Likelihood-free inference for simulator-based statistical models has developed rapidly from its infancy to a useful tool for practitioners. However, models with more than a handful of parameters still generally remain a challenge for the Approximate Bayesian Computation (ABC) based inference. To advance the possibilities for performing likelihood-free inference in higher dimensional parameter spaces, we introduce an extension of the popular Bayesian optimisation based approach to approximate discrepancy functions in a probabilistic manner which lends itself to an efficient exploration of the parameter space. Our approach achieves computational scalability for higher dimensional parameter spaces by using separate acquisition functions and discrepancies for each parameter. The efficient additive acquisition structure is combined with exponentiated loss -likelihood to provide a misspecification-robust characterisation of the marginal posterior distribution for all model parameters. The method successfully performs computationally efficient inference in a 100-dimensional space on canonical examples and compares favourably to existing modularised ABC methods. We further illustrate the potential of this approach by fitting a bacterial transmission dynamics model to a real data set, which provides biologically coherent results on strain competition in a 30-dimensional parameter space.
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Latent dynamical models are commonly used to learn the distribution of a latent dynamical process that represents a sequence of noisy data samples. However, producing samples from such models with high fidelity is challenging due to the complexity and variability of latent and observation dynamics. Recent advances in diffusion-based generative models, such as DDPM and NCSN, have shown promising alternatives to state-of-the-art latent generative models, such as Neural ODEs, RNNs, and Normalizing flow networks, for generating high-quality sequential samples from a prior distribution. However, their application in modeling sequential data with latent dynamical models is yet to be explored. Here, we propose a novel latent variable model named latent dynamical implicit diffusion processes (LDIDPs), which utilizes implicit diffusion processes to sample from dynamical latent processes and generate sequential observation samples accordingly. We tested LDIDPs on synthetic and simulated neural decoding problems. We demonstrate that LDIDPs can accurately learn the dynamics over latent dimensions. Furthermore, the implicit sampling method allows for the computationally efficient generation of high-quality sequential data samples from the latent and observation spaces.
One-shot channel simulation is a fundamental data compression problem concerned with encoding a single sample from a target distribution $Q$ using a coding distribution $P$ using as few bits as possible on average. Algorithms that solve this problem find applications in neural data compression and differential privacy and can serve as a more efficient alternative to quantization-based methods. Sadly, existing solutions are too slow or have limited applicability, preventing widespread adoption. In this paper, we conclusively solve one-shot channel simulation for one-dimensional problems where the target-proposal density ratio is unimodal by describing an algorithm with optimal runtime. We achieve this by constructing a rejection sampling procedure equivalent to greedily searching over the points of a Poisson process. Hence, we call our algorithm greedy Poisson rejection sampling (GPRS) and analyze the correctness and time complexity of several of its variants. Finally, we empirically verify our theorems, demonstrating that GPRS significantly outperforms the current state-of-the-art method, A* coding.
Doubly-stochastic point processes model the occurrence of events over a spatial domain as an inhomogeneous Poisson process conditioned on the realization of a random intensity function. They are flexible tools for capturing spatial heterogeneity and dependence. However, implementations of doubly-stochastic spatial models are computationally demanding, often have limited theoretical guarantee, and/or rely on restrictive assumptions. We propose a penalized regression method for estimating covariate effects in doubly-stochastic point processes that is computationally efficient and does not require a parametric form or stationarity of the underlying intensity. We establish the consistency and asymptotic normality of the proposed estimator, and develop a covariance estimator that leads to a conservative statistical inference procedure. A simulation study shows the validity of our approach under less restrictive assumptions on the data generating mechanism, and an application to Seattle crime data demonstrates better prediction accuracy compared with existing alternatives.
Test of independence is of fundamental importance in modern data analysis, with broad applications in variable selection, graphical models, and causal inference. When the data is high dimensional and the potential dependence signal is sparse, independence testing becomes very challenging without distributional or structural assumptions. In this paper, we propose a general framework for independence testing by first fitting a classifier that distinguishes the joint and product distributions, and then testing the significance of the fitted classifier. This framework allows us to borrow the strength of the most advanced classification algorithms developed from the modern machine learning community, making it applicable to high dimensional, complex data. By combining a sample split and a fixed permutation, our test statistic has a universal, fixed Gaussian null distribution that is independent of the underlying data distribution. Extensive simulations demonstrate the advantages of the newly proposed test compared with existing methods. We further apply the new test to a single-cell data set to test the independence between two types of single-cell sequencing measurements, whose high dimensionality and sparsity make existing methods hard to apply.
This paper studies distribution-free inference in settings where the data set has a hierarchical structure -- for example, groups of observations, or repeated measurements. In such settings, standard notions of exchangeability may not hold. To address this challenge, a hierarchical form of exchangeability is derived, facilitating extensions of distribution-free methods, including conformal prediction and jackknife+. While the standard theoretical guarantee obtained by the conformal prediction framework is a marginal predictive coverage guarantee, in the special case of independent repeated measurements, it is possible to achieve a stronger form of coverage -- the "second-moment coverage" property -- to provide better control of conditional miscoverage rates, and distribution-free prediction sets that achieve this property are constructed. Simulations illustrate that this guarantee indeed leads to uniformly small conditional miscoverage rates. Empirically, this stronger guarantee comes at the cost of a larger width of the prediction set in scenarios where the fitted model is poorly calibrated, but this cost is very mild in cases where the fitted model is accurate.
We describe a recursive algorithm that decomposes an algebraic set into locally closed equidimensional sets, i.e. sets which each have irreducible components of the same dimension. At the core of this algorithm, we combine ideas from the theory of triangular sets, a.k.a. regular chains, with Gr\"obner bases to encode and work with locally closed algebraic sets. Equipped with this, our algorithm avoids projections of the algebraic sets that are decomposed and certain genericity assumptions frequently made when decomposing polynomial systems, such as assumptions about Noether position. This makes it produce fine decompositions on more structured systems where ensuring genericity assumptions often destroys the structure of the system at hand. Practical experiments demonstrate its efficiency compared to state-of-the-art implementations.
Simulation-based inference (SBI) methods such as approximate Bayesian computation (ABC), synthetic likelihood, and neural posterior estimation (NPE) rely on simulating statistics to infer parameters of intractable likelihood models. However, such methods are known to yield untrustworthy and misleading inference outcomes under model misspecification, thus hindering their widespread applicability. In this work, we propose the first general approach to handle model misspecification that works across different classes of SBI methods. Leveraging the fact that the choice of statistics determines the degree of misspecification in SBI, we introduce a regularized loss function that penalises those statistics that increase the mismatch between the data and the model. Taking NPE and ABC as use cases, we demonstrate the superior performance of our method on high-dimensional time-series models that are artificially misspecified. We also apply our method to real data from the field of radio propagation where the model is known to be misspecified. We show empirically that the method yields robust inference in misspecified scenarios, whilst still being accurate when the model is well-specified.
In this letter, we introduce a new approach to quantify the closeness of symbolic sequences and test it in the framework of the authorship attribution problem. The method, based on a recently discovered urn representation of the Pitman-Yor process, is highly accurate compared to other state-of-the-art methods, featuring a substantial gain in computational efficiency and theoretical transparency. Our work establishes a clear connection between urn models critical in interpreting innovation processes and nonparametric Bayesian inference. It opens the way to design more efficient inference methods in the presence of complex correlation patterns and non-stationary dynamics.
Estimation of signal-to-noise ratios and residual variances in high-dimensional linear models has various important applications including, e.g. heritability estimation in bioinformatics. One commonly used estimator, usually referred to as REML, is based on the likelihood of the random effects model, in which both the regression coefficients and the noise variables are respectively assumed to be i.i.d Gaussian random variables. In this paper, we aim to establish the consistency and asymptotic distribution of the REML estimator for the SNR, when the actual coefficient vector is fixed, and the actual noise is heteroscedastic and correlated, at the cost of assuming the entries of the design matrix are independent and skew-free. The asymptotic variance can be also consistently estimated when the noise is heteroscedastic but uncorrelated. Extensive numerical simulations illustrate our theoretical findings and also suggest some assumptions imposed in our theoretical results are likely relaxable.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.
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