arXiv subjects

Jan-Willem van de Meent

Publications and source records attributed to Jan-Willem van de Meent.

At least 55 records · Page 3Linked to original sources

arXiv2021

An Introduction to Probabilistic Programming

This book is a graduate-level introduction to probabilistic programming. It not only provides a thorough background for anyone wishing to use a probabilistic programming system, but also introduces the techniques needed to design and build these systems. It is aimed at people who have an undergraduate-level understanding of either or, ideally, both probabilistic machine learning and programming languages. We start with a discussion of model-based reasoning and explain why conditioning is a foundational computation central to the fields of probabilistic machine learning and artificial intelligence. We then introduce a first-order probabilistic programming language (PPL) whose programs correspond to graphical models with a known, finite, set of random variables. In the context of this PPL we introduce fundamental inference algorithms and describe how they can be implemented. We then turn to higher-order probabilistic programming languages. Programs in such languages can define models with dynamic computation graphs, which may not instantiate the same set of random variables in each execution. Inference requires methods that generate samples by repeatedly evaluating the program. Foundational algorithms for this kind of language are discussed in the context of an interface between program executions and an inference controller. Finally we consider the intersection of probabilistic and differentiable programming. We begin with a discussion of automatic differentiation, and how it can be used to implement efficient inference methods based on Hamiltonian Monte Carlo. We then discuss gradient-based maximum likelihood estimation in programs that are parameterized using neural networks, how to amortize inference using by learning neural approximations to the program posterior, and how language features impact the design of deep probabilistic programming systems.

stat.ML↗

arXiv2021

Disentangling Representations of Text by Masking Transformers

Representations from large pretrained models such as BERT encode a range of features into monolithic vectors, affording strong predictive accuracy across a multitude of downstream tasks. In this paper we explore whether it is possible to learn disentangled representations by identifying existing subnetworks within pretrained models that encode distinct, complementary aspect representations. Concretely, we learn binary masks over transformer weights or hidden units to uncover subsets of features that correlate with a specific factor of variation; this eliminates the need to train a disentangled model from scratch for a particular task. We evaluate this method with respect to its ability to disentangle representations of sentiment from genre in movie reviews, "toxicity" from dialect in Tweets, and syntax from semantics. By combining masking with magnitude pruning we find that we can identify sparse subnetworks within BERT that strongly encode particular aspects (e.g., toxicity) while only weakly encoding others (e.g., race). Moreover, despite only learning masks, we find that disentanglement-via-masking performs as well as -- and often better than -- previously proposed methods based on variational autoencoders and adversarial training.

cs.CL↗

arXiv2021

Conjugate Energy-Based Models

In this paper, we propose conjugate energy-based models (CEBMs), a new class of energy-based models that define a joint density over data and latent variables. The joint density of a CEBM decomposes into an intractable distribution over data and a tractable posterior over latent variables. CEBMs have similar use cases as variational autoencoders, in the sense that they learn an unsupervised mapping from data to latent variables. However, these models omit a generator network, which allows them to learn more flexible notions of similarity between data points. Our experiments demonstrate that conjugate EBMs achieve competitive results in terms of image modelling, predictive power of latent space, and out-of-domain detection on a variety of datasets.

cs.LG↗

arXiv2021

Nested Variational Inference

We develop nested variational inference (NVI), a family of methods that learn proposals for nested importance samplers by minimizing an forward or reverse KL divergence at each level of nesting. NVI is applicable to many commonly-used importance sampling strategies and provides a mechanism for learning intermediate densities, which can serve as heuristics to guide the sampler. Our experiments apply NVI to (a) sample from a multimodal distribution using a learned annealing path (b) learn heuristics that approximate the likelihood of future observations in a hidden Markov model and (c) to perform amortized inference in hierarchical deep generative models. We observe that optimizing nested objectives leads to improved sample quality in terms of log average weight and effective sample size.

stat.ML↗

arXiv2021

Learning Proposals for Probabilistic Programs with Inference Combinators

We develop operators for construction of proposals in probabilistic programs, which we refer to as inference combinators. Inference combinators define a grammar over importance samplers that compose primitive operations such as application of a transition kernel and importance resampling. Proposals in these samplers can be parameterized using neural networks, which in turn can be trained by optimizing variational objectives. The result is a framework for user-programmable variational methods that are correct by construction and can be tailored to specific models. We demonstrate the flexibility of this framework by implementing advanced variational methods based on amortized Gibbs sampling and annealing.

stat.ML↗

arXiv2021

On the Impact of Random Seeds on the Fairness of Clinical Classifiers

Recent work has shown that fine-tuning large networks is surprisingly sensitive to changes in random seed(s). We explore the implications of this phenomenon for model fairness across demographic groups in clinical prediction tasks over electronic health records (EHR) in MIMIC-III -- the standard dataset in clinical NLP research. Apparent subgroup performance varies substantially for seeds that yield similar overall performance, although there is no evidence of a trade-off between overall and subgroup performance. However, we also find that the small sample sizes inherent to looking at intersections of minority groups and somewhat rare conditions limit our ability to accurately estimate disparities. Further, we find that jointly optimizing for high overall performance and low disparities does not yield statistically significant improvements. Our results suggest that fairness work using MIMIC-III should carefully account for variations in apparent differences that may arise from stochasticity and small sample sizes.

cs.CL↗

arXiv2021

Rate-Regularization and Generalization in VAEs

Variational autoencoders optimize an objective that combines a reconstruction loss (the distortion) and a KL term (the rate). The rate is an upper bound on the mutual information, which is often interpreted as a regularizer that controls the degree of compression. We here examine whether inclusion of the rate also acts as an inductive bias that improves generalization. We perform rate-distortion analyses that control the strength of the rate term, the network capacity, and the difficulty of the generalization problem. Decreasing the strength of the rate paradoxically improves generalization in most settings, and reducing the mutual information typically leads to underfitting. Moreover, we show that generalization continues to improve even after the mutual information saturates, indicating that the gap on the bound (i.e. the KL divergence relative to the inference marginal) affects generalization. This suggests that the standard Gaussian prior is not an inductive bias that typically aids generalization, prompting work to understand what choices of priors improve generalization in VAEs.

cs.LG↗

arXiv2021

Generator Surgery for Compressed Sensing

Image recovery from compressive measurements requires a signal prior for the images being reconstructed. Recent work has explored the use of deep generative models with low latent dimension as signal priors for such problems. However, their recovery performance is limited by high representation error. We introduce a method for achieving low representation error using generators as signal priors. Using a pre-trained generator, we remove one or more initial blocks at test time and optimize over the new, higher-dimensional latent space to recover a target image. Experiments demonstrate significantly improved reconstruction quality for a variety of network architectures. This approach also works well for out-of-training-distribution images and is competitive with other state-of-the-art methods. Our experiments show that test-time architectural modifications can greatly improve the recovery quality of generator signal priors for compressed sensing.

cs.CV↗

arXiv2021

Action Priors for Large Action Spaces in Robotics

In robotics, it is often not possible to learn useful policies using pure model-free reinforcement learning without significant reward shaping or curriculum learning. As a consequence, many researchers rely on expert demonstrations to guide learning. However, acquiring expert demonstrations can be expensive. This paper proposes an alternative approach where the solutions of previously solved tasks are used to produce an action prior that can facilitate exploration in future tasks. The action prior is a probability distribution over actions that summarizes the set of policies found solving previous tasks. Our results indicate that this approach can be used to solve robotic manipulation problems that would otherwise be infeasible without expert demonstrations. Source code is available at \url{https://github.com/ondrejba/action_priors}.

cs.RO↗

arXiv2021

Learning Discrete State Abstractions With Deep Variational Inference

Abstraction is crucial for effective sequential decision making in domains with large state spaces. In this work, we propose an information bottleneck method for learning approximate bisimulations, a type of state abstraction. We use a deep neural encoder to map states onto continuous embeddings. We map these embeddings onto a discrete representation using an action-conditioned hidden Markov model, which is trained end-to-end with the neural network. Our method is suited for environments with high-dimensional states and learns from a stream of experience collected by an agent acting in a Markov decision process. Through this learned discrete abstract model, we can efficiently plan for unseen goals in a multi-goal Reinforcement Learning setting. We test our method in simplified robotic manipulation domains with image states. We also compare it against previous model-based approaches to finding bisimulations in discrete grid-world-like environments. Source code is available at https://github.com/ondrejba/discrete_abstractions.

cs.LG↗

arXiv2020

Neural Topographic Factor Analysis for fMRI Data

Neuroimaging studies produce gigabytes of spatio-temporal data for a small number of participants and stimuli. Rarely do researchers attempt to model and examine how individual participants vary from each other -- a question that should be addressable even in small samples given the right statistical tools. We propose Neural Topographic Factor Analysis (NTFA), a probabilistic factor analysis model that infers embeddings for participants and stimuli. These embeddings allow us to reason about differences between participants and stimuli as signal rather than noise. We evaluate NTFA on data from an in-house pilot experiment, as well as two publicly available datasets. We demonstrate that inferring representations for participants and stimuli improves predictive generalization to unseen data when compared to previous topographic methods. We also demonstrate that the inferred latent factor representations are useful for downstream tasks such as multivoxel pattern analysis and functional connectivity.

cs.LG↗

arXiv2020

Deep Markov Spatio-Temporal Factorization

We introduce deep Markov spatio-temporal factorization (DMSTF), a generative model for dynamical analysis of spatio-temporal data. Like other factor analysis methods, DMSTF approximates high dimensional data by a product between time dependent weights and spatially dependent factors. These weights and factors are in turn represented in terms of lower dimensional latents inferred using stochastic variational inference. The innovation in DMSTF is that we parameterize weights in terms of a deep Markovian prior extendable with a discrete latent, which is able to characterize nonlinear multimodal temporal dynamics, and perform multidimensional time series forecasting. DMSTF learns a low dimensional spatial latent to generatively parameterize spatial factors or their functional forms in order to accommodate high spatial dimensionality. We parameterize the corresponding variational distribution using a bidirectional recurrent network in the low-level latent representations. This results in a flexible family of hierarchical deep generative factor analysis models that can be extended to perform time series clustering or perform factor analysis in the presence of a control signal. Our experiments, which include simulated and real-world data, demonstrate that DMSTF outperforms related methodologies in terms of predictive performance for unseen data, reveals meaningful clusters in the data, and performs forecasting in a variety of domains with potentially nonlinear temporal transitions.

cs.LG↗

arXiv2020

Amortized Population Gibbs Samplers with Neural Sufficient Statistics

We develop amortized population Gibbs (APG) samplers, a class of scalable methods that frames structured variational inference as adaptive importance sampling. APG samplers construct high-dimensional proposals by iterating over updates to lower-dimensional blocks of variables. We train each conditional proposal by minimizing the inclusive KL divergence with respect to the conditional posterior. To appropriately account for the size of the input data, we develop a new parameterization in terms of neural sufficient statistics. Experiments show that APG samplers can train highly structured deep generative models in an unsupervised manner, and achieve substantial improvements in inference accuracy relative to standard autoencoding variational methods.

stat.ML↗

arXiv2020

Query-Focused EHR Summarization to Aid Imaging Diagnosis

Electronic Health Records (EHRs) provide vital contextual information to radiologists and other physicians when making a diagnosis. Unfortunately, because a given patient's record may contain hundreds of notes and reports, identifying relevant information within these in the short time typically allotted to a case is very difficult. We propose and evaluate models that extract relevant text snippets from patient records to provide a rough case summary intended to aid physicians considering one or more diagnoses. This is hard because direct supervision (i.e., physician annotations of snippets relevant to specific diagnoses in medical records) is prohibitively expensive to collect at scale. We propose a distantly supervised strategy in which we use groups of International Classification of Diseases (ICD) codes observed in 'future' records as noisy proxies for 'downstream' diagnoses. Using this we train a transformer-based neural model to perform extractive summarization conditioned on potential diagnoses. This model defines an attention mechanism that is conditioned on potential diagnoses (queries) provided by the diagnosing physician. We train (via distant supervision) and evaluate variants of this model on EHR data from Brigham and Women's Hospital in Boston and MIMIC-III (the latter to facilitate reproducibility). Evaluations performed by radiologists demonstrate that these distantly supervised models yield better extractive summaries than do unsupervised approaches. Such models may aid diagnosis by identifying sentences in past patient reports that are clinically relevant to a potential diagnosis.

cs.LG↗

arXiv2020

Nested Reasoning About Autonomous Agents Using Probabilistic Programs

As autonomous agents become more ubiquitous, they will eventually have to reason about the plans of other agents, which is known as theory of mind reasoning. We develop a planning-as-inference framework in which agents perform nested simulation to reason about the behavior of other agents in an online manner. As a concrete application of this framework, we use probabilistic programs to model a high-uncertainty variant of pursuit-evasion games in which an agent must make inferences about the other agents' plans to craft counter-plans. Our probabilistic programs incorporate a variety of complex primitives such as field-of-view calculations and path planners, which enable us to model quasi-realistic scenarios in a computationally tractable manner. We perform extensive experimental evaluations which establish a variety of rational behaviors and quantify how allocating computation across levels of nesting affects the variance of our estimators.

cs.AI↗

arXiv2019

Structured Neural Topic Models for Reviews

We present Variational Aspect-based Latent Topic Allocation (VALTA), a family of autoencoding topic models that learn aspect-based representations of reviews. VALTA defines a user-item encoder that maps bag-of-words vectors for combined reviews associated with each paired user and item onto structured embeddings, which in turn define per-aspect topic weights. We model individual reviews in a structured manner by inferring an aspect assignment for each sentence in a given review, where the per-aspect topic weights obtained by the user-item encoder serve to define a mixture over topics, conditioned on the aspect. The result is an autoencoding neural topic model for reviews, which can be trained in a fully unsupervised manner to learn topics that are structured into aspects. Experimental evaluation on large number of datasets demonstrates that aspects are interpretable, yield higher coherence scores than non-structured autoencoding topic model variants, and can be utilized to perform aspect-based comparison and genre discovery.

cs.CL↗

arXiv2018

Can VAEs Generate Novel Examples?

An implicit goal in works on deep generative models is that such models should be able to generate novel examples that were not previously seen in the training data. In this paper, we investigate to what extent this property holds for widely employed variational autoencoder (VAE) architectures. VAEs maximize a lower bound on the log marginal likelihood, which implies that they will in principle overfit the training data when provided with a sufficiently expressive decoder. In the limit of an infinite capacity decoder, the optimal generative model is a uniform mixture over the training data. More generally, an optimal decoder should output a weighted average over the examples in the training data, where the magnitude of the weights is determined by the proximity in the latent space. This leads to the hypothesis that, for a sufficiently high capacity encoder and decoder, the VAE decoder will perform nearest-neighbor matching according to the coordinates in the latent space. To test this hypothesis, we investigate generalization on the MNIST dataset. We consider both generalization to new examples of previously seen classes, and generalization to the classes that were withheld from the training set. In both cases, we find that reconstructions are closely approximated by nearest neighbors for higher-dimensional parameterizations. When generalizing to unseen classes however, lower-dimensional parameterizations offer a clear advantage.

cs.LG↗

arXiv2018

Structured Disentangled Representations

Deep latent-variable models learn representations of high-dimensional data in an unsupervised manner. A number of recent efforts have focused on learning representations that disentangle statistically independent axes of variation by introducing modifications to the standard objective function. These approaches generally assume a simple diagonal Gaussian prior and as a result are not able to reliably disentangle discrete factors of variation. We propose a two-level hierarchical objective to control relative degree of statistical independence between blocks of variables and individual variables within blocks. We derive this objective as a generalization of the evidence lower bound, which allows us to explicitly represent the trade-offs between mutual information between data and representation, KL divergence between representation and prior, and coverage of the support of the empirical data distribution. Experiments on a variety of datasets demonstrate that our objective can not only disentangle discrete variables, but that doing so also improves disentanglement of other variables and, importantly, generalization even to unseen combinations of factors.

stat.ML↗