Miracle-dz/UniFAR-FTUs huggingface dataset:
Fully Automated Myocardial Infarction Classification using Ordinary Differential Equations

Portable, Wearable and Wireless electrocardiogram (ECG) Systems have the potential to be used as point-of-care for cardiovascular disease diagnostic systems. Such wearable and wireless ECG systems require automatic detection of cardiovascular disease. Even in the primary care, automation of ECG diagnostic systems will improve efficiency of ECG diagnosis and reduce the minimal training requirement of local healthcare workers. However, few fully automatic myocardial infarction (MI) disease detection algorithms have well been developed. This paper presents a novel automatic MI classification algorithm using second order ordinary differential equation (ODE) with time varying coefficients, which simultaneously captures morphological and dynamic feature of highly correlated ECG signals. By effectively estimating the unobserved state variables and the parameters of the second order ODE, the accuracy of the classification was significantly improved. The estimated time varying coefficients of the second order ODE were used as an input to the support vector machine (SVM) for the MI classification. The proposed method was applied to the PTB diagnostic ECG database within Physionet. The overall sensitivity, specificity, and classification accuracy of 12 lead ECGs for MI binary classifications were 98.7%, 96.4% and 98.3%, respectively. We also found that even using one lead ECG signals, we can reach accuracy as high as 97%. Multiclass MI classification is a challenging task but the developed ODE approach for 12 lead ECGs coupled with multiclass SVM reached 96.4% accuracy for classifying 5 subgroups of MI and healthy controls.
Nonparametric estimation of dynamics of monotone trajectories

We study a class of nonlinear nonparametric inverse problems. Specifically, we propose a nonparametric estimator of the dynamics of a monotonically increasing trajectory defined on a finite time interval. Under suitable regularity conditions, we prove consistency of the proposed estimator and show that in terms of $L^2$-loss, the optimal rate of convergence for the proposed estimator is the same as that for the estimation of the derivative of a trajectory. This is a new contribution to the area of nonlinear nonparametric inverse problems. We conduct a simulation study to examine the finite sample behavior of the proposed estimator and apply it to the Berkeley growth data.
Identifiability of Gaussian structural equation models with equal error variances

We consider structural equation models in which variables can be written as a function of their parents and noise terms, which are assumed to be jointly independent. Corresponding to each structural equation model is a directed acyclic graph describing the relationships between the variables. In Gaussian structural equation models with linear functions, the graph can be identified from the joint distribution only up to Markov equivalence classes, assuming faithfulness. In this work, we prove full identifiability in the case where all noise variables have the same variance: the directed acyclic graph can be recovered from the joint Gaussian distribution. Our result has direct implications for causal inference: if the data follow a Gaussian structural equation model with equal error variances, then, assuming that all variables are observed, the causal structure can be inferred from observational data only. We propose a statistical method and an algorithm based on our theoretical findings.
Bayesian and Maximum Likelihood Estimation for Gaussian Processes on an Incomplete Lattice

ABSTRACT This article proposes a new approach for Bayesian and maximum likelihood parameter estimation for stationary Gaussian processes observed on a large lattice with missing values. We propose a Markov chain Monte Carlo approach for Bayesian inference, and a Monte Carlo expectation-maximization algorithm for maximum likelihood inference. Our approach uses data augmentation and circulant embedding of the covariance matrix, and provides likelihood-based inference for the parameters and the missing data. Using simulated data and an application to satellite sea surface temperatures in the Pacific Ocean, we show that our method provides accurate inference on lattices of sizes up to 512 × 512, and is competitive with two popular methods: composite likelihood and spectral approximations.
Entropy Balancing is Doubly Robust

Abstract Covariate balance is a conventional key diagnostic for methods estimating causal effects from observational studies. Recently, there is an emerging interest in directly incorporating covariate balance in the estimation. We study a recently proposed entropy maximization method called Entropy Balancing (EB), which exactly matches the covariate moments for the different experimental groups in its optimization problem. We show EB is doubly robust with respect to linear outcome regression and logistic propensity score regression, and it reaches the asymptotic semiparametric variance bound when both regressions are correctly specified. This is surprising to us because there is no attempt to model the outcome or the treatment assignment in the original proposal of EB. Our theoretical results and simulations suggest that EB is a very appealing alternative to the conventional weighting estimators that estimate the propensity score by maximum likelihood.
A Bayesian framework for verification and recalibration of ensemble forecasts: How uncertain is NAO predictability?

Predictability estimates of ensemble prediction systems are uncertain due to limited numbers of past forecasts and observations. To account for such uncertainty, this paper proposes a Bayesian inferential framework that provides a simple 6-parameter representation of ensemble forecasting systems and the corresponding observations. The framework is probabilistic, and thus allows for quantifying uncertainty in predictability measures such as correlation skill and signal-to-noise ratios. It also provides a natural way to produce recalibrated probabilistic predictions from uncalibrated ensembles forecasts. The framework is used to address important questions concerning the skill of winter hindcasts of the North Atlantic Oscillation for 1992-2011 issued by the Met Office GloSea5 climate prediction system. Although there is much uncertainty in the correlation between ensemble mean and observations, there is strong evidence of skill: the 95% credible interval of the correlation coefficient of [0.19,0.68] does not overlap zero. There is also strong evidence that the forecasts are not exchangeable with the observations: With over 99% certainty, the signal-to-noise ratio of the forecasts is smaller than the signal-to-noise ratio of the observations, which suggests that raw forecasts should not be taken as representative scenarios of the observations. Forecast recalibration is thus required, which can be coherently addressed within the proposed framework.
A Robust Approach for Identifying Gene-Environment Interactions for Prognosis

For many complex diseases, prognosis is of essential importance. It has been shown that, beyond the main effects of genetic (G) and environmental (E) risk factors, the gene-environment (G×E) interactions also play a critical role. In practice, the prognosis outcome data can be contaminated, and most of the existing methods are not robust to data contamination. In the literature, it has been shown that even a single contaminated observation can lead to severely biased model estimation. In this study, we describe prognosis using an accelerated failure time (AFT) model. An exponential squared loss is proposed to accommodate possible data contamination. A penalization approach is adopted for regularized estimation and marker selection. The proposed method is realized using an effective coordinate descent (CD) and minorization maximization (MM) algorithm. Simulation shows that without contamination, the proposed method has performance comparable to or better than the unrobust alternative. With contamination, it outperforms the unrobust alternative and, under certain scenarios, can be superior to the robust method based on quantile regression. The proposed method is applied to the analysis of TCGA (The Cancer Genome Atlas) lung cancer data. It identifies interactions different from those using the alternatives. The identified marker have important implications and satisfactory stability.
A Fused Latent and Graphical Model for Multivariate Binary Data

We consider modeling, inference, and computation for analyzing multivariate binary data. We propose a new model that consists of a low dimensional latent variable component and a sparse graphical component. Our study is motivated by analysis of item response data in cognitive assessment and has applications to many disciplines where item response data are collected. Standard approaches to item response data in cognitive assessment adopt the multidimensional item response theory (IRT) models. However, human cognition is typically a complicated process and thus may not be adequately described by just a few factors. Consequently, a low-dimensional latent factor model, such as the multidimensional IRT models, is often insufficient to capture the structure of the data. The proposed model adds a sparse graphical component that captures the remaining ad hoc dependence. It reduces to a multidimensional IRT model when the graphical component becomes degenerate. Model selection and parameter estimation are carried out simultaneously through construction of a pseudo-likelihood function and properly chosen penalty terms. The convexity of the pseudo-likelihood function allows us to develop an efficient algorithm, while the penalty terms generate a low-dimensional latent component and a sparse graphical structure. Desirable theoretical properties are established under suitable regularity conditions. The method is applied to the revised Eysenck's personality questionnaire, revealing its usefulness in item analysis. Simulation results are reported that show the new method works well in practical situations.
Eigenvalues of sample covariance matrices of non-linear processes with infinite variance

We study the $k$-largest eigenvalues of heavy-tailed sample covariance matrices of the form $\bX\bX^\T$ in an asymptotic framework, where the dimension of the data and the sample size tend to infinity. To this end, we assume that the rows of $\bX$ are given by independent copies of some stationary process with regularly varying marginals with index $\alpha\in(0,2)$ satisfying large deviation and mixing conditions. We apply these general results to stochastic volatility and GARCH processes.
Dependent time changed processes with applications to nonlinear ocean waves

Many records in environmental sciences exhibit asymmetric trajectories and there is a need for simple and tractable models which can reproduce such features. In this paper we explore an approach based on applying both a time change and a marginal transformation on Gaussian processes. The main originality of the proposed model is that the time change depends on the observed trajectory. We first show that the proposed model is stationary and ergodic and provide an explicit characterization of the stationary distribution. This result is then used to build both parametric and non-parametric estimates of the time change function whereas the estimation of the marginal transformation is based on up-crossings. Simulation results are provided to assess the quality of the estimates. The model is applied to shallow water wave data and it is shown that the fitted model is able to reproduce important statistics of the data such as its spectrum and marginal distribution which are important quantities for practical applications. An important benefit of the proposed model is its ability to reproduce the observed asymmetries between the crest and the troughs and between the front and the back of the waves by accelerating the chronometer in the crests and in the front of the waves.
Trend extraction in functional data of R and T waves amplitudes of exercise electrocardiogram

The R and T waves amplitudes of the electrocardiogram recorded during the exercise test undergo strong modifications in response to stress. We analyze the time series of these amplitudes in a group of normal subjects in the framework of functional data, performing reduction of dimensionality, smoothing and principal component analysis. These methods show that the R and T amplitudes have opposite responses to stress, consisting respectively in a bump and a dip at the early recovery stage. We test these features computing a confidence band for the trend of the population mean and analyzing the zero crossing of its derivative. Our findings support the existence of a relationship between R and T wave amplitudes and respectively diastolic and systolic ventricular volumes.
Likelihood-based model selection for stochastic block models

The stochastic block model (SBM) provides a popular framework for modeling community structures in networks. However, more attention has been devoted to problems concerning estimating the latent node labels and the model parameters than the issue of choosing the number of blocks. We consider an approach based on the log likelihood ratio statistic and analyze its asymptotic properties under model misspecification. We show the limiting distribution of the statistic in the case of underfitting is normal and obtain its convergence rate in the case of overfitting. These conclusions remain valid when the average degree grows at a polylog rate. The results enable us to derive the correct order of the penalty term for model complexity and arrive at a likelihood-based model selection criterion that is asymptotically consistent. Our analysis can also be extended to a degree-corrected block model (DCSBM). In practice, the likelihood function can be estimated using more computationally efficient variational methods or consistent label estimation algorithms, allowing the criterion to be applied to large networks.
Matrix completion by singular value thresholding: sharp bounds

We consider the matrix completion problem where the aim is to esti-mate a large data matrix for which only a relatively small random subset of its entries is observed. Quite popular approaches to matrix completion problem are iterative thresholding methods. In spite of their empirical success, the theoretical guarantees of such iterative thresholding methods are poorly understood. The goal of this paper is to provide strong theo-retical guarantees, similar to those obtained for nuclear-norm penalization methods and one step thresholding methods, for an iterative thresholding algorithm which is a modification of the softImpute algorithm. An im-portant consequence of our result is the exact minimax optimal rates of convergence for matrix completion problem which were known until know only up to a logarithmic factor.
Bernstein polynomial model for grouped continuous data

ABSTRACT Grouped data are commonly encountered in applications. All data from a continuous population are grouped due to rounding of the individual observations. The Bernstein polynomial model is proposed as an approximate model in this paper for estimating a univariate density function based on grouped data. The coefficients of the Bernstein polynomial, as the mixture proportions of beta distributions, can be estimated using an EM algorithm. The optimal degree of the Bernstein polynomial can be determined using a change-point estimation method. The rate of convergence of the proposed density estimate to the true density is proved to be almost parametric by an acceptance–rejection argument used for generating random numbers. The proposed method is compared with some existing methods in a simulation study and is applied to the Chicken Embryo Data.
Fast Bayesian inference for exoplanet discovery in radial velocity data

Inferring the number of planets $N$ in an exoplanetary system from radial velocity (RV) data is a challenging task. Recently, it has become clear that RV data can contain periodic signals due to stellar activity, which can be difficult to distinguish from planetary signals. However, even doing the inference under a given set of simplifying assumptions (e.g. no stellar activity) can be difficult. It is common for the posterior distribution for the planet parameters, such as orbital periods, to be multimodal and to have other awkward features. In addition, when $N$ is unknown, the marginal likelihood (or evidence) as a function of $N$ is required. Rather than doing separate runs with different trial values of $N$, we propose an alternative approach using a trans-dimensional Markov Chain Monte Carlo method within Nested Sampling. The posterior distribution for $N$ can be obtained with a single run. We apply the method to $\nu$ Oph and Gliese 581, finding moderate evidence for additional signals in $\nu$ Oph with periods of 36.11 $\pm$ 0.034 days, 75.58 $\pm$ 0.80 days, and 1709 $\pm$ 183 days; the posterior probability that at least one of these exists is 85%. The results also suggest Gliese 581 hosts many (7-15) "planets" (or other causes of other periodic signals), but only 4-6 have well determined periods. The analysis of both of these datasets shows phase transitions exist which are difficult to negotiate without Nested Sampling.
Optimal scaling for the transient phase of Metropolis Hastings algorithms: The longtime behavior

We consider the Random Walk Metropolis algorithm on $\R^n$ with Gaussian proposals, and when the target probability measure is the $n$-fold product of a one dimensional law. It is well-known (see Roberts et al. (1997))) that, in the limit $n \to \infty$, starting at equilibrium and for an appropriate scaling of the variance and of the timescale as a function of the dimension $n$, a diffusive limit is obtained for each component of the Markov chain. In Jourdain et al. (2012), we generalize this result when the initial distribution is not the target probability measure. The obtained diffusive limit is the solution to a stochastic differential equation nonlinear in the sense of McKean. In the present paper, we prove convergence to equilibrium for this equation. We discuss practical counterparts in order to optimize the variance of the proposal distribution to accelerate convergence to equilibrium. Our analysis confirms the interest of the constant acceptance rate strategy (with acceptance rate between 1/4 and 1/3) first suggested in Roberts et al. (1997). We also address scaling of the Metropolis-Adjusted Langevin Algorithm. When starting at equilibrium, a diffusive limit for an optimal scaling of the variance is obtained in Roberts and Rosenthal (1998). In the transient case, we obtain formally that the optimal variance scales very differently in $n$ depending on the sign of a moment of the distribution, which vanishes at equilibrium. This suggest that it is difficult to derive practical recommendations for MALA from such asymptotic results.
Bayesian Covariance Modelling of Large Tensor-Variate Data Sets $\&$ Inverse Non-parametric Learning of the Unknown Model Parameter Vector

We present a method for modelling the covariance structure of tensor-variate data, with the ulterior aim of learning an unknown model parameter vector using such data. We express the high-dimensional observable as a function of this sought model parameter vector, and attempt to learn such a high-dimensional function given training data, by modelling it as a realisation from a tensor-variate Gaussian Process (GP). The likelihood of the unknowns given training data, is then tensor-normal. We choose vague priors on the unknown GP parameters (mean tensor and covariance matrices) and write the posterior probability density of these unknowns given the data. We perform posterior sampling using Random-Walk Metropolis-Hastings. Thereafter we learn the aforementioned unknown model parameter vector by performing posterior sampling in two different ways, given test and training data, using MCMC, to generate 95$\%$ HPD credible region on each unknown. We make an application of this method to the learning of the location of the Sun in the Milky Way disk.
MAXIMUM LIKELIHOOD ESTIMATION OF MARK-RECAPTURE-RECOVERY MODELS IN THE PRESENCE OF CONTINUOUS COVARIATES

We consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be eciently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of diusive random walks. We consider an alternative non-diusive
Posterior consistency in misspecified models for i.n.i.d response

We derive conditions for posterior consistency when the responses are independent but not identically distributed ($i.n.i.d$) and the model is "misspecified" to be a family of densities parametrized by a possibly infinite dimensional parameter. Our approach has connections to key ideas developed for $i.i.d$ models in Kleijn and van der Vaart(2006) and it's subsequent simplification in Ramamoorthi, et al.(2014) (unpublished manuscript). While key results in these two papers rely heavily on the convexity of the specified family of densities, parametric families are seldom convex. In this note, we take a direct approach to deriving posterior consistency with respect to natural topologies on the parameter space without having to impose conditions on the convex hull of the parametric family. We first derive our results for the case when the responses are $i.i.d$ and then extend it to the $i.n. i.d$ case. As an example, we demonstrate the applicability of the results to the Bayesian quantile estimation problem.
Joint Dispersion Model with a Flexible Link

The objective is to model longitudinal and survival data jointly taking into account the dependence between the two responses in a real HIV/AIDS dataset using a shared parameter approach inside a Bayesian framework. We propose a linear mixed effects dispersion model to adjust the CD4 longitudinal biomarker data with a between-individual heterogeneity in the mean and variance. In doing so we are relaxing the usual assumption of a common variance for the longitudinal residuals. A hazard regression model is considered in addition to model the time since HIV/AIDS diagnostic until failure, being the coefficients, accounting for the linking between the longitudinal and survival processes, time-varying. This flexibility is specified using Penalized Splines and allows the relationship to vary in time. Because heteroscedasticity may be related with the survival, the standard deviation is considered as a covariate in the hazard model, thus enabling to study the effect of the CD4 counts' stability on the survival. The proposed framework outperforms the most used joint models, highlighting the importance in correctly taking account the individual heterogeneity for the measurement errors variance and the evolution of the disease over time in bringing new insights to better understand this biomarker-survival relation.