Author name cluster

S. T. John

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

7 papers

1 author row

ICLR Conference 2025 Conference Paper

Identifying latent state transitions in non-linear dynamical systems

Caglar Hizli
Çagatay Yildiz
Matthias Bethge
S. T. John
Pekka Marttinen

This work aims to recover the underlying states and their time evolution in a latent dynamical system from high-dimensional sensory measurements. Previous works on identifiable representation learning in dynamical systems focused on identifying the latent states, often with linear transition approximations. As such, they cannot identify nonlinear transition dynamics, and hence fail to reliably predict complex future behavior. Inspired by the advances in nonlinear ICA, we propose a state-space modeling framework in which we can identify not just the latent states but also the unknown transition function that maps the past states to the present. Our identifiability theory relies on two key assumptions: (i) sufficient variability in the latent noise, and (ii) the bijectivity of the augmented transition function. Drawing from this theory, we introduce a practical algorithm based on variational auto-encoders. We empirically demonstrate that it improves generalization and interpretability of target dynamical systems by (i) recovering latent state dynamics with high accuracy, (ii) correspondingly achieving high future prediction accuracy, and (iii) adapting fast to new environments. Additionally, for complex real-world dynamics, (iv) it produces state-of the-art future prediction results for long horizons, highlighting its usefulness for practical scenarios.

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UAI Conference 2024 Conference Paper

Learning relevant contextual variables within Bayesian optimization

Julien Martinelli
Ayush Bharti
Armi Tiihonen
S. T. John
Louis Filstroff
Sabina J. Sloman
Patrick Rinke
Samuel Kaski

Contextual Bayesian Optimization (CBO) efficiently optimizes black-box functions with respect to design variables, while simultaneously integrating _contextual_ information regarding the environment, such as experimental conditions. However, the relevance of contextual variables is not necessarily known beforehand. Moreover, contextual variables can sometimes be optimized themselves at additional cost, a setting overlooked by current CBO algorithms. Cost-sensitive CBO would simply include optimizable contextual variables as part of the design variables based on their cost. Instead, we adaptively select a subset of contextual variables to include in the optimization, based on the trade-off between their _relevance_ and the additional cost incurred by optimizing them compared to leaving them to be determined by the environment. We learn the relevance of contextual variables by sensitivity analysis of the posterior surrogate model while minimizing the cost of optimization by leveraging recent developments on early stopping for BO. We empirically evaluate our proposed Sensitivity-Analysis-Driven Contextual BO (_SADCBO_) method against alternatives on both synthetic and real-world experiments, together with extensive ablation studies, and demonstrate a consistent improvement across examples.

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ICML Conference 2023 Conference Paper

Causal Modeling of Policy Interventions From Treatment-Outcome Sequences

Caglar Hizli
S. T. John
Anne Tuulikki Juuti
Tuure Tapani Saarinen
Kirsi Hannele Pietiläinen
Pekka Marttinen

A treatment policy defines when and what treatments are applied to affect some outcome of interest. Data-driven decision-making requires the ability to predict what happens if a policy is changed. Existing methods that predict how the outcome evolves under different scenarios assume that the tentative sequences of future treatments are fixed in advance, while in practice the treatments are determined stochastically by a policy and may depend, for example, on the efficiency of previous treatments. Therefore, the current methods are not applicable if the treatment policy is unknown or a counterfactual analysis is needed. To handle these limitations, we model the treatments and outcomes jointly in continuous time, by combining Gaussian processes and point processes. Our model enables the estimation of a treatment policy from observational sequences of treatments and outcomes, and it can predict the interventional and counterfactual progression of the outcome after an intervention on the treatment policy (in contrast with the causal effect of a single treatment). We show with real-world and semi-synthetic data on blood glucose progression that our method can answer causal queries more accurately than existing alternatives.

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ICML Conference 2023 Conference Paper

Improving Hyperparameter Learning under Approximate Inference in Gaussian Process Models

Rui Li
S. T. John
Arno Solin

Approximate inference in Gaussian process (GP) models with non-conjugate likelihoods gets entangled with the learning of the model hyperparameters. We improve hyperparameter learning in GP models and focus on the interplay between variational inference (VI) and the learning target. While VI’s lower bound to the marginal likelihood is a suitable objective for inferring the approximate posterior, we show that a direct approximation of the marginal likelihood as in Expectation Propagation (EP) is a better learning objective for hyperparameter optimization. We design a hybrid training procedure to bring the best of both worlds: it leverages conjugate-computation VI for inference and uses an EP-like marginal likelihood approximation for hyperparameter learning. We compare VI, EP, Laplace approximation, and our proposed training procedure and empirically demonstrate the effectiveness of our proposal across a wide range of data sets.

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ICML Conference 2023 Conference Paper

Memory-Based Dual Gaussian Processes for Sequential Learning

Paul Edmund Chang
Prakhar Verma
S. T. John
Arno Solin
Mohammad Emtiyaz Khan

Sequential learning with Gaussian processes (GPs) is challenging when access to past data is limited, for example, in continual and active learning. In such cases, errors can accumulate over time due to inaccuracies in the posterior, hyperparameters, and inducing points, making accurate learning challenging. Here, we present a method to keep all such errors in check using the recently proposed dual sparse variational GP. Our method enables accurate inference for generic likelihoods and improves learning by actively building and updating a memory of past data. We demonstrate its effectiveness in several applications involving Bayesian optimization, active learning, and continual learning.

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UAI Conference 2020 Conference Paper

Amortized variance reduction for doubly stochastic objective

Ayman Boustati
Sattar Vakili
James Hensman
S. T. John

Approximate inference in complex probabilistic models such as deep Gaussian processes requires the optimisation of doubly stochastic objective functions. These objectives incorporate randomness both from mini-batch subsampling of the data and from Monte Carlo estimation of expectations. If the gradient variance is high, the stochastic optimisation problem becomes difficult with a slow rate of convergence. Control variates can be used to reduce the variance, but past approaches do not take into account how mini-batch stochasticity affects sampling stochasticity, resulting in sub-optimal variance reduction. We propose a new approach in which we use a recognition network to cheaply approximate the optimal control variate for each mini-batch, with no additional model gradient computations. We illustrate the properties of this proposal and test its performance on logistic regression and deep Gaussian processes.

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ICML Conference 2018 Conference Paper

Large-Scale Cox Process Inference using Variational Fourier Features

S. T. John
James Hensman

Gaussian process modulated Poisson processes provide a flexible framework for modeling spatiotemporal point patterns. So far this had been restricted to one dimension, binning to a pre-determined grid, or small data sets of up to a few thousand data points. Here we introduce Cox process inference based on Fourier features. This sparse representation induces global rather than local constraints on the function space and is computationally efficient. This allows us to formulate a grid-free approximation that scales well with the number of data points and the size of the domain. We demonstrate that this allows MCMC approximations to the non-Gaussian posterior. In practice, we find that Fourier features have more consistent optimization behavior than previous approaches. Our approximate Bayesian method can fit over 100 000 events with complex spatiotemporal patterns in three dimensions on a single GPU.

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