When estimating an effect of an action with a randomized or observational study, that study is often not a random sample of the desired target population. Instead, estimates from that study can be transported to the target population. However, transportability methods generally rely on a positivity assumption, such that all relevant covariate patterns in the target population are also observed in the study sample. Strict eligibility criteria, particularly in the context of randomized trials, may lead to violations of this assumption. Two common approaches to address positivity violations are restricting the target population and restricting the relevant covariate set. As neither of these restrictions are ideal, we instead propose a synthesis of statistical and simulation models to address positivity violations. We propose corresponding g-computation and inverse probability weighting estimators. The restriction and synthesis approaches to addressing positivity violations are contrasted with a simulation experiment and an illustrative example in the context of sexually transmitted infection testing uptake. In both cases, the proposed synthesis approach accurately addressed the original research question when paired with a thoughtfully selected simulation model. Neither of the restriction approaches were able to accurately address the motivating question. As public health decisions must often be made with imperfect target population information, model synthesis is a viable approach given a combination of empirical data and external information based on the best available knowledge.
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This work introduces an empirical quadrature-based hyperreduction procedure and greedy training algorithm to effectively reduce the computational cost of solving convection-dominated problems with limited training. The proposed approach circumvents the slowly decaying $n$-width limitation of linear model reduction techniques applied to convection-dominated problems by using a nonlinear approximation manifold systematically defined by composing a low-dimensional affine space with bijections of the underlying domain. The reduced-order model is defined as the solution of a residual minimization problem over the nonlinear manifold. An online-efficient method is obtained by using empirical quadrature to approximate the optimality system such that it can be solved with mesh-independent operations. The proposed reduced-order model is trained using a greedy procedure to systematically sample the parameter domain. The effectiveness of the proposed approach is demonstrated on two shock-dominated computational fluid dynamics benchmarks.
The spectral clustering algorithm is often used as a binary clustering method for unclassified data by applying the principal component analysis. To study theoretical properties of the algorithm, the assumption of homoscedasticity is often supposed in existing studies. However, this assumption is restrictive and often unrealistic in practice. Therefore, in this paper, we consider the allometric extension model, that is, the directions of the first eigenvectors of two covariance matrices and the direction of the difference of two mean vectors coincide, and we provide a non-asymptotic bound of the error probability of the spectral clustering algorithm for the allometric extension model. As a byproduct of the result, we obtain the consistency of the clustering method in high-dimensional settings.
Science mapping is an important tool to gain insight into scientific fields, to identify emerging research trends, and to support science policy. Understanding the different ways in which different science mapping approaches capture the structure of scientific fields is critical. This paper presents a comparative analysis of two commonly used approaches, topic modeling (TM) and citation-based clustering (CC), to assess their respective strengths, weaknesses, and the characteristics of their results. We compare the two approaches using cluster-to-topic and topic-to-cluster mappings based on science maps of cardiovascular research (CVR) generated by TM and CC. Our findings reveal that relations between topics and clusters are generally weak, with limited overlap between topics and clusters. Only in a few exceptional cases do more than one-third of the documents in a topic belong to the same cluster, or vice versa. CC excels at identifying diseases and generating specialized clusters in Clinical Treatment & Surgical Procedures, while TM focuses on sub-techniques within diagnostic techniques, provides a general perspective on Clinical Treatment & Surgical Procedures, and identifies distinct topics related to practical guidelines. Our work enhances the understanding of science mapping approaches based on TM and CC and delivers practical guidance for scientometricians on how to apply these approaches effectively.
Quantum computing devices are believed to be powerful in solving the prime factorization problem, which is at the heart of widely deployed public-key cryptographic tools. However, the implementation of Shor's quantum factorization algorithm requires significant resources scaling linearly with the number size; taking into account an overhead that is required for quantum error correction the estimation is that 20 millions of (noisy) physical qubits are required for factoring 2048-bit RSA key in 8 hours. Recent proposal by Yan et. al. claims a possibility of solving the factorization problem with sublinear quantum resources. As we demonstrate in our work, this proposal lacks systematic analysis of the computational complexity of the classical part of the algorithm, which exploits the Schnorr's lattice-based approach. We provide several examples illustrating the need in additional resource analysis for the proposed quantum factorization algorithm.
It is crucial to detect when an instance lies downright too far from the training samples for the machine learning model to be trusted, a challenge known as out-of-distribution (OOD) detection. For neural networks, one approach to this task consists of learning a diversity of predictors that all can explain the training data. This information can be used to estimate the epistemic uncertainty at a given newly observed instance in terms of a measure of the disagreement of the predictions. Evaluation and certification of the ability of a method to detect OOD require specifying instances which are likely to occur in deployment yet on which no prediction is available. Focusing on regression tasks, we choose a simple yet insightful model for this OOD distribution and conduct an empirical evaluation of the ability of various methods to discriminate OOD samples from the data. Moreover, we exhibit evidence that a diversity of parameters may fail to translate to a diversity of predictors. Based on the choice of an OOD distribution, we propose a new way of estimating the entropy of a distribution on predictors based on nearest neighbors in function space. This leads to a variational objective which, combined with the family of distributions given by a generative neural network, systematically produces a diversity of predictors that provides a robust way to detect OOD samples.
We explore a link between complexity and physics for circuits of given functionality. Taking advantage of the connection between circuit counting problems and the derivation of ensembles in statistical mechanics, we tie the entropy of circuits of a given functionality and fixed number of gates to circuit complexity. We use thermodynamic relations to connect the quantity analogous to the equilibrium temperature to the exponent describing the exponential growth of the number of distinct functionalities as a function of complexity. This connection is intimately related to the finite compressibility of typical circuits. Finally, we use the thermodynamic approach to formulate a framework for the obfuscation of programs of arbitrary length -- an important problem in cryptography -- as thermalization through recursive mixing of neighboring sections of a circuit, which can viewed as the mixing of two containers with ``gases of gates''. This recursive process equilibrates the average complexity and leads to the saturation of the circuit entropy, while preserving functionality of the overall circuit. The thermodynamic arguments hinge on ergodicity in the space of circuits which we conjecture is limited to disconnected ergodic sectors due to fragmentation. The notion of fragmentation has important implications for the problem of circuit obfuscation as it implies that there are circuits with same size and functionality that cannot be connected via local moves. Furthermore, we argue that fragmentation is unavoidable unless the complexity classes NP and coNP coincide, a statement that implies the collapse of the polynomial hierarchy of complexity theory to its first level.
Permutation tests are widely recognized as robust alternatives to tests based on the normal theory. Random permutation tests have been frequently employed to assess the significance of variables in linear models. Despite their widespread use, existing random permutation tests lack finite-sample and assumption-free guarantees for controlling type I error in partial correlation tests. To address this standing challenge, we develop a conformal test through permutation-augmented regressions, which we refer to as PALMRT. PALMRT not only achieves power competitive with conventional methods but also provides reliable control of type I errors at no more than $2\alpha$ given any targeted level $\alpha$, for arbitrary fixed-designs and error distributions. We confirmed this through extensive simulations. Compared to the cyclic permutation test (CPT), which also offers theoretical guarantees, PALMRT does not significantly compromise power or set stringent requirements on the sample size, making it suitable for diverse biomedical applications. We further illustrate their differences in a long-Covid study where PALMRT validated key findings previously identified using the t-test, while CPT suffered from a drastic loss of power. We endorse PALMRT as a robust and practical hypothesis test in scientific research for its superior error control, power preservation, and simplicity.
泛函
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It is disproved the Tokareva's conjecture that any balanced boolean function of appropriate degree is a derivative of some bent function. This result is based on new upper bounds for the numbers of bent and plateaued functions.
Gene set analysis is a mainstay of functional genomics, but it relies on manually curated databases of gene functions that are incomplete and unaware of biological context. Here we evaluate the ability of OpenAI's GPT-4, a Large Language Model (LLM), to develop hypotheses about common gene functions from its embedded biomedical knowledge. We created a GPT-4 pipeline to label gene sets with names that summarize their consensus functions, substantiated by analysis text and citations. Benchmarking against named gene sets in the Gene Ontology, GPT-4 generated very similar names in 50% of cases, while in most remaining cases it recovered the name of a more general concept. In gene sets discovered in 'omics data, GPT-4 names were more informative than gene set enrichment, with supporting statements and citations that largely verified in human review. The ability to rapidly synthesize common gene functions positions LLMs as valuable functional genomics assistants.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.
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