Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages. Thus, there is a need for computational host prediction. Despite some promising results, computational host prediction remains a challenge because of the limited known interactions and the sheer amount of sequenced phages by high-throughput sequencing technologies. The state-of-the-art methods can only achieve 43\% accuracy at the species level. In this work, we formulate host prediction as link prediction in a knowledge graph that integrates multiple protein and DNA-based sequence features. Our implementation named CHERRY can be applied to predict hosts for newly discovered viruses and to identify viruses infecting targeted bacteria. We demonstrated the utility of CHERRY for both applications and compared its performance with 11 popular host prediction methods. To our best knowledge, CHERRY has the highest accuracy in identifying virus-prokaryote interactions. It outperforms all the existing methods at the species level with an accuracy increase of 37\%. In addition, CHERRY's performance on short contigs is more stable than other tools.

We investigate the usage of a Schlieren imaging setup to measure the geometrical dimensions of a plasma channel in atomic vapor. Near resonant probe light is used to image the plasma channel in a tenuous vapor and machine learning techniques are tested for extracting quantitative information from the images. By building a database of simulated signals with a range of plasma parameters for training Deep Neural Networks, we demonstrate that they can extract from the Schlieren images reliably and with high accuracy the location, the radius and the maximum ionization fraction of the plasma channel as well as the width of the transition region between the core of the plasma channel and the unionized vapor. We test several different neural network architectures with supervised learning and show that the parameter estimations supplied by the networks are resilient with respect to slight changes of the experimental parameters that may occur in the course of a measurement.

Complex distributions of the healthcare expenditure pose challenges to statistical modeling via a single model. Super learning, an ensemble method that combines a range of candidate models, is a promising alternative for cost estimation and has shown benefits over a single model. However, standard approaches to super learning may have poor performance in settings where extreme values are present, such as healthcare expenditure data. We propose a super learner based on the Huber loss, a "robust" loss function that combines squared error loss with absolute loss to down-weight the influence of outliers. We derive oracle inequalities that establish bounds on the finite-sample and asymptotic performance of the method. We show that the proposed method can be used both directly to optimize Huber risk, as well as in finite-sample settings where optimizing mean squared error is the ultimate goal. For this latter scenario, we provide two methods for performing a grid search for values of the robustification parameter indexing the Huber loss. Simulations and real data analysis demonstrate appreciable finite-sample gains in cost prediction and causal effect estimation using our proposed method.

This paper studies the cooperative learning of two generative flow models, in which the two models are iteratively updated based on the jointly synthesized examples. The first flow model is a normalizing flow that transforms an initial simple density into a target density by applying a sequence of invertible transformations. The second flow model is a Langevin flow that runs finite steps of gradient-based MCMC toward an energy-based model. We start from proposing a generative framework that trains an energy-based model with a normalizing flow as an amortized sampler to initialize the MCMC chains of the energy-based model. In each learning iteration, we generate synthesized examples by using a normalizing flow initialization followed by a short-run Langevin flow revision toward the current energy-based model. Then we treat the synthesized examples as fair samples from the energy-based model and update the model parameters with the maximum likelihood learning gradient, while the normalizing flow directly learns from the synthesized examples by maximizing the tractable likelihood. Under the short-run non-mixing MCMC scenario, the estimation of the energy-based model is shown to follow the perturbation of maximum likelihood, and the short-run Langevin flow and the normalizing flow form a two-flow generator that we call CoopFlow. We provide an understating of the CoopFlow algorithm by information geometry and show that it is a valid generator as it converges to a moment matching estimator. We demonstrate that the trained CoopFlow is capable of synthesizing realistic images, reconstructing images, and interpolating between images. Normalizing flows (Dinh et al., 2015; 2017; Kingma & Dhariwal, 2018) are a family of generative models that construct a complex distribution by transforming a simple probability density, such as Gaussian distribution, through a sequence of invertible and differentiable mappings. Due to the tractability of the exact log-likelihood and the efficiency of the inference and synthesis, normalizing flows have gained popularity in density estimation (Kingma & Dhariwal, 2018; Ho et al., 2019; Yang et al., 2019; Prenger et al., 2019; Kumar et al., 2020) and variational inference (Rezende & Mohamed, 2015; Kingma et al., 2016).

In this thesis, we focus on the design of an automatic algorithms that provide personalized ranking by adapting to the current conditions. To demonstrate the empirical efficiency of the proposed approaches we investigate their applications for decision making in recommender systems and energy systems domains. For the former, we propose novel algorithm called SAROS that take into account both kinds of feedback for learning over the sequence of interactions. The proposed approach consists in minimizing pairwise ranking loss over blocks constituted by a sequence of non-clicked items followed by the clicked one for each user. We also explore the influence of long memory on the accurateness of predictions. SAROS shows highly competitive and promising results based on quality metrics and also it turn out faster in terms of loss convergence than stochastic gradient descent and batch classical approaches. Regarding power systems, we propose an algorithm for faulted lines detection based on focusing of misclassifications in lines close to the true event location. The proposed idea of taking into account the neighbour lines shows statistically significant results in comparison with the initial approach based on convolutional neural networks for faults detection in power grid.

Data Science and Machine Learning has been the latest talk right now and companies are looking for data scientists and machine learning engineers to handle their data and make significant contributions to them. Whenever data is given to data scientists, they must take the right steps to process them and ensure that the transformed data can be used to train various machine learning models optimally while ensuring maximum efficiency. It is often found that the data that is present in real-world is oftentimes incomplete and inaccurate along with containing a lot of outliers which some machine learning models cannot handle, leading to suboptimal training performance. It is also important to note that there might be duplicate rows or columns in the data which must be dealt with before giving it to machine learning models. Addressing these issues along with many others can be crucial, especially when one wants to improve model performance and generalizing ability of the model.

Whenever we debate with other devs about the best programming language, we talk about JavaScript and Python for hours. Both are powerful, flexible languages that are dominating the world today. But a dead end to Python is its inability to run on browsers. JavaScript (JS), with the discovery of Node, runs on almost any platform. It even has modules to build machine learning algorithms.

The Plackett-Luce (PL) model is ubiquitous in learning-to-rank (LTR) because it provides a useful and intuitive probabilistic model for sampling ranked lists. Counterfactual offline evaluation and optimization of ranking metrics are pivotal for using LTR methods in production. When adopting the PL model as a ranking policy, both tasks require the computation of expectations with respect to the model. These are usually approximated via Monte-Carlo (MC) sampling, since the combinatorial scaling in the number of items to be ranked makes their analytical computation intractable. Despite recent advances in improving the computational efficiency of the sampling process via the Gumbel top-k trick, the MC estimates can suffer from high variance. We develop a novel approach to producing more sample-efficient estimators of expectations in the PL model by combining the Gumbel top-k trick with quasi-Monte Carlo (QMC) sampling, a well-established technique for variance reduction. We illustrate our findings both theoretically and empirically using real-world recommendation data from Amazon Music and the Yahoo learning-to-rank challenge.

In this project we will be working with a data set, indicating whether or not a particular internet user clicked on an Advertisement. We will try to create a model that will predict whether or not they will click on an ad based off the features of that user. Welcome to this project on predict Ads Click in Apache Spark Machine Learning using Databricks platform community edition server which allows you to execute your spark code, free of cost on their server just by registering through email id. In this project, we explore Apache Spark and Machine Learning on the Databricks platform. I am a firm believer that the best way to learn is by doing.

Problem Statement A target marketing campaign for a bank was undertaken to identify a segment of customers who are likely to respond to an insurance product. Here, the target variable is whether or not the customers bought insurance product and it depends on factors like Product usage in three months, demographics, transaction patterns as like deposit amount, checking account, a branch of the bank, Residential information (like urban, rural) and so on.