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The Poisson-Nernst-Planck (PNP) equations are one of the most effective model for describing electrostatic interactions and diffusion processes in ion solution systems, and have been widely used in the numerical simulations of biological ion channels, semiconductor devices, and nanopore systems. Due to the characteristics of strong coupling, convection dominance, nonlinearity and multiscale, the classic Gummel iteration for the nonlinear discrete system of PNP equations converges slowly or even diverges. We focus on fast algorithms of nonlinear discrete system for the general PNP equations, which have better adaptability, friendliness and efficiency than the Gummel iteration. First, a geometric full approximation storage (FAS) algorithm is proposed to improve the slow convergence speed of the Gummel iteration. Second, an algebraic FAS algorithm is designed, which does not require multi-level geometric information and is more suitable for practical computation compared with the geometric one. Finally, improved algorithms based on the acceleration technique and adaptive method are proposed to solve the problems of excessive coarse grid iterations and insufficient adaptability to the size of computational domain in the algebraic FAS algorithm. The numerical experiments are shown for the geometric, algebraic FAS and improved algorithms respectively to illustrate the effiency of the algorithms.

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Most mathematical distortions used in ML are fundamentally integral in nature: $f$-divergences, Bregman divergences, (regularized) optimal transport distances, integral probability metrics, geodesic distances, etc. In this paper, we unveil a grounded theory and tools which can help improve these distortions to better cope with ML requirements. We start with a generalization of Riemann integration that also encapsulates functions that are not strictly additive but are, more generally, $t$-additive, as in nonextensive statistical mechanics. Notably, this recovers Volterra's product integral as a special case. We then generalize the Fundamental Theorem of calculus using an extension of the (Euclidean) derivative. This, along with a series of more specific Theorems, serves as a basis for results showing how one can specifically design, alter, or change fundamental properties of distortion measures in a simple way, with a special emphasis on geometric- and ML-related properties that are the metricity, hyperbolicity, and encoding. We show how to apply it to a problem that has recently gained traction in ML: hyperbolic embeddings with a "cheap" and accurate encoding along the hyperbolic vs Euclidean scale. We unveil a new application for which the Poincar\'e disk model has very appealing features, and our theory comes in handy: \textit{model} embeddings for boosted combinations of decision trees, trained using the log-loss (trees) and logistic loss (combinations).

Inferring brain connectivity and structure \textit{in-vivo} requires accurate estimation of the orientation distribution function (ODF), which encodes key local tissue properties. However, estimating the ODF from diffusion MRI (dMRI) signals is a challenging inverse problem due to obstacles such as significant noise, high-dimensional parameter spaces, and sparse angular measurements. In this paper, we address these challenges by proposing a novel deep-learning based methodology for continuous estimation and uncertainty quantification of the spatially varying ODF field. We use a neural field (NF) to parameterize a random series representation of the latent ODFs, implicitly modeling the often ignored but valuable spatial correlation structures in the data, and thereby improving efficiency in sparse and noisy regimes. An analytic approximation to the posterior predictive distribution is derived which can be used to quantify the uncertainty in the ODF estimate at any spatial location, avoiding the need for expensive resampling-based approaches that are typically employed for this purpose. We present empirical evaluations on both synthetic and real in-vivo diffusion data, demonstrating the advantages of our method over existing approaches.

Optimal Transport (OT) problem investigates a transport map that bridges two distributions while minimizing a given cost function. In this regard, OT between tractable prior distribution and data has been utilized for generative modeling tasks. However, OT-based methods are susceptible to outliers and face optimization challenges during training. In this paper, we propose a novel generative model based on the semi-dual formulation of Unbalanced Optimal Transport (UOT). Unlike OT, UOT relaxes the hard constraint on distribution matching. This approach provides better robustness against outliers, stability during training, and faster convergence. We validate these properties empirically through experiments. Moreover, we study the theoretical upper-bound of divergence between distributions in UOT. Our model outperforms existing OT-based generative models, achieving FID scores of 2.97 on CIFAR-10 and 6.36 on CelebA-HQ-256. The code is available at \url{//github.com/Jae-Moo/UOTM}.

We conduct a systematic study of the approximation properties of Transformer for sequence modeling with long, sparse and complicated memory. We investigate the mechanisms through which different components of Transformer, such as the dot-product self-attention, positional encoding and feed-forward layer, affect its expressive power, and we study their combined effects through establishing explicit approximation rates. Our study reveals the roles of critical parameters in the Transformer, such as the number of layers and the number of attention heads, and these insights also provide natural suggestions for alternative architectures.

The Weisfeiler-Leman (WL) dimension is an established measure for the inherent descriptive complexity of graphs and relational structures. It corresponds to the number of variables that are needed and sufficient to define the object of interest in a counting version of first-order logic (FO). These bounded-variable counting logics were even candidates to capture graph isomorphism, until a celebrated construction due to Cai, F\"urer, and Immerman [Combinatorica 1992] showed that $\Omega(n)$ variables are required to distinguish all non-isomorphic $n$-vertex graphs. Still, very little is known about the precise number of variables required and sufficient to define every $n$-vertex graph. For the bounded-variable (non-counting) FO fragments, Pikhurko, Veith, and Verbitsky [Discret. Appl. Math. 2006] provided an upper bound of $\frac{n+3}{2}$ and showed that it is essentially tight. Our main result yields that, in the presence of counting quantifiers, $\frac{n}{4} + o(n)$ variables suffice. This shows that counting does allow us to save variables when defining graphs. As an application of our techniques, we also show new bounds in terms of the vertex cover number of the graph. To obtain the results, we introduce a new concept called the WL depth of a graph. We use it to analyze branching trees within the Individualization/Refinement (I/R) paradigm from the domain of isomorphism algorithms. We extend the recursive procedure from the I/R paradigm by the possibility of splitting the graphs into independent parts. Then we bound the depth of the obtained branching trees, which translates into bounds on the WL dimension and thereby on the number of variables that suffice to define the graphs.

The Gottesman-Kitaev-Preskill (GKP) code, being information theoretically near optimal for quantum communication over Gaussian thermal-loss optical channels, is likely to be the encoding of choice for advanced quantum networks of the future. Quantum repeaters based on GKP-encoded light have been shown to support high end-to-end entanglement rates across large distances despite realistic finite squeezing in GKP code preparation and homodyne detection inefficiencies. Here, we introduce a quantum switch for GKP-qubit-based quantum networks, whose architecture involves multiplexed GKP-qubit-based entanglement link generation with clients, and their all-photonic storage, together enabled by GKP-qubit graph state resources. For bipartite entanglement distribution between clients via entanglement swapping, the switch uses a multi-client generalization of a recently introduced $\textit{entanglement-ranking-based link matching}$ protocol heuristic. Since generating the GKP-qubit graph state resource is hardware intensive, given a total resource budget and an arbitrary layout of clients, we address the question of their optimal allocation towards the different client-pair connections served by the switch such that the sum throughput of the switch is maximized while also being fair in terms of the individual entanglement rates. We illustrate our results for an exemplary data center network, where the data center is a client of a switch and all of its other clients aim to connect to the data center alone -- a scenario that also captures the general case of a gateway router connecting a local area network to a global network. Together with compatible quantum repeaters, our quantum switch provides a way to realize quantum networks of arbitrary topology.

Ordinary differential equation (ODE) is an important tool to study the dynamics of a system of biological and physical processes. A central question in ODE modeling is to infer the significance of individual regulatory effect of one signal variable on another. However, building confidence band for ODE with unknown regulatory relations is challenging, and it remains largely an open question. In this article, we construct post-regularization confidence band for individual regulatory function in ODE with unknown functionals and noisy data observations. Our proposal is the first of its kind, and is built on two novel ingredients. The first is a new localized kernel learning approach that combines reproducing kernel learning with local Taylor approximation, and the second is a new de-biasing method that tackles infinite-dimensional functionals and additional measurement errors. We show that the constructed confidence band has the desired asymptotic coverage probability, and the recovered regulatory network approaches the truth with probability tending to one. We establish the theoretical properties when the number of variables in the system can be either smaller or larger than the number of sampling time points, and we study the regime-switching phenomenon. We demonstrate the efficacy of the proposed method through both simulations and illustrations with two data applications.

Most identification laws of unknown parameters of linear regression equations (LRE) ensure only boundedness of a parametric error in the presence of additive perturbations, which is almost always unacceptable for practical scenarios. In this paper, a new identification law is proposed to overcome this drawback and guarantee asymptotic convergence of the unknown parameters estimation error to zero in case the mentioned additive perturbation meets special averaging conditions. Such law is successfully applied to state reconstruction problem. Theoretical results are illustrated by numerical simulations.

Quantum annealing (QA) is a type of analog quantum computation that is a relaxed form of adiabatic quantum computation and uses quantum fluctuations in order to search for ground state solutions of a programmable Ising model. Here we present extensive experimental random number results from a D-Wave 2000Q quantum annealer, totaling over 20 billion bits of QA measurements, which is significantly larger than previous D-Wave QA random number generator studies. Current quantum annealers are susceptible to noise from environmental sources and calibration errors, and are not in general unbiased samplers. Therefore, it is of interest to quantify whether noisy quantum annealers can effectively function as an unbiased QRNG. The amount of data that was collected from the quantum annealer allows a comprehensive analysis of the random bits to be performed using the NIST SP 800-22 Rev 1a testsuite, as well as min-entropy estimates from NIST SP 800-90B. The randomness tests show that the generated random bits from the D-Wave 2000Q are biased, and not unpredictable random bit sequences. With no server-side sampling post-processing, the $1$ microsecond annealing time measurements had a min-entropy of $0.824$.

Graph Convolutional Networks (GCNs) have been widely applied in various fields due to their significant power on processing graph-structured data. Typical GCN and its variants work under a homophily assumption (i.e., nodes with same class are prone to connect to each other), while ignoring the heterophily which exists in many real-world networks (i.e., nodes with different classes tend to form edges). Existing methods deal with heterophily by mainly aggregating higher-order neighborhoods or combing the immediate representations, which leads to noise and irrelevant information in the result. But these methods did not change the propagation mechanism which works under homophily assumption (that is a fundamental part of GCNs). This makes it difficult to distinguish the representation of nodes from different classes. To address this problem, in this paper we design a novel propagation mechanism, which can automatically change the propagation and aggregation process according to homophily or heterophily between node pairs. To adaptively learn the propagation process, we introduce two measurements of homophily degree between node pairs, which is learned based on topological and attribute information, respectively. Then we incorporate the learnable homophily degree into the graph convolution framework, which is trained in an end-to-end schema, enabling it to go beyond the assumption of homophily. More importantly, we theoretically prove that our model can constrain the similarity of representations between nodes according to their homophily degree. Experiments on seven real-world datasets demonstrate that this new approach outperforms the state-of-the-art methods under heterophily or low homophily, and gains competitive performance under homophily.

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