Principal variables analysis (PVA) is a technique for selecting a subset of variables that capture as much of the information in a dataset as possible. Existing approaches for PVA are based on the Pearson correlation matrix, which is not well-suited to describing the relationships between non-Gaussian variables. We propose a generalized approach to PVA enabling the use of different types of correlation, and we explore using Spearman, Gaussian copula, and polychoric correlations as alternatives to Pearson correlation when performing PVA. We compare performance in simulation studies varying the form of the true multivariate distribution over a wide range of possibilities. Our results show that on continuous non-Gaussian data, using generalized PVA with Gaussian copula or Spearman correlations provides a major improvement in performance compared to Pearson. Meanwhile, on ordinal data, generalized PVA with polychoric correlations outperforms the rest by a wide margin. We apply generalized PVA to a dataset of 102 clinical variables measured on individuals with X-linked dystonia parkinsonism (XDP), a rare neurodegenerative disorder, and we find that using different types of correlation yields substantively different sets of principal variables.
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Learning tasks play an increasingly prominent role in quantum information and computation. They range from fundamental problems such as state discrimination and metrology over the framework of quantum probably approximately correct (PAC) learning, to the recently proposed shadow variants of state tomography. However, the many directions of quantum learning theory have so far evolved separately. We propose a general mathematical formalism for describing quantum learning by training on classical-quantum data and then testing how well the learned hypothesis generalizes to new data. In this framework, we prove bounds on the expected generalization error of a quantum learner in terms of classical and quantum information-theoretic quantities measuring how strongly the learner's hypothesis depends on the specific data seen during training. To achieve this, we use tools from quantum optimal transport and quantum concentration inequalities to establish non-commutative versions of decoupling lemmas that underlie recent information-theoretic generalization bounds for classical machine learning. Our framework encompasses and gives intuitively accessible generalization bounds for a variety of quantum learning scenarios such as quantum state discrimination, PAC learning quantum states, quantum parameter estimation, and quantumly PAC learning classical functions. Thereby, our work lays a foundation for a unifying quantum information-theoretic perspective on quantum learning.
Bayesian inference and kernel methods are well established in machine learning. The neural network Gaussian process in particular provides a concept to investigate neural networks in the limit of infinitely wide hidden layers by using kernel and inference methods. Here we build upon this limit and provide a field-theoretic formalism which covers the generalization properties of infinitely wide networks. We systematically compute generalization properties of linear, non-linear, and deep non-linear networks for kernel matrices with heterogeneous entries. In contrast to currently employed spectral methods we derive the generalization properties from the statistical properties of the input, elucidating the interplay of input dimensionality, size of the training data set, and variability of the data. We show that data variability leads to a non-Gaussian action reminiscent of a ($\varphi^3+\varphi^4$)-theory. Using our formalism on a synthetic task and on MNIST we obtain a homogeneous kernel matrix approximation for the learning curve as well as corrections due to data variability which allow the estimation of the generalization properties and exact results for the bounds of the learning curves in the case of infinitely many training data points.
As the IT industry advances, system log data becomes increasingly crucial. Many computer systems rely on log texts for management due to restricted access to source code. The need for log anomaly detection is growing, especially in real-world applications, but identifying anomalies in rapidly accumulating logs remains a challenging task. Traditional deep learning-based anomaly detection models require dataset-specific training, leading to corresponding delays. Notably, most methods only focus on sequence-level log information, which makes the detection of subtle anomalies harder, and often involve inference processes that are difficult to utilize in real-time. We introduce RAPID, a model that capitalizes on the inherent features of log data to enable anomaly detection without training delays, ensuring real-time capability. RAPID treats logs as natural language, extracting representations using pre-trained language models. Given that logs can be categorized based on system context, we implement a retrieval-based technique to contrast test logs with the most similar normal logs. This strategy not only obviates the need for log-specific training but also adeptly incorporates token-level information, ensuring refined and robust detection, particularly for unseen logs. We also propose the core set technique, which can reduce the computational cost needed for comparison. Experimental results show that even without training on log data, RAPID demonstrates competitive performance compared to prior models and achieves the best performance on certain datasets. Through various research questions, we verified its capability for real-time detection without delay.
Causal representation learning algorithms discover lower-dimensional representations of data that admit a decipherable interpretation of cause and effect; as achieving such interpretable representations is challenging, many causal learning algorithms utilize elements indicating prior information, such as (linear) structural causal models, interventional data, or weak supervision. Unfortunately, in exploratory causal representation learning, such elements and prior information may not be available or warranted. Alternatively, scientific datasets often have multiple modalities or physics-based constraints, and the use of such scientific, multimodal data has been shown to improve disentanglement in fully unsupervised settings. Consequently, we introduce a causal representation learning algorithm (causalPIMA) that can use multimodal data and known physics to discover important features with causal relationships. Our innovative algorithm utilizes a new differentiable parametrization to learn a directed acyclic graph (DAG) together with a latent space of a variational autoencoder in an end-to-end differentiable framework via a single, tractable evidence lower bound loss function. We place a Gaussian mixture prior on the latent space and identify each of the mixtures with an outcome of the DAG nodes; this novel identification enables feature discovery with causal relationships. Tested against a synthetic and a scientific dataset, our results demonstrate the capability of learning an interpretable causal structure while simultaneously discovering key features in a fully unsupervised setting.
A method for the analysis of superresolution microscopy images is presented. This method is based on the analysis of stochastic trajectories of particles moving on the membrane of a cell with the assumption that this motion is determined by the properties of this membrane. Thus, the purpose of this method is to recover the structural properties of the membrane by solving an inverse problem governed by the Fokker-Planck equation related to the stochastic trajectories. Results of numerical experiments demonstrate the ability of the proposed method to reconstruct the potential of a cell membrane by using synthetic data similar those captured by superresolution microscopy of luminescent activated proteins.
The remarkable generative capabilities of denoising diffusion models have raised new concerns regarding the authenticity of the images we see every day on the Internet. However, the vast majority of existing deepfake detection models are tested against previous generative approaches (e.g. GAN) and usually provide only a "fake" or "real" label per image. We believe a more informative output would be to augment the per-image label with a localization map indicating which regions of the input have been manipulated. To this end, we frame this task as a weakly-supervised localization problem and identify three main categories of methods (based on either explanations, local scores or attention), which we compare on an equal footing by using the Xception network as the common backbone architecture. We provide a careful analysis of all the main factors that parameterize the design space: choice of method, type of supervision, dataset and generator used in the creation of manipulated images; our study is enabled by constructing datasets in which only one of the components is varied. Our results show that weakly-supervised localization is attainable, with the best performing detection method (based on local scores) being less sensitive to the looser supervision than to the mismatch in terms of dataset or generator.
We combine Kronecker products, and quantitative information flow, to give a novel formal analysis for the fine-grained verification of utility in complex privacy pipelines. The combination explains a surprising anomaly in the behaviour of utility of privacy-preserving pipelines -- that sometimes a reduction in privacy results also in a decrease in utility. We use the standard measure of utility for Bayesian analysis, introduced by Ghosh at al., to produce tractable and rigorous proofs of the fine-grained statistical behaviour leading to the anomaly. More generally, we offer the prospect of formal-analysis tools for utility that complement extant formal analyses of privacy. We demonstrate our results on a number of common privacy-preserving designs.
Permutation tests enable testing statistical hypotheses in situations when the distribution of the test statistic is complicated or not available. In some situations, the test statistic under investigation is multivariate, with the multiple testing problem being an important example. The corresponding multivariate permutation tests are then typically based on a suitableone-dimensional transformation of the vector of partial permutation p-values via so called combining functions. This paper proposes a new approach that utilizes the optimal measure transportation concept. The final single p-value is computed from the empirical center-outward distribution function of the permuted multivariate test statistics. This method avoids computation of the partial p-values and it is easy to be implemented. In addition, it allows to compute and interpret contributions of the components of the multivariate test statistic to the non-conformity score and to the rejection of the null hypothesis. Apart from this method, the measure transportation is applied also to the vector of partial p-values as an alternative to the classical combining functions. Both techniques are compared with the standard approaches using various practical examples in a Monte Carlo study. An application on a functional data set is provided as well.
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.
Block majorization-minimization (BMM) is a simple iterative algorithm for nonconvex constrained optimization that sequentially minimizes majorizing surrogates of the objective function in each block coordinate while the other coordinates are held fixed. BMM entails a large class of optimization algorithms such as block coordinate descent and its proximal-point variant, expectation-minimization, and block projected gradient descent. We establish that for general constrained nonconvex optimization, BMM with strongly convex surrogates can produce an $\epsilon$-stationary point within $O(\epsilon^{-2}(\log \epsilon^{-1})^{2})$ iterations and asymptotically converges to the set of stationary points. Furthermore, we propose a trust-region variant of BMM that can handle surrogates that are only convex and still obtain the same iteration complexity and asymptotic stationarity. These results hold robustly even when the convex sub-problems are inexactly solved as long as the optimality gaps are summable. As an application, we show that a regularized version of the celebrated multiplicative update algorithm for nonnegative matrix factorization by Lee and Seung has iteration complexity of $O(\epsilon^{-2}(\log \epsilon^{-1})^{2})$. The same result holds for a wide class of regularized nonnegative tensor decomposition algorithms as well as the classical block projected gradient descent algorithm. These theoretical results are validated through various numerical experiments.
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