We study self-regulating processes modeling biological transportation networks as presented in \cite{portaro2023}. In particular, we focus on the 1D setting for Dirichlet and Neumann boundary conditions. We prove an existence and uniqueness result under the assumption of positivity of the diffusivity $D$. We explore systematically various scenarios and gain insights into the behavior of $D$ and its impact on the studied system. This involves analyzing the system with a signed measure distribution of sources and sinks. Finally, we perform several numerical tests in which the solution $D$ touches zero, confirming the previous hints of local existence in particular cases.
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We introduce a flexible method to simultaneously infer both the drift and volatility functions of a discretely observed scalar diffusion. We introduce spline bases to represent these functions and develop a Markov chain Monte Carlo algorithm to infer, a posteriori, the coefficients of these functions in the spline basis. A key innovation is that we use spline bases to model transformed versions of the drift and volatility functions rather than the functions themselves. The output of the algorithm is a posterior sample of plausible drift and volatility functions that are not constrained to any particular parametric family. The flexibility of this approach provides practitioners a powerful investigative tool, allowing them to posit a variety of parametric models to better capture the underlying dynamics of their processes of interest. We illustrate the versatility of our method by applying it to challenging datasets from finance, paleoclimatology, and astrophysics. In view of the parametric diffusion models widely employed in the literature for those examples, some of our results are surprising since they call into question some aspects of these models.
Many real-world processes have complex tail dependence structures that cannot be characterized using classical Gaussian processes. More flexible spatial extremes models exhibit appealing extremal dependence properties but are often exceedingly prohibitive to fit and simulate from in high dimensions. In this paper, we develop a new spatial extremes model that has flexible and non-stationary dependence properties, and we integrate it in the encoding-decoding structure of a variational autoencoder (XVAE), whose parameters are estimated via variational Bayes combined with deep learning. The XVAE can be used as a spatio-temporal emulator that characterizes the distribution of potential mechanistic model output states and produces outputs that have the same statistical properties as the inputs, especially in the tail. As an aside, our approach also provides a novel way of making fast inference with complex extreme-value processes. Through extensive simulation studies, we show that our XVAE is substantially more time-efficient than traditional Bayesian inference while also outperforming many spatial extremes models with a stationary dependence structure. To further demonstrate the computational power of the XVAE, we analyze a high-resolution satellite-derived dataset of sea surface temperature in the Red Sea, which includes 30 years of daily measurements at 16703 grid cells. We find that the extremal dependence strength is weaker in the interior of Red Sea and it has decreased slightly over time.
Gaussian processes (GPs) are popular nonparametric statistical models for learning unknown functions and quantifying the spatiotemporal uncertainty in data. Recent works have extended GPs to model scalar and vector quantities distributed over non-Euclidean domains, including smooth manifolds appearing in numerous fields such as computer vision, dynamical systems, and neuroscience. However, these approaches assume that the manifold underlying the data is known, limiting their practical utility. We introduce RVGP, a generalisation of GPs for learning vector signals over latent Riemannian manifolds. Our method uses positional encoding with eigenfunctions of the connection Laplacian, associated with the tangent bundle, readily derived from common graph-based approximation of data. We demonstrate that RVGP possesses global regularity over the manifold, which allows it to super-resolve and inpaint vector fields while preserving singularities. Furthermore, we use RVGP to reconstruct high-density neural dynamics derived from low-density EEG recordings in healthy individuals and Alzheimer's patients. We show that vector field singularities are important disease markers and that their reconstruction leads to a comparable classification accuracy of disease states to high-density recordings. Thus, our method overcomes a significant practical limitation in experimental and clinical applications.
We develop lower bounds on communication in the memory hierarchy or between processors for nested bilinear algorithms, such as Strassen's algorithm for matrix multiplication. We build on a previous framework that establishes communication lower bounds by use of the rank expansion, or the minimum rank of any fixed size subset of columns of a matrix, for each of the three matrices encoding a bilinear algorithm. This framework provides lower bounds for a class of dependency directed acyclic graphs (DAGs) corresponding to the execution of a given bilinear algorithm, in contrast to other approaches that yield bounds for specific DAGs. However, our lower bounds only apply to executions that do not compute the same DAG node multiple times. Two bilinear algorithms can be nested by taking Kronecker products between their encoding matrices. Our main result is a lower bound on the rank expansion of a matrix constructed by a Kronecker product derived from lower bounds on the rank expansion of the Kronecker product's operands. We apply the rank expansion lower bounds to obtain novel communication lower bounds for nested Toom-Cook convolution, Strassen's algorithm, and fast algorithms for contraction of partially symmetric tensors.
Langevin dynamics are widely used in sampling high-dimensional, non-Gaussian distributions whose densities are known up to a normalizing constant. In particular, there is strong interest in unadjusted Langevin algorithms (ULA), which directly discretize Langevin dynamics to estimate expectations over the target distribution. We study the use of transport maps that approximately normalize a target distribution as a way to precondition and accelerate the convergence of Langevin dynamics. We show that in continuous time, when a transport map is applied to Langevin dynamics, the result is a Riemannian manifold Langevin dynamics (RMLD) with metric defined by the transport map. We also show that applying a transport map to an irreversibly-perturbed ULA results in a geometry-informed irreversible perturbation (GiIrr) of the original dynamics. These connections suggest more systematic ways of learning metrics and perturbations, and also yield alternative discretizations of the RMLD described by the map, which we study. Under appropriate conditions, these discretized processes can be endowed with non-asymptotic bounds describing convergence to the target distribution in 2-Wasserstein distance. Illustrative numerical results complement our theoretical claims.
Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how weakly supervised and self-supervised deep learning approaches scale when training larger models on larger datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised models. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 95-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised models at inferring known biological relationships curated from public databases.
We show how quantum-inspired 2d tensor networks can be used to efficiently and accurately simulate the largest quantum processors from IBM, namely Eagle (127 qubits), Osprey (433 qubits) and Condor (1121 qubits). We simulate the dynamics of a complex quantum many-body system -- specifically, the kicked Ising experiment considered recently by IBM in Nature 618, p. 500-505 (2023) -- using graph-based Projected Entangled Pair States (gPEPS), which was proposed by some of us in PRB 99, 195105 (2019). Our results show that simple tensor updates are already sufficient to achieve very large unprecedented accuracy with remarkably low computational resources for this model. Apart from simulating the original experiment for 127 qubits, we also extend our results to 433 and 1121 qubits, thus setting a benchmark for the newest IBM quantum machines. We also report accurate simulations for infinitely-many qubits. Our results show that gPEPS are a natural tool to efficiently simulate quantum computers with an underlying lattice-based qubit connectivity, such as all quantum processors based on superconducting qubits.
Effective application of mathematical models to interpret biological data and make accurate predictions often requires that model parameters are identifiable. Approaches to assess the so-called structural identifiability of models are well-established for ordinary differential equation models, yet there are no commonly adopted approaches that can be applied to assess the structural identifiability of the partial differential equation (PDE) models that are requisite to capture spatial features inherent to many phenomena. The differential algebra approach to structural identifiability has recently been demonstrated to be applicable to several specific PDE models. In this brief article, we present general methodology for performing structural identifiability analysis on partially observed linear reaction-advection-diffusion (RAD) PDE models. We show that the differential algebra approach can always, in theory, be applied to linear RAD models. Moreover, despite the perceived complexity introduced by the addition of advection and diffusion terms, identifiability of spatial analogues of non-spatial models cannot decrease structural identifiability. Finally, we show that our approach can also be applied to a class of non-linear PDE models that are linear in the unobserved variables, and conclude by discussing future possibilities and computational cost of performing structural identifiability analysis on more general PDE models in mathematical biology.
We study the multivariate deconvolution problem of recovering the distribution of a signal from independent and identically distributed observations additively contaminated with random errors (noise) from a known distribution. For errors with independent coordinates having ordinary smooth densities, we derive an inversion inequality relating the $L^1$-Wasserstein distance between two distributions of the signal to the $L^1$-distance between the corresponding mixture densities of the observations. This smoothing inequality outperforms existing inversion inequalities. As an application of the inversion inequality to the Bayesian framework, we consider $1$-Wasserstein deconvolution with Laplace noise in dimension one using a Dirichlet process mixture of normal densities as a prior measure on the mixing distribution (or distribution of the signal). We construct an adaptive approximation of the sampling density by convolving the Laplace density with a well-chosen mixture of normal densities and show that the posterior measure concentrates around the sampling density at a nearly minimax rate, up to a log-factor, in the $L^1$-distance. The same posterior law is also shown to automatically adapt to the unknown Sobolev regularity of the mixing density, thus leading to a new Bayesian adaptive estimation procedure for mixing distributions with regular densities under the $L^1$-Wasserstein metric. We illustrate utility of the inversion inequality also in a frequentist setting by showing that an appropriate isotone approximation of the classical kernel deconvolution estimator attains the minimax rate of convergence for $1$-Wasserstein deconvolution in any dimension $d\geq 1$, when only a tail condition is required on the latent mixing density and we derive sharp lower bounds for these problems
Optimal transport (OT) offers a versatile framework to compare complex data distributions in a geometrically meaningful way. Traditional methods for computing the Wasserstein distance and geodesic between probability measures require mesh-dependent domain discretization and suffer from the curse-of-dimensionality. We present GeONet, a mesh-invariant deep neural operator network that learns the non-linear mapping from the input pair of initial and terminal distributions to the Wasserstein geodesic connecting the two endpoint distributions. In the offline training stage, GeONet learns the saddle point optimality conditions for the dynamic formulation of the OT problem in the primal and dual spaces that are characterized by a coupled PDE system. The subsequent inference stage is instantaneous and can be deployed for real-time predictions in the online learning setting. We demonstrate that GeONet achieves comparable testing accuracy to the standard OT solvers on simulation examples and the MNIST dataset with considerably reduced inference-stage computational cost by orders of magnitude.
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