arXiv subjects

Frank Wood

Publications and source records attributed to Frank Wood.

At least 73 records · Page 4Linked to original sources

arXiv2020

Improved Few-Shot Visual Classification

Few-shot learning is a fundamental task in computer vision that carries the promise of alleviating the need for exhaustively labeled data. Most few-shot learning approaches to date have focused on progressively more complex neural feature extractors and classifier adaptation strategies, as well as the refinement of the task definition itself. In this paper, we explore the hypothesis that a simple class-covariance-based distance metric, namely the Mahalanobis distance, adopted into a state of the art few-shot learning approach (CNAPS) can, in and of itself, lead to a significant performance improvement. We also discover that it is possible to learn adaptive feature extractors that allow useful estimation of the high dimensional feature covariances required by this metric from surprisingly few samples. The result of our work is a new "Simple CNAPS" architecture which has up to 9.2% fewer trainable parameters than CNAPS and performs up to 6.1% better than state of the art on the standard few-shot image classification benchmark dataset.

cs.CV↗

arXiv2020

Coping With Simulators That Don't Always Return

Deterministic models are approximations of reality that are easy to interpret and often easier to build than stochastic alternatives. Unfortunately, as nature is capricious, observational data can never be fully explained by deterministic models in practice. Observation and process noise need to be added to adapt deterministic models to behave stochastically, such that they are capable of explaining and extrapolating from noisy data. We investigate and address computational inefficiencies that arise from adding process noise to deterministic simulators that fail to return for certain inputs; a property we describe as "brittle." We show how to train a conditional normalizing flow to propose perturbations such that the simulator succeeds with high probability, increasing computational efficiency.

cs.LG↗

arXiv2020

Efficient Probabilistic Inference in the Quest for Physics Beyond the Standard Model

We present a novel probabilistic programming framework that couples directly to existing large-scale simulators through a cross-platform probabilistic execution protocol, which allows general-purpose inference engines to record and control random number draws within simulators in a language-agnostic way. The execution of existing simulators as probabilistic programs enables highly interpretable posterior inference in the structured model defined by the simulator code base. We demonstrate the technique in particle physics, on a scientifically accurate simulation of the tau lepton decay, which is a key ingredient in establishing the properties of the Higgs boson. Inference efficiency is achieved via inference compilation where a deep recurrent neural network is trained to parameterize proposal distributions and control the stochastic simulator in a sequential importance sampling scheme, at a fraction of the computational cost of a Markov chain Monte Carlo baseline.

cs.LG↗

arXiv2019

Attention for Inference Compilation

We present a new approach to automatic amortized inference in universal probabilistic programs which improves performance compared to current methods. Our approach is a variation of inference compilation (IC) which leverages deep neural networks to approximate a posterior distribution over latent variables in a probabilistic program. A challenge with existing IC network architectures is that they can fail to model long-range dependencies between latent variables. To address this, we introduce an attention mechanism that attends to the most salient variables previously sampled in the execution of a probabilistic program. We demonstrate that the addition of attention allows the proposal distributions to better match the true posterior, enhancing inference about latent variables in simulators.

cs.LG↗

arXiv2019

Revisiting Reweighted Wake-Sleep for Models with Stochastic Control Flow

Stochastic control-flow models (SCFMs) are a class of generative models that involve branching on choices from discrete random variables. Amortized gradient-based learning of SCFMs is challenging as most approaches targeting discrete variables rely on their continuous relaxations---which can be intractable in SCFMs, as branching on relaxations requires evaluating all (exponentially many) branching paths. Tractable alternatives mainly combine REINFORCE with complex control-variate schemes to improve the variance of naive estimators. Here, we revisit the reweighted wake-sleep (RWS) (Bornschein and Bengio, 2015) algorithm, and through extensive evaluations, show that it outperforms current state-of-the-art methods in learning SCFMs. Further, in contrast to the importance weighted autoencoder, we observe that RWS learns better models and inference networks with increasing numbers of particles. Our results suggest that RWS is a competitive, often preferable, alternative for learning SCFMs.

stat.ML↗

arXiv2019

Etalumis: Bringing Probabilistic Programming to Scientific Simulators at Scale

Probabilistic programming languages (PPLs) are receiving widespread attention for performing Bayesian inference in complex generative models. However, applications to science remain limited because of the impracticability of rewriting complex scientific simulators in a PPL, the computational cost of inference, and the lack of scalable implementations. To address these, we present a novel PPL framework that couples directly to existing scientific simulators through a cross-platform probabilistic execution protocol and provides Markov chain Monte Carlo (MCMC) and deep-learning-based inference compilation (IC) engines for tractable inference. To guide IC inference, we perform distributed training of a dynamic 3DCNN--LSTM architecture with a PyTorch-MPI-based framework on 1,024 32-core CPU nodes of the Cori supercomputer with a global minibatch size of 128k: achieving a performance of 450 Tflop/s through enhancements to PyTorch. We demonstrate a Large Hadron Collider (LHC) use-case with the C++ Sherpa simulator and achieve the largest-scale posterior inference in a Turing-complete PPL.

cs.LG↗

arXiv2019

The Virtual Patch Clamp: Imputing C. elegans Membrane Potentials from Calcium Imaging

We develop a stochastic whole-brain and body simulator of the nematode roundworm Caenorhabditis elegans (C. elegans) and show that it is sufficiently regularizing to allow imputation of latent membrane potentials from partial calcium fluorescence imaging observations. This is the first attempt we know of to "complete the circle," where an anatomically grounded whole-connectome simulator is used to impute a time-varying "brain" state at single-cell fidelity from covariates that are measurable in practice. The sequential Monte Carlo (SMC) method we employ not only enables imputation of said latent states but also presents a strategy for learning simulator parameters via variational optimization of the noisy model evidence approximation provided by SMC. Our imputation and parameter estimation experiments were conducted on distributed systems using novel implementations of the aforementioned techniques applied to synthetic data of dimension and type representative of that which are measured in laboratories currently.

q-bio.NC↗

arXiv2019

Amortized Monte Carlo Integration

Current approaches to amortizing Bayesian inference focus solely on approximating the posterior distribution. Typically, this approximation is, in turn, used to calculate expectations for one or more target functions - a computational pipeline which is inefficient when the target function(s) are known upfront. In this paper, we address this inefficiency by introducing AMCI, a method for amortizing Monte Carlo integration directly. AMCI operates similarly to amortized inference but produces three distinct amortized proposals, each tailored to a different component of the overall expectation calculation. At runtime, samples are produced separately from each amortized proposal, before being combined to an overall estimate of the expectation. We show that while existing approaches are fundamentally limited in the level of accuracy they can achieve, AMCI can theoretically produce arbitrarily small errors for any integrable target function using only a single sample from each proposal at runtime. We further show that it is able to empirically outperform the theoretically optimal self-normalized importance sampler on a number of example problems. Furthermore, AMCI allows not only for amortizing over datasets but also amortizing over target functions.

stat.ML↗

arXiv2019

LF-PPL: A Low-Level First Order Probabilistic Programming Language for Non-Differentiable Models

We develop a new Low-level, First-order Probabilistic Programming Language (LF-PPL) suited for models containing a mix of continuous, discrete, and/or piecewise-continuous variables. The key success of this language and its compilation scheme is in its ability to automatically distinguish parameters the density function is discontinuous with respect to, while further providing runtime checks for boundary crossings. This enables the introduction of new inference engines that are able to exploit gradient information, while remaining efficient for models which are not everywhere differentiable. We demonstrate this ability by incorporating a discontinuous Hamiltonian Monte Carlo (DHMC) inference engine that is able to deliver automated and efficient inference for non-differentiable models. Our system is backed up by a mathematical formalism that ensures that any model expressed in this language has a density with measure zero discontinuities to maintain the validity of the inference engine.

cs.LG↗

arXiv2019

Tighter Variational Bounds are Not Necessarily Better

We provide theoretical and empirical evidence that using tighter evidence lower bounds (ELBOs) can be detrimental to the process of learning an inference network by reducing the signal-to-noise ratio of the gradient estimator. Our results call into question common implicit assumptions that tighter ELBOs are better variational objectives for simultaneous model learning and inference amortization schemes. Based on our insights, we introduce three new algorithms: the partially importance weighted auto-encoder (PIWAE), the multiply importance weighted auto-encoder (MIWAE), and the combination importance weighted auto-encoder (CIWAE), each of which includes the standard importance weighted auto-encoder (IWAE) as a special case. We show that each can deliver improvements over IWAE, even when performance is measured by the IWAE target itself. Furthermore, our results suggest that PIWAE may be able to deliver simultaneous improvements in the training of both the inference and generative networks.

stat.ML↗

arXiv2019

Hamiltonian Monte Carlo for Probabilistic Programs with Discontinuities

Hamiltonian Monte Carlo (HMC) is arguably the dominant statistical inference algorithm used in most popular "first-order differentiable" Probabilistic Programming Languages (PPLs). However, the fact that HMC uses derivative information causes complications when the target distribution is non-differentiable with respect to one or more of the latent variables. In this paper, we show how to use extensions to HMC to perform inference in probabilistic programs that contain discontinuities. To do this, we design a Simple first-order Probabilistic Programming Language (SPPL) that contains a sufficient set of language restrictions together with a compilation scheme. This enables us to preserve both the statistical and syntactic interpretation of if-else statements in the probabilistic program, within the scope of first-order PPLs. We also provide a corresponding mathematical formalism that ensures any joint density denoted in such a language has a suitably low measure of discontinuities.

stat.CO↗

arXiv2018

Faithful Inversion of Generative Models for Effective Amortized Inference

Inference amortization methods share information across multiple posterior-inference problems, allowing each to be carried out more efficiently. Generally, they require the inversion of the dependency structure in the generative model, as the modeller must learn a mapping from observations to distributions approximating the posterior. Previous approaches have involved inverting the dependency structure in a heuristic way that fails to capture these dependencies correctly, thereby limiting the achievable accuracy of the resulting approximations. We introduce an algorithm for faithfully, and minimally, inverting the graphical model structure of any generative model. Such inverses have two crucial properties: (a) they do not encode any independence assertions that are absent from the model and; (b) they are local maxima for the number of true independencies encoded. We prove the correctness of our approach and empirically show that the resulting minimally faithful inverses lead to better inference amortization than existing heuristic approaches.

stat.ML↗

arXiv2018

Inference Trees: Adaptive Inference with Exploration

We introduce inference trees (ITs), a new class of inference methods that build on ideas from Monte Carlo tree search to perform adaptive sampling in a manner that balances exploration with exploitation, ensures consistency, and alleviates pathologies in existing adaptive methods. ITs adaptively sample from hierarchical partitions of the parameter space, while simultaneously learning these partitions in an online manner. This enables ITs to not only identify regions of high posterior mass, but also maintain uncertainty estimates to track regions where significant posterior mass may have been missed. ITs can be based on any inference method that provides a consistent estimate of the marginal likelihood. They are particularly effective when combined with sequential Monte Carlo, where they capture long-range dependencies and yield improvements beyond proposal adaptation alone.

stat.CO↗

arXiv2018

Deep Variational Reinforcement Learning for POMDPs

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.

cs.LG↗

arXiv2018

On Nesting Monte Carlo Estimators

Many problems in machine learning and statistics involve nested expectations and thus do not permit conventional Monte Carlo (MC) estimation. For such problems, one must nest estimators, such that terms in an outer estimator themselves involve calculation of a separate, nested, estimation. We investigate the statistical implications of nesting MC estimators, including cases of multiple levels of nesting, and establish the conditions under which they converge. We derive corresponding rates of convergence and provide empirical evidence that these rates are observed in practice. We further establish a number of pitfalls that can arise from naive nesting of MC estimators, provide guidelines about how these can be avoided, and lay out novel methods for reformulating certain classes of nested expectation problems into single expectations, leading to improved convergence rates. We demonstrate the applicability of our work by using our results to develop a new estimator for discrete Bayesian experimental design problems and derive error bounds for a class of variational objectives.

stat.CO↗

arXiv2018

Auto-Encoding Sequential Monte Carlo

We build on auto-encoding sequential Monte Carlo (AESMC): a method for model and proposal learning based on maximizing the lower bound to the log marginal likelihood in a broad family of structured probabilistic models. Our approach relies on the efficiency of sequential Monte Carlo (SMC) for performing inference in structured probabilistic models and the flexibility of deep neural networks to model complex conditional probability distributions. We develop additional theoretical insights and introduce a new training procedure which improves both model and proposal learning. We demonstrate that our approach provides a fast, easy-to-implement and scalable means for simultaneous model learning and proposal adaptation in deep generative models.

stat.ML↗

arXiv2018

High Throughput Synchronous Distributed Stochastic Gradient Descent

We introduce a new, high-throughput, synchronous, distributed, data-parallel, stochastic-gradient-descent learning algorithm. This algorithm uses amortized inference in a compute-cluster-specific, deep, generative, dynamical model to perform joint posterior predictive inference of the mini-batch gradient computation times of all worker-nodes in a parallel computing cluster. We show that a synchronous parameter server can, by utilizing such a model, choose an optimal cutoff time beyond which mini-batch gradient messages from slow workers are ignored that maximizes overall mini-batch gradient computations per second. In keeping with earlier findings we observe that, under realistic conditions, eagerly discarding the mini-batch gradient computations of stragglers not only increases throughput but actually increases the overall rate of convergence as a function of wall-clock time by virtue of eliminating idleness. The principal novel contribution and finding of this work goes beyond this by demonstrating that using the predicted run-times from a generative model of cluster worker performance to dynamically adjust the cutoff improves substantially over the static-cutoff prior art, leading to, among other things, significantly reduced deep neural net training times on large computer clusters.

cs.DC↗

arXiv2018

Inference Networks for Sequential Monte Carlo in Graphical Models

We introduce a new approach for amortizing inference in directed graphical models by learning heuristic approximations to stochastic inverses, designed specifically for use as proposal distributions in sequential Monte Carlo methods. We describe a procedure for constructing and learning a structured neural network which represents an inverse factorization of the graphical model, resulting in a conditional density estimator that takes as input particular values of the observed random variables, and returns an approximation to the distribution of the latent variables. This recognition model can be learned offline, independent from any particular dataset, prior to performing inference. The output of these networks can be used as automatically-learned high-quality proposal distributions to accelerate sequential Monte Carlo across a diverse range of problem settings.

stat.ML↗