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Elimination of unknowns in a system of differential equations is often required when analysing (possibly nonlinear) dynamical systems models, where only a subset of variables are observable. One such analysis, identifiability, often relies on computing input-output relations via differential algebraic elimination. Determining identifiability, a natural prerequisite for meaningful parameter estimation, is often prohibitively expensive for medium to large systems due to the computationally expensive task of elimination. We propose an algorithm that computes a description of the set of differential-algebraic relations between the input and output variables of a dynamical system model. The resulting algorithm outperforms general-purpose software for differential elimination on a set of benchmark models from literature. We use the designed elimination algorithm to build a new randomized algorithm for assessing structural identifiability of a parameter in a parametric model. A parameter is said to be identifiable if its value can be uniquely determined from input-output data assuming the absence of noise and sufficiently exciting inputs. Our new algorithm allows the identification of models that could not be tackled before. Our implementation is publicly available as a Julia package at //github.com/SciML/StructuralIdentifiability.jl.

We consider Bayesian optimization of the output of a network of functions, where each function takes as input the output of its parent nodes, and where the network takes significant time to evaluate. Such problems arise, for example, in reinforcement learning, engineering design, and manufacturing. While the standard Bayesian optimization approach observes only the final output, our approach delivers greater query efficiency by leveraging information that the former ignores: intermediate output within the network. This is achieved by modeling the nodes of the network using Gaussian processes and choosing the points to evaluate using, as our acquisition function, the expected improvement computed with respect to the implied posterior on the objective. Although the non-Gaussian nature of this posterior prevents computing our acquisition function in closed form, we show that it can be efficiently maximized via sample average approximation. In addition, we prove that our method is asymptotically consistent, meaning that it finds a globally optimal solution as the number of evaluations grows to infinity, thus generalizing previously known convergence results for the expected improvement. Notably, this holds even though our method might not evaluate the domain densely, instead leveraging problem structure to leave regions unexplored. Finally, we show that our approach dramatically outperforms standard Bayesian optimization methods in several synthetic and real-world problems.

In many practical settings control decisions must be made under partial/imperfect information about the evolution of a relevant state variable. Partially Observable Markov Decision Processes (POMDPs) is a relatively well-developed framework for modeling and analyzing such problems. In this paper we consider the structural estimation of the primitives of a POMDP model based upon the observable history of the process. We analyze the structural properties of POMDP model with random rewards and specify conditions under which the model is identifiable without knowledge of the state dynamics. We consider a soft policy gradient algorithm to compute a maximum likelihood estimator and provide a finite-time characterization of convergence to a stationary point. We illustrate the estimation methodology with an application to optimal equipment replacement. In this context, replacement decisions must be made under partial/imperfect information on the true state (i.e. condition of the equipment). We use synthetic and real data to highlight the robustness of the proposed methodology and characterize the potential for misspecification when partial state observability is ignored.

We give an exact characterization of admissibility in statistical decision problems in terms of Bayes optimality in a so-called nonstandard extension of the original decision problem, as introduced by Duanmu and Roy. Unlike the consideration of improper priors or other generalized notions of Bayes optimalitiy, the nonstandard extension is distinguished, in part, by having priors that can assign "infinitesimal" mass in a sense that can be made rigorous using results from nonstandard analysis. With these additional priors, we find that, informally speaking, a decision procedure $\delta_0$ is admissible in the original statistical decision problem if and only if, in the nonstandard extension of the problem, the nonstandard extension of $\delta_0$ is Bayes optimal among the extensions of standard decision procedures with respect to a nonstandard prior that assigns at least infinitesimal mass to every standard parameter value. We use the above theorem to give further characterizations of admissibility, one related to Blyth's method, one to a condition due to Stein which characterizes admissibility under some regularity assumptions; and finally, a characterization using finitely additive priors in decision problems meeting certain regularity requirements. Our results imply that Blyth's method is a sound and complete method for establishing admissibility. Buoyed by this result, we revisit the univariate two-sample common-mean problem, and show that the Graybill--Deal estimator is admissible among a certain class of unbiased decision procedures.

Causality can be described in terms of a structural causal model (SCM) that carries information on the variables of interest and their mechanistic relations. For most processes of interest the underlying SCM will only be partially observable, thus causal inference tries to leverage any exposed information. Graph neural networks (GNN) as universal approximators on structured input pose a viable candidate for causal learning, suggesting a tighter integration with SCM. To this effect we present a theoretical analysis from first principles that establishes a novel connection between GNN and SCM while providing an extended view on general neural-causal models. We then establish a new model class for GNN-based causal inference that is necessary and sufficient for causal effect identification. Our empirical illustration on simulations and standard benchmarks validate our theoretical proofs.

Unpaired image-to-image translation has been applied successfully to natural images but has received very little attention for manifold-valued data such as in diffusion tensor imaging (DTI). The non-Euclidean nature of DTI prevents current generative adversarial networks (GANs) from generating plausible images and has mainly limited their application to diffusion MRI scalar maps, such as fractional anisotropy (FA) or mean diffusivity (MD). Even if these scalar maps are clinically useful, they mostly ignore fiber orientations and therefore have limited applications for analyzing brain fibers. Here, we propose a manifold-aware CycleGAN that learns the generation of high-resolution DTI from unpaired T1w images. We formulate the objective as a Wasserstein distance minimization problem of data distributions on a Riemannian manifold of symmetric positive definite 3x3 matrices SPD(3), using adversarial and cycle-consistency losses. To ensure that the generated diffusion tensors lie on the SPD(3) manifold, we exploit the theoretical properties of the exponential and logarithm maps of the Log-Euclidean metric. We demonstrate that, unlike standard GANs, our method is able to generate realistic high-resolution DTI that can be used to compute diffusion-based metrics and potentially run fiber tractography algorithms. To evaluate our model's performance, we compute the cosine similarity between the generated tensors principal orientation and their ground-truth orientation, the mean squared error (MSE) of their derived FA values and the Log-Euclidean distance between the tensors. We demonstrate that our method produces 2.5 times better FA MSE than a standard CycleGAN and up to 30% better cosine similarity than a manifold-aware Wasserstein GAN while synthesizing sharp high-resolution DTI.

Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph nodes. A recent breakthrough formulates the problem as a continuous optimization with a structural constraint that ensures acyclicity (Zheng et al., 2018). The authors apply the approach to the linear structural equation model (SEM) and the least-squares loss function that are statistically well justified but nevertheless limited. Motivated by the widespread success of deep learning that is capable of capturing complex nonlinear mappings, in this work we propose a deep generative model and apply a variant of the structural constraint to learn the DAG. At the heart of the generative model is a variational autoencoder parameterized by a novel graph neural network architecture, which we coin DAG-GNN. In addition to the richer capacity, an advantage of the proposed model is that it naturally handles discrete variables as well as vector-valued ones. We demonstrate that on synthetic data sets, the proposed method learns more accurate graphs for nonlinearly generated samples; and on benchmark data sets with discrete variables, the learned graphs are reasonably close to the global optima. The code is available at \url{//github.com/fishmoon1234/DAG-GNN}.

Classification tasks are usually analysed and improved through new model architectures or hyperparameter optimisation but the underlying properties of datasets are discovered on an ad-hoc basis as errors occur. However, understanding the properties of the data is crucial in perfecting models. In this paper we analyse exactly which characteristics of a dataset best determine how difficult that dataset is for the task of text classification. We then propose an intuitive measure of difficulty for text classification datasets which is simple and fast to calculate. We show that this measure generalises to unseen data by comparing it to state-of-the-art datasets and results. This measure can be used to analyse the precise source of errors in a dataset and allows fast estimation of how difficult a dataset is to learn. We searched for this measure by training 12 classical and neural network based models on 78 real-world datasets, then use a genetic algorithm to discover the best measure of difficulty. Our difficulty-calculating code ( //github.com/Wluper/edm ) and datasets ( //data.wluper.com ) are publicly available.

Deep structured models are widely used for tasks like semantic segmentation, where explicit correlations between variables provide important prior information which generally helps to reduce the data needs of deep nets. However, current deep structured models are restricted by oftentimes very local neighborhood structure, which cannot be increased for computational complexity reasons, and by the fact that the output configuration, or a representation thereof, cannot be transformed further. Very recent approaches which address those issues include graphical model inference inside deep nets so as to permit subsequent non-linear output space transformations. However, optimization of those formulations is challenging and not well understood. Here, we develop a novel model which generalizes existing approaches, such as structured prediction energy networks, and discuss a formulation which maintains applicability of existing inference techniques.

Developing classification algorithms that are fair with respect to sensitive attributes of the data has become an important problem due to the growing deployment of classification algorithms in various social contexts. Several recent works have focused on fairness with respect to a specific metric, modeled the corresponding fair classification problem as a constrained optimization problem, and developed tailored algorithms to solve them. Despite this, there still remain important metrics for which we do not have fair classifiers and many of the aforementioned algorithms do not come with theoretical guarantees; perhaps because the resulting optimization problem is non-convex. The main contribution of this paper is a new meta-algorithm for classification that takes as input a large class of fairness constraints, with respect to multiple non-disjoint sensitive attributes, and which comes with provable guarantees. This is achieved by first developing a meta-algorithm for a large family of classification problems with convex constraints, and then showing that classification problems with general types of fairness constraints can be reduced to those in this family. We present empirical results that show that our algorithm can achieve near-perfect fairness with respect to various fairness metrics, and that the loss in accuracy due to the imposed fairness constraints is often small. Overall, this work unifies several prior works on fair classification, presents a practical algorithm with theoretical guarantees, and can handle fairness metrics that were previously not possible.