Bayesian graphical models are powerful tools to infer complex relationships in high dimension, yet are often fraught with computational and statistical challenges. If exploited in a principled way, the increasing information collected alongside the data of primary interest constitutes an opportunity to mitigate these difficulties by guiding the detection of dependence structures. For instance, gene network inference may be informed by the use of publicly available summary statistics on the regulation of genes by genetic variants. Here we present a novel Gaussian graphical modelling framework to identify and leverage information on the centrality of nodes in conditional independence graphs. Specifically, we consider a fully joint hierarchical model to simultaneously infer (i) sparse precision matrices and (ii) the relevance of node-level information for uncovering the sought-after network structure. We encode such information as candidate auxiliary variables using a spike-and-slab submodel on the propensity of nodes to be hubs, which allows hypothesis-free selection and interpretation of a sparse subset of relevant variables. As efficient exploration of large posterior spaces is needed for real-world applications, we develop a variational expectation conditional maximisation algorithm that scales inference to hundreds of samples, nodes and auxiliary variables. We illustrate and exploit the advantages of our approach in simulations and in a gene network study which identifies hub genes involved in biological pathways relevant to immune-mediated diseases.
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Neural oscillations are considered to be brain-specific signatures of information processing and communication in the brain. They also reflect pathological brain activity in neurological disorders, thus offering a basis for diagnoses and forecasting. Epilepsy is one of the most common neurological disorders, characterized by abnormal synchronization and desynchronization of the oscillations in the brain. About one third of epilepsy cases are pharmacoresistant, and as such emphasize the need for novel therapy approaches, where brain stimulation appears to be a promising therapeutic option. The development of brain stimulation paradigms, however, is often based on generalized assumptions about brain dynamics, although it is known that significant differences occur between patients and brain states. We developed a framework to extract individualized predictive models of epileptic network dynamics directly from EEG data. The models are based on the dominant coherent oscillations and their dynamical coupling, thus combining an established interpretation of dynamics through neural oscillations, with accurate patient-specific features. We show that it is possible to build a direct correspondence between the models of brain-network dynamics under periodic driving, and the mechanism of neural entrainment via periodic stimulation. When our framework is applied to EEG recordings of patients in status epilepticus (a brain state of perpetual seizure activity), it yields a model-driven predictive analysis of the therapeutic performance of periodic brain stimulation. This suggests that periodic brain stimulation can drive pathological states of epileptic network dynamics towards a healthy functional brain state.
Models of complex technological systems inherently contain interactions and dependencies among their input variables that affect their joint influence on the output. Such models are often computationally expensive and few sensitivity analysis methods can effectively process such complexities. Moreover, the sensitivity analysis field as a whole pays limited attention to the nature of interaction effects, whose understanding can prove to be critical for the design of safe and reliable systems. In this paper, we introduce and extensively test a simple binning approach for computing sensitivity indices and demonstrate how complementing it with the smart visualization method, simulation decomposition (SimDec), can permit important insights into the behavior of complex engineering models. The simple binning approach computes first-, second-order effects, and a combined sensitivity index, and is considerably more computationally efficient than Sobol' indices. The totality of the sensitivity analysis framework provides an efficient and intuitive way to analyze the behavior of complex systems containing interactions and dependencies.
We propose an approach to 3D reconstruction via inverse procedural modeling and investigate two variants of this approach. The first option consists in the fitting set of input parameters using a genetic algorithm. We demonstrate the results of our work on tree models, complex objects, with the reconstruction of which most existing methods cannot handle. The second option allows us to significantly improve the precision by using gradients within memetic algorithm, differentiable rendering and also differentiable procedural generators. In our work we see 2 main contributions. First, we propose a method to join differentiable rendering and inverse procedural modeling. This gives us an opportunity to reconstruct 3D model more accurately than existing approaches when a small number of input images are available (even for single image). Second, we join both differentiable and non-differentiable procedural generators in a single framework which allow us to apply inverse procedural modeling to fairly complex generators: when gradient is available, reconstructions is precise, when gradient is not available, reconstruction is approximate, but always high quality without visual artifacts.
A new mechanical model on noncircular shallow tunnelling considering initial stress field is proposed in this paper by constraining far-field ground surface to eliminate displacement singularity at infinity, and the originally unbalanced tunnel excavation problem in existing solutions is turned to an equilibrium one of mixed boundaries. By applying analytic continuation, the mixed boundaries are transformed to a homogenerous Riemann-Hilbert problem, which is subsequently solved via an efficient and accurate iterative method with boundary conditions of static equilibrium, displacement single-valuedness, and traction along tunnel periphery. The Lanczos filtering technique is used in the final stress and displacement solution to reduce the Gibbs phenomena caused by the constrained far-field ground surface for more accurte results. Several numerical cases are conducted to intensively verify the proposed solution by examining boundary conditions and comparing with existing solutions, and all the results are in good agreements. Then more numerical cases are conducted to investigate the stress and deformation distribution along ground surface and tunnel periphery, and several engineering advices are given. Further discussions on the defects of the proposed solution are also conducted for objectivity.
Rational function approximations provide a simple but flexible alternative to polynomial approximation, allowing one to capture complex non-linearities without oscillatory artifacts. However, there have been few attempts to use rational functions on noisy data due to the likelihood of creating spurious singularities. To avoid the creation of singularities, we use Bernstein polynomials and appropriate conditions on their coefficients to force the denominator to be strictly positive. While this reduces the range of rational polynomials that can be expressed, it keeps all the benefits of rational functions while maintaining the robustness of polynomial approximation in noisy data scenarios. Our numerical experiments on noisy data show that existing rational approximation methods continually produce spurious poles inside the approximation domain. This contrasts our method, which cannot create poles in the approximation domain and provides better fits than a polynomial approximation and even penalized splines on functions with multiple variables. Moreover, guaranteeing pole-free in an interval is critical for estimating non-constant coefficients when numerically solving differential equations using spectral methods. This provides a compact representation of the original differential equation, allowing numeric solvers to achieve high accuracy quickly, as seen in our experiments.
Insurers usually turn to generalized linear models for modelling claim frequency and severity data. Due to their success in other fields, machine learning techniques are gaining popularity within the actuarial toolbox. Our paper contributes to the literature on frequency-severity insurance pricing with machine learning via deep learning structures. We present a benchmark study on four insurance data sets with frequency and severity targets in the presence of multiple types of input features. We compare in detail the performance of: a generalized linear model on binned input data, a gradient-boosted tree model, a feed-forward neural network (FFNN), and the combined actuarial neural network (CANN). Our CANNs combine a baseline prediction established with a GLM and GBM, respectively, with a neural network correction. We explain the data preprocessing steps with specific focus on the multiple types of input features typically present in tabular insurance data sets, such as postal codes, numeric and categorical covariates. Autoencoders are used to embed the categorical variables into the neural network and we explore their potential advantages in a frequency-severity setting. Finally, we construct global surrogate models for the neural nets' frequency and severity models. These surrogates enable the translation of the essential insights captured by the FFNNs or CANNs to GLMs. As such, a technical tariff table results that can easily be deployed in practice.
phyloDB is a modular and extensible framework for large-scale phylogenetic analyses, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an API for representing and querying phylogenetic data. Custom algorithms are also supported, allowing to perform heavy computations directly over the data, and to store results in the database. Multiple computation results are stored as multilayer networks, promoting and facilitating comparative analyses, as well as avoiding unnecessary ab initio computations. The experimental evaluation results showcase that phyloDB is efficient and scalable with respect to both API operations and algorithms execution.
Factor models are widely used for dimension reduction in the analysis of multivariate data. This is achieved through decomposition of a p x p covariance matrix into the sum of two components. Through a latent factor representation, they can be interpreted as a diagonal matrix of idiosyncratic variances and a shared variation matrix, that is, the product of a p x k factor loadings matrix and its transpose. If k << p, this defines a sparse factorisation of the covariance matrix. Historically, little attention has been paid to incorporating prior information in Bayesian analyses using factor models where, at best, the prior for the factor loadings is order invariant. In this work, a class of structured priors is developed that can encode ideas of dependence structure about the shared variation matrix. The construction allows data-informed shrinkage towards sensible parametric structures while also facilitating inference over the number of factors. Using an unconstrained reparameterisation of stationary vector autoregressions, the methodology is extended to stationary dynamic factor models. For computational inference, parameter-expanded Markov chain Monte Carlo samplers are proposed, including an efficient adaptive Gibbs sampler. Two substantive applications showcase the scope of the methodology and its inferential benefits.
Within the realm of image recognition, a specific category of multi-label classification (MLC) challenges arises when objects within the visual field may occlude one another, demanding simultaneous identification of both occluded and occluding objects. Traditional convolutional neural networks (CNNs) can tackle these challenges; however, those models tend to be bulky and can only attain modest levels of accuracy. Leveraging insights from cutting-edge neural science research, specifically the Holistic Bursting (HB) cell, this paper introduces a pioneering integrated network framework named HB-net. Built upon the foundation of HB cell clusters, HB-net is designed to address the intricate task of simultaneously recognizing multiple occluded objects within images. Various Bursting cell cluster structures are introduced, complemented by an evidence accumulation mechanism. Testing is conducted on multiple datasets comprising digits and letters. The results demonstrate that models incorporating the HB framework exhibit a significant $2.98\%$ enhancement in recognition accuracy compared to models without the HB framework ($1.0298$ times, $p=0.0499$). Although in high-noise settings, standard CNNs exhibit slightly greater robustness when compared to HB-net models, the models that combine the HB framework and EA mechanism achieve a comparable level of accuracy and resilience to ResNet50, despite having only three convolutional layers and approximately $1/30$ of the parameters. The findings of this study offer valuable insights for improving computer vision algorithms. The essential code is provided at //github.com/d-lab438/hb-net.git.
HyperNetX (HNX) is an open source Python library for the analysis and visualization of complex network data modeled as hypergraphs. Initially released in 2019, HNX facilitates exploratory data analysis of complex networks using algebraic topology, combinatorics, and generalized hypergraph and graph theoretical methods on structured data inputs. With its 2023 release, the library supports attaching metadata, numerical and categorical, to nodes (vertices) and hyperedges, as well as to node-hyperedge pairings (incidences). HNX has a customizable Matplotlib-based visualization module as well as HypernetX-Widget, its JavaScript addon for interactive exploration and visualization of hypergraphs within Jupyter Notebooks. Both packages are available on GitHub and PyPI. With a growing community of users and collaborators, HNX has become a preeminent tool for hypergraph analysis.
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