arXiv subjects

Veronica Vinciotti

Publications and source records attributed to Veronica Vinciotti.

30 records · Page 2Linked to original sources

arXiv2019

Does hospital cooperation increase the quality of healthcare?

Motivated by reasons such as altruism, managers from different hospitals may engage in cooperative behaviours, which shape the networked healthcare economy. In this paper we study the determinants of hospital cooperation and its association with the quality delivered by hospitals, using Italian administrative data. We explore the impact on patient transfers between hospitals (cooperation/network) of a set of demand-supply factors, as well as distance-based centrality measures. We then use this framework to assess how such cooperation is related to the overall quality for the hospital of origin and of destination of the patient transfer. The over-dispersed Poisson mixed model that we propose, inspired by the literature on social relations models, is suitably defined to handle network data, which are rarely used in health economics. The results show that distance plays an important role in hospital cooperation, though there are other factors that matter such as geographical centrality. Another empirical finding is the existence of a positive relationship between hospital cooperation and the overall quality of the connected hospitals. The absence of a source of information on the quality of hospitals accessible to all providers, such as in the form of star ratings, may prevent some hospitals to engage and cooperate with other hospitals of potentially higher quality. This may result in a lower degree of cooperation among hospitals and a reduction in quality overall.

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arXiv2019

The conditional censored graphical lasso estimator

In many applied fields, such as genomics, different types of data are collected on the same system, and it is not uncommon that some of these datasets are subject to censoring as a result of the measurement technologies used, such as data generated by polymerase chain reactions and flow cytometer. When the overall objective is that of network inference, at possibly different levels of a system, information coming from different sources and/or different steps of the analysis can be integrated into one model with the use of conditional graphical models. In this paper, we develop a doubly penalized inferential procedure for a conditional Gaussian graphical model when data can be subject to censoring. The computational challenges of handling censored data in high dimensionality are met with the development of an efficient Expectation-Maximization algorithm, based on approximate calculations of the moments of truncated Gaussian distributions and on a suitably derived two-step procedure alternating graphical lasso with a novel block-coordinate multivariate lasso approach. We evaluate the performance of this approach on an extensive simulation study and on gene expression data generated by RT-qPCR technologies, where we are able to integrate network inference, differential expression detection and data normalization into one model.

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arXiv2018

A computationally efficient correlated mixed Probit for credit risk modelling

Mixed Probit models are widely applied in many fields where prediction of a binary response is of interest. Typically, the random effects are assumed to be independent but this is seldom the case for many real applications. In the credit risk application considered in this paper, random effects are present at the level of industrial sectors and they are expected to be correlated due to inter-firm credit links inducing dependencies in the firms' risk to default. Unfortunately, existing inferential procedures for correlated mixed Probit models are computationally very intensive already for a moderate number of effects. Borrowing from the literature on large network inference, we propose an efficient Expectation-Maximization algorithm for unconstrained and penalised likelihood estimation and derive the asymptotic standard errors of the estimates. An extensive simulation study shows that the proposed approach enjoys substantial computational gains relative to standard Monte Carlo approaches, while still providing accurate parameter estimates. Using data on nearly 64,000 accounts for small and medium-sized enterprises in the United Kingdom in 2013 across 14 industrial sectors, we find that accounting for network effects via a correlated mixed Probit model increases significantly the default prediction power of the model compared to conventional default prediction models, making efficient inferential procedures for these models particularly useful in this field.

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arXiv2018

A Simple and Adaptive Dispersion Regression Model for Count Data

Regression for count data is widely performed by models such as Poisson, negative binomial (NB) and zero-inflated regression. A challenge often faced by practitioners is the selection of the right model to take into account dispersion, which typically occurs in count datasets. It is highly desirable to have a unified model that can automatically adapt to the underlying dispersion and that can be easily implemented in practice. In this paper, a discrete Weibull regression model is shown to be able to adapt in a simple way to different types of dispersions relative to Poisson regression: overdispersion, underdispersion and covariate-specific dispersion. Maximum likelihood can be used for efficient parameter estimation. The description of the model, parameter inference and model diagnostics is accompanied by simulated and real data analyses.

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arXiv2018

L1-Penalized Censored Gaussian Graphical Model

Graphical lasso is one of the most used estimators for inferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern measurement technologies make the use of this estimator theoretically unfounded, even when the assumption of a multivariate Gaussian distribution is satisfied. Typical examples are data generated by polymerase chain reactions and flow cytometer. The combination of censoring and high-dimensionality make inference of the underlying genetic networks from these data very challenging. In this paper we propose an $\ell_1$-penalized Gaussian graphical model for censored data and derive two EM-like algorithms for inference. By an extensive simulation study, we evaluate the computational efficiency of the proposed algorithms and show that our proposal overcomes existing competitors when censored data are available. We apply the proposed method to gene expression data coming from microfluidic RT-qPCR technology in order to make inference on the regulatory mechanisms of blood development.

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arXiv2018

Discrete Weibull generalised additive model: an application to count fertility data

Fertility plans, measured by the number of planned children, have been found to be affected by education and family background via complex tail dependencies. This challenge was previously met with the use of non-parametric jittering approaches. This paper shows how a novel generalized additive model based on a discrete Weibull distribution provides partial effects of the covariates on fertility plans which are comparable to jittering, without the inherent drawback of crossing conditional quantiles. The model has some additional desirable features: both over- and under-dispersed data can be modelled by this distribution, the conditional quantiles have a simple analytic form and the likelihood is the same of that of a continuous Weibull distribution with interval-censored data. The latter means that efficient implementations are already available, in the R package gamlss, for a range of models and inferential procedures, and at a fraction of the time compared to the jittering and COM-Poisson approaches, showing potential for the wide applicability of this approach to the modelling of count data.

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arXiv2017

Do pay-for-performance incentives lead to a better health outcome?

Pay-for-performance approaches have been widely adopted in order to drive improvements in the quality of healthcare provision. Previous studies evaluating the impact of these programs are either limited by the number of health outcomes or of medical conditions considered. In this paper, we evaluate the effectiveness of a pay-for-performance program on the basis of five health outcomes and across a wide range of medical conditions. The context of the study is the Lombardy region in Italy, where a rewarding program was introduced in 2012. The policy evaluation is based on a difference-in-differences approach. The model includes multiple dependent outcomes, that allow quantifying the joint effect of the program, and random effects, that account for the heterogeneity of the data at the ward and hospital level. Our results show that the policy had a positive effect on the hospitals' performance in terms of those outcomes that can be more influenced by a managerial activity, namely the number of readmissions, transfers and returns to the surgery room. No significant changes which can be related to the pay-for-performance introduction are observed for the number of voluntary discharges and for mortality. Finally, our study shows evidence that the medical wards have reacted more strongly to the pay-for-performance program than the surgical ones, whereas only limited evidence is found in support of a different policy reaction across different types of hospital ownership.

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arXiv2016

NEAT: an efficient network enrichment analysis test

Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and are based on normality assumptions. We propose NEAT, a test for network enrichment analysis. The test is based on the hypergeometric distribution, which naturally arises as the null distribution in this context. NEAT can be applied not only to undirected, but to directed and partially directed networks as well. Our simulations indicate that NEAT is considerably faster than alternative resampling-based methods, and that its capacity to detect enrichments is at least as good as the one of alternative tests. We discuss applications of NEAT to network analyses in yeast by testing for enrichment of the Environmental Stress Response target gene set with GO Slim and KEGG functional gene sets, and also by testing for associations between GO Slim categories themselves. NEAT is a flexible and efficient test for network enrichment analysis that aims to overcome some limitations of existing resampling-based tests. The method is implemented in the R package neat, which can be freely downloaded from CRAN (http://cran.r-project.org/package=neat).

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arXiv2016

A Differentiable Alternative to the Lasso Penalty

Regularized regression has become very popular nowadays, particularly on high-dimensional problems where the addition of a penalty term to the log-likelihood allows inference where traditional methods fail. A number of penalties have been proposed in the literature, such as lasso, SCAD, ridge and elastic net to name a few. Despite their advantages and remarkable performance in rather extreme settings, where $p \gg n$, all these penalties, with the exception of ridge, are non-differentiable at zero. This can be a limitation in certain cases, such as computational efficiency of parameter estimation in non-linear models or derivation of estimators of the degrees of freedom for model selection criteria. With this paper, we provide the scientific community with a differentiable penalty, which can be used in any situation, but particularly where differentiability plays a key role. We show some desirable features of this function and prove theoretical properties of the resulting estimators within a regularized regression context. A simulation study and the analysis of a real dataset show overall a good performance under different scenarios. The method is implemented in the R package DLASSO freely available from CRAN.

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arXiv2016

A new Bayesian regression model for counts in medicine

Discrete data are collected in many application areas and are often characterised by highly skewed and power-lawlike distributions. An example of this, which is considered in this paper, is the number of visits to a specialist, often taken as a measure of demand in healthcare. A discrete Weibull regression model was recently proposed for regression problems with a discrete response and it was shown to possess two important features: the ability to capture over and under-dispersion simultaneously and a closed-form analytical expression of the quantiles of the conditional distribution. In this paper, we propose the first Bayesian implementation of a discrete Weibull regression model. The implementation considers a novel parameterization, where both parameters of the discrete Weibull distribution can be made dependent on the predictors. In addition, prior distributions can be imposed that encourage parameter shrinkage and that lead to variable selection. As with Bayesian procedures, the full posterior distribution of the parameters is returned, from which credible intervals can be readily calculated. A simulation study and the analysis of four real datasets of medical records show promises for the wide applicability of this approach to the analysis of count data. The method is implemented in the R package BDWreg.

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arXiv2015

Penalised inference for autoregressive moving average models with time-dependent predictors

Linear models that contain a time-dependent response and explanatory variables have attracted much interest in recent years. The most general form of the existing approaches is of a linear regression model with autoregressive moving average residuals. The addition of the moving average component results in a complex model with a very challenging implementation. In this paper, we propose to account for the time dependency in the data by explicitly adding autoregressive terms of the response variable in the linear model. In addition, we consider an autoregressive process for the errors in order to capture complex dynamic relationships parsimoniously. To broaden the application of the model, we present an $l_1$ penalized likelihood approach for the estimation of the parameters and show how the adaptive lasso penalties lead to an estimator which enjoys the oracle property. Furthermore, we prove the consistency of the estimators with respect to the mean squared prediction error in high-dimensional settings, an aspect that has not been considered by the existing time-dependent regression models. A simulation study and real data analysis show the successful applications of the model on financial data on stock indexes.

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arXiv2013

Joint modelling of ChIP-seq data via a Markov random field model

Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein binding sites. In this paper, we present a Markov random field model for the joint analysis of multiple ChIP-seq experiments. The proposed model naturally accounts for spatial dependencies in the data, by assuming first order Markov properties, and for the large proportion of zero counts, by using zero-inflated mixture distributions. In contrast to all other available implementations, the model allows for the joint modelling of multiple experiments, by incorporating key aspects of the experimental design. In particular, the model uses the information about replicates and about the different antibodies used in the experiments. An extensive simulation study shows a lower false non-discovery rate for the proposed method, compared to existing methods, at the same false discovery rate. Finally, we present an analysis on real data for the detection of histone modifications of two chromatin modifiers from eight ChIP-seq experiments, including technical replicates with different IP efficiencies.

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