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We import the algebro-geometric notion of a complete collineation into the study of maximum likelihood estimation in directed Gaussian graphical models. A complete collineation produces a perturbation of sample data, which we call a stabilisation of the sample. While a maximum likelihood estimate (MLE) may not exist or be unique given sample data, it is always unique given a stabilisation. We relate the MLE given a stabilisation to the MLE given original sample data, when one exists, providing necessary and sufficient conditions for the MLE given a stabilisation to be one given the original sample. For linear regression models, we show that the MLE given any stabilisation is the minimal norm choice among the MLEs given an original sample. We show that the MLE has a well-defined limit as the stabilisation of a sample tends to the original sample, and that the limit is an MLE given the original sample, when one exists. Finally, we study which MLEs given a sample can arise as such limits. We reduce this to a question regarding the non-emptiness of certain algebraic varieties.

Batch effects are pervasive in biomedical studies. One approach to address the batch effects is repeatedly measuring a subset of samples in each batch. These remeasured samples are used to estimate and correct the batch effects. However, rigorous statistical methods for batch effect correction with remeasured samples are severely under-developed. In this study, we developed a framework for batch effect correction using remeasured samples in highly confounded case-control studies. We provided theoretical analyses of the proposed procedure, evaluated its power characteristics, and provided a power calculation tool to aid in the study design. We found that the number of samples that need to be remeasured depends strongly on the between-batch correlation. When the correlation is high, remeasuring a small subset of samples is possible to rescue most of the power.

The meteoric rise in the adoption of deep neural networks as computational models of vision has inspired efforts to "align" these models with humans. One dimension of interest for alignment includes behavioral choices, but moving beyond characterizing choice patterns to capturing temporal aspects of visual decision-making has been challenging. Here, we sketch a general-purpose methodology to construct computational accounts of reaction times from a stimulus-computable, task-optimized model. Specifically, we introduce a novel metric leveraging insights from subjective logic theory summarizing evidence accumulation in recurrent vision models. We demonstrate that our metric aligns with patterns of human reaction times for stimulus manipulations across four disparate visual decision-making tasks spanning perceptual grouping, mental simulation, and scene categorization. This work paves the way for exploring the temporal alignment of model and human visual strategies in the context of various other cognitive tasks toward generating testable hypotheses for neuroscience. Links to the code and data can be found on the project page: //serre-lab.github.io/rnn_rts_site.

We consider the efficient estimation of total causal effects in the presence of unmeasured confounding using conditional instrumental sets. Specifically, we consider the two-stage least squares estimator in the setting of a linear structural equation model with correlated errors that is compatible with a known acyclic directed mixed graph. To set the stage for our results, we characterize the class of linearly valid conditional instrumental sets that yield consistent two-stage least squares estimators for the target total effect and derive a new asymptotic variance formula for these estimators. Equipped with these results, we provide three graphical tools for selecting more efficient linearly valid conditional instrumental sets. First, a graphical criterion that for certain pairs of linearly valid conditional instrumental sets identifies which of the two corresponding estimators has the smaller asymptotic variance. Second, an algorithm that greedily adds covariates that reduce the asymptotic variance to a given linearly valid conditional instrumental set. Third, a linearly valid conditional instrumental set for which the corresponding estimator has the smallest asymptotic variance that can be ensured with a graphical criterion.

Thanks to the singularity of the solution of linear subdiffusion problems, most time-stepping methods on uniform meshes can result in $O(\tau)$ accuracy where $\tau$ denotes the time step. The present work aims to discover the reason why some type of Crank-Nicolson schemes (the averaging Crank-Nicolson scheme) for the subdiffusion can only yield $O(\tau^\alpha)$$(\alpha<1)$ accuracy, which is much lower than the desired. The existing well developed error analysis for the subdiffusion, which has been successfully applied to many time-stepping methods such as the fractional BDF-$p (1\leq p\leq 6)$, all requires singular points be out of the path of contour integrals involved. The averaging Crank-Nicolson scheme in this work is quite natural but fails to meet this requirement. By resorting to the residue theorem, some novel sharp error analysis is developed in this study, upon which correction methods are further designed to obtain the optimal $O(\tau^2)$ accuracy. All results are verified by numerical tests.

Quantum computing has recently emerged as a transformative technology. Yet, its promised advantages rely on efficiently translating quantum operations into viable physical realizations. In this work, we use generative machine learning models, specifically denoising diffusion models (DMs), to facilitate this transformation. Leveraging text-conditioning, we steer the model to produce desired quantum operations within gate-based quantum circuits. Notably, DMs allow to sidestep during training the exponential overhead inherent in the classical simulation of quantum dynamics -- a consistent bottleneck in preceding ML techniques. We demonstrate the model's capabilities across two tasks: entanglement generation and unitary compilation. The model excels at generating new circuits and supports typical DM extensions such as masking and editing to, for instance, align the circuit generation to the constraints of the targeted quantum device. Given their flexibility and generalization abilities, we envision DMs as pivotal in quantum circuit synthesis, enhancing both practical applications but also insights into theoretical quantum computation.

We establish conditions under which latent causal graphs are nonparametrically identifiable and can be reconstructed from unknown interventions in the latent space. Our primary focus is the identification of the latent structure in measurement models without parametric assumptions such as linearity or Gaussianity. Moreover, we do not assume the number of hidden variables is known, and we show that at most one unknown intervention per hidden variable is needed. This extends a recent line of work on learning causal representations from observations and interventions. The proofs are constructive and introduce two new graphical concepts -- imaginary subsets and isolated edges -- that may be useful in their own right. As a matter of independent interest, the proofs also involve a novel characterization of the limits of edge orientations within the equivalence class of DAGs induced by unknown interventions. These are the first results to characterize the conditions under which causal representations are identifiable without making any parametric assumptions in a general setting with unknown interventions and without faithfulness.

This paper investigates the multiple testing problem for high-dimensional sparse binary sequences, motivated by the crowdsourcing problem in machine learning. We study the empirical Bayes approach for multiple testing on the high-dimensional Bernoulli model with a conjugate spike and uniform slab prior. We first show that the hard thresholding rule deduced from the posterior distribution is suboptimal. Consequently, the $\ell$-value procedure constructed using this posterior tends to be overly conservative in estimating the false discovery rate (FDR). We then propose two new procedures based on $\adj\ell$-values and $q$-values to correct this issue. Sharp frequentist theoretical results are obtained, demonstrating that both procedures can effectively control the FDR under sparsity. Numerical experiments are conducted to validate our theory in finite samples. To our best knowledge, this work provides the first uniform FDR control result in multiple testing for high-dimensional sparse binary data.

To improve the predictability of complex computational models in the experimentally-unknown domains, we propose a Bayesian statistical machine learning framework utilizing the Dirichlet distribution that combines results of several imperfect models. This framework can be viewed as an extension of Bayesian stacking. To illustrate the method, we study the ability of Bayesian model averaging and mixing techniques to mine nuclear masses. We show that the global and local mixtures of models reach excellent performance on both prediction accuracy and uncertainty quantification and are preferable to classical Bayesian model averaging. Additionally, our statistical analysis indicates that improving model predictions through mixing rather than mixing of corrected models leads to more robust extrapolations.

Palimpsests refer to historical manuscripts where erased writings have been partially covered by the superimposition of a second writing. By employing imaging techniques, e.g., multispectral imaging, it becomes possible to identify features that are imperceptible to the naked eye, including faded and erased inks. When dealing with overlapping inks, Artificial Intelligence techniques can be utilized to disentangle complex nodes of overlapping letters. In this work, we propose deep learning-based semantic segmentation as a method for identifying and segmenting individual letters in overlapping characters. The experiment was conceived as a proof of concept, focusing on the palimpsests of the Ars Grammatica by Prisciano as a case study. Furthermore, caveats and prospects of our approach combined with multispectral imaging are also discussed.