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While a difference-in-differences (DID) design was originally developed with one pre- and one post-treatment period, data from additional pre-treatment periods are often available. How can researchers improve the DID design with such multiple pre-treatment periods under what conditions? We first use potential outcomes to clarify three benefits of multiple pre-treatment periods: (1) assessing the parallel trends assumption, (2) improving estimation accuracy, and (3) allowing for a more flexible parallel trends assumption. We then propose a new estimator, double DID, which combines all the benefits through the generalized method of moments and contains the two-way fixed effects regression as a special case. We show that the double DID requires a weaker assumption about outcome trends and is more efficient than existing DID estimators. We also generalize the double DID to the staggered adoption design where different units can receive the treatment in different time periods. We illustrate the proposed method with two empirical applications, covering both the basic DID and staggered adoption designs. We offer an open-source R package that implements the proposed methodologies.

Brain tumors analysis is important in timely diagnosis and effective treatment to cure patients. Tumor analysis is challenging because of tumor morphology like size, location, texture, and heteromorphic appearance in the medical images. In this regard, a novel two-phase deep learning-based framework is proposed to detect and categorize brain tumors in magnetic resonance images (MRIs). In the first phase, a novel deep boosted features and ensemble classifiers (DBF-EC) scheme is proposed to detect tumor MRI images from healthy individuals effectively. The deep boosted feature space is achieved through the customized and well-performing deep convolutional neural networks (CNNs), and consequently, fed into the ensemble of machine learning (ML) classifiers. While in the second phase, a new hybrid features fusion-based brain tumor classification approach is proposed, comprised of dynamic-static feature and ML classifier to categorize different tumor types. The dynamic features are extracted from the proposed BRAIN-RENet CNN, which carefully learns heteromorphic and inconsistent behavior of various tumors, while the static features are extracted using HOG. The effectiveness of the proposed two-phase brain tumor analysis framework is validated on two standard benchmark datasets; collected from Kaggle and Figshare containing different types of tumor, including glioma, meningioma, pituitary, and normal images. Experimental results proved that the proposed DBF-EC detection scheme outperforms and achieved accuracy (99.56%), precision (0.9991), recall (0.9899), F1-Score (0.9945), MCC (0.9892), and AUC-PR (0.9990). While the classification scheme, the joint employment of the deep features fusion of proposed BRAIN-RENet and HOG features improves performance significantly in terms of recall (0.9913), precision (0.9906), F1-Score (0.9909), and accuracy (99.20%) on diverse datasets.

We study full Bayesian procedures for high-dimensional linear regression. We adopt data-dependent empirical priors introduced in [1]. In their paper, these priors have nice posterior contraction properties and are easy to compute. Our paper extend their theoretical results to the case of unknown error variance . Under proper sparsity assumption, we achieve model selection consistency, posterior contraction rates as well as Bernstein von-Mises theorem by analyzing multivariate t-distribution.

Music Structure Analysis (MSA) consists in segmenting a music piece in several distinct sections. We approach MSA within a compression framework, under the hypothesis that the structure is more easily revealed by a simplified representation of the original content of the song. More specifically, under the hypothesis that MSA is correlated with similarities occurring at the bar scale, linear and non-linear compression schemes can be applied to barwise audio signals. Compressed representations capture the most salient components of the different bars in the song and are then used to infer the song structure using a dynamic programming algorithm. This work explores both low-rank approximation models such as Principal Component Analysis or Nonnegative Matrix Factorization and "piece-specific" Auto-Encoding Neural Networks, with the objective to learn latent representations specific to a given song. Such approaches do not rely on supervision nor annotations, which are well-known to be tedious to collect and possibly ambiguous in MSA description. In our experiments, several unsupervised compression schemes achieve a level of performance comparable to that of state-of-the-art supervised methods (for 3s tolerance) on the RWC-Pop dataset, showcasing the importance of the barwise compression processing for MSA.

Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic biological processes involving composite genomic aberrations, key challenges are to effectively assimilate information from these domains to identify genomic signatures and biological entities that are druggable, develop accurate risk prediction profiles for future patients, and identify novel patient subgroups for tailored therapy and monitoring. We propose integrative probabilistic frameworks for high-dimensional multiple-domain cancer data that coherently incorporate dependence within and between domains to accurately detect tumor subtypes, thus providing a catalogue of genomic aberrations associated with cancer taxonomy. We propose an innovative, flexible and scalable Bayesian nonparametric framework for simultaneous clustering of both tumor samples and genomic probes. We describe an efficient variable selection procedure to identify relevant genomic aberrations that can potentially reveal underlying drivers of a disease. Although the work is motivated by several investigations related to lung cancer, the proposed methods are broadly applicable in a variety of contexts involving high-dimensional data. The success of the methodology is demonstrated using artificial data and lung cancer omics profiles publicly available from The Cancer Genome Atlas.

In this study, a longitudinal regression model for covariance matrix outcomes is introduced. The proposal considers a multilevel generalized linear model for regressing covariance matrices on (time-varying) predictors. This model simultaneously identifies covariate associated components from covariance matrices, estimates regression coefficients, and estimates the within-subject variation in the covariance matrices. Optimal estimators are proposed for both low-dimensional and high-dimensional cases by maximizing the (approximated) hierarchical likelihood function and are proved to be asymptotically consistent, where the proposed estimator is the most efficient under the low-dimensional case and achieves the uniformly minimum quadratic loss among all linear combinations of the identity matrix and the sample covariance matrix under the high-dimensional case. Through extensive simulation studies, the proposed approach achieves good performance in identifying the covariate related components and estimating the model parameters. Applying to a longitudinal resting-state fMRI dataset from the Alzheimer's Disease Neuroimaging Initiative (ADNI), the proposed approach identifies brain networks that demonstrate the difference between males and females at different disease stages. The findings are in line with existing knowledge of AD and the method improves the statistical power over the analysis of cross-sectional data.

We present a novel hybrid strategy based on machine learning to improve curvature estimation in the level-set method. The proposed inference system couples enhanced neural networks with standard numerical schemes to compute curvature more accurately. The core of our hybrid framework is a switching mechanism that relies on well established numerical techniques to gauge curvature. If the curvature magnitude is larger than a resolution-dependent threshold, it uses a neural network to yield a better approximation. Our networks are multilayer perceptrons fitted to synthetic data sets composed of sinusoidal- and circular-interface samples at various configurations. To reduce data set size and training complexity, we leverage the problem's characteristic symmetry and build our models on just half of the curvature spectrum. These savings lead to a powerful inference system able to outperform any of its numerical or neural component alone. Experiments with stationary, smooth interfaces show that our hybrid solver is notably superior to conventional numerical methods in coarse grids and along steep interface regions. Compared to prior research, we have observed outstanding gains in precision after training the regression model with data pairs from more than a single interface type and transforming data with specialized input preprocessing. In particular, our findings confirm that machine learning is a promising venue for reducing or removing mass loss in the level-set method.

The availability of large microarray data has led to a growing interest in biclustering methods in the past decade. Several algorithms have been proposed to identify subsets of genes and conditions according to different similarity measures and under varying constraints. In this paper we focus on the exclusive row biclustering problem for gene expression data sets, in which each row can only be a member of a single bicluster while columns can participate in multiple ones. This type of biclustering may be adequate, for example, for clustering groups of cancer patients where each patient (row) is expected to be carrying only a single type of cancer, while each cancer type is associated with multiple (and possibly overlapping) genes (columns). We present a novel method to identify these exclusive row biclusters through a combination of existing biclustering algorithms and combinatorial auction techniques. We devise an approach for tuning the threshold for our algorithm based on comparison to a null model in the spirit of the Gap statistic approach. We demonstrate our approach on both synthetic and real-world gene expression data and show its power in identifying large span non-overlapping rows sub matrices, while considering their unique nature. The Gap statistic approach succeeds in identifying appropriate thresholds in all our examples.

Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.

In this paper we introduce a covariance framework for the analysis of EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. We perform a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. Apart from that, we illustrate our method on real EEG and MEG data sets. The proposed covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed for accurate dipole localization, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, such as in combined EEG/fMRI experiments in which the correlation between EEG and fMRI signals is investigated.