Disaggregation regression has become an important tool in spatial disease mapping for making fine-scale predictions of disease risk from aggregated response data. By including high resolution covariate information and modelling the data generating process on a fine scale, it is hoped that these models can accurately learn the relationships between covariates and response at a fine spatial scale. However, validating these high resolution predictions can be a challenge, as often there is no data observed at this spatial scale. In this study, disaggregation regression was performed on simulated data in various settings and the resulting fine-scale predictions are compared to the simulated ground truth. Performance was investigated with varying numbers of data points, sizes of aggregated areas and levels of model misspecification. The effectiveness of cross validation on the aggregate level as a measure of fine-scale predictive performance was also investigated. Predictive performance improved as the number of observations increased and as the size of the aggregated areas decreased. When the model was well-specified, fine-scale predictions were accurate even with small numbers of observations and large aggregated areas. Under model misspecification predictive performance was significantly worse for large aggregated areas but remained high when response data was aggregated over smaller regions. Cross-validation correlation on the aggregate level was a moderately good predictor of fine-scale predictive performance. While the simulations are unlikely to capture the nuances of real-life response data, this study gives insight into the effectiveness of disaggregation regression in different contexts.

In many Machine Learning domains, datasets are characterized by highly imbalanced and overlapping classes. Particularly in the medical domain, a specific list of symptoms can be labeled as one of various different conditions. Some of these conditions may be more prevalent than others by several orders of magnitude. Here we present a novel unsupervised Domain Adaptation scheme for such datasets. The scheme, based on a specific type of Quantification, is designed to work under both label and conditional shifts. It is demonstrated on datasets generated from Electronic Health Records and provides high quality results for both Quantification and Domain Adaptation in very challenging scenarios. Potential benefits of using this scheme in the current COVID-19 outbreak, for estimation of prevalence and probability of infection, are discussed.

Early detection of patients vulnerable to infections acquired in the hospital environment is a challenge in current health systems given the impact that such infections have on patient mortality and healthcare costs. This work is focused on both the identification of risk factors and the prediction of healthcare-associated infections in intensive-care units by means of machine-learning methods. The aim is to support decision making addressed at reducing the incidence rate of infections. In this field, it is necessary to deal with the problem of building reliable classifiers from imbalanced datasets. We propose a clustering-based undersampling strategy to be used in combination with ensemble classifiers. A comparative study with data from 4616 patients was conducted in order to validate our proposal. We applied several single and ensemble classifiers both to the original dataset and to data preprocessed by means of different resampling methods. The results were analyzed by means of classic and recent metrics specifically designed for imbalanced data classification. They revealed that the proposal is more efficient in comparison with other approaches.

In the field of numerical weather prediction (NWP), the probabilistic distribution of the future state of the atmosphere is sampled with Monte-Carlo-like simulations, called ensembles. These ensembles have deficiencies (such as conditional biases) that can be corrected thanks to statistical post-processing methods. Several ensembles exist and may be corrected with different statistiscal methods. A further step is to combine these raw or post-processed ensembles. The theory of prediction with expert advice allows us to build combination algorithms with theoretical guarantees on the forecast performance. This article adapts this theory to the case of probabilistic forecasts issued as step-wise cumulative distribution functions (CDF). The theory is applied to wind speed forecasting, by combining several raw or post-processed ensembles, considered as CDFs. The second goal of this study is to explore the use of two forecast performance criteria: the Continous ranked probability score (CRPS) and the Jolliffe-Primo test. Comparing the results obtained with both criteria leads to reconsidering the usual way to build skillful probabilistic forecasts, based on the minimization of the CRPS. Minimizing the CRPS does not necessarily produce reliable forecasts according to the Jolliffe-Primo test. The Jolliffe-Primo test generally selects reliable forecasts, but could lead to issuing suboptimal forecasts in terms of CRPS. It is proposed to use both criterion to achieve reliable and skillful probabilistic forecasts.

Machine learning models with both good predictability and high interpretability are crucial for decision support systems. Linear regression is one of the most interpretable prediction models. However, the linearity in a simple linear regression worsens its predictability. In this work, we introduce a locally adaptive interpretable regression (LoAIR). In LoAIR, a metamodel parameterized by neural networks predicts percentile of a Gaussian distribution for the regression coefficients for a rapid adaptation. Our experimental results on public benchmark datasets show that our model not only achieves comparable or better predictive performance than the other state-of-the-art baselines but also discovers some interesting relationships between input and target variables such as a parabolic relationship between CO2 emissions and Gross National Product (GNP). Therefore, LoAIR is a step towards bridging the gap between econometrics, statistics, and machine learning by improving the predictive ability of linear regression without depreciating its interpretability.

Graph Neural Networks (GNNs) are powerful and flexible neural networks that use the naturally sparse connectivity information of the data. GNNs represent this connectivity as sparse matrices, which have lower arithmetic intensity and thus higher communication costs compared to dense matrices, making GNNs harder to scale to high concurrencies than convolutional or fully-connected neural networks.

We present a family of parallel algorithms for training GNNs. These algorithms are based on their counterparts in dense and sparse linear algebra, but they had not been previously applied to GNN training. We show that they can asymptotically reduce communication compared to existing parallel GNN training methods. We implement a promising and practical version that is based on 2D sparse-dense matrix multiplication using torch.distributed. Our implementation parallelizes over GPU-equipped clusters. We train GNNs on up to a hundred GPUs on datasets that include a protein network with over a billion edges.

An accurate and prompt diagnosis of pediatric pneumonia is imperative for successful treatment intervention. One approach to diagnose pneumonia cases is using radiographic data. In this article, we propose a novel parsimonious scalar-on-image classification model adopting the ideas of functional data analysis. Our main idea is to treat images as functional measurements and exploit underlying covariance structures to select basis functions; these bases are then used in approximating both image profiles and corresponding regression coefficient. We re-express the regression model into a standard generalized linear model where the functional principal component scores are treated as covariates. We apply the method to (1) classify pneumonia against healthy and viral against bacterial pneumonia patients, and (2) test the null effect about the association between images and responses. Extensive simulation studies show excellent numerical performance in terms of classification, hypothesis testing, and efficient computation.

Reducing domain divergence is a key step in transfer learning problems. Existing works focus on the minimization of global domain divergence. However, two domains may consist of several shared subdomains, and differ from each other in each subdomain. In this paper, we take the local divergence of subdomains into account in transfer. Specifically, we propose to use low-dimensional manifold to represent subdomain, and align the local data distribution discrepancy in each manifold across domains. A Manifold Maximum Mean Discrepancy (M3D) is developed to measure the local distribution discrepancy in each manifold. We then propose a general framework, called Transfer with Manifolds Discrepancy Alignment (TMDA), to couple the discovery of data manifolds with the minimization of M3D. We instantiate TMDA in the subspace learning case considering both the linear and nonlinear mappings. We also instantiate TMDA in the deep learning framework. Extensive experimental studies demonstrate that TMDA is a promising method for various transfer learning tasks.

Effective property prediction methods can help accelerate the search for COVID-19 antivirals either through accurate in-silico screens or by effectively guiding on-going at-scale experimental efforts. However, existing prediction tools have limited ability to accommodate scarce or fragmented training data currently available. In this paper, we introduce a novel approach to learn predictors that can generalize or extrapolate beyond the heterogeneous data. Our method builds on and extends recently proposed invariant risk minimization, adaptively forcing the predictor to avoid nuisance variation. We achieve this by continually exercising and manipulating latent representations of molecules to highlight undesirable variation to the predictor. To test the method we use a combination of three data sources: SARS-CoV-2 antiviral screening data, molecular fragments that bind to SARS-CoV-2 main protease and large screening data for SARS-CoV-1. Our predictor outperforms state-of-the-art transfer learning methods by significant margin. We also report the top 20 predictions of our model on Broad drug repurposing hub.

We present the R package mgm for the estimation of k-order mixed graphical models (MGMs) and mixed vector autoregressive (mVAR) models in high-dimensional data. These are a useful extensions of graphical models for only one variable type, since data sets consisting of mixed types of variables (continuous, count, categorical) are ubiquitous. In addition, we allow to relax the stationarity assumption of both models by introducing time-varying versions of MGMs and mVAR models based on a kernel weighting approach. Time-varying models offer a rich description of temporally evolving systems and allow to identify external influences on the model structure such as the impact of interventions. We provide the background of all implemented methods and provide fully reproducible examples that illustrate how to use the package.