Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the Chemical Master Equation. Despite its simple structure, no analytic solutions to the Chemical Master Equation are known for most systems. Moreover, stochastic simulations are computationally expensive, making systematic analysis and statistical inference a challenging task. Consequently, significant effort has been spent in recent decades on the development of efficient approximation and inference methods. This article gives an introduction to basic modelling concepts as well as an overview of state of the art methods. First, we motivate and introduce deterministic and stochastic methods for modelling chemical networks, and give an overview of simulation and exact solution methods. Next, we discuss several approximation methods, including the chemical Langevin equation, the system size expansion, moment closure approximations, time-scale separation approximations and hybrid methods. We discuss their various properties and review recent advances and remaining challenges for these methods. We present a comparison of several of these methods by means of a numerical case study and highlight some of their respective advantages and disadvantages. Finally, we discuss the problem of inference from experimental data in the Bayesian framework and review recent methods developed the literature. In summary, this review gives a self-contained introduction to modelling, approximations and inference methods for stochastic chemical kinetics.

We propose a modified expectation-maximization algorithm by introducing the concept of quantum annealing, which we call the deterministic quantum annealing expectation-maximization (DQAEM) algorithm. The expectation-maximization (EM) algorithm is an established algorithm to compute maximum likelihood estimates and applied to many practical applications. However, it is known that EM heavily depends on initial values and its estimates are sometimes trapped by local optima. To solve such a problem, quantum annealing (QA) was proposed as a novel optimization approach motivated by quantum mechanics. By employing QA, we then formulate DQAEM and present a theorem that supports its stability. Finally, we demonstrate numerical simulations to confirm its efficiency.

The focus in this paper is Bayesian system identification based on noisy incomplete modal data where we can impose spatially-sparse stiffness changes when updating a structural model. To this end, based on a similar hierarchical sparse Bayesian learning model from our previous work, we propose two Gibbs sampling algorithms. The algorithms differ in their strategies to deal with the posterior uncertainty of the equation-error precision parameter, but both sample from the conditional posterior probability density functions (PDFs) for the structural stiffness parameters and system modal parameters. The effective dimension for the Gibbs sampling is low because iterative sampling is done from only three conditional posterior PDFs that correspond to three parameter groups, along with sampling of the equation-error precision parameter from another conditional posterior PDF in one of the algorithms where it is not integrated out as a "nuisance" parameter. A nice feature from a computational perspective is that it is not necessary to solve a nonlinear eigenvalue problem of a structural model. The effectiveness and robustness of the proposed algorithms are illustrated by applying them to the IASE-ASCE Phase II simulated and experimental benchmark studies. The goal is to use incomplete modal data identified before and after possible damage to detect and assess spatially-sparse stiffness reductions induced by any damage. Our past and current focus on meeting challenges arising from Bayesian inference of structural stiffness serve to strengthen the capability of vibration-based structural system identification but our methods also have much broader applicability for inverse problems in science and technology where system matrices are to be inferred from noisy partial information about their eigenquantities.

With the development of free, open-source machine learning and artificial intelligence tools like Google's TensorFlow and sci-kit learn, as well as "ML-as-a-service" products like Google's Cloud Prediction API and Microsoft's Azure Machine Learning platform, it's never been easier for companies of all sizes to harness the power of data. But machine learning is such a vast, complex field. Where do you start learning how to use it in your business? In this article, we'll survey the current landscape of machine learning algorithms and explain how they work, provide example applications, share how other companies use them, and provide further resources on learning about them. This executive overview will provide the first step in learning how to apply machine learning algorithm(s) to make your business more efficient, more effective, and more profitable.

Crowdsourcing systems are popular for solving large-scale labelling tasks with low-paid workers. We study the problem of recovering the true labels from the possibly erroneous crowdsourced labels under the popular Dawid-Skene model. To address this inference problem, several algorithms have recently been proposed, but the best known guarantee is still significantly larger than the fundamental limit. We close this gap by introducing a tighter lower bound on the fundamental limit and proving that Belief Propagation (BP) exactly matches this lower bound. The guaranteed optimality of BP is the strongest in the sense that it is information-theoretically impossible for any other algorithm to correctly label a larger fraction of the tasks. Experimental results suggest that BP is close to optimal for all regimes considered and improves upon competing state-of-the-art algorithms.

Grasping is a complex process involving knowledge of the object, the surroundings, and of oneself. While humans are able to integrate and process all of the sensory information required for performing this task, equipping machines with this capability is an extremely challenging endeavor. In this paper, we investigate how deep learning techniques can allow us to translate high-level concepts such as motor imagery to the problem of robotic grasp synthesis. We explore a paradigm based on generative models for learning integrated object-action representations, and demonstrate its capacity for capturing and generating multimodal, multi-finger grasp configurations on a simulated grasping dataset.

How do you know what machine learning algorithm to choose for your classification problem? Of course, if you really care about accuracy, your best bet is to test out a couple different ones (making sure to try different parameters within each algorithm as well), and select the best one by cross-validation. But if you're simply looking for a "good enough" algorithm for your problem, or a place to start, here are some general guidelines I've found to work well over the years. If your training set is small, high bias/low variance classifiers (e.g., Naive Bayes) have an advantage over low bias/high variance classifiers (e.g., kNN), since the latter will overfit. But low bias/high variance classifiers start to win out as your training set grows (they have lower asymptotic error), since high bias classifiers aren't powerful enough to provide accurate models.

In many real applications of statistical learning, a decision made from misclassification can be too costly to afford; in this case, a reject option, which defers the decision until further investigation is conducted, is often preferred. In recent years, there has been much development for binary classification with a reject option. Yet, little progress has been made for the multicategory case. In this article, we propose margin-based multicategory classification methods with a reject option. In addition, and more importantly, we introduce a new and unique refine option for the multicategory problem, where the class of an observation is predicted to be from a set of class labels, whose cardinality is not necessarily one. The main advantage of both options lies in their capacity of identifying error-prone observations. Moreover, the refine option can provide more constructive information for classification by effectively ruling out implausible classes. Efficient implementations have been developed for the proposed methods. On the theoretical side, we offer a novel statistical learning theory and show a fast convergence rate of the excess $\ell$-risk of our methods with emphasis on diverging dimensionality and number of classes. The results can be further improved under a low noise assumption. A set of comprehensive simulation and real data studies has shown the usefulness of the new learning tools compared to regular multicategory classifiers. Detailed proofs of theorems and extended numerical results are included in the supplemental materials available online.

For example, genes may regulate each other in different ways when external conditions are changed; the number of daily flu-like symptom reports in nearby hospitals may become correlated when a major epidemic disease breaks out; EEG signals from different regions of the brain may be synchronized/desynchronized when the subject is performing different activities. Spotting such changes in interactions may provide key insights into the underlying system. The interactions among random variables can be formulated as undirected probabilistic graphical models, or Markov Networks (MNs) [Koller and Friedman, 2009], expressing the interactions via the conditional independence. We consider a simple model: the pairwise MNs where the links are only encoded for single or pairs of random variables. Due to the Hammersley-Clifford theorem [Hammersley and Clifford, 1971], the underlying joint probability density function can be represented as the product of univariate and bivariate factors.

In this article, we investigate large sample properties of model selection procedures in a general Bayesian framework when a closed form expression of the marginal likelihood function is not available or a local asymptotic quadratic approximation of the log-likelihood function does not exist. Under appropriate identifiability assumptions on the true model, we provide sufficient conditions for a Bayesian model selection procedure to be consistent and obey the Occam's razor phenomenon, i.e., the probability of selecting the "smallest" model that contains the truth tends to one as the sample size goes to infinity. In order to show that a Bayesian model selection procedure selects the smallest model containing the truth, we impose a prior anti-concentration condition, requiring the prior mass assigned by large models to a neighborhood of the truth to be sufficiently small. In a more general setting where the strong model identifiability assumption may not hold, we introduce the notion of local Bayesian complexity and develop oracle inequalities for Bayesian model selection procedures. Our Bayesian oracle inequality characterizes a trade-off between the approximation error and a Bayesian characterization of the local complexity of the model, illustrating the adaptive nature of averaging-based Bayesian procedures towards achieving an optimal rate of posterior convergence. Specific applications of the model selection theory are discussed in the context of high-dimensional nonparametric regression and density regression where the regression function or the conditional density is assumed to depend on a fixed subset of predictors. As a result of independent interest, we propose a general technique for obtaining upper bounds of certain small ball probability of stationary Gaussian processes.