Effectively modeling phenomena present in highly nonlinear dynamical systems whilst also accurately quantifying uncertainty is a challenging task, which often requires problem-specific techniques. We present a novel, domain-agnostic approach to tackling this problem, using compositions of physics-informed random features, derived from ordinary differential equations. The architecture of our model leverages recent advances in approximate inference for deep Gaussian processes, such as layer-wise weight-space approximations which allow us to incorporate random Fourier features, and stochastic variational inference for approximate Bayesian inference. We provide evidence that our model is capable of capturing highly nonlinear behaviour in real-world multivariate time series data. In addition, we find that our approach achieves comparable performance to a number of other probabilistic models on benchmark regression tasks.
In this work, we study the problem of clustering survival data $-$ a challenging and so far under-explored task. We introduce a novel semi-supervised probabilistic approach to cluster survival data by leveraging recent advances in stochastic gradient variational inference. In contrast to previous work, our proposed method employs a deep generative model to uncover the underlying distribution of both the explanatory variables and censored survival times. We compare our model to the related work on clustering and mixture models for survival data in comprehensive experiments on a wide range of synthetic, semi-synthetic, and real-world datasets, including medical imaging data. Our method performs better at identifying clusters and is competitive at predicting survival times. Relying on novel generative assumptions, the proposed model offers a holistic perspective on clustering survival data and holds a promise of discovering subpopulations whose survival is regulated by different generative mechanisms.
This paper introduces a method for the nonparametric Bayesian learning of nonlinear operators, through the use of the Volterra series with kernels represented using Gaussian processes (GPs), which we term the nonparametric Volterra kernels model (NVKM). When the input function to the operator is unobserved and has a GP prior, the NVKM constitutes a powerful method for both single and multiple output regression, and can be viewed as a nonlinear and nonparametric latent force model. When the input function is observed, the NVKM can be used to perform Bayesian system identification. We use recent advances in efficient sampling of explicit functions from GPs to map process realisations through the Volterra series without resorting to numerical integration, allowing scalability through doubly stochastic variational inference, and avoiding the need for Gaussian approximations of the output processes. We demonstrate the performance of the model for both multiple output regression and system identification using standard benchmarks.
We propose probabilistic task modelling -- a generative probabilistic model for collections of tasks used in meta-learning. The proposed model combines variational auto-encoding and latent Dirichlet allocation to model each task as a mixture of Gaussian distribution in an embedding space. Such modelling provides an explicit representation of a task through its task-theme mixture. We present an efficient approximation inference technique based on variational inference method for empirical Bayes parameter estimation. We perform empirical evaluations to validate the task uncertainty and task distance produced by the proposed method through correlation diagrams of the prediction accuracy on testing tasks. We also carry out experiments of task selection in meta-learning to demonstrate how the task relatedness inferred from the proposed model help to facilitate meta-learning algorithms.
A critical challenge faced by supervised word sense disambiguation (WSD) is the lack of large annotated datasets with sufficient coverage of words in their diversity of senses. This inspired recent research on few-shot WSD using meta-learning. While such work has successfully applied meta-learning to learn new word senses from very few examples, its performance still lags behind its fully supervised counterpart. Aiming to further close this gap, we propose a model of semantic memory for WSD in a meta-learning setting. Semantic memory encapsulates prior experiences seen throughout the lifetime of the model, which aids better generalization in limited data settings. Our model is based on hierarchical variational inference and incorporates an adaptive memory update rule via a hypernetwork. We show our model advances the state of the art in few-shot WSD, supports effective learning in extremely data scarce (e.g. one-shot) scenarios and produces meaning prototypes that capture similar senses of distinct words.
We study the role of information complexity in privacy leakage about an attribute of an adversary's interest, which is not known a priori to the system designer. Considering the supervised representation learning setup and using neural networks to parameterize the variational bounds of information quantities, we study the impact of the following factors on the amount of information leakage: information complexity regularizer weight, latent space dimension, the cardinalities of the known utility and unknown sensitive attribute sets, the correlation between utility and sensitive attributes, and a potential bias in a sensitive attribute of adversary's interest. We conduct extensive experiments on Colored-MNIST and CelebA datasets to evaluate the effect of information complexity on the amount of intrinsic leakage.
Quantification of uncertainty in point cloud matching is critical in many tasks such as pose estimation, sensor fusion, and grasping. Iterative closest point (ICP) is a commonly used pose estimation algorithm which provides a point estimate of the transformation between two point clouds. There are many sources of uncertainty in this process that may arise due to sensor noise, ambiguous environment, and occlusion. However, for safety critical problems such as autonomous driving, a point estimate of the pose transformation is not sufficient as it does not provide information about the multiple solutions. Current probabilistic ICP methods usually do not capture all sources of uncertainty and may provide unreliable transformation estimates which can have a detrimental effect in state estimation or decision making tasks that use this information. In this work we propose a new algorithm to align two point clouds that can precisely estimate the uncertainty of ICP's transformation parameters. We develop a Stein variational inference framework with gradient based optimization of ICP's cost function. The method provides a non-parametric estimate of the transformation, can model complex multi-modal distributions, and can be effectively parallelized on a GPU. Experiments using 3D kinect data as well as sparse indoor/outdoor LiDAR data show that our method is capable of efficiently producing accurate pose uncertainty estimates.
Modern time series data often display complex nonlinear dependencies along with irregular regime-switching behaviors. These features present technical challenges in modeling, inference, and in offering insightful understanding into the underlying stochastic phenomena. To tackle these challenges, we introduce a novel modeling framework known as the Deep Switching State Space Model (DS$^3$M). This framework is engineered to make accurate forecasts for such time series while adeptly identifying the irregular regimes hidden within the dynamics. These identifications not only have significant economic ramifications but also contribute to a deeper understanding of the underlying phenomena. In DS$^3$M, the architecture employs discrete latent variables to represent regimes and continuous latent variables to account for random driving factors. By melding a Recurrent Neural Network (RNN) with a nonlinear Switching State Space Model (SSSM), we manage to capture the nonlinear dependencies and irregular regime-switching behaviors, governed by a Markov chain and parameterized using multilayer perceptrons. We validate the effectiveness and regime identification capabilities of DS$^3$M through short- and long-term forecasting tests on a wide array of simulated and real-world datasets, spanning sectors such as healthcare, economics, traffic, meteorology, and energy. Experimental results reveal that DS$^3$M outperforms several state-of-the-art models in terms of forecasting accuracy, while providing meaningful regime identifications.
This paper is concerned about a learning algorithm for a probabilistic model of spiking neural networks (SNNs). Jimenez Rezende & Gerstner (2014) proposed a stochastic variational inference algorithm to train SNNs with hidden neurons. The algorithm updates the variational distribution using the score function gradient estimator, whose high variance often impedes the whole learning algorithm. This paper presents an alternative gradient estimator for SNNs based on the path-wise gradient estimator. The main technical difficulty is a lack of a general method to differentiate a realization of an arbitrary point process, which is necessary to derive the path-wise gradient estimator. We develop a differentiable point process, which is the technical highlight of this paper, and apply it to derive the path-wise gradient estimator for SNNs. We investigate the effectiveness of our gradient estimator through numerical simulation.
The main challenge in Bayesian models is to determine the posterior for the model parameters. Already, in models with only one or few parameters, the analytical posterior can only be determined in special settings. In Bayesian neural networks, variational inference is widely used to approximate difficult-to-compute posteriors by variational distributions. Usually, Gaussians are used as variational distributions (Gaussian-VI) which limits the quality of the approximation due to their limited flexibility. Transformation models on the other hand are flexible enough to fit any distribution. Here we present transformation model-based variational inference (TM-VI) and demonstrate that it allows to accurately approximate complex posteriors in models with one parameter and also works in a mean-field fashion for multi-parameter models like neural networks.
We adopt the interpretability offered by a parametric, Hawkes-process-inspired conditional probability mass function for the marks and apply variational inference techniques to derive a general and scalable inferential framework for marked point processes. The framework can handle both exchangeable and non-exchangeable event sequences with minimal tuning and without any pre-training. This contrasts with many parametric and non-parametric state-of-the-art methods that typically require pre-training and/or careful tuning, and can only handle exchangeable event sequences. The framework's competitive computational and predictive performance against other state-of-the-art methods are illustrated through real data experiments. Its attractiveness for large-scale applications is demonstrated through a case study involving all events occurring in an English Premier League season.
Variational auto-encoders (VAEs) are a powerful approach to unsupervised learning. They enable scalable approximate posterior inference in latent-variable models using variational inference (VI). A VAE posits a variational family parameterized by a deep neural network called an encoder that takes data as input. This encoder is shared across all the observations, which amortizes the cost of inference. However the encoder of a VAE has the undesirable property that it maps a given observation and a semantics-preserving transformation of it to different latent representations. This "inconsistency" of the encoder lowers the quality of the learned representations, especially for downstream tasks, and also negatively affects generalization. In this paper, we propose a regularization method to enforce consistency in VAEs. The idea is to minimize the Kullback-Leibler (KL) divergence between the variational distribution when conditioning on the observation and the variational distribution when conditioning on a random semantic-preserving transformation of this observation. This regularization is applicable to any VAE. In our experiments we apply it to four different VAE variants on several benchmark datasets and found it always improves the quality of the learned representations but also leads to better generalization. In particular, when applied to the Nouveau Variational Auto-Encoder (NVAE), our regularization method yields state-of-the-art performance on MNIST and CIFAR-10. We also applied our method to 3D data and found it learns representations of superior quality as measured by accuracy on a downstream classification task.
We report on the potential for using algorithms for non-negative matrix factorization (NMF) to improve parameter estimation in topic models. While several papers have studied connections between NMF and topic models, none have suggested leveraging these connections to develop new algorithms for fitting topic models. NMF avoids the "sum-to-one" constraints on the topic model parameters, resulting in an optimization problem with simpler structure and more efficient computations. Building on recent advances in optimization algorithms for NMF, we show that first solving the NMF problem then recovering the topic model fit can produce remarkably better fits, and in less time, than standard algorithms for topic models. While we focus primarily on maximum likelihood estimation, we show that this approach also has the potential to improve variational inference for topic models. Our methods are implemented in the R package fastTopics.
Bayesian structure learning allows inferring Bayesian network structure from data while reasoning about the epistemic uncertainty -- a key element towards enabling active causal discovery and designing interventions in real world systems. In this work, we propose a general, fully differentiable framework for Bayesian structure learning (DiBS) that operates in the continuous space of a latent probabilistic graph representation. Contrary to existing work, DiBS is agnostic to the form of the local conditional distributions and allows for joint posterior inference of both the graph structure and the conditional distribution parameters. This makes our formulation directly applicable to posterior inference of complex Bayesian network models, e.g., with nonlinear dependencies encoded by neural networks. Using DiBS, we devise an efficient, general purpose variational inference method for approximating distributions over structural models. In evaluations on simulated and real-world data, our method significantly outperforms related approaches to joint posterior inference.
Physical processes, camera movement, and unpredictable environmental conditions like the presence of dust can induce noise and artifacts in video feeds. We observe that popular unsupervised MOT methods are dependent on noise-free inputs. We show that the addition of a small amount of artificial random noise causes a sharp degradation in model performance on benchmark metrics. We resolve this problem by introducing a robust unsupervised multi-object tracking (MOT) model: AttU-Net. The proposed single-head attention model helps limit the negative impact of noise by learning visual representations at different segment scales. AttU-Net shows better unsupervised MOT tracking performance over variational inference-based state-of-the-art baselines. We evaluate our method in the MNIST-MOT and the Atari game video benchmark. We also provide two extended video datasets: ``Kuzushiji-MNIST MOT'' which consists of moving Japanese characters and ``Fashion-MNIST MOT'' to validate the effectiveness of the MOT models.
AtomAI is an open-source software package bridging instrument-specific Python libraries, deep learning, and simulation tools into a single ecosystem. AtomAI allows direct applications of the deep convolutional neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically-resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders (VAEs). The latter consists of VAEs with rotational and (optionally) translational invariance for unsupervised and class-conditioned disentanglement of categorical and continuous data representations. In addition, AtomAI provides utilities for mapping structure-property relationships via im2spec and spec2im type of encoder-decoder models. Finally, AtomAI allows seamless connection to the first principles modeling with a Python interface, including molecular dynamics and density functional theory calculations on the inferred atomic position. While the majority of applications to date were based on atomically resolved electron microscopy, the flexibility of AtomAI allows straightforward extension towards the analysis of mesoscopic imaging data once the labels and feature identification workflows are established/available. The source code and example notebooks are available at https://github.com/pycroscopy/atomai.
Observing a set of images and their corresponding paragraph-captions, a challenging task is to learn how to produce a semantically coherent paragraph to describe the visual content of an image. Inspired by recent successes in integrating semantic topics into this task, this paper develops a plug-and-play hierarchical-topic-guided image paragraph generation framework, which couples a visual extractor with a deep topic model to guide the learning of a language model. To capture the correlations between the image and text at multiple levels of abstraction and learn the semantic topics from images, we design a variational inference network to build the mapping from image features to textual captions. To guide the paragraph generation, the learned hierarchical topics and visual features are integrated into the language model, including Long Short-Term Memory (LSTM) and Transformer, and jointly optimized. Experiments on public datasets demonstrate that the proposed models, which are competitive with many state-of-the-art approaches in terms of standard evaluation metrics, can be used to both distill interpretable multi-layer semantic topics and generate diverse and coherent captions. We release our code at https://github.com/DandanGuo1993/VTCM-based-image-paragraph-caption.git
Bayesian inference on non-Gaussian data is often non-analytic and requires computationally expensive approximations such as sampling or variational inference. We propose an approximate inference framework primarily designed to be computationally cheap while still achieving high approximation quality. The concept, which we call Laplace Matching, involves closed-form, approximate, bi-directional transformations between the parameter spaces of exponential families. These are constructed from Laplace approximations under custom-designed basis transformations. The mappings can then be leveraged to effectively turn a latent Gaussian distribution into an approximate conjugate prior to a rich class of observable variables. This allows us to train latent Gaussian models such as Gaussian Processes on non-Gaussian data at nearly no additional cost. The method can be thought of as a pre-processing step which can be implemented in <5 lines of code and runs in less than a second. Furthermore, Laplace Matching yields a simple way to group similar data points together, e.g. to produce inducing points for GPs. We empirically evaluate the method with experiments for four different exponential distributions, namely the Beta, Gamma, Dirichlet and inverse Wishart, showing approximation quality comparable to state-of-the-art approximate inference techniques at a drastic reduction in computational cost.
Motivation: Electronic health record (EHR) data provides a new venue to elucidate disease comorbidities and latent phenotypes for precision medicine. To fully exploit its potential, a realistic data generative process of the EHR data needs to be modelled. We present MixEHR-S to jointly infer specialist-disease topics from the EHR data. As the key contribution, we model the specialist assignments and ICD-coded diagnoses as the latent topics based on patient's underlying disease topic mixture in a novel unified supervised hierarchical Bayesian topic model. For efficient inference, we developed a closed-form collapsed variational inference algorithm to learn the model distributions of MixEHR-S. We applied MixEHR-S to two independent large-scale EHR databases in Quebec with three targeted applications: (1) Congenital Heart Disease (CHD) diagnostic prediction among 154,775 patients; (2) Chronic obstructive pulmonary disease (COPD) diagnostic prediction among 73,791 patients; (3) future insulin treatment prediction among 78,712 patients diagnosed with diabetes as a mean to assess the disease exacerbation. In all three applications, MixEHR-S conferred clinically meaningful latent topics among the most predictive latent topics and achieved superior target prediction accuracy compared to the existing methods, providing opportunities for prioritizing high-risk patients for healthcare services. MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS
The posterior over Bayesian neural network (BNN) parameters is extremely high-dimensional and non-convex. For computational reasons, researchers approximate this posterior using inexpensive mini-batch methods such as mean-field variational inference or stochastic-gradient Markov chain Monte Carlo (SGMCMC). To investigate foundational questions in Bayesian deep learning, we instead use full-batch Hamiltonian Monte Carlo (HMC) on modern architectures. We show that (1) BNNs can achieve significant performance gains over standard training and deep ensembles; (2) a single long HMC chain can provide a comparable representation of the posterior to multiple shorter chains; (3) in contrast to recent studies, we find posterior tempering is not needed for near-optimal performance, with little evidence for a "cold posterior" effect, which we show is largely an artifact of data augmentation; (4) BMA performance is robust to the choice of prior scale, and relatively similar for diagonal Gaussian, mixture of Gaussian, and logistic priors; (5) Bayesian neural networks show surprisingly poor generalization under domain shift; (6) while cheaper alternatives such as deep ensembles and SGMCMC methods can provide good generalization, they provide distinct predictive distributions from HMC. Notably, deep ensemble predictive distributions are similarly close to HMC as standard SGLD, and closer than standard variational inference.