Stochastic kinetic models (SKMs) are increasingly used to account for the inherent stochasticity exhibited by interacting populations of species in areas such as epidemiology, population ecology and systems biology. Species numbers are modelled using a continuous-time stochastic process, and, depending on the application area of interest, this will typically take the form of a Markov jump process or an It\^o diffusion process. Widespread use of these models is typically precluded by their computational complexity. In particular, performing exact fully Bayesian inference in either modelling framework is challenging due to the intractability of the observed data likelihood, necessitating the use of computationally intensive techniques such as particle Markov chain Monte Carlo (particle MCMC). We propose to increase the computational and statistical efficiency of this approach by leveraging the tractability of an inexpensive surrogate derived directly from either the jump or diffusion process. The surrogate is used in three ways: in the design of a gradient-based parameter proposal, to construct an appropriate bridge construct and in the first stage of a delayed-acceptance step. We find that the resulting approach offers substantial gains in efficiency over a standard particle MCMC implementation.
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Uncertainty quantification techniques such as the time-dependent generalized polynomial chaos (TD-gPC) use an adaptive orthogonal basis to better represent the stochastic part of the solution space (aka random function space) in time. However, because the random function space is constructed using tensor products, TD-gPC-based methods are known to suffer from the curse of dimensionality. In this paper, we introduce a new numerical method called the 'flow-driven spectral chaos' (FSC) which overcomes this curse of dimensionality at the random-function-space level. The proposed method is not only computationally more efficient than existing TD-gPC-based methods but is also far more accurate. The FSC method uses the concept of 'enriched stochastic flow maps' to track the evolution of a finite-dimensional random function space efficiently in time. To transfer the probability information from one random function space to another, two approaches are developed and studied herein. In the first approach, the probability information is transferred in the mean-square sense, whereas in the second approach the transfer is done exactly using a new theorem that was developed for this purpose. The FSC method can quantify uncertainties with high fidelity, especially for the long-time response of stochastic dynamical systems governed by ODEs of arbitrary order. Six representative numerical examples, including a nonlinear problem (the Van-der-Pol oscillator), are presented to demonstrate the performance of the FSC method and corroborate the claims of its superior numerical properties. Finally, a parametric, high-dimensional stochastic problem is used to demonstrate that when the FSC method is used in conjunction with Monte Carlo integration, the curse of dimensionality can be overcome altogether.
For decades, uncertainty quantification techniques based on the spectral approach have been demonstrated to be computationally more efficient than the Monte Carlo method for a wide variety of problems, particularly when the dimensionality of the probability space is relatively low. The time-dependent generalized polynomial chaos (TD-gPC) is one such technique that uses an evolving orthogonal basis to better represent the stochastic part of the solution space in time. In this paper, we present a new numerical method that uses the concept of 'enriched stochastic flow maps' to track the evolution of the stochastic part of the solution space in time. The computational cost of this proposed flow-driven stochastic chaos (FSC) method is an order of magnitude lower than TD-gPC for comparable solution accuracy. This gain in computational cost is realized because, unlike most existing methods, the number of basis vectors required to track the stochastic part of the solution space, and consequently the computational cost associated with the solution of the resulting system of equations, does not depend upon the dimensionality of the probability space. Four representative numerical examples are presented to demonstrate the performance of the FSC method for long-time integration of second-order stochastic dynamical systems in the context of stochastic dynamics of structures.
Heterogeneity is a dominant factor in the behaviour of many biological processes. Despite this, it is common for mathematical and statistical analyses to ignore biological heterogeneity as a source of variability in experimental data. Therefore, methods for exploring the identifiability of models that explicitly incorporate heterogeneity through variability in model parameters are relatively underdeveloped. We develop a new likelihood-based framework, based on moment matching, for inference and identifiability analysis of differential equation models that capture biological heterogeneity through parameters that vary according to probability distributions. As our novel method is based on an approximate likelihood function, it is highly flexible; we demonstrate identifiability analysis using both a frequentist approach based on profile likelihood, and a Bayesian approach based on Markov-chain Monte Carlo. Through three case studies, we demonstrate our method by providing a didactic guide to inference and identifiability analysis of hyperparameters that relate to the statistical moments of model parameters from independent observed data. Our approach has a computational cost comparable to analysis of models that neglect heterogeneity, a significant improvement over many existing alternatives. We demonstrate how analysis of random parameter models can aid better understanding of the sources of heterogeneity from biological data.
The seminal paper by Mazumdar and Saha \cite{MS17a} introduced an extensive line of work on clustering with noisy queries. Yet, despite significant progress on the problem, the proposed methods depend crucially on knowing the exact probabilities of errors of the underlying fully-random oracle. In this work, we develop robust learning methods that tolerate general semi-random noise obtaining qualitatively the same guarantees as the best possible methods in the fully-random model. More specifically, given a set of $n$ points with an unknown underlying partition, we are allowed to query pairs of points $u,v$ to check if they are in the same cluster, but with probability $p$, the answer may be adversarially chosen. We show that information theoretically $O\left(\frac{nk \log n} {(1-2p)^2}\right)$ queries suffice to learn any cluster of sufficiently large size. Our main result is a computationally efficient algorithm that can identify large clusters with $O\left(\frac{nk \log n} {(1-2p)^2}\right) + \text{poly}\left(\log n, k, \frac{1}{1-2p} \right)$ queries, matching the guarantees of the best known algorithms in the fully-random model. As a corollary of our approach, we develop the first parameter-free algorithm for the fully-random model, answering an open question by \cite{MS17a}.
In this paper, we show how the It\^o-stochastic Magnus expansion can be used to efficiently solve stochastic partial differential equations (SPDE) with two space variables numerically. To this end, we will first discretize the SPDE in space only by utilizing finite difference methods and vectorize the resulting equation exploiting its sparsity. As a benchmark, we will apply it to the case of the stochastic Langevin equation with constant coefficients, where an explicit solution is available, and compare the Magnus scheme with the Euler-Maruyama scheme. We will see that the Magnus expansion is superior in terms of both accuracy and especially computational time by using a single GPU and verify it in a variable coefficient case. Notably, we will see speed-ups of order ranging form 20 to 200 compared to the Euler-Maruyama scheme, depending on the accuracy target and the spatial resolution.
Profile hidden Markov models (pHMMs) are widely used in many bioinformatics applications to accurately identify similarities between biological sequences (e.g., DNA or protein sequences). PHMMs use a commonly-adopted and highly-accurate method, called the Baum-Welch algorithm, to calculate these similarities. However, the Baum-Welch algorithm is computationally expensive, and existing works provide either software- or hardware-only solutions for a fixed pHMM design. When we analyze the state-of-the-art works, we find that there is a pressing need for a flexible, high-performant, and energy-efficient hardware-software co-design to efficiently and effectively solve all the major inefficiencies in the Baum-Welch algorithm for pHMMs. We propose ApHMM, the first flexible acceleration framework that can significantly reduce computational and energy overheads of the Baum-Welch algorithm for pHMMs. ApHMM leverages hardware-software co-design to solve the major inefficiencies in the Baum-Welch algorithm by 1) designing a flexible hardware to support different pHMMs designs, 2) exploiting the predictable data dependency pattern in an on-chip memory with memoization techniques, 3) quickly eliminating negligible computations with a hardware-based filter, and 4) minimizing the redundant computations. We implement our 1) hardware-software optimizations on a specialized hardware and 2) software optimizations for GPUs to provide the first flexible Baum-Welch accelerator for pHMMs. ApHMM provides significant speedups of 15.55x-260.03x, 1.83x-5.34x, and 27.97x compared to CPU, GPU, and FPGA implementations of the Baum-Welch algorithm, respectively. ApHMM outperforms the state-of-the-art CPU implementations of three important bioinformatics applications, 1) error correction, 2) protein family search, and 3) multiple sequence alignment, by 1.29x-59.94x, 1.03x-1.75x, and 1.03x-1.95x, respectively.
Language is not only used to inform. We often seek to persuade by arguing in favor of a particular view. Persuasion raises a number of challenges for classical accounts of belief updating, as information cannot be taken at face value. How should listeners account for a speaker's "hidden agenda" when incorporating new information? Here, we extend recent probabilistic models of recursive social reasoning to allow for persuasive goals and show that our model provides a new pragmatic explanation for why weakly favorable arguments may backfire, a phenomenon known as the weak evidence effect. Critically, our model predicts a relationship between belief updating and speaker expectations: weak evidence should only backfire when speakers are expected to act under persuasive goals, implying the absence of stronger evidence. We introduce a simple experimental paradigm called the Stick Contest to measure the extent to which the weak evidence effect depends on speaker expectations, and show that a pragmatic listener model accounts for the empirical data better than alternative models. Our findings suggest potential avenues for rational models of social reasoning to further illuminate decision-making phenomena.
Score-based generative models (SGMs) have recently emerged as a promising class of generative models. However, a fundamental limitation is that their inference is very slow due to a need for many (e.g., 2000) iterations of sequential computations. An intuitive acceleration method is to reduce the sampling iterations which however causes severe performance degradation. We investigate this problem by viewing the diffusion sampling process as a Metropolis adjusted Langevin algorithm, which helps reveal the underlying cause to be ill-conditioned curvature. Under this insight, we propose a model-agnostic preconditioned diffusion sampling (PDS) method that leverages matrix preconditioning to alleviate the aforementioned problem. Crucially, PDS is proven theoretically to converge to the original target distribution of a SGM, no need for retraining. Extensive experiments on three image datasets with a variety of resolutions and diversity validate that PDS consistently accelerates off-the-shelf SGMs whilst maintaining the synthesis quality. In particular, PDS can accelerate by up to 29x on more challenging high resolution (1024x1024) image generation.
The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.
As soon as abstract mathematical computations were adapted to computation on digital computers, the problem of efficient representation, manipulation, and communication of the numerical values in those computations arose. Strongly related to the problem of numerical representation is the problem of quantization: in what manner should a set of continuous real-valued numbers be distributed over a fixed discrete set of numbers to minimize the number of bits required and also to maximize the accuracy of the attendant computations? This perennial problem of quantization is particularly relevant whenever memory and/or computational resources are severely restricted, and it has come to the forefront in recent years due to the remarkable performance of Neural Network models in computer vision, natural language processing, and related areas. Moving from floating-point representations to low-precision fixed integer values represented in four bits or less holds the potential to reduce the memory footprint and latency by a factor of 16x; and, in fact, reductions of 4x to 8x are often realized in practice in these applications. Thus, it is not surprising that quantization has emerged recently as an important and very active sub-area of research in the efficient implementation of computations associated with Neural Networks. In this article, we survey approaches to the problem of quantizing the numerical values in deep Neural Network computations, covering the advantages/disadvantages of current methods. With this survey and its organization, we hope to have presented a useful snapshot of the current research in quantization for Neural Networks and to have given an intelligent organization to ease the evaluation of future research in this area.
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