The novel severe acute respiratory syndrome coronavirus type-2 (SARS-CoV-2) caused a global pandemic that has taken more than 4.5 million lives and severely affected the global economy. To curb the spread of the virus, an accurate, cost-effective, and quick testing for large populations is exceedingly important in order to identify, isolate, and treat infected people. Current testing methods commonly use PCR (Polymerase Chain Reaction) based equipment that have limitations on throughput, cost-effectiveness, and simplicity of procedure which creates a compelling need for developing additional coronavirus disease-2019 (COVID-19) testing mechanisms, that are highly sensitive, rapid, trustworthy, and convenient to use by the public. We propose a COVID-19 testing method using artificial intelligence (AI) techniques on MALDI-ToF (matrix-assisted laser desorption/ionization time-of-flight) data extracted from 152 human gargle samples (60 COVID-19 positive tests and 92 COVID-19 negative tests). Our AI-based approach leverages explainable-AI (X-AI) methods to explain the decision rules behind the predictive algorithm both on a local (per-sample) and global (all-samples) basis to make the AI model more trustworthy. Finally, we evaluated our proposed method using a 70%-30% train-test-split strategy and achieved a training accuracy of 86.79% and a testing accuracy of 91.30%.

In the early 1990s, the first signs of life of the CNN era were given: LeCun et al. proposed a CNN model trained by the backpropagation algorithm to classify low-resolution images of handwritten digits. Undoubtedly, it was a breakthrough in the field of computer vision. But with the rise of other classification methods, it fell out fashion. That was until 2012, when Krizhevsky et al. revived the interest in CNNs by exhibiting considerably higher image classification accuracy on the ImageNet challenge. Since then, the complexity of the architectures are exponentially increasing and many structures are rapidly becoming obsolete. Using multistream networks as a base and the feature infusion precept, we explore the proposed LCNN cross-fusion strategy to use the backbones of former state-of-the-art networks on image classification in order to discover if the technique is able to put these designs back in the game. In this paper, we showed that we can obtain an increase of accuracy up to 63.21% on the NORB dataset we comparing with the original structure. However, no technique is definitive. While our goal is to try to reuse previous state-of-the-art architectures with few modifications, we also expose the disadvantages of our explored strategy.

Intelligent data-driven fault diagnosis methods have been widely applied, but most of these methods need a large number of high-quality labeled samples. It costs a lot of labor and time to label data in actual industrial processes, which challenges the application of intelligent fault diagnosis methods. To solve this problem, a multi-stage semi-supervised improved deep embedded clustering (MS-SSIDEC) method is proposed for the bearing fault diagnosis under the insufficient labeled samples situation. This method includes three stages: pre-training, deep clustering and enhanced supervised learning. In the first stage, a skip-connection based convolutional auto-encoder (SCCAE) is proposed and pre-trained to automatically learn low-dimensional representations. In the second stage, a semi-supervised improved deep embedded clustering (SSIDEC) model that integrates the pre-trained auto-encoder with a clustering layer is proposed for deep clustering. Additionally, virtual adversarial training (VAT) is introduced as a regularization term to overcome the overfitting in the model's training. In the third stage, high-quality clustering results obtained in the second stage are assigned to unlabeled samples as pseudo labels. The labeled dataset is augmented by those pseudo-labeled samples and used to train a bearing fault discriminative model. The effectiveness of the method is evaluated on the Case Western Reserve University (CWRU) bearing dataset. The results show that the method can not only satisfy the semi-supervised learning under a small number of labeled samples, but also solve the problem of unsupervised learning, and has achieved better results than traditional diagnosis methods. This method provides a new research idea for fault diagnosis with limited labeled samples by effectively using unsupervised data.

Program optimization is the process of modifying software to execute more efficiently. Because finding the optimal program is generally undecidable, modern compilers usually resort to expert-written heuristic optimizations. In contrast, superoptimizers attempt to find the optimal program by employing significantly more expensive search and constraint solving techniques. Generally, these methods do not scale well to programs in real development scenarios, and as a result superoptimization has largely been confined to small-scale, domain-specific, and/or synthetic program benchmarks. In this paper, we propose a framework to learn to superoptimize real-world programs by using neural sequence-to-sequence models. We introduce the Big Assembly benchmark, a dataset consisting of over 25K real-world functions mined from open-source projects in x86-64 assembly, which enables experimentation on large-scale optimization of real-world programs. We propose an approach, Self Imitation Learning for Optimization (SILO) that is easy to implement and outperforms a standard policy gradient learning approach on our Big Assembly benchmark. Our method, SILO, superoptimizes programs an expected 6.2% of our test set when compared with the gcc version 10.3 compiler's aggressive optimization level -O3. We also report that SILO's rate of superoptimization on our test set is over five times that of a standard policy gradient approach and a model pre-trained on compiler optimization demonstration.

Children's health studies support an association between maternal environmental exposures and children's birth and health outcomes. A common goal in such studies is to identify critical windows of susceptibility -- periods during gestation with increased association between maternal exposures and a future outcome. The associations and timings of critical windows are likely heterogeneous across different levels of individual, family, and neighborhood characteristics. However, the few studies that have considered effect modification were limited to a few pre-specified subgroups. We propose a statistical learning method to estimate critical windows at the individual level and identify important characteristics that induce heterogeneity. The proposed approach uses distributed lag models (DLMs) modified by Bayesian additive regression trees to account for effect heterogeneity based on a potentially high-dimensional set of modifying factors. We show in a simulation study that our model can identify both critical windows and modifiers responsible for DLM heterogeneity. We estimate the relationship between weekly exposures to fine particulate matter during gestation and birth weight in an administrative Colorado birth cohort. We identify maternal body mass index (BMI), age, Hispanic designation, and education as modifiers of the distributed lag effects and find non-Hispanics with increased BMI to be a susceptible population.

High-dimensional classification and feature selection tasks are ubiquitous with the recent advancement in data acquisition technology. In several application areas such as biology, genomics and proteomics, the data are often functional in their nature and exhibit a degree of roughness and non-stationarity. These structures pose additional challenges to commonly used methods that rely mainly on a two-stage approach performing variable selection and classification separately. We propose in this work a novel Gaussian process discriminant analysis (GPDA) that combines these steps in a unified framework. Our model is a two-layer non-stationary Gaussian process coupled with an Ising prior to identify differentially-distributed locations. Scalable inference is achieved via developing a variational scheme that exploits advances in the use of sparse inverse covariance matrices. We demonstrate the performance of our methodology on simulated datasets and two proteomics datasets: breast cancer and SARS-CoV-2. Our approach distinguishes itself by offering explainability as well as uncertainty quantification in addition to low computational cost, which are crucial to increase trust and social acceptance of data-driven tools.

This paper introduces a new simulation-based inference procedure to model and sample from multi-dimensional probability distributions given access to i.i.d. samples, circumventing usual approaches of explicitly modeling the density function or designing Markov chain Monte Carlo. Motivated by the seminal work of M\'emoli (2011) and Sturm (2012) on distance and isomorphism between metric measure spaces, we propose a new notion called the Reversible Gromov-Monge (RGM) distance and study how RGM can be used to design new transform samplers in order to perform simulation-based inference. Our RGM sampler can also estimate optimal alignments between two heterogenous metric measure spaces $(\mathcal{X}, \mu, c_{\mathcal{X}})$ and $(\mathcal{Y}, \nu, c_{\mathcal{Y}})$ from empirical data sets, with estimated maps that approximately push forward one measure $\mu$ to the other $\nu$, and vice versa. Analytic properties of RGM distance are derived; statistical rate of convergence, representation, and optimization questions regarding the induced sampler are studied. Synthetic and real-world examples showcasing the effectiveness of the RGM sampler are also demonstrated.

Objectives: This paper develops two algorithms to achieve federated generalized linear mixed effect models (GLMM), and compares the developed model's outcomes with each other, as well as that from the standard R package (`lme4'). Methods: The log-likelihood function of GLMM is approximated by two numerical methods (Laplace approximation and Gaussian Hermite approximation), which supports federated decomposition of GLMM to bring computation to data. Results: Our developed method can handle GLMM to accommodate hierarchical data with multiple non-independent levels of observations in a federated setting. The experiment results demonstrate comparable (Laplace) and superior (Gaussian-Hermite) performances with simulated and real-world data. Conclusion: We developed and compared federated GLMMs with different approximations, which can support researchers in analyzing biomedical data to accommodate mixed effects and address non-independence due to hierarchical structures (i.e., institutes, region, country, etc.).

Deep neural networks (DNNs) have shown their success as high-dimensional function approximators in many applications; however, training DNNs can be challenging in general. DNN training is commonly phrased as a stochastic optimization problem whose challenges include non-convexity, non-smoothness, insufficient regularization, and complicated data distributions. Hence, the performance of DNNs on a given task depends crucially on tuning hyperparameters, especially learning rates and regularization parameters. In the absence of theoretical guidelines or prior experience on similar tasks, this requires solving many training problems, which can be time-consuming and demanding on computational resources. This can limit the applicability of DNNs to problems with non-standard, complex, and scarce datasets, e.g., those arising in many scientific applications. To remedy the challenges of DNN training, we propose slimTrain, a stochastic optimization method for training DNNs with reduced sensitivity to the choice hyperparameters and fast initial convergence. The central idea of slimTrain is to exploit the separability inherent in many DNN architectures; that is, we separate the DNN into a nonlinear feature extractor followed by a linear model. This separability allows us to leverage recent advances made for solving large-scale, linear, ill-posed inverse problems. Crucially, for the linear weights, slimTrain does not require a learning rate and automatically adapts the regularization parameter. Since our method operates on mini-batches, its computational overhead per iteration is modest. In our numerical experiments, slimTrain outperforms existing DNN training methods with the recommended hyperparameter settings and reduces the sensitivity of DNN training to the remaining hyperparameters.

We present a two-stage Metropolis-Hastings algorithm for sampling probabilistic models, whose log-likelihood is computationally expensive to evaluate, by using a surrogate Gaussian Process (GP) model. The key feature of the approach, and the difference w.r.t. previous works, is the ability to learn the target distribution from scratch (while sampling), and so without the need of pre-training the GP. This is fundamental for automatic and inference in Probabilistic Programming Languages In particular, we present an alternative first stage acceptance scheme by marginalising out the GP distributed function, which makes the acceptance ratio explicitly dependent on the variance of the GP. This approach is extended to Metropolis-Adjusted Langevin algorithm (MALA).