Early evaluation of patients who require special care and who have high death-expectancy in COVID-19, and the effective determination of relevant biomarkers on large sample-groups are important to reduce mortality. This study aimed to reveal the routine blood-value predictors of COVID-19 mortality and to determine the lethal-risk levels of these predictors during the disease process. The dataset of the study consists of 38 routine blood-values of 2597 patients who died (n = 233) and those who recovered (n = 2364) from COVID-19 in August-December, 2021. In this study, the histogram-based gradient-boosting (HGB) model was the most successful machine-learning classifier in detecting living and deceased COVID-19 patients (with squared F1 metrics F1^2 = 1). The most efficient binary combinations with procalcitonin were obtained with D-dimer, ESR, D-Bil and ferritin. The HGB model operated with these feature pairs correctly detected almost all of the patients who survived and those who died (precision > 0.98, recall > 0.98, F1^2 > 0.98). Furthermore, in the HGB model operated with a single feature, the most efficient features were procalcitonin (F1^2 = 0.96) and ferritin (F1^2 = 0.91). In addition, according to the two-threshold approach, ferritin values between 376.2 mkg/L and 396.0 mkg/L (F1^2 = 0.91) and pro-calcitonin values between 0.2 mkg/L and 5.2 mkg/L (F1^2 = 0.95) were found to be fatal risk levels for COVID-19. Considering all the results, we suggest that many features combined with these features, especially procalcitonin and ferritin, operated with the HGB model, can be used to achieve very successful results in the classification of those who live, and those who die from COVID-19. Moreover, we strongly recommend that clinicians consider the critical levels we have found for procalcitonin and ferritin properties, to reduce the lethality of the COVID-19 disease.

Linear regression is a statistical technique for estimating the relationship between two variables. A simple example of linear regression is to predict the height of someone based on the square root of the person’s weight (that’s what BMI is based on). To do this, we need to find the slope and intercept of the line. […]

One hundred seventy-four new packages made it to CRAN in October. Here are my “Top 40” selections in sixteen categories: Astronomy, Biology, Business, Computational Methods, Data, Ecology, Finance, Genomics, Mathematics, Machine Learning, Medicine, Pharma, Statistics, Time Series, Utilities, Visualization. Astronomy skylight v1.1: Provides a function to calculate sky illuminance values (in lux) for both the sun and moon. The model is a verbatim translation of the code by Janiczek and DeYoung (1987). There are vignettes for Use and Advanced Use. Biology palaeoverse v1.0.0: Provides tools to support data preparation and exploration for palaeobiological analyses including functions for data cleaning, binning (time and space), summarisation and visualisation with the goals of improving code reproducibility and accessibility and establishing standards for the palaeobiological community. See Jones et al. for details, and the contribution guide to get involved. pirouette v1.6.5: Implements a method to create a Bayesian posterior from a phylogeny that depicts the true evolutionary relationships. See Richèl et al. (2020) for background. There are several vignettes including a Tutorial, a demo, and a guide showing how to use the package in a scientific experiment. Business bupaverse v0.1.0: Facilitates loading the packages comprising the bupaverse, an integrated suite of R packages for handling and analysing business process data, developed by the Business Informatics research group at Hasselt University, Belgium. See the Getting Started Guide. Computational Methods fastWavelets v1.0.1: Provides an Rcpp implementation of the Maximal Overlap Discrete Wavelet Transform (MODWT) and the À Trous Discrete Wavelet Transform. See Quilty & Adamowski (2018) for background and README for examples. gips v1.0.0: Employs the methods described in Graczyk et al. (2022) to find the permutation symmetry group under which the covariance matrix of the data is invariant. See the vignettes Optimizers, Theory, and gips. HomomorphicEncryption v0.1.0: Implements the Brakerski-Fan-Vercauteren (2012), Brakerski-Gentry-Vaikuntanathan (2014), and Cheon-Kim-Kim-Song (2016) schema for fully homomorphic encryption. There are seven short vignettes including BFV, BGV, and CKKS. rxode2random v2.0.9: Implements parallel random number generation. See Wang et al. (2016) and Fidler et al (2019) for background and README for an example.. Data airnow v0.1.0: Provides functions to retrieve U.S. Government AirNow air quality data. See README to get started. amazonadsR v0.1.0: Provides functions to collect data on digital marketing campaigns using the Windsor.ai API. See the tutorial for an example and also look at the related new packages: bingadsR, facebookadsR, googleadsR, instagramadsR, linkedinadsR, pinterestadsR, redditadsR, snapchatadsR, ticktokadsR, twitteradsR. Pablo Sanchez was on a roll in October. congress v0.0.1: Provides functions to download and read data on United States congressional proceedings through the Congress.gov API of the Library of Congress. See README for an example. Ecology canaper v1.0.0: Provides functions to analyze the spatial distribution of biodiversity especially useful in the categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al. (2014) and for statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species. There are vignettes on CANAPE, randomization, and parallel computing. EcoEnsemble v1.0.1: Provides functions to fit and sample from the ensemble model described in Spence et al (2018). There is an Introduction and there are two additional vignettes: ExploringPriors and SyntheticData. rTRIPLEXCWFlux v0.2.0: Encodes the carbon uptake submodule and evapotranspiration submodule of the TRIPLEX-CW-Flux model to run the simulation of carbon-water coupling. See Zhou et al. (2008) Monteith (1965) for background and the vignette for examples. stopdetection v0.1.1: Enables stop detection in time stamped trajectory by implementing the Stay Point detection algorithm originally described in Ye (2009) that uses time and distance thresholds to characterize spatial regions as stops. See the vignette for examples. Finance highOrderPortfolios v0.1.0: Implements methods to select portfolios using high order moments to characterize return distributions. See Zhou & Palomar (2021) and Wang et al. (2022) for the theory and the vignette to get started. MSTest v0.1.0: Implements hypothesis testing procedures described in Hansen (1992), Carrasco, Hu, & Ploberger (2014) and Dufour & Luger (2017) that can be used to identify the number of regimes in Markov switching models. See README for an example. Genomics metevalue v0.1.13: Implements the e-value method to correct p-values in omics data association studies. See Hebestreit & Klein (2022) and Akalin et.al (2012) for background and the vignette for an example. SCpubr v1.0.4: Implements a system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data. Look here for an online reference manual. Mathematics Boov v1.0.0: Provides functions to perform the Boolean operations union, difference and intersection on volumes. Computations are done by the C++ library CGAL. See README for some examples. Also, have a look at the package MinkowskiSum. fitode v0.1.1: Provides methods and functions for fitting ordinary differential equations that use sensitivity equations to compute gradients of ODE trajectories with respect to underlying parameters. See the vignette for details. manifold v0.1.1: Implements operations for Riemannian manifolds including geodesic distance, Riemannian metric, and exponential and logarithm maps, and also incorporates a random object generator on the manifolds. See Dai, Lin, and Müller (2021) for details. Machine Learning SoftBart v1.0.1: Implements the SoftBart model of described by Linero and Yang (2018) with the optional use of a sparsity-inducing prior to allow for variable selection. The vignette contains theory and examples. tidyfit v0.5.1: Extends the tidy data environment with functions to fit and cross validate linear regression and classification algorithms on grouped data. There are several vignettes including Predicting Boston House Prices, Multinomial Classification, and Rolling Window Time Series Regression. Medicine cities v0.1.0: Provides functions to simulate clinical trials and summarize causal effects and treatment policy estimands in the presence of intercurrent events. Have a look at the demo. RCT2 v0.0.1: Implements various statistical methods for designing and analyzing two-stage randomized controlled trials using the methods developed by Imai, Jiang, and Malani (2021) and Imai, Jiang, and Malani (2022). There are vignettes on Interference and Causal Inference. Pharma DTSEA v0.0.3: Implements a novel tool to identify candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. See Gómez-Carballa et al. (2022) and Feng et al. (2022) for disease expression profiles, Wishart et al. (2018) and Gaulton et al. (2017) for drug target information, and Kanehisa et al. (2021) for the details of KEGG database. There is a vignette. nlmixr2lib v0.1.0: Provides tools to create model libraries for nlmixr2. Models include pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. See the vignette Creating a model library. Statistics aIc v1.0: Implements set of tests for compositional pathologies including for coherence of correlations as suggested by Erb et al. (2020), compositional dominance of distance, compositional perturbation invariance as suggested by (Aitchison (1992) and singularity of the covariation matrix. See the vignette for details and examples. ktweedie v1.0.1: Uses Reproducing Kernel Hilbert Space methods to implement Tweedie compound Poisson gamma models with high-dimensional predictors for the analyses of zero-inflated response variables. See the vignette for examples. missoNet v1.0.0: Implements efficient procedures for fitting conditional graphical lasso models linking predictor variables to response variables or tasks, when the response data may contain missing values. See the vignette for examples. ShalpeyOutlier v0.1.0: Provides methods to use Shapley values to detect, explain, and cell wise impute multivariate outliers. See Mayrhofer and Filzmoser (2022) for details and the vignette for examples. SpatialfdaR v1.0.0: Provides functions to that implement finite element analysis methods to spatial functional data analysis. See Sangalli et al. (2013) and Bernardi et al. (2018) for background and the vignette for an example. Time Series dfms v0..1.3: Provides a user friendly and computationally efficient approach to estimate linear Gaussian dynamic factor models using Kalman filter and EM algorithm methods. See Doz et al. (2011) and Banbura & Modugno (2014) for background and the vignette for examples. Utilities ExclusionTable v1.0.0: Provides functions for creating tables of excluded observations by reporting the number before and after each subset() call together with the number of observations that have been excluded. See the vignette. shiny.tailwind v0.2.2: Allows TailwindCSS to be used in Shiny apps with just-in-time compiling including custom CSS with @apply directive, and custom tailwind configurations. See README for examples. Visualization AlphaHull3D v1.1.0: Provides functions to compute the alpha hull of a set of points (informallly: the shape formed by these points) in 3D space. See README for some visualizations, and also have a look at the related packages MeshesTools, and PolygonSoup. bangladesh v1.0.0: Provides sf objects, shape files, and functions to draw regional chorpleth maps for Bangladesh. See the vignette. ggstats v0.1.0: Provides functions to create forest plots of regression model coefficients along with new statistics to compute proportions, weighted mean and cross-tabulation statistics, as well as new geometries to add alternative background color to a plot. There are vignettes on plotting coefficients and on computing cross-tabulation, custom proportions, and weighted means. jagshelper v0.1.11: Provides tools to streamline Bayesian analyses in JAGSincluding functions for extracting output, streamlining assessment of convergence, and producing summary plots. See the vignette for examples. roughsf v1.0.0: Provides functions to draw maps, including “sketchy”, hand-drawn-like maps using the Javascript library Roughjs. See README for examples.

Abstract: The use of machine learning methods helps to improve decision making in different fields. In particular, the idea of bridging predictions (machine learning models) and prescriptions (optimization problems) is gaining attention within the scientific community. One of the main ideas to address this trade-off is the so-called Constraint Learning (CL) methodology, where the structures of the machine learning model can be treated as a set of constraints to be embedded within the optimization problem, establishing the relationship between a direct decision variable x and a response variable y. However, most CL approaches have focused on making point predictions for a certain variable, not taking into account the statistical and external uncertainty faced in the modeling process. In this paper, we extend the CL methodology to deal with uncertainty in the response variable y. The novel Distributional Constraint Learning (DCL) methodology makes use of a piece-wise linearizable neural network-based model to estimate the parameters of the conditional distribution of y (dependent on decisions x and contextual information), which can be embedded within mixed-integer optimization problems.

Abstract: In this paper, we propose a weak approximation of the reflection coupling (RC) for stochastic differential equations (SDEs), and prove it converges weakly to the desired coupling. In contrast to the RC, the proposed approximate reflection coupling (ARC) need not take the hitting time of processes to the diagonal set into consideration and can be defined as the solution of some SDEs on the whole time interval. Therefore, ARC can work effectively against SDEs with different drift terms. As an application of ARC, an evaluation on the effectiveness of the stochastic gradient descent in a non-convex setting is also described. Abstract: The online optimization problem with non-convex loss functions over a closed convex set, coupled with a set of inequality (possibly non-convex) constraints is a challenging online learning problem.

This paper describes several improvements to a new method for signal decomposition that we recently formulated under the name of Differentiable Dictionary Search (DDS). The fundamental idea of DDS is to exploit a class of powerful deep invertible density estimators called normalizing flows, to model the dictionary in a linear decomposition method such as NMF, effectively creating a bijection between the space of dictionary elements and the associated probability space, allowing a differentiable search through the dictionary space, guided by the estimated densities. As the initial formulation was a proof of concept with some practical limitations, we will present several steps towards making it scalable, hoping to improve both the computational complexity of the method and its signal decomposition capabilities. As a testbed for experimental evaluation, we choose the task of frame-level piano transcription, where the signal is to be decomposed into sources whose activity is attributed to individual piano notes. To highlight the impact of improved non-linear modelling of sources, we compare variants of our method to a linear overcomplete NMF baseline. Experimental results will show that even in the absence of additional constraints, our models produce increasingly sparse and precise decompositions, according to two pertinent evaluation measures.

Medical treatments tailored to a patient's baseline characteristics hold the potential of improving patient outcomes while reducing negative side effects. Learning individualized treatment rules (ITRs) often requires aggregation of multiple datasets(sites); however, current ITR methodology does not take between-site heterogeneity into account, which can hurt model generalizability when deploying back to each site. To address this problem, we develop a method for individual-level meta-analysis of ITRs, which jointly learns site-specific ITRs while borrowing information about feature sign-coherency via a scientifically-motivated directionality principle. We also develop an adaptive procedure for model tuning, using information criteria tailored to the ITR learning problem. We study the proposed methods through numerical experiments to understand their performance under different levels of between-site heterogeneity and apply the methodology to estimate ITRs in a large multi-center database of electronic health records. This work extends several popular methodologies for estimating ITRs (A-learning, weighted learning) to the multiple-sites setting.

We present MEM: Multi-view Exploration Maximization for tackling complex visual control tasks. To the best of our knowledge, MEM is the first approach that combines multi-view representation learning and intrinsic reward-driven exploration in reinforcement learning (RL). More specifically, MEM first extracts the specific and shared information of multi-view observations to form high-quality features before performing RL on the learned features, enabling the agent to fully comprehend the environment and yield better actions. Furthermore, MEM transforms the multi-view features into intrinsic rewards based on entropy maximization to encourage exploration. As a result, MEM can significantly promote the sample-efficiency and generalization ability of the RL agent, facilitating solving real-world problems with high-dimensional observations and spare-reward space. We evaluate MEM on various tasks from DeepMind Control Suite and Procgen games. Extensive simulation results demonstrate that MEM can achieve superior performance and outperform the benchmarking schemes with simple architecture and higher efficiency.

Deep metric learning (DML) aims to automatically construct task-specific distances or similarities of data, resulting in a low-dimensional representation. Several significant metric-learning methods have been proposed. Nonetheless, no approach guarantees the preservation of the ordinal nature of the original data in a low-dimensional space. Ordinal data are ubiquitous in real-world problems, such as the severity of symptoms in biomedical cases, production quality in manufacturing, rating level in businesses, and aging level in face recognition. This study proposes a novel angular triangle distance (ATD) and ordinal triplet network (OTD) to obtain an accurate and meaningful embedding space representation for ordinal data. The ATD projects the ordinal relation of data in the angular space, whereas the OTD learns its ordinal projection. We also demonstrated that our new distance measure satisfies the distance metric properties mathematically. The proposed method was assessed using real-world data with an ordinal nature, such as biomedical, facial, and hand-gestured images. Extensive experiments have been conducted, and the results show that our proposed method not only semantically preserves the ordinal nature but is also more accurate than existing DML models. Moreover, we also demonstrate that our proposed method outperforms the state-of-the-art ordinal metric learning method.

Graphs are ubiquitous representation for structured data. They model naturally occurring relations between objects and, in a sense, generalize sequential data to more complex dependencies. Many algorithms originally designed for learning from sequential data are thus generalized to learning from graphs. Learning continuous vector representations of graph nodes, or node embeddings, have become an integral part of the graph learning toolbox, with applications ranging from link prediction [9] to graph compression [2]. The first algorithm [18] for learning node embeddings generates random walks, starting from each node in the graph, and then feeds the sequences of visited nodes into a word embedding learning algorithm such as word2vec [15]. The approach was extended to a more general setting where random walks can consider different properties of the local neighborhood [9, 26, 27]. An alternative method for training continuous node embeddings is based on matrix factorization of (powers of) the graph adjacency matrix. As an alternative, researchers proposed to use coordinated node sampling for training discrete node embeddings [28, 29]. In this setting, each sample is an independent estimator of the similarity between nodes.