The aim of this short Python tutorial is to introduce the uniform manifold approximation and projection (UMAP) algorithm, using 76,533 single-cell expression profiles from the human primary motor cortex. The data are available from the Cell Types database, which is part of the Allen Brain Map platform. The UMAP has quickly established itself as a go-to clustering tool well poised to expand our knowledge of various many things, including the human brain. I hope by the end of this tutorial you will have a broad understanding of the UMAP algorithm and how to implement it. Uniform manifold approximation and projection (UMAP)1 is a scalable and efficient dimension reduction algorithm that performs competitively among state-of-the-art methods such as t-SNE2, and widely applied for unsupervised clustering.

Created by Lazy Programmer Inc. Cluster analysis is a staple of unsupervised machine learning and data science. It is very useful for data mining and big data because it automatically finds patterns in the data, without the need for labels, unlike supervised machine learning. In a real-world environment, you can imagine that a robot or an artificial intelligence won't always have access to the optimal answer, or maybe there isn't an optimal correct answer. You'd want that robot to be able to explore the world on its own, and learn things just by looking for patterns. Do you ever wonder how we get the data that we use in our supervised machine learning algorithms?

Deep neural networks (DNNs) are being widely applied for various real-world applications across domains due to their high performance (e.g., high accuracy on image classification). Nevertheless, a well-trained DNN after deployment could oftentimes raise errors during practical use in the operational environment due to the mismatching between distributions of the training dataset and the potential unknown noise factors in the operational environment, e.g., weather, blur, noise etc. Hence, it poses a rather important problem for the DNNs' real-world applications: how to repair the deployed DNNs for correcting the failure samples (i.e., incorrect prediction) under the deployed operational environment while not harming their capability of handling normal or clean data. The number of failure samples we can collect in practice, caused by the noise factors in the operational environment, is often limited. Therefore, It is rather challenging how to repair more similar failures based on the limited failure samples we can collect. In this paper, we propose a style-guided data augmentation for repairing DNN in the operational environment. We propose a style transfer method to learn and introduce the unknown failure patterns within the failure data into the training data via data augmentation. Moreover, we further propose the clustering-based failure data generation for much more effective style-guided data augmentation. We conduct a large-scale evaluation with fifteen degradation factors that may happen in the real world and compare with four state-of-the-art data augmentation methods and two DNN repairing methods, demonstrating that our method can significantly enhance the deployed DNNs on the corrupted data in the operational environment, and with even better accuracy on clean datasets.

COVID-19, the disease caused by the SARS-CoV-2 virus, has been declared a pandemic by the World Health Organization, which has reported over 18 million confirmed cases as of August 5, 2020. In this review, we present an overview of recent studies using Machine Learning and, more broadly, Artificial Intelligence, to tackle many aspects of the COVID-19 crisis. We have identified applications that address challenges posed by COVID-19 at different scales, including: molecular, by identifying new or existing drugs for treatment; clinical, by supporting diagnosis and evaluating prognosis based on medical imaging and non-invasive measures; and societal, by tracking both the epidemic and the accompanying infodemic using multiple data sources. We also review datasets, tools, and resources needed to facilitate Artificial Intelligence research, and discuss strategic considerations related to the operational implementation of multidisciplinary partnerships and open science. We highlight the need for international cooperation to maximize the potential of AI in this and future pandemics.

In many numerical schemes, the computational complexity scales non-linearly with the problem size. Solving a linear system of equations using direct methods or most iterative methods is a typical example. Algebraic multi-grid (AMG) methods are numerical methods used to solve large linear systems of equations efficiently. One of the main differences between AMG methods is how the coarser grid is constructed from a given fine grid. There are two main classes of AMG methods; graph and aggregation based coarsening methods. Here we propose an aggregation-based coarsening framework leveraging graph representation learning and clustering algorithms. Our method introduces the power of machine learning into the AMG research field and opens a new perspective for future researches. The proposed method uses graph representation learning techniques to learn latent features of the graph obtained from the underlying matrix of coefficients. Using these extracted features, we generated a coarser grid from the fine grid. The proposed method is highly capable of parallel computations. Our experiments show that the proposed method's efficiency in solving large systems is closely comparable with other aggregation-based methods, demonstrating the high capability of graph representation learning in designing multi-grid solvers.

This paper presents an eXplainable Fault Detection and Diagnosis System (XFDDS) for incipient faults in PV panels. The XFDDS is a hybrid approach that combines the model-based and data-driven framework. Model-based FDD for PV panels lacks high fidelity models at low irradiance conditions for detecting incipient faults. To overcome this, a novel irradiance based three diode model (IB3DM) is proposed. It is a nine parameter model that provides higher accuracy even at low irradiance conditions, an important aspect for detecting incipient faults from noise. To exploit PV data, extreme gradient boosting (XGBoost) is used due to its ability to detecting incipient faults. Lack of explainability, feature variability for sample instances, and false alarms are challenges with data-driven FDD methods. These shortcomings are overcome by hybridization of XGBoost and IB3DM, and using eXplainable Artificial Intelligence (XAI) techniques. To combine the XGBoost and IB3DM, a fault-signature metric is proposed that helps reducing false alarms and also trigger an explanation on detecting incipient faults. To provide explainability, an eXplainable Artificial Intelligence (XAI) application is developed. It uses the local interpretable model-agnostic explanations (LIME) framework and provides explanations on classifier outputs for data instances. These explanations help field engineers/technicians for performing troubleshooting and maintenance operations. The proposed XFDDS is illustrated using experiments on different PV technologies and our results demonstrate the perceived benefits.

Air quality has become one of the main issues in public health and urban planning management, due to the proven adverse effects of high pollutant concentrations. Considering the mitigation measures that cities all over the world are taking in order to face frequent low air quality episodes, the capability of foreseeing future pollutant concentrations is of great importance. Through this paper, we present SOCAIRE, an operational tool based on a Bayesian and spatiotemporal ensemble of neural and statistical nested models. SOCAIRE integrates endogenous and exogenous information in order to predict and monitor future distributions of the concentration for several pollutants in the city of Madrid. It focuses on modeling each and every available component which might play a role in air quality: past concentrations of pollutants, human activity, numerical pollution estimation, and numerical weather predictions. This tool is currently in operation in Madrid, producing daily air quality predictions for the next 48 hours and anticipating the probability of the activation of the measures included in the city's official air quality \no protocols through probabilistic inferences about compound events.

Acceleration of first order methods is mainly obtained via inertial techniques \`a la Nesterov, or via nonlinear extrapolation. The latter has known a recent surge of interest, with successful applications to gradient and proximal gradient techniques. On multiple Machine Learning problems, coordinate descent achieves performance significantly superior to full-gradient methods. Speeding up coordinate descent in practice is not easy: inertially accelerated versions of coordinate descent are theoretically accelerated, but might not always lead to practical speed-ups. We propose an accelerated version of coordinate descent using extrapolation, showing considerable speed up in practice, compared to inertial accelerated coordinate descent and extrapolated (proximal) gradient descent. Experiments on least squares, Lasso, elastic net and logistic regression validate the approach.

Identification of a linear time-invariant dynamical system from partial observations is a fundamental problem in control theory. A natural question is how to do so with non-asymptotic statistical rates depending on the inherent dimensionality (order) $d$ of the system, rather than on the sufficient rollout length or on $\frac1{1-\rho(A)}$, where $\rho(A)$ is the spectral radius of the dynamics matrix. We develop the first algorithm that given a single trajectory of length $T$ with gaussian observation noise, achieves a near-optimal rate of $\widetilde O\left(\sqrt\frac{d}{T}\right)$ in $\mathcal{H}_2$ error for the learned system. We also give bounds under process noise and improved bounds for learning a realization of the system. Our algorithm is based on low-rank approximation of Hankel matrices of geometrically increasing sizes.

Traditionally, robust statistics has focused on designing estimators tolerant to a minority of contaminated data. Robust list-decodable learning focuses on the more challenging regime where only a minority $\frac 1 k$ fraction of the dataset is drawn from the distribution of interest, and no assumptions are made on the remaining data. We study the fundamental task of list-decodable mean estimation in high dimensions. Our main result is a new list-decodable mean estimation algorithm for bounded covariance distributions with optimal sample complexity and error rate, running in nearly-PCA time. Assuming the ground truth distribution on $\mathbb{R}^d$ has bounded covariance, our algorithm outputs a list of $O(k)$ candidate means, one of which is within distance $O(\sqrt{k})$ from the truth. Our algorithm runs in time $\widetilde{O}(ndk)$ for all $k = O(\sqrt{d}) \cup \Omega(d)$, where $n$ is the size of the dataset. We also show that a variant of our algorithm has runtime $\widetilde{O}(ndk)$ for all $k$, at the expense of an $O(\sqrt{\log k})$ factor in the recovery guarantee. This runtime matches up to logarithmic factors the cost of performing a single $k$-PCA on the data, which is a natural bottleneck of known algorithms for (very) special cases of our problem, such as clustering well-separated mixtures. Prior to our work, the fastest list-decodable mean estimation algorithms had runtimes $\widetilde{O}(n^2 d k^2)$ and $\widetilde{O}(nd k^{\ge 6})$. Our approach builds on a novel soft downweighting method, $\mathsf{SIFT}$, which is arguably the simplest known polynomial-time mean estimation technique in the list-decodable learning setting. To develop our fast algorithms, we boost the computational cost of $\mathsf{SIFT}$ via a careful "win-win-win" analysis of an approximate Ky Fan matrix multiplicative weights procedure we develop, which we believe may be of independent interest.