Driven by the critical needs of biomanufacturing 4.0, we introduce a probabilistic knowledge graph hybrid model characterizing the risk- and science-based understanding of bioprocess mechanisms. It can faithfully capture the important properties, including nonlinear reactions, partially observed state, and nonstationary dynamics. Given very limited real process observations, we derive a posterior distribution quantifying model estimation uncertainty. To avoid the evaluation of intractable likelihoods, Approximate Bayesian Computation sampling with Sequential Monte Carlo (ABC-SMC) is utilized to approximate the posterior distribution. Under high stochastic and model uncertainties, it is computationally expensive to match output trajectories. Therefore, we create a linear Gaussian dynamic Bayesian network (LG-DBN) auxiliary likelihood-based ABC-SMC approach. Through matching the summary statistics driven through LG-DBN likelihood that can capture critical interactions and variations, the proposed algorithm can accelerate hybrid model inference, support process monitoring, and facilitate mechanism learning and robust control.
Probabilistic models for sequential data are the basis for a variety of applications concerned with processing timely ordered information. The predominant approach in this domain is given by recurrent neural networks, implementing either an approximate Bayesian approach (e.g. Variational Autoencoders or Generative Adversarial Networks) or a regression-based approach, i.e. variations of Mixture Density networks (MDN). In this paper, we focus on the $\mathcal{N}$-MDN variant, which parameterizes (mixtures of) probabilistic B\'ezier curves ($\mathcal{N}$-Curves) for modeling stochastic processes. While in favor in terms of computational cost and stability, MDNs generally fall behind approximate Bayesian approaches in terms of expressiveness. Towards this end, we present an approach for closing this gap by enabling full Bayesian inference on top of $\mathcal{N}$-MDNs. For this, we show that $\mathcal{N}$-Curves are a special case of Gaussian processes (denoted as $\mathcal{N}$-GP) and then derive corresponding mean and kernel functions for different modalities. Following this, we propose the use of the $\mathcal{N}$-MDN as a data-dependent generator for $\mathcal{N}$-GP prior distributions. We show the advantages granted by this combined model in an application context, using human trajectory prediction as an example.
Most of the current inference techniques rely upon Bayesian inference on Probabilistic Graphical Models of observations and do predictions and classification on observations. However, there is very little literature on the mining of relationships between observations and building models of the relationship between sets of observations or the generating context of the observations. Moreover, event understanding of machines with observation inputs needs to understand the relationship between observations. Thus there is a crucial need to build models and develop effective data structures to accumulate and organize relationships between observations. Given a PGM model, this paper attempts to fit a permutation of states to a sequence of observation tokens (The Travelling Photographer Problem). We have devised a machine learning inspired architecture for randomized approximation of state permutation, facilitating parallelization of heuristic search of permutations. As a result, our algorithm can solve The Travelling Photographer Problem with minimal error. Furthermore, we demonstrate that by mimicking machine learning components such as normalization, dropout, and lambda layer with a randomized algorithm, we can devise an architecture that solves TPP, a permutation NP-Hard problem. Other than TPP, we can also provide a 2-Local improvement heuristic for the Travelling Salesman Problem (TSP) with similar ideas.
Deep Ensemble (DE) is an effective alternative to Bayesian neural networks for uncertainty quantification in deep learning. The uncertainty of DE is usually conveyed by the functional inconsistency among the ensemble members, say, the disagreement among their predictions. Yet, the functional inconsistency stems from unmanageable randomness and may easily collapse in specific cases. To render the uncertainty of DE reliable, we propose a refinement of DE where the functional inconsistency is explicitly characterized, and further tuned w.r.t. the training data and certain priori beliefs. Specifically, we describe the functional inconsistency with the empirical covariance of the functions dictated by ensemble members, which, along with the mean, define a Gaussian process (GP). Then, with specific priori uncertainty imposed, we maximize functional evidence lower bound to make the GP specified by DE approximate the Bayesian posterior. In this way, we relate DE to Bayesian inference to enjoy reliable Bayesian uncertainty. Moreover, we provide strategies to make the training efficient. Our approach consumes only marginally added training cost than the standard DE, but achieves better uncertainty quantification than DE and its variants across diverse scenarios.
Low-dose CT (LDCT) imaging attracted a considerable interest for the reduction of the object's exposure to X-ray radiation. In recent years, supervised deep learning (DL) has been extensively studied for LDCT image reconstruction, which trains a network over a dataset containing many pairs of normal-dose and low-dose images. However, the challenge on collecting many such pairs in the clinical setup limits the application of such supervised-learning-based methods for LDCT image reconstruction in practice. Aiming at addressing the challenges raised by the collection of training dataset, this paper proposed a unsupervised deep learning method for LDCT image reconstruction, which does not require any external training data. The proposed method is built on a re-parametrization technique for Bayesian inference via deep network with random weights, combined with additional total variational~(TV) regularization. The experiments show that the proposed method noticeably outperforms existing dataset-free image reconstruction methods on the test data.
The likelihood function plays a crucial role in statistical inference and experimental design. However, it is computationally intractable for several important classes of statistical models, including energy-based models and simulator-based models. Contrastive learning is an intuitive and computationally feasible alternative to likelihood-based learning. We here first provide an introduction to contrastive learning and then show how we can use it to derive methods for diverse statistical problems, namely parameter estimation for energy-based models, Bayesian inference for simulator-based models, as well as experimental design.
A new algorithm based on bayesian inference for learning local graph conductance based on Gaussian Process(GP) is given that uses advanced MCMC convergence ideas to create a scalable and fast algorithm for convergence to stationary distribution which is provided to learn the bahavior of conductance when traversing the indirected weighted graph. First metric embedding is used to represent the vertices of the graph. Then, uniform induced conductance is calculated for training points. Finally, in the learning step, a gaussian process is used to approximate the uniform induced conductance. MCMC is used to measure uncertainty of estimated hyper-parameters.
We design new visual illusions by finding "adversarial examples" for principled models of human perception -- specifically, for probabilistic models, which treat vision as Bayesian inference. To perform this search efficiently, we design a differentiable probabilistic programming language, whose API exposes MCMC inference as a first-class differentiable function. We demonstrate our method by automatically creating illusions for three features of human vision: color constancy, size constancy, and face perception.
Semantic-descriptor-based Generalized Zero-Shot Learning (GZSL) poses challenges in recognizing novel classes in the test phase. The development of generative models enables current GZSL techniques to probe further into the semantic-visual link, culminating in a two-stage form that includes a generator and a classifier. However, existing generation-based methods focus on enhancing the generator's effect while neglecting the improvement of the classifier. In this paper, we first analyze of two properties of the generated pseudo unseen samples: bias and homogeneity. Then, we perform variational Bayesian inference to back-derive the evaluation metrics, which reflects the balance of the seen and unseen classes. As a consequence of our derivation, the aforementioned two properties are incorporated into the classifier training as seen-unseen priors via logit adjustment. The Zero-Shot Logit Adjustment further puts semantic-based classifiers into effect in generation-based GZSL. Our experiments demonstrate that the proposed technique achieves state-of-the-art when combined with the basic generator, and it can improve various generative Zero-Shot Learning frameworks. Our codes are available on https://github.com/cdb342/IJCAI-2022-ZLA.
Models of human behavior for prediction and collaboration tend to fall into two categories: ones that learn from large amounts of data via imitation learning, and ones that assume human behavior to be noisily-optimal for some reward function. The former are very useful, but only when it is possible to gather a lot of human data in the target environment and distribution. The advantage of the latter type, which includes Boltzmann rationality, is the ability to make accurate predictions in new environments without extensive data when humans are actually close to optimal. However, these models fail when humans exhibit systematic suboptimality, i.e. when their deviations from optimal behavior are not independent, but instead consistent over time. Our key insight is that systematic suboptimality can be modeled by predicting policies, which couple action choices over time, instead of trajectories. We introduce the Boltzmann policy distribution (BPD), which serves as a prior over human policies and adapts via Bayesian inference to capture systematic deviations by observing human actions during a single episode. The BPD is difficult to compute and represent because policies lie in a high-dimensional continuous space, but we leverage tools from generative and sequence models to enable efficient sampling and inference. We show that the BPD enables prediction of human behavior and human-AI collaboration equally as well as imitation learning-based human models while using far less data.
This paper tackles the problem of decomposing binary data using matrix factorization. We consider the family of mean-parametrized Bernoulli models, a class of generative models that are well suited for modeling binary data and enables interpretability of the factors. We factorize the Bernoulli parameter and consider an additional Beta prior on one of the factors to further improve the model's expressive power. While similar models have been proposed in the literature, they only exploit the Beta prior as a proxy to ensure a valid Bernoulli parameter in a Bayesian setting; in practice it reduces to a uniform or uninformative prior. Besides, estimation in these models has focused on costly Bayesian inference. In this paper, we propose a simple yet very efficient majorization-minimization algorithm for maximum a posteriori estimation. Our approach leverages the Beta prior whose parameters can be tuned to improve performance in matrix completion tasks. Experiments conducted on three public binary datasets show that our approach offers an excellent trade-off between prediction performance, computational complexity, and interpretability.
Stein variational gradient descent (SVGD) is a general-purpose optimization-based sampling algorithm that has recently exploded in popularity, but is limited by two issues: it is known to produce biased samples, and it can be slow to converge on complicated distributions. A recently proposed stochastic variant of SVGD (sSVGD) addresses the first issue, producing unbiased samples by incorporating a special noise into the SVGD dynamics such that asymptotic convergence is guaranteed. Meanwhile, Stein variational Newton (SVN), a Newton-like extension of SVGD, dramatically accelerates the convergence of SVGD by incorporating Hessian information into the dynamics, but also produces biased samples. In this paper we derive, and provide a practical implementation of, a stochastic variant of SVN (sSVN) which is both asymptotically correct and converges rapidly. We demonstrate the effectiveness of our algorithm on a difficult class of test problems -- the Hybrid Rosenbrock density -- and show that sSVN converges using three orders of magnitude fewer gradient evaluations of the log likelihood than its stochastic SVGD counterpart. Our results show that sSVN is a promising approach to accelerating high-precision Bayesian inference tasks with modest-dimension, $d\sim\mathcal{O}(10)$.
Model-based fault-tolerant control (FTC) often consists of two distinct steps: fault detection & isolation (FDI), and fault accommodation. In this work we investigate posing fault-tolerant control as a single Bayesian inference problem. Previous work showed that precision learning allows for stochastic FTC without an explicit fault detection step. While this leads to implicit fault recovery, information on sensor faults is not provided, which may be essential for triggering other impact-mitigation actions. In this paper, we introduce a precision-learning based Bayesian FTC approach and a novel beta residual for fault detection. Simulation results are presented, supporting the use of beta residual against competing approaches.
This letter proposes a learning-based bounded synthesis for a semi-Markov decision process (SMDP) with a linear temporal logic (LTL) specification. In the product of the SMDP and the deterministic $K$-co-B\"uchi automaton (d$K$cBA) converted from the LTL specification, we learn both the winning region of satisfying the LTL specification and the dynamics therein based on reinforcement learning and Bayesian inference. Then, we synthesize an optimal policy satisfying the following two conditions. (1) It maximizes the probability of reaching the wining region. (2) It minimizes a long-term risk for the dwell time within the winning region. The minimization of the long-term risk is done based on the estimated dynamics and a value iteration. We show that, if the discount factor is sufficiently close to one, the synthesized policy converges to the optimal policy as the number of the data obtained by the exploration goes to the infinity.
How is information processed in the brain during perception? Mechanistic insight is achieved only when experiments are employed to test formal or computational models. In analogy to lesion studies, phantom perception may serve as a vehicle to understand the fundamental processing principles underlying auditory perception. With a special focus on tinnitus -- as the prime example of auditory phantom perception -- we review recent work at the intersection of artificial intelligence, psychology, and neuroscience. In particular, we discuss why everyone with tinnitus suffers from hearing loss, but not everyone with hearing loss suffers from tinnitus. We argue that the increase of sensory precision due to Bayesian inference could be caused by intrinsic neural noise and lead to a prediction error in the cerebral cortex. Hence, two fundamental processing principles - being ubiquitous in the brain - provide the most explanatory power for the emergence of tinnitus: predictive coding as a top-down, and stochastic resonance as a complementary bottom-up mechanism. We conclude that both principles play a crucial role in healthy auditory perception.
We introduce a deep learning accelerated methodology to solve PDE-based Bayesian inverse problems with guaranteed accuracy. This is motivated by the ill-posed problem of inferring a spatio-temporal heat-flux parameter known as the Biot number given temperature data, however the methodology is generalisable to other settings. To accelerate Bayesian inference, we develop a novel training scheme that uses data to adaptively train a neural-network surrogate simulating the parametric forward model. By simultaneously identifying an approximate posterior distribution over the Biot number, and weighting a physics-informed training loss according to this, our approach approximates forward and inverse solution together without any need for external solves. Using a random Chebyshev series, we outline how to approximate a Gaussian process prior, and using the surrogate we apply Hamiltonian Monte Carlo (HMC) to sample from the posterior distribution. We derive convergence of the surrogate posterior to the true posterior distribution in the Hellinger metric as our adaptive loss approaches zero. Additionally, we describe how this surrogate-accelerated HMC approach can be combined with traditional PDE solvers in a delayed-acceptance scheme to a-priori control the posterior accuracy. This overcomes a major limitation of deep learning-based surrogate approaches, which do not achieve guaranteed accuracy a-priori due to their non-convex training. Biot number calculations are involved in turbo-machinery design, which is safety critical and highly regulated, therefore it is important that our results have such mathematical guarantees. Our approach achieves fast mixing in high dimensions whilst retaining the convergence guarantees of a traditional PDE solver, and without the burden of evaluating this solver for proposals that are likely to be rejected. Numerical results are given using real and simulated data.
In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods for synthetic route design using deep neural networks have been studied intensively in recent years. However, little progress has been made in designing molecules and their synthetic routes simultaneously. Here, we formulate the problem of simultaneously designing molecules with the desired set of properties and their synthetic routes within the framework of Bayesian inference. The design variables consist of a set of reactants in a reaction network and its network topology. The design space is extremely large because it consists of all combinations of purchasable reactants, often in the order of millions or more. In addition, the designed reaction networks can adopt any topology beyond simple multistep linear reaction routes. To solve this hard combinatorial problem, we present a powerful sequential Monte Carlo algorithm that recursively designs a synthetic reaction network by sequentially building up single-step reactions. In a case study of designing drug-like molecules based on commercially available compounds, compared with heuristic combinatorial search methods, the proposed method shows overwhelming performance in terms of computational efficiency and coverage and novelty with respect to existing compounds.
Predictive coding is an influential model of cortical neural activity. It proposes that perceptual beliefs are furnished by sequentially minimising "prediction errors" - the differences between predicted and observed data. Implicit in this proposal is the idea that perception requires multiple cycles of neural activity. This is at odds with evidence that several aspects of visual perception - including complex forms of object recognition - arise from an initial "feedforward sweep" that occurs on fast timescales which preclude substantial recurrent activity. Here, we propose that the feedforward sweep can be understood as performing amortized inference and recurrent processing can be understood as performing iterative inference. We propose a hybrid predictive coding network that combines both iterative and amortized inference in a principled manner by describing both in terms of a dual optimization of a single objective function. We show that the resulting scheme can be implemented in a biologically plausible neural architecture that approximates Bayesian inference utilising local Hebbian update rules. We demonstrate that our hybrid predictive coding model combines the benefits of both amortized and iterative inference -- obtaining rapid and computationally cheap perceptual inference for familiar data while maintaining the context-sensitivity, precision, and sample efficiency of iterative inference schemes. Moreover, we show how our model is inherently sensitive to its uncertainty and adaptively balances iterative and amortized inference to obtain accurate beliefs using minimum computational expense. Hybrid predictive coding offers a new perspective on the functional relevance of the feedforward and recurrent activity observed during visual perception and offers novel insights into distinct aspects of visual phenomenology.
We propose a variational Bayesian inference procedure for online nonlinear system identification. For each output observation, a set of parameter posterior distributions is updated, which is then used to form a posterior predictive distribution for future outputs. We focus on the class of polynomial NARMAX models, which we cast into probabilistic form and represent in terms of a Forney-style factor graph. Inference in this graph is efficiently performed by a variational message passing algorithm. We show empirically that our variational Bayesian estimator outperforms an online recursive least-squares estimator, most notably in small sample size settings and low noise regimes, and performs on par with an iterative least-squares estimator trained offline.
The Cut posterior and related Semi-Modular Inference are Generalised Bayes methods for Modular Bayesian evidence combination. Analysis is broken up over modular sub-models of the joint posterior distribution. Model-misspecification in multi-modular models can be hard to fix by model elaboration alone and the Cut posterior and SMI offer a way round this. Information entering the analysis from misspecified modules is controlled by an influence parameter $\eta$ related to the learning rate. This paper contains two substantial new methods. First, we give variational methods for approximating the Cut and SMI posteriors which are adapted to the inferential goals of evidence combination. We parameterise a family of variational posteriors using a Normalising Flow for accurate approximation and end-to-end training. Secondly, we show that analysis of models with multiple cuts is feasible using a new Variational Meta-Posterior. This approximates a family of SMI posteriors indexed by $\eta$ using a single set of variational parameters.