3,000 research outputs found

    Transferable neural networks for enhanced sampling of protein dynamics

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    Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable and is generally applicable to sets of related simulations, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.Comment: 20 pages, 10 figure

    Lightweight Probabilistic Deep Networks

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    Even though probabilistic treatments of neural networks have a long history, they have not found widespread use in practice. Sampling approaches are often too slow already for simple networks. The size of the inputs and the depth of typical CNN architectures in computer vision only compound this problem. Uncertainty in neural networks has thus been largely ignored in practice, despite the fact that it may provide important information about the reliability of predictions and the inner workings of the network. In this paper, we introduce two lightweight approaches to making supervised learning with probabilistic deep networks practical: First, we suggest probabilistic output layers for classification and regression that require only minimal changes to existing networks. Second, we employ assumed density filtering and show that activation uncertainties can be propagated in a practical fashion through the entire network, again with minor changes. Both probabilistic networks retain the predictive power of the deterministic counterpart, but yield uncertainties that correlate well with the empirical error induced by their predictions. Moreover, the robustness to adversarial examples is significantly increased.Comment: To appear at CVPR 201

    Deep Variational Reinforcement Learning for POMDPs

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    Many real-world sequential decision making problems are partially observable by nature, and the environment model is typically unknown. Consequently, there is great need for reinforcement learning methods that can tackle such problems given only a stream of incomplete and noisy observations. In this paper, we propose deep variational reinforcement learning (DVRL), which introduces an inductive bias that allows an agent to learn a generative model of the environment and perform inference in that model to effectively aggregate the available information. We develop an n-step approximation to the evidence lower bound (ELBO), allowing the model to be trained jointly with the policy. This ensures that the latent state representation is suitable for the control task. In experiments on Mountain Hike and flickering Atari we show that our method outperforms previous approaches relying on recurrent neural networks to encode the past

    Matrix Completion With Variational Graph Autoencoders: Application in Hyperlocal Air Quality Inference

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    Inferring air quality from a limited number of observations is an essential task for monitoring and controlling air pollution. Existing inference methods typically use low spatial resolution data collected by fixed monitoring stations and infer the concentration of air pollutants using additional types of data, e.g., meteorological and traffic information. In this work, we focus on street-level air quality inference by utilizing data collected by mobile stations. We formulate air quality inference in this setting as a graph-based matrix completion problem and propose a novel variational model based on graph convolutional autoencoders. Our model captures effectively the spatio-temporal correlation of the measurements and does not depend on the availability of additional information apart from the street-network topology. Experiments on a real air quality dataset, collected with mobile stations, shows that the proposed model outperforms state-of-the-art approaches

    Decomposing feature-level variation with Covariate Gaussian Process Latent Variable Models

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    The interpretation of complex high-dimensional data typically requires the use of dimensionality reduction techniques to extract explanatory low-dimensional representations. However, in many real-world problems these representations may not be sufficient to aid interpretation on their own, and it would be desirable to interpret the model in terms of the original features themselves. Our goal is to characterise how feature-level variation depends on latent low-dimensional representations, external covariates, and non-linear interactions between the two. In this paper, we propose to achieve this through a structured kernel decomposition in a hybrid Gaussian Process model which we call the Covariate Gaussian Process Latent Variable Model (c-GPLVM). We demonstrate the utility of our model on simulated examples and applications in disease progression modelling from high-dimensional gene expression data in the presence of additional phenotypes. In each setting we show how the c-GPLVM can extract low-dimensional structures from high-dimensional data sets whilst allowing a breakdown of feature-level variability that is not present in other commonly used dimensionality reduction approaches
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