Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression between two groups (e.g., treatment vs. control). But there is increasing interest in multi-condition differential expression analyses in which expression is measured in many conditions, and the aim is to accurately detect and estimate expression differences in all conditions. We show that directly modeling single-cell RNA-seq counts in all conditions simultaneously, while also inferring how expression differences are shared across conditions, leads to greatly improved performance for detecting and estimating expression differences compared to existing methods. We illustrate the potential of this new approach by analyzing data from a single-cell experiment studying the effects of cytokine stimulation on gene expression. We call our new method "Poisson multivariate adaptive shrinkage", and it is implemented in an R package available online at //github.com/stephenslab/poisson.mash.alpha.
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Prediction is a central problem in Statistics, and there is currently a renewed interest for the so-called predictive approach in Bayesian statistics. What is the latter about? One has to return on foundational concepts, which we do in this paper, moving from the role of exchangeability and reviewing forms of partial exchangeability for more structured data, with the aim of discussing their use and implications in Bayesian statistics. There we show the underlying concept that, in Bayesian statistics, a predictive rule is meant as a learning rule - how one conveys past information to information on future events. This concept has implications on the use of exchangeability and generally invests all statistical problems, also in inference. It applies to classic contexts and to less explored situations, such as the use of predictive algorithms that can be read as Bayesian learning rules. The paper offers a historical overview, but also includes a few new results, presents some recent developments and poses some open questions.
We introduce a fast and explainable clustering method called CLASSIX. It consists of two phases, namely a greedy aggregation phase of the sorted data into groups of nearby data points, followed by the merging of groups into clusters. The algorithm is controlled by two scalar parameters, namely a distance parameter for the aggregation and another parameter controlling the minimal cluster size. Extensive experiments are conducted to give a comprehensive evaluation of the clustering performance on synthetic and real-world datasets, with various cluster shapes and low to high feature dimensionality. Our experiments demonstrate that CLASSIX competes with state-of-the-art clustering algorithms. The algorithm has linear space complexity and achieves near linear time complexity on a wide range of problems. Its inherent simplicity allows for the generation of intuitive explanations of the computed clusters.
Deep neural networks used for reconstructing sparse-view CT data are typically trained by minimizing a pixel-wise mean-squared error or similar loss function over a set of training images. However, networks trained with such pixel-wise losses are prone to wipe out small, low-contrast features that are critical for screening and diagnosis. To remedy this issue, we introduce a novel training loss inspired by the model observer framework to enhance the detectability of weak signals in the reconstructions. We evaluate our approach on the reconstruction of synthetic sparse-view breast CT data, and demonstrate an improvement in signal detectability with the proposed loss.
Non-Hermitian topological phases can produce some remarkable properties, compared with their Hermitian counterpart, such as the breakdown of conventional bulk-boundary correspondence and the non-Hermitian topological edge mode. Here, we introduce several algorithms with multi-layer perceptron (MLP), and convolutional neural network (CNN) in the field of deep learning, to predict the winding of eigenvalues non-Hermitian Hamiltonians. Subsequently, we use the smallest module of the periodic circuit as one unit to construct high-dimensional circuit data features. Further, we use the Dense Convolutional Network (DenseNet), a type of convolutional neural network that utilizes dense connections between layers to design a non-Hermitian topolectrical Chern circuit, as the DenseNet algorithm is more suitable for processing high-dimensional data. Our results demonstrate the effectiveness of the deep learning network in capturing the global topological characteristics of a non-Hermitian system based on training data.
The broad class of multivariate unified skew-normal (SUN) distributions has been recently shown to possess fundamental conjugacy properties. When used as priors for the vector of parameters in general probit, tobit, and multinomial probit models, these distributions yield posteriors that still belong to the SUN family. Although such a core result has led to important advancements in Bayesian inference and computation, its applicability beyond likelihoods associated with fully-observed, discretized, or censored realizations from multivariate Gaussian models remains yet unexplored. This article covers such an important gap by proving that the wider family of multivariate unified skew-elliptical (SUE) distributions, which extends SUNs to more general perturbations of elliptical densities, guarantees conjugacy for broader classes of models, beyond those relying on fully-observed, discretized or censored Gaussians. Such a result leverages the closure under linear combinations, conditioning and marginalization of SUE to prove that such a family is conjugate to the likelihood induced by general multivariate regression models for fully-observed, censored or dichotomized realizations from skew-elliptical distributions. This advancement substantially enlarges the set of models that enable conjugate Bayesian inference to general formulations arising from elliptical and skew-elliptical families, including the multivariate Student's t and skew-t, among others.
Untargeted metabolomic profiling through liquid chromatography-mass spectrometry (LC-MS) measures a vast array of metabolites within biospecimens, advancing drug development, disease diagnosis, and risk prediction. However, the low throughput of LC-MS poses a major challenge for biomarker discovery, annotation, and experimental comparison, necessitating the merging of multiple datasets. Current data pooling methods encounter practical limitations due to their vulnerability to data variations and hyperparameter dependence. Here we introduce GromovMatcher, a flexible and user-friendly algorithm that automatically combines LC-MS datasets using optimal transport. By capitalizing on feature intensity correlation structures, GromovMatcher delivers superior alignment accuracy and robustness compared to existing approaches. This algorithm scales to thousands of features requiring minimal hyperparameter tuning. Applying our method to experimental patient studies of liver and pancreatic cancer, we discover shared metabolic features related to patient alcohol intake, demonstrating how GromovMatcher facilitates the search for biomarkers associated with lifestyle risk factors linked to several cancer types.
Mesh-based Graph Neural Networks (GNNs) have recently shown capabilities to simulate complex multiphysics problems with accelerated performance times. However, mesh-based GNNs require a large number of message-passing (MP) steps and suffer from over-smoothing for problems involving very fine mesh. In this work, we develop a multiscale mesh-based GNN framework mimicking a conventional iterative multigrid solver, coupled with adaptive mesh refinement (AMR), to mitigate challenges with conventional mesh-based GNNs. We use the framework to accelerate phase field (PF) fracture problems involving coupled partial differential equations with a near-singular operator due to near-zero modulus inside the crack. We define the initial graph representation using all mesh resolution levels. We perform a series of downsampling steps using Transformer MP GNNs to reach the coarsest graph followed by upsampling steps to reach the original graph. We use skip connectors from the generated embedding during coarsening to prevent over-smoothing. We use Transfer Learning (TL) to significantly reduce the size of training datasets needed to simulate different crack configurations and loading conditions. The trained framework showed accelerated simulation times, while maintaining high accuracy for all cases compared to physics-based PF fracture model. Finally, this work provides a new approach to accelerate a variety of mesh-based engineering multiphysics problems
We study the problem of training diffusion models to sample from a distribution with a given unnormalized density or energy function. We benchmark several diffusion-structured inference methods, including simulation-based variational approaches and off-policy methods (continuous generative flow networks). Our results shed light on the relative advantages of existing algorithms while bringing into question some claims from past work. We also propose a novel exploration strategy for off-policy methods, based on local search in the target space with the use of a replay buffer, and show that it improves the quality of samples on a variety of target distributions. Our code for the sampling methods and benchmarks studied is made public at //github.com/GFNOrg/gfn-diffusion as a base for future work on diffusion models for amortized inference.
This paper considers the problem of manifold functional multiple regression with functional response, time--varying scalar regressors, and functional error term displaying Long Range Dependence (LRD) in time. Specifically, the error term is given by a manifold multifractionally integrated functional time series (see, e.g., Ovalle--Mu\~noz \& Ruiz--Medina, 2024)). The manifold is defined by a connected and compact two--point homogeneous space. The functional regression parameters have support in the manifold. The Generalized Least--Squares (GLS) estimator of the vector functional regression parameter is computed, and its asymptotic properties are analyzed under a totally specified and misspecified model scenario. A multiscale residual correlation analysis in the simulation study undertaken illustrates the empirical distributional properties of the errors at different spherical resolution levels.
Signal processing in the time-frequency plane has a long history and remains a field of methodological innovation. For instance, detection and denoising based on the zeros of the spectrogram have been proposed since 2015, contrasting with a long history of focusing on larger values of the spectrogram. Yet, unlike neighboring fields like optimization and machine learning, time-frequency signal processing lacks widely-adopted benchmarking tools. In this work, we contribute an open-source, Python-based toolbox termed MCSM-Benchs for benchmarking multi-component signal analysis methods, and we demonstrate our toolbox on three time-frequency benchmarks. First, we compare different methods for signal detection based on the zeros of the spectrogram, including unexplored variations of previously proposed detection tests. Second, we compare zero-based denoising methods to both classical and novel methods based on large values and ridges of the spectrogram. Finally, we compare the denoising performance of these methods against typical spectrogram thresholding strategies, in terms of post-processing artifacts commonly referred to as musical noise. At a low level, the obtained results provide new insight on the assessed approaches, and in particular research directions to further develop zero-based methods. At a higher level, our benchmarks exemplify the benefits of using a public, collaborative, common framework for benchmarking.
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