In this chapter, we identify fundamental geometric structures that underlie the problems of sampling, optimisation, inference and adaptive decision-making. Based on this identification, we derive algorithms that exploit these geometric structures to solve these problems efficiently. We show that a wide range of geometric theories emerge naturally in these fields, ranging from measure-preserving processes, information divergences, Poisson geometry, and geometric integration. Specifically, we explain how (i) leveraging the symplectic geometry of Hamiltonian systems enable us to construct (accelerated) sampling and optimisation methods, (ii) the theory of Hilbertian subspaces and Stein operators provides a general methodology to obtain robust estimators, (iii) preserving the information geometry of decision-making yields adaptive agents that perform active inference. Throughout, we emphasise the rich connections between these fields; e.g., inference draws on sampling and optimisation, and adaptive decision-making assesses decisions by inferring their counterfactual consequences. Our exposition provides a conceptual overview of underlying ideas, rather than a technical discussion, which can be found in the references herein.

Frequently asked questions What are the benefits of using CausalNex? When should you consider using CausalNex?

Training and testing supervised object detection models require a large collection of images with ground truth labels. Labels define object classes in the image, as well as their locations, shape, and possibly other information such as pose. The labeling process has proven extremely time consuming, even with the presence of manpower. We introduce a novel labeling tool for 2D images as well as 3D triangular meshes: 3D Labeling Tool (3DLT). This is a standalone, feature-heavy and cross-platform software that does not require installation and can run on Windows, macOS and Linux-based distributions. Instead of labeling the same object on every image separately like current tools, we use depth information to reconstruct a triangular mesh from said images and label the object only once on the aforementioned mesh. We use registration to simplify 3D labeling, outlier detection to improve 2D bounding box calculation and surface reconstruction to expand labeling possibility to large point clouds. Our tool is tested against state of the art methods and it greatly surpasses them in terms of speed while preserving accuracy and ease of use.

We study the performance -- and specifically the rate at which the error probability converges to zero -- of Machine Learning (ML) classification techniques. Leveraging the theory of large deviations, we provide the mathematical conditions for a ML classifier to exhibit error probabilities that vanish exponentially, say $\sim \exp\left(-n\,I + o(n) \right)$, where $n$ is the number of informative observations available for testing (or another relevant parameter, such as the size of the target in an image) and $I$ is the error rate. Such conditions depend on the Fenchel-Legendre transform of the cumulant-generating function of the Data-Driven Decision Function (D3F, i.e., what is thresholded before the final binary decision is made) learned in the training phase. As such, the D3F and, consequently, the related error rate $I$, depend on the given training set, which is assumed of finite size. Interestingly, these conditions can be verified and tested numerically exploiting the available dataset, or a synthetic dataset, generated according to the available information on the underlying statistical model. In other words, the classification error probability convergence to zero and its rate can be computed on a portion of the dataset available for training. Coherently with the large deviations theory, we can also establish the convergence, for $n$ large enough, of the normalized D3F statistic to a Gaussian distribution. This property is exploited to set a desired asymptotic false alarm probability, which empirically turns out to be accurate even for quite realistic values of $n$. Furthermore, approximate error probability curves $\sim \zeta_n \exp\left(-n\,I \right)$ are provided, thanks to the refined asymptotic derivation (often referred to as exact asymptotics), where $\zeta_n$ represents the most representative sub-exponential terms of the error probabilities.

This work presents a new procedure for obtaining predictive distributions in the context of Gaussian process (GP) modeling, with a relaxation of the interpolation constraints outside some ranges of interest: the mean of the predictive distributions no longer necessarily interpolates the observed values when they are outside ranges of interest, but are simply constrained to remain outside. This method called relaxed Gaussian process (reGP) interpolation provides better predictive distributions in ranges of interest, especially in cases where a stationarity assumption for the GP model is not appropriate. It can be viewed as a goal-oriented method and becomes particularly interesting in Bayesian optimization, for example, for the minimization of an objective function, where good predictive distributions for low function values are important. When the expected improvement criterion and reGP are used for sequentially choosing evaluation points, the convergence of the resulting optimization algorithm is theoretically guaranteed (provided that the function to be optimized lies in the reproducing kernel Hilbert spaces attached to the known covariance of the underlying Gaussian process). Experiments indicate that using reGP instead of stationary GP models in Bayesian optimization is beneficial.

In this work, we investigated the application of score-based gradient learning in discriminative and generative classification settings. Score function can be used to characterize data distribution as an alternative to density. It can be efficiently learned via score matching, and used to flexibly generate credible samples to enhance discriminative classification quality, to recover density and to build generative classifiers. We analysed the decision theories involving score-based representations, and performed experiments on simulated and real-world datasets, demonstrating its effectiveness in achieving and improving binary classification performance, and robustness to perturbations, particularly in high dimensions and imbalanced situations.

A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses, including diagnosis or prognosis of diseases and finding effective treatments for chronic diseases such as cancer. Boolean networks have emerged as a successful class of models for capturing the behavior of GRNs. In most practical settings, inference of GRNs should be achieved through limited and temporally sparse genomics data. A large number of genes in GRNs leads to a large possible topology candidate space, which often cannot be exhaustively searched due to the limitation in computational resources. This paper develops a scalable and efficient topology inference for GRNs using Bayesian optimization and kernel-based methods. Rather than an exhaustive search over possible topologies, the proposed method constructs a Gaussian Process (GP) with a topology-inspired kernel function to account for correlation in the likelihood function. Then, using the posterior distribution of the GP model, the Bayesian optimization efficiently searches for the topology with the highest likelihood value by optimally balancing between exploration and exploitation. The performance of the proposed method is demonstrated through comprehensive numerical experiments using a well-known mammalian cell-cycle network.

Using Bayes's theorem, we derive a unit-wise recurrence as well as a backward recursion similar to the forward-backward algorithm. The resulting Bayesian recurrent units can be integrated as recurrent neural networks within deep learning frameworks, while retaining a probabilistic interpretation from the direct correspondence with hidden Markov models. Whilst the contribution is mainly theoretical, experiments on speech recognition indicate that adding the derived units at the end of state-of-the-art recurrent architectures can improve the performance at a very low cost in terms of trainable parameters.

Target detection in hyperspectral imagery is the process of locating pixels from an image which are likely to contain target, typically done by comparing one or more spectra for the desired target material to each pixel in the image. Target identification is the process of target detection incorporating an additional process to identify more specifically the material that is present in each pixel that scored high in detection. Detection is generally a 2-class problem of target vs. background, and identification is a many class problem including target, background, and additional know materials. The identification process we present is probabilistic and hierarchical which provides transparency to the process and produces trustworthy output. In this paper we show that target identification has a much lower false alarm rate than detection alone, and provide a detailed explanation of a robust identification method using probabilistic hierarchical classification that handles the vague categories of materials that depend on users which are different than the specific physical categories of chemical constituents. Identification is often done by comparing mixtures of materials including the target spectra to mixtures of materials that do not include the target spectra, possibly with other steps. (band combinations, feature checking, background removal, etc.) Standard linear regression does not handle these problems well because the number of regressors (identification spectra) is greater than the number of feature variables (bands), and there are multiple correlated spectra. Our proposed method handles these challenges efficiently and provides additional important practical information in the form of hierarchical probabilities computed from Bayesian model averaging.

In this paper we provide classification In this paper we will be working hyperspectral pixel data methods for determining crop type in the USGS collected using the NASA Hyperion satellite [3] and organized GHISACONUS data, which contains around 7,000 pixel spectra and meticulously labeled by the USGS. This data, available from the five major U.S. agricultural crops (winter wheat, online from the USGS as the Global Hyperspectral Imaging rice, corn, soybeans, and cotton) collected by the NASA Spectral-library of Agricultural crops for Conterminous United Hyperion satellite, and includes the spectrum, geolocation, States (GHISACONUS) [4], is a library of 6,988 spectra, each crop type, and stage of growth for each pixel. We apply of which is labeled as one of the five major agricultural crops standard LDA and QDA as well as Bayesian custom versions (e.g., winter wheat, rice, corn, soybeans, and cotton) collected that compute the joint probability of crop type and stage, and between 2008 and 2015. The locations for the spectra in the then the marginal probability for crop type, outperforming GHISACONUS library are shown in Figure 1.