Cell type deconvolution is a computational approach to infer proportions of individual cell types from bulk transcriptomics data. Though many new methods have been developed for cell type deconvolution, most of them only provide point estimation of the cell type proportions. On the other hand, estimates of the cell type proportions can be very noisy due to various sources of bias and randomness, and ignoring their uncertainty may greatly affect the validity of downstream analyses. In this paper, we propose a comprehensive statistical framework for cell type deconvolution and construct asymptotically valid confidence intervals both for each individual's cell type proportion and for quantifying how cell type proportions change across multiple bulk individuals in downstream regression analyses. Our analysis takes into account various factors including the biological randomness of gene expressions across cells and individuals, gene-gene dependence, and the cross-platform biases and sequencing errors, and avoids any parametric assumptions on the data distributions. We also provide identification conditions of the cell type proportions when there are arbitrary platforms-specific bias across sequencing technologies.
An automated and accurate fabric defect inspection system is in high demand as a replacement for slow, inconsistent, error-prone, and expensive human operators in the textile industry. Previous efforts focused on certain types of fabrics or defects, which is not an ideal solution. In this paper, we propose a novel one-class model that is capable of detecting various defects on different fabric types. Our model takes advantage of a well-designed Gabor filter bank to analyze fabric texture. We then leverage an advanced deep learning algorithm, autoencoder, to learn general feature representations from the outputs of the Gabor filter bank. Lastly, we develop a nearest neighbor density estimator to locate potential defects and draw them on the fabric images. We demonstrate the effectiveness and robustness of the proposed model by testing it on various types of fabrics such as plain, patterned, and rotated fabrics. Our model also achieves a true positive rate (a.k.a recall) value of 0.895 with no false alarms on our dataset based upon the Standard Fabric Defect Glossary.
In Statistical Relational Artificial Intelligence, a branch of AI and machine learning which combines the logical and statistical schools of AI, one uses the concept {\em para\-metrized probabilistic graphical model (PPGM)} to model (conditional) dependencies between random variables and to make probabilistic inferences about events on a space of "possible worlds". The set of possible worlds with underlying domain $D$ (a set of objects) can be represented by the set $\mathbf{W}_D$ of all first-order structures (for a suitable signature) with domain $D$. Using a formal logic we can describe events on $\mathbf{W}_D$. By combining a logic and a PPGM we can also define a probability distribution $\mathbb{P}_D$ on $\mathbf{W}_D$ and use it to compute the probability of an event. We consider a logic, denoted $PLA$, with truth values in the unit interval, which uses aggregation functions, such as arithmetic mean, geometric mean, maximum and minimum instead of quantifiers. However we face the problem of computational efficiency and this problem is an obstacle to the wider use of methods from Statistical Relational AI in practical applications. We address this problem by proving that the described probability will, under certain assumptions on the PPGM and the sentence $\varphi$, converge as the size of $D$ tends to infinity. The convergence result is obtained by showing that every formula $\varphi(x_1, \ldots, x_k)$ which contains only "admissible" aggregation functions (e.g. arithmetic and geometric mean, max and min) is asymptotically equivalent to a formula $\psi(x_1, \ldots, x_k)$ without aggregation functions.
Anomaly detection among a large number of processes arises in many applications ranging from dynamic spectrum access to cybersecurity. In such problems one can often obtain noisy observations aggregated from a chosen subset of processes that conforms to a tree structure. The distribution of these observations, based on which the presence of anomalies is detected, may be only partially known. This gives rise to the need for a search strategy designed to account for both the sample complexity and the detection accuracy, as well as cope with statistical models that are known only up to some missing parameters. In this work we propose a sequential search strategy using two variations of the Generalized Local Likelihood Ratio statistic. Our proposed Hierarchical Dynamic Search (HDS) strategy is shown to be order-optimal with respect to the size of the search space and asymptotically optimal with respect to the detection accuracy. An explicit upper bound on the error probability of HDS is established for the finite sample regime. Extensive experiments are conducted, demonstrating the performance gains of HDS over existing methods.
Graph Convolutional Networks (GCNs) are one of the most popular architectures that are used to solve classification problems accompanied by graphical information. We present a rigorous theoretical understanding of the effects of graph convolutions in multi-layer networks. We study these effects through the node classification problem of a non-linearly separable Gaussian mixture model coupled with a stochastic block model. First, we show that a single graph convolution expands the regime of the distance between the means where multi-layer networks can classify the data by a factor of at least $1/\sqrt[4]{\mathbb{E}{\rm deg}}$, where $\mathbb{E}{\rm deg}$ denotes the expected degree of a node. Second, we show that with a slightly stronger graph density, two graph convolutions improve this factor to at least $1/\sqrt[4]{n}$, where $n$ is the number of nodes in the graph. Finally, we provide both theoretical and empirical insights into the performance of graph convolutions placed in different combinations among the layers of a network, concluding that the performance is mutually similar for all combinations of the placement. We present extensive experiments on both synthetic and real-world data that illustrate our results.
Covariance estimation for matrix-valued data has received an increasing interest in applications. Unlike previous works that rely heavily on matrix normal distribution assumption and the requirement of fixed matrix size, we propose a class of distribution-free regularized covariance estimation methods for high-dimensional matrix data under a separability condition and a bandable covariance structure. Under these conditions, the original covariance matrix is decomposed into a Kronecker product of two bandable small covariance matrices representing the variability over row and column directions. We formulate a unified framework for estimating bandable covariance, and introduce an efficient algorithm based on rank one unconstrained Kronecker product approximation. The convergence rates of the proposed estimators are established, and the derived minimax lower bound shows our proposed estimator is rate-optimal under certain divergence regimes of matrix size. We further introduce a class of robust covariance estimators and provide theoretical guarantees to deal with heavy-tailed data. We demonstrate the superior finite-sample performance of our methods using simulations and real applications from a gridded temperature anomalies dataset and a S&P 500 stock data analysis.
Low-rank matrix estimation under heavy-tailed noise is challenging, both computationally and statistically. Convex approaches have been proven statistically optimal but suffer from high computational costs, especially since robust loss functions are usually non-smooth. More recently, computationally fast non-convex approaches via sub-gradient descent are proposed, which, unfortunately, fail to deliver a statistically consistent estimator even under sub-Gaussian noise. In this paper, we introduce a novel Riemannian sub-gradient (RsGrad) algorithm which is not only computationally efficient with linear convergence but also is statistically optimal, be the noise Gaussian or heavy-tailed. Convergence theory is established for a general framework and specific applications to absolute loss, Huber loss, and quantile loss are investigated. Compared with existing non-convex methods, ours reveals a surprising phenomenon of dual-phase convergence. In phase one, RsGrad behaves as in a typical non-smooth optimization that requires gradually decaying stepsizes. However, phase one only delivers a statistically sub-optimal estimator which is already observed in the existing literature. Interestingly, during phase two, RsGrad converges linearly as if minimizing a smooth and strongly convex objective function and thus a constant stepsize suffices. Underlying the phase-two convergence is the smoothing effect of random noise to the non-smooth robust losses in an area close but not too close to the truth. Lastly, RsGrad is applicable for low-rank tensor estimation under heavy-tailed noise where a statistically optimal rate is attainable with the same phenomenon of dual-phase convergence, and a novel shrinkage-based second-order moment method is guaranteed to deliver a warm initialization. Numerical simulations confirm our theoretical discovery and showcase the superiority of RsGrad over prior methods.
Bayesian model selection provides a powerful framework for objectively comparing models directly from observed data, without reference to ground truth data. However, Bayesian model selection requires the computation of the marginal likelihood (model evidence), which is computationally challenging, prohibiting its use in many high-dimensional Bayesian inverse problems. With Bayesian imaging applications in mind, in this work we present the proximal nested sampling methodology to objectively compare alternative Bayesian imaging models for applications that use images to inform decisions under uncertainty. The methodology is based on nested sampling, a Monte Carlo approach specialised for model comparison, and exploits proximal Markov chain Monte Carlo techniques to scale efficiently to large problems and to tackle models that are log-concave and not necessarily smooth (e.g., involving l_1 or total-variation priors). The proposed approach can be applied computationally to problems of dimension O(10^6) and beyond, making it suitable for high-dimensional inverse imaging problems. It is validated on large Gaussian models, for which the likelihood is available analytically, and subsequently illustrated on a range of imaging problems where it is used to analyse different choices of dictionary and measurement model.
One of the most important problems in system identification and statistics is how to estimate the unknown parameters of a given model. Optimization methods and specialized procedures, such as Empirical Minimization (EM) can be used in case the likelihood function can be computed. For situations where one can only simulate from a parametric model, but the likelihood is difficult or impossible to evaluate, a technique known as the Two-Stage (TS) Approach can be applied to obtain reliable parametric estimates. Unfortunately, there is currently a lack of theoretical justification for TS. In this paper, we propose a statistical decision-theoretical derivation of TS, which leads to Bayesian and Minimax estimators. We also show how to apply the TS approach on models for independent and identically distributed samples, by computing quantiles of the data as a first step, and using a linear function as the second stage. The proposed method is illustrated via numerical simulations.
Event detection (ED), a sub-task of event extraction, involves identifying triggers and categorizing event mentions. Existing methods primarily rely upon supervised learning and require large-scale labeled event datasets which are unfortunately not readily available in many real-life applications. In this paper, we consider and reformulate the ED task with limited labeled data as a Few-Shot Learning problem. We propose a Dynamic-Memory-Based Prototypical Network (DMB-PN), which exploits Dynamic Memory Network (DMN) to not only learn better prototypes for event types, but also produce more robust sentence encodings for event mentions. Differing from vanilla prototypical networks simply computing event prototypes by averaging, which only consume event mentions once, our model is more robust and is capable of distilling contextual information from event mentions for multiple times due to the multi-hop mechanism of DMNs. The experiments show that DMB-PN not only deals with sample scarcity better than a series of baseline models but also performs more robustly when the variety of event types is relatively large and the instance quantity is extremely small.
In this paper, we propose Latent Relation Language Models (LRLMs), a class of language models that parameterizes the joint distribution over the words in a document and the entities that occur therein via knowledge graph relations. This model has a number of attractive properties: it not only improves language modeling performance, but is also able to annotate the posterior probability of entity spans for a given text through relations. Experiments demonstrate empirical improvements over both a word-based baseline language model and a previous approach that incorporates knowledge graph information. Qualitative analysis further demonstrates the proposed model's ability to learn to predict appropriate relations in context.