Uncertainty
Unlocking the Power of Artificial Intelligence and Big Data in Medicine
Most of the daily news and recently published scientific papers on research, innovations, and applications in artificial intelligence (AI) refer to what is known as machine learning--algorithms using massive amounts of data and various methodologies to find patterns, support decisions, make predictions, or, for the deep learning part, self-identify important features in data. However, AI is a complex concept to grasp, and most people have little understanding of what it really is. AI was founded as an academic discipline in 1956 and, despite its youth, already has a rich history [1,2]. In more than 60 years of exploration and progress, AI has become a large field of research and development involving multidisciplinary approaches to address many challenges, from theoretical frameworks, methods, and tools to real implementations, risk analysis, and impact measures. The definition of AI is a moving target and changes over time with the evolution of the field. Since its early days, the field of AI has allowed the development of many techniques supporting decision support and prediction, as it is usually made by humans. As early as 1958, a perceptron was expected to be able "to walk, talk, see, write, reproduce itself and be conscious of its existence," which led a large scientific controversy between neural network and symbolic reasoning approaches [3].
Basic concepts, definitions, and methods in D number theory
Although DST has many advantages in representing and dealing with uncertainty, but it is limited by some hypotheses and constraints that are hardly satisfied in some situation [3-6]. There are two main aspects. First, in DST a frame of discernment (FOD) must be composed of mutually exclusive elements, which is called the FOD's exclusiveness hypothesis. Second, in DST the sum of basic probabilities or belief m(.) in a basic probability assignment (BPA) must be 1 (or basic probabilities can not be assigned to elements outside the FOD), which is called the BPA's completeness constraint. To overcome the above-mentioned limitations in DST, a new generalization of DST, called D number theory (DNT), has been proposed in recently [7, 8] for the fusion of uncertain information with non-exclusiveness and incompleteness. The theory of DNT stems from the concept of D numbers [9-16], and aims to build a more sophisticated framework for representing and reasoning with uncertain information similar to DST from a generic setmembership perspective, in which DNT relaxes the exclusiveness constraint of elements in FOD and completeness assumption of BPA in DST.
Neural Networks are Function Approximation Algorithms
Supervised learning in machine learning can be described in terms of function approximation. Given a dataset comprised of inputs and outputs, we assume that there is an unknown underlying function that is consistent in mapping inputs to outputs in the target domain and resulted in the dataset. We then use supervised learning algorithms to approximate this function. Neural networks are an example of a supervised machine learning algorithm that is perhaps best understood in the context of function approximation. This can be demonstrated with examples of neural networks approximating simple one-dimensional functions that aid in developing the intuition for what is being learned by the model.
Probabilistic learning of boolean functions applied to the binary classification problem with categorical covariates
Consider a sample y {0, 1} n generated by two different Bernoulli distributions with parameters ฯ 0 and ฯ 1, and consider the set S {1,..., n} as the set of all indices i such that P (y i) ฯ 1 . Assuming that the components of the vector y i are conditionally independent given ฮธ (S, ฯ 0, ฯ 1), the likelihood function is the product of two Binomial distribution functions, and will attain a global maximum at the set S L(y) {i: 1 i n y i 1} (let's call this set the onset of the vector y), with maximum likelihood estimators given by หฯ 0 0 and หฯ 1 1. Now consider a design matrix X R n p and a function f: R p {0, 1} such that ฯ(X i) 1 i S, where X i is the i-th row of X. Again, if the function f is not constrained in any way, the problem is the same and the same trivial solution applies, with function f defined only in the set of rows of X. In this extreme case, the solution will usually not generalize well, and also will not provide any interesting interpretation (since f is just an enumeration based on the onset of y). Standard methods for the binary classification problem are concerned with the task of estimating f constraining it in different ways such that this trivial solution (associated with the problem of overfitting) is avoided.
Sequential Bayesian Experimental Design for Implicit Models via Mutual Information
Kleinegesse, Steven, Drovandi, Christopher, Gutmann, Michael U.
Bayesian experimental design (BED) is a framework that uses statistical models and decision making under uncertainty to optimise the cost and performance of a scientific experiment. Sequential BED, as opposed to static BED, considers the scenario where we can sequentially update our beliefs about the model parameters through data gathered in the experiment. A class of models of particular interest for the natural and medical sciences are implicit models, where the data generating distribution is intractable, but sampling from it is possible. Even though there has been a lot of work on static BED for implicit models in the past few years, the notoriously difficult problem of sequential BED for implicit models has barely been touched upon. We address this gap in the literature by devising a novel sequential design framework for parameter estimation that uses the Mutual Information (MI) between model parameters and simulated data as a utility function to find optimal experimental designs, which has not been done before for implicit models. Our approach uses likelihood-free inference by ratio estimation to simultaneously estimate posterior distributions and the MI. During the sequential BED procedure we utilise Bayesian optimisation to help us optimise the MI utility. We find that our framework is efficient for the various implicit models tested, yielding accurate parameter estimates after only a few iterations.
Query-Aware MCMC
Wick, Michael L., McCallum, Andrew
Traditional approaches to probabilistic inference such as loopy belief propagation and Gibbs sampling typically compute marginals for it all the unobserved variables in a graphical model. However, in many real-world applications the user's interests are focused on a subset of the variables, specified by a query. In this case it would be wasteful to uniformly sample, say, one million variables when the query concerns only ten. In this paper we propose a query-specific approach to MCMC that accounts for the query variables and their generalized mutual information with neighboring variables in order to achieve higher computational efficiency. Surprisingly there has been almost no previous work on query-aware MCMC.
On Lifting the Gibbs Sampling Algorithm
Venugopal, Deepak, Gogate, Vibhav
Statistical relational learning models combine the power of first-order logic, the de facto tool for handling relational structure, with that of probabilistic graphical models, the de facto tool for handling uncertainty. Lifted probabilistic inference algorithms for them have been the subject of much recent research. The main idea in these algorithms is to improve the speed, accuracy and scalability of existing graphical models' inference algorithms by exploiting symmetry in the first-order representation. In this paper, we consider blocked Gibbs sampling, an advanced variation of the classic Gibbs sampling algorithm and lift it to the first-order level. We propose to achieve this by partitioning the first-order atoms in the relational model into a set of disjoint clusters such that exact lifted inference is polynomial in each cluster given an assignment to all other atoms not in the cluster.
Model-based Bayesian inference of neural activity and connectivity from all-optical interrogation of a neural circuit
Aitchison, Laurence, Russell, Lloyd, Packer, Adam M., Yan, Jinyao, Castonguay, Philippe, Hausser, Michael, Turaga, Srinivas C.
Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons.
On the equivalence between graph isomorphism testing and function approximation with GNNs
Chen, Zhengdao, Villar, Soledad, Chen, Lei, Bruna, Joan
Graph neural networks (GNNs) have achieved lots of success on graph-structured data. In light of this, there has been increasing interest in studying their representation power. One line of work focuses on the universal approximation of permutation-invariant functions by certain classes of GNNs, and another demonstrates the limitation of GNNs via graph isomorphism tests. Our work connects these two perspectives and proves their equivalence. We further develop a framework of the representation power of GNNs with the language of sigma-algebra, which incorporates both viewpoints.
Space and Time Efficient Kernel Density Estimation in High Dimensions
Backurs, Arturs, Indyk, Piotr, Wagner, Tal
Recently, Charikar and Siminelakis (2017) presented a framework for kernel density estimation in provably sublinear query time, for kernels that possess a certain hashing-based property. However, their data structure requires a significantly increased super-linear storage space, as well as super-linear preprocessing time. These limitations inhibit the practical applicability of their approach on large datasets. In this work, we present an improvement to their framework that retains the same query time, while requiring only linear space and linear preprocessing time. We instantiate our framework with the Laplacian and Exponential kernels, two popular kernels which possess the aforementioned property.