In applications such as gene regulatory network analysis based on single-cell RNA sequencing data, samples often come from a mixture of different populations and each population has its own unique network. Available graphical models often assume that all samples are from the same population and share the same network. One has to first cluster the samples and use available methods to infer the network for every cluster separately. However, this two-step procedure ignores uncertainty in the clustering step and thus could lead to inaccurate network estimation. Motivated by these applications, we consider the mixture Poisson log-normal model for network inference of count data from mixed populations. The latent precision matrices of the mixture model correspond to the networks of different populations and can be jointly estimated by maximizing the lasso-penalized log-likelihood. Under rather mild conditions, we show that the mixture Poisson log-normal model is identifiable and has the positive definite Fisher information matrix. Consistency of the maximum lasso-penalized log-likelihood estimator is also established. To avoid the intractable optimization of the log-likelihood, we develop an algorithm called VMPLN based on the variational inference method. Comprehensive simulation and real single-cell RNA sequencing data analyses demonstrate the superior performance of VMPLN.
We consider the setting of online convex optimization (OCO) with \textit{exp-concave} losses. The best regret bound known for this setting is $O(n\log{}T)$, where $n$ is the dimension and $T$ is the number of prediction rounds (treating all other quantities as constants and assuming $T$ is sufficiently large), and is attainable via the well-known Online Newton Step algorithm (ONS). However, ONS requires on each iteration to compute a projection (according to some matrix-induced norm) onto the feasible convex set, which is often computationally prohibitive in high-dimensional settings and when the feasible set admits a non-trivial structure. In this work we consider projection-free online algorithms for exp-concave and smooth losses, where by projection-free we refer to algorithms that rely only on the availability of a linear optimization oracle (LOO) for the feasible set, which in many applications of interest admits much more efficient implementations than a projection oracle. We present an LOO-based ONS-style algorithm, which using overall $O(T)$ calls to a LOO, guarantees in worst case regret bounded by $\widetilde{O}(n^{2/3}T^{2/3})$ (ignoring all quantities except for $n,T$). However, our algorithm is most interesting in an important and plausible low-dimensional data scenario: if the gradients (approximately) span a subspace of dimension at most $\rho$, $\rho << n$, the regret bound improves to $\widetilde{O}(\rho^{2/3}T^{2/3})$, and by applying standard deterministic sketching techniques, both the space and average additional per-iteration runtime requirements are only $O(\rho{}n)$ (instead of $O(n^2)$). This improves upon recently proposed LOO-based algorithms for OCO which, while having the same state-of-the-art dependence on the horizon $T$, suffer from regret/oracle complexity that scales with $\sqrt{n}$ or worse.
Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome wide human data we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.
This paper studies covariate adjusted estimation of the average treatment effect (ATE) in stratified experiments. We work in the stratified randomization framework of Cytrynbaum (2021), which includes matched tuples designs (e.g. matched pairs), coarse stratification, and complete randomization as special cases. Interestingly, we show that the Lin (2013) interacted regression is generically asymptotically inefficient, with efficiency only in the edge case of complete randomization. Motivated by this finding, we derive the optimal linear covariate adjustment for a given stratified design, constructing several new estimators that achieve the minimal variance. Conceptually, we show that optimal linear adjustment of a stratified design is equivalent in large samples to doubly-robust semiparametric adjustment of an independent design. We also develop novel asymptotically exact inference for the ATE over a general family of adjusted estimators, showing in simulations that the usual Eicker-Huber-White confidence intervals can significantly overcover. Our inference methods produce shorter confidence intervals by fully accounting for the precision gains from both covariate adjustment and stratified randomization. Simulation experiments and an empirical application to the Oregon Health Insurance Experiment data (Finkelstein et al. (2012)) demonstrate the value of our proposed methods.
The last decades are marked by massive and diverse image data, which shows increasingly high resolution and quality. However, some images we obtained may be corrupted, affecting the perception and the application of downstream tasks. A generic method for generating a high-quality image from the degraded one is in demand. In this paper, we present a novel GAN inversion framework that utilizes the powerful generative ability of StyleGAN-XL for this problem. To ease the inversion challenge with StyleGAN-XL, Clustering \& Regularize Inversion (CRI) is proposed. Specifically, the latent space is firstly divided into finer-grained sub-spaces by clustering. Instead of initializing the inversion with the average latent vector, we approximate a centroid latent vector from the clusters, which generates an image close to the input image. Then, an offset with a regularization term is introduced to keep the inverted latent vector within a certain range. We validate our CRI scheme on multiple restoration tasks (i.e., inpainting, colorization, and super-resolution) of complex natural images, and show preferable quantitative and qualitative results. We further demonstrate our technique is robust in terms of data and different GAN models. To our best knowledge, we are the first to adopt StyleGAN-XL for generating high-quality natural images from diverse degraded inputs. Code is available at //github.com/Booooooooooo/CRI.
Federated learning methods, that is, methods that perform model training using data situated across different sources, whilst simultaneously not having the data leave their original source, are of increasing interest in a number of fields. However, despite this interest, the classes of models for which easily-applicable and sufficiently general approaches are available is limited, excluding many structured probabilistic models. We present a general yet elegant resolution to the aforementioned issue. The approach is based on adopting structured variational inference, an approach widely used in Bayesian machine learning, to the federated setting. Additionally, a communication-efficient variant analogous to the canonical FedAvg algorithm is explored. The effectiveness of the proposed algorithms are demonstrated, and their performance is compared on Bayesian multinomial regression, topic modelling, and mixed model examples.
We create a mixed-integer optimization (MIO) approach for doing cluster-aware regression, i.e. linear regression that takes into account the inherent clustered structure of the data. We compare to the linear mixed effects regression (LMEM) which is the most used current method, and design simulation experiments to show superior performance to LMEM in terms of both predictive and inferential metrics in silico. Furthermore, we show how our method is formulated in a very interpretable way; LMEM cannot generalize and make cluster-informed predictions when the cluster of new data points is unknown, but we solve this problem by training an interpretable classification tree that can help decide cluster effects for new data points, and demonstrate the power of this generalizability on a real protein expression dataset.
We investigate solution methods for large-scale inverse problems governed by partial differential equations (PDEs) via Bayesian inference. The Bayesian framework provides a statistical setting to infer uncertain parameters from noisy measurements. To quantify posterior uncertainty, we adopt Markov Chain Monte Carlo (MCMC) approaches for generating samples. To increase the efficiency of these approaches in high-dimension, we make use of local information about gradient and Hessian of the target potential, also via Hamiltonian Monte Carlo (HMC). Our target application is inferring the field of soil permeability processing observations of pore pressure, using a nonlinear PDE poromechanics model for predicting pressure from permeability. We compare the performance of different sampling approaches in this and other settings. We also investigate the effect of dimensionality and non-gaussianity of distributions on the performance of different sampling methods.
Multivariate time series forecasting is extensively studied throughout the years with ubiquitous applications in areas such as finance, traffic, environment, etc. Still, concerns have been raised on traditional methods for incapable of modeling complex patterns or dependencies lying in real word data. To address such concerns, various deep learning models, mainly Recurrent Neural Network (RNN) based methods, are proposed. Nevertheless, capturing extremely long-term patterns while effectively incorporating information from other variables remains a challenge for time-series forecasting. Furthermore, lack-of-explainability remains one serious drawback for deep neural network models. Inspired by Memory Network proposed for solving the question-answering task, we propose a deep learning based model named Memory Time-series network (MTNet) for time series forecasting. MTNet consists of a large memory component, three separate encoders, and an autoregressive component to train jointly. Additionally, the attention mechanism designed enable MTNet to be highly interpretable. We can easily tell which part of the historic data is referenced the most.
We propose a novel approach to multimodal sentiment analysis using deep neural networks combining visual analysis and natural language processing. Our goal is different than the standard sentiment analysis goal of predicting whether a sentence expresses positive or negative sentiment; instead, we aim to infer the latent emotional state of the user. Thus, we focus on predicting the emotion word tags attached by users to their Tumblr posts, treating these as "self-reported emotions." We demonstrate that our multimodal model combining both text and image features outperforms separate models based solely on either images or text. Our model's results are interpretable, automatically yielding sensible word lists associated with emotions. We explore the structure of emotions implied by our model and compare it to what has been posited in the psychology literature, and validate our model on a set of images that have been used in psychology studies. Finally, our work also provides a useful tool for the growing academic study of images - both photographs and memes - on social networks.
Aspect based sentiment analysis (ABSA) can provide more detailed information than general sentiment analysis, because it aims to predict the sentiment polarities of the given aspects or entities in text. We summarize previous approaches into two subtasks: aspect-category sentiment analysis (ACSA) and aspect-term sentiment analysis (ATSA). Most previous approaches employ long short-term memory and attention mechanisms to predict the sentiment polarity of the concerned targets, which are often complicated and need more training time. We propose a model based on convolutional neural networks and gating mechanisms, which is more accurate and efficient. First, the novel Gated Tanh-ReLU Units can selectively output the sentiment features according to the given aspect or entity. The architecture is much simpler than attention layer used in the existing models. Second, the computations of our model could be easily parallelized during training, because convolutional layers do not have time dependency as in LSTM layers, and gating units also work independently. The experiments on SemEval datasets demonstrate the efficiency and effectiveness of our models.