scholarly journals History Marginalization Improves Forecasting in Variational Recurrent Neural Networks

Entropy ◽  
2021 ◽  
Vol 23 (12) ◽  
pp. 1563
Author(s):  
Chen Qiu ◽  
Stephan Mandt ◽  
Maja Rudolph

Deep probabilistic time series forecasting models have become an integral part of machine learning. While several powerful generative models have been proposed, we provide evidence that their associated inference models are oftentimes too limited and cause the generative model to predict mode-averaged dynamics. Mode-averaging is problematic since many real-world sequences are highly multi-modal, and their averaged dynamics are unphysical (e.g., predicted taxi trajectories might run through buildings on the street map). To better capture multi-modality, we develop variational dynamic mixtures (VDM): a new variational family to infer sequential latent variables. The VDM approximate posterior at each time step is a mixture density network, whose parameters come from propagating multiple samples through a recurrent architecture. This results in an expressive multi-modal posterior approximation. In an empirical study, we show that VDM outperforms competing approaches on highly multi-modal datasets from different domains.

2017 ◽  
Author(s):  
Takafumi Arakaki ◽  
G. Barello ◽  
Yashar Ahmadian

AbstractTuning curves characterizing the response selectivities of biological neurons often exhibit large degrees of irregularity and diversity across neurons. Theoretical network models that feature heterogeneous cell populations or random connectivity also give rise to diverse tuning curves. However, a general framework for fitting such models to experimentally measured tuning curves is lacking. We address this problem by proposing to view mechanistic network models as generative models whose parameters can be optimized to fit the distribution of experimentally measured tuning curves. A major obstacle for fitting such models is that their likelihood function is not explicitly available or is highly intractable to compute. Recent advances in machine learning provide ways for fitting generative models without the need to evaluate the likelihood and its gradient. Generative Adversarial Networks (GAN) provide one such framework which has been successful in traditional machine learning tasks. We apply this approach in two separate experiments, showing how GANs can be used to fit commonly used mechanistic models in theoretical neuroscience to datasets of measured tuning curves. This fitting procedure avoids the computationally expensive step of inferring latent variables, e.g., the biophysical parameters of individual cells or the particular realization of the full synaptic connectivity matrix, and directly learns model parameters which characterize the statistics of connectivity or of single-cell properties. Another strength of this approach is that it fits the entire, joint distribution of experimental tuning curves, instead of matching a few summary statistics picked a priori by the user. More generally, this framework opens the door to fitting theoretically motivated dynamical network models directly to simultaneously or non-simultaneously recorded neural responses.


2019 ◽  
Author(s):  
Amrit Kashyap ◽  
Shella Keilholz

AbstractLarge scale patterns of spontaneous whole brain activity seen in resting state functional Magnetic Resonance Imaging (rsfMRI), are in part believed to arise from neural populations interacting through the structural fiber network [18]. Generative models that simulate this network activity, called Brain Network Models (BNM), are able to reproduce global averaged properties of empirical rsfMRI activity such as functional connectivity (FC) [7, 27]. However, they perform poorly in reproducing unique trajectories and state transitions that are observed over the span of minutes in whole brain data [20]. At very short timescales between measurements, it is not known how much of the variance these BNM can explain because they are not currently synchronized with the measured rsfMRI. We demonstrate that by solving for the initial conditions of BNM from an observed data point using Recurrent Neural Networks (RNN) and integrating it to predict the next time step, the trained network can explain large amounts of variance for the 5 subsequent time points of unseen future trajectory. The RNN and BNM combined system essentially models the network component of rsfMRI, and where future activity is solely based on previous neural activity propagated through the structural network. Longer instantiations of this generative model simulated over the span of minutes can reproduce average FC and the 1/f power spectrum from 0.01 to 0.3 Hz seen in fMRI. Simulated data also contain interesting resting state dynamics, such as unique repeating trajectories, called QPPs [22] that are highly correlated to the empirical trajectory which spans over 20 seconds. Moreover, it exhibits complex states and transitions as seen using k-Means analysis on windowed FC matrices [1]. This suggests that by combining BNMs with RNN to accurately predict future resting state activity at short timescales, it is learning the manifold of the network dynamics, allowing it to simulate complex resting state trajectories at longer time scales. We believe that our technique will be useful in understanding the large-scale functional organization of the brain and how different BNMs recapitulate different aspects of the system dynamics.


2020 ◽  
Author(s):  
Amol Thakkar ◽  
Veronika Chadimova ◽  
Esben Jannik Bjerrum ◽  
Ola Engkvist ◽  
Jean-Louis Reymond

<p>Computer aided synthesis planning (CASP) is part of a suite of artificial intelligence (AI) based tools that are able to propose synthesis to a wide range of compounds. However, at present they are too slow to be used to screen the synthetic feasibility of millions of generated or enumerated compounds before identification of potential bioactivity by virtual screening (VS) workflows. Herein we report a machine learning (ML) based method capable of classifying whether a synthetic route can be identified for a particular compound or not by the CASP tool AiZynthFinder. The resulting ML models return a retrosynthetic accessibility score (RAscore) of any molecule of interest, and computes 4,500 times faster than retrosynthetic analysis performed by the underlying CASP tool. The RAscore should be useful for the pre-screening millions of virtual molecules from enumerated databases or generative models for synthetic accessibility and produce higher quality databases for virtual screening of biological activity. </p>


2021 ◽  
Author(s):  
Herdiantri Sufriyana ◽  
Yu Wei Wu ◽  
Emily Chia-Yu Su

Abstract We aimed to provide a resampling protocol for dimensional reduction resulting a few latent variables. The applicability focuses on but not limited for developing a machine learning prediction model in order to improve the number of sample size in relative to the number of candidate predictors. By this feature representation technique, one can improve generalization by preventing latent variables to overfit data used to conduct the dimensional reduction. However, this technique may warrant more computational capacity and time to conduct the procedure. The key stages consisted of derivation of latent variables from multiple resampling subsets, parameter estimation of latent variables in population, and selection of latent variables transformed by the estimated parameters.


2021 ◽  
Author(s):  
◽  
Mouna Hakami

<p><b>This thesis presents two studies on non-intrusive speech quality assessment methods. The first applies supervised learning methods to speech quality assessment, which is a common approach in machine learning based quality assessment. To outperform existing methods, we concentrate on enhancing the feature set. In the second study, we analyse quality assessment from a different point of view inspired by the biological brain and present the first unsupervised learning based non-intrusive quality assessment that removes the need for labelled training data.</b></p> <p>Supervised learning based, non-intrusive quality predictors generally involve the development of a regressor that maps signal features to a representation of perceived quality. The performance of the predictor largely depends on 1) how sensitive the features are to the different types of distortion, and 2) how well the model learns the relation between the features and the quality score. We improve the performance of the quality estimation by enhancing the feature set and using a contemporary machine learning model that fits this objective. We propose an augmented feature set that includes raw features that are presumably redundant. The speech quality assessment system benefits from this redundancy as it results in reducing the impact of unwanted noise in the input. Feature set augmentation generally leads to the inclusion of features that have non-smooth distributions. We introduce a new pre-processing method and re-distribute the features to facilitate the training. The evaluation of the system on the ITU-T Supplement23 database illustrates that the proposed system outperforms the popular standards and contemporary methods in the literature.</p> <p>The unsupervised learning quality assessment approach presented in this thesis is based on a model that is learnt from clean speech signals. Consequently, it does not need to learn the statistics of any corruption that exists in the degraded speech signals and is trained only with unlabelled clean speech samples. The quality has a new definition, which is based on the divergence between 1) the distribution of the spectrograms of test signals, and 2) the pre-existing model that represents the distribution of the spectrograms of good quality speech. The distribution of the spectrogram of the speech is complex, and hence comparing them is not trivial. To tackle this problem, we propose to map the spectrograms of speech signals to a simple latent space.</p> <p>Generative models that map simple latent distributions into complex distributions are excellent platforms for our work. Generative models that are trained on the spectrograms of clean speech signals learned to map the latent variable $Z$ from a simple distribution $P_Z$ into a spectrogram $X$ from the distribution of good quality speech.</p> <p>Consequently, an inference model is developed by inverting the pre-trained generator, which maps spectrograms of the signal under the test, $X_t$, into its relevant latent variable, $Z_t$, in the latent space. We postulate the divergence between the distribution of the latent variable and the prior distribution $P_Z$ is a good measure of the quality of speech.</p> <p>Generative adversarial nets (GAN) are an effective training method and work well in this application. The proposed system is a novel application for a GAN. The experimental results with the TIMIT and NOIZEUS databases show that the proposed measure correlates positively with the objective quality scores.</p>


Author(s):  
David Opeoluwa Oyewola ◽  
Emmanuel Gbenga Dada ◽  
Juliana Ngozi Ndunagu ◽  
Terrang Abubakar Umar ◽  
Akinwunmi S.A

Since the declaration of COVID-19 as a global pandemic, it has been transmitted to more than 200 nations of the world. The harmful impact of the pandemic on the economy of nations is far greater than anything suffered in almost a century. The main objective of this paper is to apply Structural Equation Modeling (SEM) and Machine Learning (ML) to determine the relationships among COVID-19 risk factors, epidemiology factors and economic factors. Structural equation modeling is a statistical technique for calculating and evaluating the relationships of manifest and latent variables. It explores the causal relationship between variables and at the same time taking measurement error into account. Bagging (BAG), Boosting (BST), Support Vector Machine (SVM), Decision Tree (DT) and Random Forest (RF) Machine Learning techniques was applied to predict the impact of COVID-19 risk factors. Data from patients who came into contact with coronavirus disease were collected from Kaggle database between 23 January 2020 and 24 June 2020. Results indicate that COVID-19 risk factors have negative effects on epidemiology factors. It also has negative effects on economic factors.


2022 ◽  
Author(s):  
Leon Faure ◽  
Bastien Mollet ◽  
Wolfram Liebermeister ◽  
Jean-Loup Faulon

Metabolic networks have largely been exploited as mechanistic tools to predict the behavior of microorganisms with a defined genotype in different environments. However, flux predictions by constraint-based modeling approaches are limited in quality unless labor-intensive experiments including the measurement of media intake fluxes, are performed. Using machine learning instead of an optimization of biomass flux - on which most existing constraint-based methods are based - provides ways to improve flux and growth rate predictions. In this paper, we show how Recurrent Neural Networks can surrogate constraint-based modeling and make metabolic networks suitable for backpropagation and consequently be used as an architecture for machine learning. We refer to our hybrid - mechanistic and neural network - models as Artificial Metabolic Networks (AMN). We showcase AMN and illustrate its performance with an experimental dataset of Escherichia coli growth rates in 73 different media compositions. We reach a regression coefficient of R2=0.78 on cross-validation sets. We expect AMNs to provide easier discovery of metabolic insights and prompt new biotechnological applications.


2019 ◽  
Author(s):  
Miguel Oyler-Castrillo ◽  
Nicolas Bohm Agostini ◽  
Gadiel Sznaier ◽  
David Kaeli

Author(s):  
Ben Tribelhorn ◽  
H. E. Dillon

Abstract This paper is a preliminary report on work done to explore the use of unsupervised machine learning methods to predict the onset of turbulent transitions in natural convection systems. The Lorenz system was chosen to test the machine learning methods due to the relative simplicity of the dynamic system. We developed a robust numerical solution to the Lorenz equations using a fourth order Runge-Kutta method with a time step of 0.001 seconds. We solved the Lorenz equations for a large range of Raleigh ratios from 1–1000 while keeping the geometry and Prandtl number constant. We calculated the spectral density, various descriptive statistics, and a cluster analysis using unsupervised machine learning. We examined the performance of the machine learning system for different Raleigh ratio ranges. We found that the automated cluster analysis aligns well with well known key transition regions of the convection system. We determined that considering smaller ranges of Raleigh ratios may improve the performance of the machine learning tools. We also identified possible additional behaviors not shown in z-axis bifurcation plots. This unsupervised learning approach can be leveraged on other systems where numerical analysis is computationally intractable or more difficult. The results are interesting and provide a foundation for expanding the study for Prandtl number and geometry variations. Future work will focus on applying the methods to more complex natural convection systems, including the development of new methods for Nusselt correlations.


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