stat.AP↗

arXiv2015

A Parzen-based distance between probability measures as an alternative of summary statistics in Approximate Bayesian Computation

Approximate Bayesian Computation (ABC) are likelihood-free Monte Carlo methods. ABC methods use a comparison between simulated data, using different parameters drew from a prior distribution, and observed data. This comparison process is based on computing a distance between the summary statistics from the simulated data and the observed data. For complex models, it is usually difficult to define a methodology for choosing or constructing the summary statistics. Recently, a nonparametric ABC has been proposed, that uses a dissimilarity measure between discrete distributions based on empirical kernel embeddings as an alternative for summary statistics. The nonparametric ABC outperforms other methods including ABC, kernel ABC or synthetic likelihood ABC. However, it assumes that the probability distributions are discrete, and it is not robust when dealing with few observations. In this paper, we propose to apply kernel embeddings using an smoother density estimator or Parzen estimator for comparing the empirical data distributions, and computing the ABC posterior. Synthetic data and real data were used to test the Bayesian inference of our method. We compare our method with respect to state-of-the-art methods, and demonstrate that our method is a robust estimator of the posterior distribution in terms of the number of observations.

stat.ML↗

arXiv2015

Indian Buffet process for model selection in convolved multiple-output Gaussian processes

Multi-output Gaussian processes have received increasing attention during the last few years as a natural mechanism to extend the powerful flexibility of Gaussian processes to the setup of multiple output variables. The key point here is the ability to design kernel functions that allow exploiting the correlations between the outputs while fulfilling the positive definiteness requisite for the covariance function. Alternatives to construct these covariance functions are the linear model of coregionalization and process convolutions. Each of these methods demand the specification of the number of latent Gaussian process used to build the covariance function for the outputs. We propose in this paper, the use of an Indian Buffet process as a way to perform model selection over the number of latent Gaussian processes. This type of model is particularly important in the context of latent force models, where the latent forces are associated to physical quantities like protein profiles or latent forces in mechanical systems. We use variational inference to estimate posterior distributions over the variables involved, and show examples of the model performance over artificial data, a motion capture dataset, and a gene expression dataset.

stat.ML↗

arXiv2015

Discriminative training for Convolved Multiple-Output Gaussian processes

Multi-output Gaussian processes (MOGP) are probability distributions over vector-valued functions, and have been previously used for multi-output regression and for multi-class classification. A less explored facet of the multi-output Gaussian process is that it can be used as a generative model for vector-valued random fields in the context of pattern recognition. As a generative model, the multi-output GP is able to handle vector-valued functions with continuous inputs, as opposed, for example, to hidden Markov models. It also offers the ability to model multivariate random functions with high dimensional inputs. In this report, we use a discriminative training criteria known as Minimum Classification Error to fit the parameters of a multi-output Gaussian process. We compare the performance of generative training and discriminative training of MOGP in emotion recognition, activity recognition, and face recognition. We also compare the proposed methodology against hidden Markov models trained in a generative and in a discriminative way.

stat.ML↗

arXiv2009

Variational Inducing Kernels for Sparse Convolved Multiple Output Gaussian Processes

Interest in multioutput kernel methods is increasing, whether under the guise of multitask learning, multisensor networks or structured output data. From the Gaussian process perspective a multioutput Mercer kernel is a covariance function over correlated output functions. One way of constructing such kernels is based on convolution processes (CP). A key problem for this approach is efficient inference. Alvarez and Lawrence (2009) recently presented a sparse approximation for CPs that enabled efficient inference. In this paper, we extend this work in two directions: we introduce the concept of variational inducing functions to handle potential non-smooth functions involved in the kernel CP construction and we consider an alternative approach to approximate inference based on variational methods, extending the work by Titsias (2009) to the multiple output case. We demonstrate our approaches on prediction of school marks, compiler performance and financial time series.

stat.ML↗

arXiv2009

Sparse Convolved Multiple Output Gaussian Processes

Recently there has been an increasing interest in methods that deal with multiple outputs. This has been motivated partly by frameworks like multitask learning, multisensor networks or structured output data. From a Gaussian processes perspective, the problem reduces to specifying an appropriate covariance function that, whilst being positive semi-definite, captures the dependencies between all the data points and across all the outputs. One approach to account for non-trivial correlations between outputs employs convolution processes. Under a latent function interpretation of the convolution transform we establish dependencies between output variables. The main drawbacks of this approach are the associated computational and storage demands. In this paper we address these issues. We present different sparse approximations for dependent output Gaussian processes constructed through the convolution formalism. We exploit the conditional independencies present naturally in the model. This leads to a form of the covariance similar in spirit to the so called PITC and FITC approximations for a single output. We show experimental results with synthetic and real data, in particular, we show results in pollution prediction, school exams score prediction and gene expression data.

stat.ML↗