Instrumental variables are widely used in econometrics and epidemiology for identifying and estimating causal effects when an exposure of interest is confounded by unmeasured factors. Despite this popularity, the assumptions invoked to justify the use of instruments differ substantially across the literature. Similarly, statistical approaches for estimating the resulting causal quantities vary considerably, and often rely on strong parametric assumptions. In this work, we compile and organize structural conditions that nonparametrically identify conditional average treatment effects, average treatment effects among the treated, and local average treatment effects, with a focus on identification formulae invoking the conditional Wald estimand. Moreover, we build upon existing work and propose nonparametric efficient estimators of functionals corresponding to marginal and conditional causal contrasts resulting from the various identification paradigms. We illustrate the proposed methods on an observational study examining the effects of operative care on adverse events for cholecystitis patients, and a randomized trial assessing the effects of market participation on political views.
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Antibodies are proteins produced by the immune system that can identify and neutralise a wide variety of antigens with high specificity and affinity, and constitute the most successful class of biotherapeutics. With the advent of next-generation sequencing, billions of antibody sequences have been collected in recent years, though their application in the design of better therapeutics has been constrained by the sheer volume and complexity of the data. To address this challenge, we present IgBert and IgT5, the best performing antibody-specific language models developed to date which can consistently handle both paired and unpaired variable region sequences as input. These models are trained comprehensively using the more than two billion unpaired sequences and two million paired sequences of light and heavy chains present in the Observed Antibody Space dataset. We show that our models outperform existing antibody and protein language models on a diverse range of design and regression tasks relevant to antibody engineering. This advancement marks a significant leap forward in leveraging machine learning, large scale data sets and high-performance computing for enhancing antibody design for therapeutic development.
During an epidemic outbreak of a new disease, the probability of dying once infected is considered an important though difficult task to be computed. Since it is very hard to know the true number of infected people, the focus is placed on estimating the case fatality rate, which is defined as the probability of dying once tested and confirmed as infected. The estimation of this rate at the beginning of an epidemic remains challenging for several reasons, including the time gap between diagnosis and death, and the rapid growth in the number of confirmed cases. In this work, an unbiased estimator of the case fatality rate of a virus is presented. The consistency of the estimator is demonstrated, and its asymptotic distribution is derived, enabling the corresponding confidence intervals (C.I.) to be established. The proposed method is based on the distribution F of the time between confirmation and death of individuals who die because of the virus. The estimator's performance is analyzed in both simulation scenarios and the real-world context of Argentina in 2020 for the COVID-19 pandemic, consistently achieving excellent results when compared to an existing proposal as well as to the conventional \naive" estimator that was employed to report the case fatality rates during the last COVID-19 pandemic. In the simulated scenarios, the empirical coverage of our C.I. is studied, both using the F employed to generate the data and an estimated F, and it is observed that the desired level of confidence is reached quickly when using real F and in a reasonable period of time when estimating F.
Experiments studying get-out-the-vote (GOTV) efforts estimate the causal effect of various mobilization efforts on voter turnout. However, there is often substantial noncompliance in these studies. A usual approach is to use an instrumental variable (IV) analysis to estimate impacts for compliers, here being those actually contacted by the investigators. Unfortunately, popular IV estimators can be unstable in studies with a small fraction of compliers. We explore post-stratifying the data (e.g., taking a weighted average of IV estimates within each stratum) using variables that predict complier status (and, potentially, the outcome) to mitigate this. We present the benefits of post-stratification in terms of bias, variance, and improved standard error estimates, and provide a finite-sample asymptotic variance formula. We also compare the performance of different IV approaches and discuss the advantages of our design-based post-stratification approach over incorporating compliance-predictive covariates into the two-stage least squares estimator. In the end, we show that covariates predictive of compliance can increase precision, but only if one is willing to make a bias-variance trade-off by down-weighting or dropping strata with few compliers. By contrast, standard approaches such as two-stage least squares fail to use such information. We finally examine the benefits of our approach in two GOTV applications.
Quantifying the heterogeneity is an important issue in meta-analysis, and among the existing measures, the $I^2$ statistic is most commonly used. In this paper, we first illustrate with a simple example that the $I^2$ statistic is heavily dependent on the study sample sizes, mainly because it is used to quantify the heterogeneity between the observed effect sizes. To reduce the influence of sample sizes, we introduce an alternative measure that aims to directly measure the heterogeneity between the study populations involved in the meta-analysis. We further propose a new estimator, namely the $I_A^2$ statistic, to estimate the newly defined measure of heterogeneity. For practical implementation, the exact formulas of the $I_A^2$ statistic are also derived under two common scenarios with the effect size as the mean difference (MD) or the standardized mean difference (SMD). Simulations and real data analysis demonstrate that the $I_A^2$ statistic provides an asymptotically unbiased estimator for the absolute heterogeneity between the study populations, and it is also independent of the study sample sizes as expected. To conclude, our newly defined $I_A^2$ statistic can be used as a supplemental measure of heterogeneity to monitor the situations where the study effect sizes are indeed similar with little biological difference. In such scenario, the fixed-effect model can be appropriate; nevertheless, when the sample sizes are sufficiently large, the $I^2$ statistic may still increase to 1 and subsequently suggest the random-effects model for meta-analysis.
We consider a discrete best approximation problem formulated in the framework of tropical algebra, which deals with the theory and applications of algebraic systems with idempotent operations. Given a set of samples of input and output of an unknown function, the problem is to construct a generalized tropical Puiseux polynomial that best approximates the function in the sense of a tropical distance function. The construction of an approximate polynomial involves the evaluation of both unknown coefficient and exponent of each monomial in the polynomial. To solve the approximation problem, we first reduce the problem to an equation in unknown vector of coefficients, which is given by a matrix with entries parameterized by unknown exponents. We derive a best approximate solution of the equation, which yields both vector of coefficients and approximation error parameterized by the exponents. Optimal values of exponents are found by minimization of the approximation error, which is reduced to a minimization of a function of exponents over all partitions of a finite set. We solve this minimization problem in terms of max-plus algebra (where addition is defined as maximum and multiplication as arithmetic addition) by using a computational procedure based on the agglomerative clustering technique. This solution is extended to the minimization problem of finding optimal exponents in the polynomial in terms of max-algebra (where addition is defined as maximum). The results obtained are applied to develop new solutions for conventional problems of discrete best approximation of real functions by piecewise linear functions and piecewise Puiseux polynomials. We discuss computational complexity of the proposed solution and estimate upper bounds on the computational time. We demonstrate examples of approximation problems solved in terms of max-plus and max-algebra, and give graphical illustrations.
We address the problem of the best uniform approximation of a continuous function on a convex domain. The approximation is by linear combinations of a finite system of functions (not necessarily Chebyshev) under arbitrary linear constraints. By modifying the concept of alternance and of the Remez iterative procedure we present a method, which demonstrates its efficiency in numerical problems. The linear rate of convergence is proved under some favourable assumptions. A special attention is paid to systems of complex exponents, Gaussian functions, lacunar algebraic and trigonometric polynomials. Applications to signal processing, linear ODE, switching dynamical systems, and to Markov-Bernstein type inequalities are considered.
We propose a method for obtaining parsimonious decompositions of networks into higher order interactions which can take the form of arbitrary motifs.The method is based on a class of analytically solvable generative models, where vertices are connected via explicit copies of motifs, which in combination with non-parametric priors allow us to infer higher order interactions from dyadic graph data without any prior knowledge on the types or frequencies of such interactions. Crucially, we also consider 'degree--corrected' models that correctly reflect the degree distribution of the network and consequently prove to be a better fit for many real world--networks compared to non-degree corrected models. We test the presented approach on simulated data for which we recover the set of underlying higher order interactions to a high degree of accuracy. For empirical networks the method identifies concise sets of atomic subgraphs from within thousands of candidates that cover a large fraction of edges and include higher order interactions of known structural and functional significance. The method not only produces an explicit higher order representation of the network but also a fit of the network to analytically tractable models opening new avenues for the systematic study of higher order network structures.
The univariate dimension reduction (UDR) method stands as a way to estimate the statistical moments of the output that is effective in a large class of uncertainty quantification (UQ) problems. UDR's fundamental strategy is to approximate the original function using univariate functions so that the UQ cost only scales linearly with the dimension of the problem. Nonetheless, UDR's effectiveness can diminish when uncertain inputs have high variance, particularly when assessing the output's second and higher-order statistical moments. This paper proposes a new method, gradient-enhanced univariate dimension reduction (GUDR), that enhances the accuracy of UDR by incorporating univariate gradient function terms into the UDR approximation function. Theoretical results indicate that the GUDR approximation is expected to be one order more accurate than UDR in approximating the original function, and it is expected to generate more accurate results in computing the output's second and higher-order statistical moments. Our proposed method uses a computational graph transformation strategy to efficiently evaluate the GUDR approximation function on tensor-grid quadrature inputs, and use the tensor-grid input-output data to compute the statistical moments of the output. With an efficient automatic differentiation method to compute the gradients, our method preserves UDR's linear scaling of computation time with problem dimension. Numerical results show that the GUDR is more accurate than UDR in estimating the standard deviation of the output and has a performance comparable to the method of moments using a third-order Taylor series expansion.
Decision making and learning in the presence of uncertainty has attracted significant attention in view of the increasing need to achieve robust and reliable operations. In the case where uncertainty stems from the presence of adversarial attacks this need is becoming more prominent. In this paper we focus on linear and nonlinear classification problems and propose a novel adversarial training method for robust classifiers, inspired by Support Vector Machine (SVM) margins. We view robustness under a data driven lens, and derive finite sample complexity bounds for both linear and non-linear classifiers in binary and multi-class scenarios. Notably, our bounds match natural classifiers' complexity. Our algorithm minimizes a worst-case surrogate loss using Linear Programming (LP) and Second Order Cone Programming (SOCP) for linear and non-linear models. Numerical experiments on the benchmark MNIST and CIFAR10 datasets show our approach's comparable performance to state-of-the-art methods, without needing adversarial examples during training. Our work offers a comprehensive framework for enhancing binary linear and non-linear classifier robustness, embedding robustness in learning under the presence of adversaries.
Due to their flexibility to represent almost any kind of relational data, graph-based models have enjoyed a tremendous success over the past decades. While graphs are inherently only combinatorial objects, however, many prominent analysis tools are based on the algebraic representation of graphs via matrices such as the graph Laplacian, or on associated graph embeddings. Such embeddings associate to each node a set of coordinates in a vector space, a representation which can then be employed for learning tasks such as the classification or alignment of the nodes of the graph. As the geometric picture provided by embedding methods enables the use of a multitude of methods developed for vector space data, embeddings have thus gained interest both from a theoretical as well as a practical perspective. Inspired by trace-optimization problems, often encountered in the analysis of graph-based data, here we present a method to derive ellipsoidal embeddings of the nodes of a graph, in which each node is assigned a set of coordinates on the surface of a hyperellipsoid. Our method may be seen as an alternative to popular spectral embedding techniques, to which it shares certain similarities we discuss. To illustrate the utility of the embedding we conduct a case study in which analyse synthetic and real world networks with modular structure, and compare the results obtained with known methods in the literature.
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