The differential network (DN) analysis identifies changes in measures of association among genes under two or more experimental conditions. In this article, we introduce a Pseudo-value Regression Approach for Network Analysis (PRANA). This is a novel method of differential network analysis that also adjusts for additional clinical covariates. We start from mutual information (MI) criteria, followed by pseudo-value calculations, which are then entered into a robust regression model. This article assesses the model performances of PRANA in a multivariable setting, followed by a comparison to dnapath and DINGO in both univariable and multivariable settings through variety of simulations. Performance in terms of precision, recall, and F1 score of differentially connected (DC) genes is assessed. By and large, PRANA outperformed dnapath and DINGO, neither of which is equipped to adjust for available covariates such as patient-age. Lastly, we employ PRANA in a real data application from the Gene Expression Omnibus (GEO) database to identify DC genes that are associated with chronic obstructive pulmonary disease (COPD) to demonstrate its utility. To the best of our knowledge, this is the first attempt of utilizing a regression modeling for DN analysis by collective gene expression levels between two or more groups with the inclusion of additional clinical covariates. By and large, adjusting for available covariates improves accuracy of a DN analysis.
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This paper introduces a novel probabilistic forecasting technique called Smoothing Quantile Regression Averaging (SQRA). It combines Quantile Regression Averaging - a well performing load and price forecasting approach - with kernel estimation to improve the reliability of the estimates. Three variants of SQRA are evaluated across datasets from four power markets and compared against well-established benchmarks. Empirical evidence indicates superior predictive performance of the method in terms of the Kupiec test, the pinball score, and the conditional predictive accuracy test. Moreover, considering a day-ahead market trading strategy that utilizes probabilistic price predictions and battery storage, the study shows that profits of up to 9 EUR per 1 MW traded can be achieved when forecasts are generated using SQRA.
Probabilistic sensitivity analysis identifies the influential uncertain input to guide decision-making. We propose a general sensitivity framework with respect to the input distribution parameters that unifies a wide range of sensitivity measures, including information theoretical metrics such as the Fisher information. The framework is derived analytically via a constrained maximization and the sensitivity analysis is reformulated into an eigenvalue problem. There are only two main steps to implement the sensitivity framework utilising the likelihood ratio/score function method, a Monte Carlo type sampling followed by solving an eigenvalue equation. The resulting eigenvectors then provide the directions for simultaneous variations of the input parameters and guide the focus to perturb uncertainty the most. Not only is it conceptually simple, but numerical examples demonstrate that the proposed framework also provides new sensitivity insights, such as the combined sensitivity of multiple correlated uncertainty metrics, robust sensitivity analysis with an entropic constraint, and approximation of deterministic sensitivities. Three different examples, ranging from a simple cantilever beam to an offshore marine riser, are used to demonstrate the potential applications of the proposed sensitivity framework to applied mechanics problems.
Improving road safety is hugely important with the number of deaths on the world's roads remaining unacceptably high; an estimated 1.35 million people die each year (WHO, 2020). Current practice for treating collision hotspots is almost always reactive: once a threshold level of collisions has been exceeded during some predetermined observation period, treatment is applied (e.g. road safety cameras). However, more recently, methodology has been developed to predict collision counts at potential hotspots in future time periods, with a view to a more proactive treatment of road safety hotspots. Dynamic linear models provide a flexible framework for predicting collisions and thus enabling such a proactive treatment. In this paper, we demonstrate how such models can be used to capture both seasonal variability and spatial dependence in time course collision rates at several locations. The model allows for within- and out-of-sample forecasting for locations which are fully observed and for locations where some data are missing. We illustrate our approach using collision rate data from 8 Traffic Administration Zones in North Florida, USA, and find that the model provides a good description of the underlying process and reasonable forecast accuracy.
In order to apply canonical labelling of graphs and isomorphism checking in interactive theorem provers, these checking algorithms must either be mechanically verified or their results must be verifiable by independent checkers. We analyze a state-of-the-art algorithm for canonical labelling of graphs (described by McKay and Piperno) and formulate it in terms of a formal proof system. We provide an implementation that can export a proof that the obtained graph is the canonical form of a given graph. Such proofs are then verified by our independent checker and can be used to confirm that two given graphs are not isomorphic.
The paper tackles the problem of clustering multiple networks, that do not share the same set of vertices, into groups of networks with similar topology. A statistical model-based approach based on a finite mixture of stochastic block models is proposed. A clustering is obtained by maximizing the integrated classification likelihood criterion. This is done by a hierarchical agglomerative algorithm, that starts from singleton clusters and successively merges clusters of networks. As such, a sequence of nested clusterings is computed that can be represented by a dendrogram providing valuable insights on the collection of networks. Using a Bayesian framework, model selection is performed in an automated way since the algorithm stops when the best number of clusters is attained. The algorithm is computationally efficient, when carefully implemented. The aggregation of groups of networks requires a means to overcome the label-switching problem of the stochastic block model and to match the block labels of the graphs. To address this problem, a new tool is proposed based on a comparison of the graphons of the associated stochastic block models. The clustering approach is assessed on synthetic data. An application to a collection of ecological networks illustrates the interpretability of the obtained results.
Functional data such as curves and surfaces have become more and more common with modern technological advancements. The use of functional predictors remains challenging due to its inherent infinite-dimensionality. The common practice is to project functional data into a finite dimensional space. The popular partial least square (PLS) method has been well studied for the functional linear model [1]. As an alternative, quantile regression provides a robust and more comprehensive picture of the conditional distribution of a response when it is non-normal, heavy-tailed, or contaminated by outliers. While partial quantile regression (PQR) was proposed in [2], no theoretical guarantees were provided due to the iterative nature of the algorithm and the non-smoothness of quantile loss function. To address these issues, we propose an alternative PQR (APQR) formulation with guaranteed convergence. This novel formulation motivates new theories and allows us to establish asymptotic properties. Numerical studies on a benchmark dataset show the superiority of our new approach. We also apply our novel method to a functional magnetic resonance imaging (fMRI) data to predict attention deficit hyperactivity disorder (ADHD) and a diffusion tensor imaging (DTI) dataset to predict Alzheimer's disease (AD).
We examine the evolutionary basis for risk aversion with respect to aggregate risk. We study populations in which agents face choices between alternatives with different levels of aggregate risk. We show that the choices that maximize the long-run growth rate are induced by a heterogeneous population in which the least and most risk-averse agents are indifferent between facing an aggregate risk and obtaining its linear and harmonic mean for sure, respectively. Moreover, approximately optimal behavior can be induced by a simple distribution according to which all agents have constant relative risk aversion, and the coefficient of relative risk aversion is uniformly distributed between zero and two.
Transfer learning for partial differential equations (PDEs) is to develop a pre-trained neural network that can be used to solve a wide class of PDEs. Existing transfer learning approaches require much information of the target PDEs such as its formulation and/or data of its solution for pre-training. In this work, we propose to construct transferable neural feature spaces from purely function approximation perspectives without using PDE information. The construction of the feature space involves re-parameterization of the hidden neurons and uses auxiliary functions to tune the resulting feature space. Theoretical analysis shows the high quality of the produced feature space, i.e., uniformly distributed neurons. Extensive numerical experiments verify the outstanding performance of our method, including significantly improved transferability, e.g., using the same feature space for various PDEs with different domains and boundary conditions, and the superior accuracy, e.g., several orders of magnitude smaller mean squared error than the state of the art methods.
The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.
Seeking the equivalent entities among multi-source Knowledge Graphs (KGs) is the pivotal step to KGs integration, also known as \emph{entity alignment} (EA). However, most existing EA methods are inefficient and poor in scalability. A recent summary points out that some of them even require several days to deal with a dataset containing 200,000 nodes (DWY100K). We believe over-complex graph encoder and inefficient negative sampling strategy are the two main reasons. In this paper, we propose a novel KG encoder -- Dual Attention Matching Network (Dual-AMN), which not only models both intra-graph and cross-graph information smartly, but also greatly reduces computational complexity. Furthermore, we propose the Normalized Hard Sample Mining Loss to smoothly select hard negative samples with reduced loss shift. The experimental results on widely used public datasets indicate that our method achieves both high accuracy and high efficiency. On DWY100K, the whole running process of our method could be finished in 1,100 seconds, at least 10* faster than previous work. The performances of our method also outperform previous works across all datasets, where Hits@1 and MRR have been improved from 6% to 13%.
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