The Gaussian process state space model (GPSSM) is a non-linear dynamical system, where unknown transition and/or measurement mappings are described by GPs. Most research in GPSSMs has focussed on the state estimation problem, i.e., computing a posterior of the latent state given the model. However, the key challenge in GPSSMs has not been satisfactorily addressed yet: system identification, i.e., learning the model. To address this challenge, we impose a structured Gaussian variational posterior distribution over the latent states, which is parameterised by a recognition model in the form of a bi-directional recurrent neural network. Inference with this structure allows us to recover a posterior smoothed over sequences of data. We provide a practical algorithm for efficiently computing a lower bound on the marginal likelihood using the reparameterisation trick. This further allows for the use of arbitrary kernels within the GPSSM. We demonstrate that the learnt GPSSM can efficiently generate plausible future trajectories of the identified system after only observing a small number of episodes from the true system.

The Gaussian process state space model (GPSSM) is a non-linear dynamical system, where unknown transition and/or measurement mappings are described by GPs. Most research in GPSSMs has focussed on the state estimation problem, i.e., computing a posterior of the latent state given the model. However, the key challenge in GPSSMs has not been satisfactorily addressed yet: system identification, i.e., learning the model. To address this challenge, we impose a structured Gaussian variational posterior distribution over the latent states, which is parameterised by a recognition model in the form of a bi-directional recurrent neural network. Inference with this structure allows us to recover a posterior smoothed over sequences of data. We provide a practical algorithm for efficiently computing a lower bound on the marginal likelihood using the reparameterisation trick. This further allows for the use of arbitrary kernels within the GPSSM. We demonstrate that the learnt GPSSM can efficiently generate plausible future trajectories of the identified system after only observing a small number of episodes from the true system.

Neural Information Processing Systems http://nips.cc/

Learning dynamical models from data is not only fundamental but also holds great promise for advancing principle discovery, time-series prediction, and controller design. Among various approaches, Gaussian Process State-Space Models (GPSSMs) have recently gained significant attention due to their combination of flexibility and interpretability. However, for online learning, the field lacks an efficient method suitable for scenarios where prior information regarding data distribution and model function is limited. To address this issue, this paper proposes a recursive GPSSM method with adaptive capabilities for both operating domains and Gaussian process (GP) hyperparameters. Specifically, we first utilize first-order linearization to derive a Bayesian update equation for the joint distribution between the system state and the GP model, enabling closed-form and domain-independent learning. Second, an online selection algorithm for inducing points is developed based on informative criteria to achieve lightweight learning. Third, to support online hyperparameter optimization, we recover historical measurement information from the current filtering distribution. Comprehensive evaluations on both synthetic and real-world datasets demonstrate the superior accuracy, computational efficiency, and adaptability of our method compared to state-of-the-art online GPSSM techniques.

The Gaussian process state space model (GPSSM) is a non-linear dynamical system, where unknown transition and/or measurement mappings are described by GPs. Most research in GPSSMs has focussed on the state estimation problem, i.e., computing a posterior of the latent state given the model. However, the key challenge in GPSSMs has not been satisfactorily addressed yet: system identification, i.e., learning the model. To address this challenge, we impose a structured Gaussian variational posterior distribution over the latent states, which is parameterised by a recognition model in the form of a bi-directional recurrent neural network. Inference with this structure allows us to recover a posterior smoothed over sequences of data. We provide a practical algorithm for efficiently computing a lower bound on the marginal likelihood using the reparameterisation trick. This further allows for the use of arbitrary kernels within the GPSSM. We demonstrate that the learnt GPSSM can efficiently generate plausible future trajectories of the identified system after only observing a small number of episodes from the true system.

Gaussian process state-space models (GPSSMs) are a versatile and principled family of nonlinear dynamical system models. However, existing variational learning and inference methods for GPSSMs often necessitate optimizing a substantial number of variational parameters, leading to inadequate performance and efficiency. To overcome this issue, we propose incorporating the ensemble Kalman filter (EnKF), a well-established model-based filtering technique, into the variational inference framework to approximate the posterior distribution of latent states. This utilization of EnKF can effectively exploit the dependencies between latent states and GP dynamics, while eliminating the need for parameterizing the variational distribution, thereby significantly reducing the number of variational parameters. Moreover, we show that our proposed algorithm allows straightforward evaluation of an approximated evidence lower bound (ELBO) in variational inference via simply summating multiple terms with readily available closed-form solutions. Leveraging automatic differentiation tools, we hence can maximize the ELBO and train the GPSSM efficiently. We also extend the proposed algorithm to accommodate an online setting and provide detailed algorithmic analyses and insights. Extensive evaluation on diverse real and synthetic datasets demonstrates the superiority of our EnKF-aided variational inference algorithms in terms of learning and inference performance compared to existing methods.

The rapid mutation of the influenza virus threatens public health. Reassortment among viruses with different hosts can lead to a fatal pandemic. However, it is difficult to detect the original host of the virus during or after an outbreak as influenza viruses can circulate between different species. Therefore, early and rapid detection of the viral host would help reduce the further spread of the virus. We use various machine learning models with features derived from the position-specific scoring matrix (PSSM) and features learned from word embedding and word encoding to infer the origin host of viruses. The results show that the performance of the PSSM-based model reaches the MCC around 95%, and the F1 around 96%. The MCC obtained using the model with word embedding is around 96%, and the F1 is around 97%.

In order for robots to safely navigate in unseen scenarios using learning-based methods, it is important to accurately detect out-of-training-distribution (OoD) situations online. Recently, Gaussian process state-space models (GPSSMs) have proven useful to discriminate unexpected observations by comparing them against probabilistic predictions. However, the capability for the model to correctly distinguish between in- and out-of-training distribution observations hinges on the accuracy of these predictions, primarily affected by the class of functions the GPSSM kernel can represent. In this paper, we propose (i) a novel approach to embed existing domain knowledge in the kernel and (ii) an OoD online runtime monitor, based on receding-horizon predictions. Domain knowledge is provided in the form of a dataset, collected either in simulation or by using a nominal model. Numerical results show that the informed kernel yields better regression quality with smaller datasets, as compared to standard kernel choices. We demonstrate the effectiveness of the OoD monitor on a real quadruped navigating an indoor setting, which reliably classifies previously unseen terrains.

The Gaussian process state-space model (GPSSM) has attracted extensive attention for modeling complex nonlinear dynamical systems. However, the existing GPSSM employs separate Gaussian processes (GPs) for each latent state dimension, leading to escalating computational complexity and parameter proliferation, thus posing challenges for modeling dynamical systems with high-dimensional latent states. To surmount this obstacle, we propose to integrate the efficient transformed Gaussian process (ETGP) into the GPSSM, which involves pushing a shared GP through multiple normalizing flows to efficiently model the transition function in high-dimensional latent state space. Additionally, we develop a corresponding variational inference algorithm that surpasses existing methods in terms of parameter count and computational complexity. Experimental results on diverse synthetic and real-world datasets corroborate the efficiency of the proposed method, while also demonstrating its ability to achieve similar inference performance compared to existing methods. Code is available at \url{https://github.com/zhidilin/gpssmProj}.

Gaussian process state-space model (GPSSM) is a fully probabilistic state-space model that has attracted much attention over the past decade. However, the outputs of the transition function in the existing GPSSMs are assumed to be independent, meaning that the GPSSMs cannot exploit the inductive biases between different outputs and lose certain model capacities. To address this issue, this paper proposes an output-dependent and more realistic GPSSM by utilizing the well-known, simple yet practical linear model of coregionalization (LMC) framework to represent the output dependency. To jointly learn the output-dependent GPSSM and infer the latent states, we propose a variational sparse GP-based learning method that only gently increases the computational complexity. Experiments on both synthetic and real datasets demonstrate the superiority of the output-dependent GPSSM in terms of learning and inference performance.