Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular localization tools to study molecular structure at the nanoscale level in the intact cell, bridging the mesoscale gap to classical structural biology methodologies. Analysis of super-resolution data by artificial intelligence (AI), such as machine learning, offers tremendous potential for discovery of new biology, that, by definition, is not known and lacks ground truth. Herein, we describe the application of weakly supervised paradigms to super-resolution microscopy and its potential to enable the accelerated exploration of the nanoscale architecture of subcellular macromolecules and organelles.
The influence of natural image transformations on receptive field responses is crucial for modelling visual operations in computer vision and biological vision. In this regard, covariance properties with respect to geometric image transformations in the earliest layers of the visual hierarchy are essential for expressing robust image operations, and for formulating invariant visual operations at higher levels. This paper defines and proves a set of joint covariance properties for spatio-temporal receptive fields in terms of spatio-temporal derivative operators applied to spatio-temporally smoothed image data under compositions of spatial scaling transformations, spatial affine transformations, Galilean transformations and temporal scaling transformations. Specifically, the derived relations show how the parameters of the receptive fields need to be transformed, in order to match the output from spatio-temporal receptive fields under composed spatio-temporal image transformations. For this purpose, we also fundamentally extend the notion of scale-normalized derivatives to affine-normalized derivatives, that are computed based on spatial smoothing with affine Gaussian kernels, and analyze the covariance properties of the resulting affine-normalized derivatives for the affine group as well as for important subgroups thereof. We conclude with a geometric analysis, showing how the derived joint covariance properties make it possible to relate or match spatio-temporal receptive field responses, when observing, possibly moving, local surface patches from different views, under locally linearized perspective or projective transformations, as well as when observing different instances of spatio-temporal events, that may occur either faster or slower between different views of similar spatio-temporal events.
This study devised a physics-informed neural network (PINN) framework to solve the wave equation for acoustic resonance analysis. The proposed analytical model, ResoNet, minimizes the loss function for periodic solutions and conventional PINN loss functions, thereby effectively using the function approximation capability of neural networks while performing resonance analysis. Additionally, it can be easily applied to inverse problems. The resonance in a one-dimensional acoustic tube, and the effectiveness of the proposed method was validated through the forward and inverse analyses of the wave equation with energy-loss terms. In the forward analysis, the applicability of PINN to the resonance problem was evaluated via comparison with the finite-difference method. The inverse analysis, which included identifying the energy loss term in the wave equation and design optimization of the acoustic tube, was performed with good accuracy.
We discuss a connection between a generative model, called the diffusion model, and nonequilibrium thermodynamics for the Fokker-Planck equation, called stochastic thermodynamics. Based on the techniques of stochastic thermodynamics, we derive the speed-accuracy trade-off for the diffusion models, which is a trade-off relationship between the speed and accuracy of data generation in diffusion models. Our result implies that the entropy production rate in the forward process affects the errors in data generation. From a stochastic thermodynamic perspective, our results provide quantitative insight into how best to generate data in diffusion models. The optimal learning protocol is introduced by the conservative force in stochastic thermodynamics and the geodesic of space by the 2-Wasserstein distance in optimal transport theory. We numerically illustrate the validity of the speed-accuracy trade-off for the diffusion models with different noise schedules such as the cosine schedule, the conditional optimal transport, and the optimal transport.
We investigate a Tikhonov regularization scheme specifically tailored for shallow neural networks within the context of solving a classic inverse problem: approximating an unknown function and its derivatives within a unit cubic domain based on noisy measurements. The proposed Tikhonov regularization scheme incorporates a penalty term that takes three distinct yet intricately related network (semi)norms: the extended Barron norm, the variation norm, and the Radon-BV seminorm. These choices of the penalty term are contingent upon the specific architecture of the neural network being utilized. We establish the connection between various network norms and particularly trace the dependence of the dimensionality index, aiming to deepen our understanding of how these norms interplay with each other. We revisit the universality of function approximation through various norms, establish rigorous error-bound analysis for the Tikhonov regularization scheme, and explicitly elucidate the dependency of the dimensionality index, providing a clearer understanding of how the dimensionality affects the approximation performance and how one designs a neural network with diverse approximating tasks.
We discuss a connection between a generative model, called the diffusion model, and nonequilibrium thermodynamics for the Fokker-Planck equation, called stochastic thermodynamics. Based on the techniques of stochastic thermodynamics, we derive the speed-accuracy trade-off for the diffusion models, which is a trade-off relationship between the speed and accuracy of data generation in diffusion models. Our result implies that the entropy production rate in the forward process affects the errors in data generation. From a stochastic thermodynamic perspective, our results provide quantitative insight into how best to generate data in diffusion models. The optimal learning protocol is introduced by the conservative force in stochastic thermodynamics and the geodesic of space by the 2-Wasserstein distance in optimal transport theory. We numerically illustrate the validity of the speed-accuracy trade-off for the diffusion models with different noise schedules such as the cosine schedule, the conditional optimal transport, and the optimal transport.
We propose an extremely versatile approach to address a large family of matrix nearness problems, possibly with additional linear constraints. Our method is based on splitting a matrix nearness problem into two nested optimization problems, of which the inner one can be solved either exactly or cheaply, while the outer one can be recast as an unconstrained optimization task over a smooth real Riemannian manifold. We observe that this paradigm applies to many matrix nearness problems of practical interest appearing in the literature, thus revealing that they are equivalent in this sense to a Riemannian optimization problem. We also show that the objective function to be minimized on the Riemannian manifold can be discontinuous, thus requiring regularization techniques, and we give conditions for this to happen. Finally, we demonstrate the practical applicability of our method by implementing it for a number of matrix nearness problems that are relevant for applications and are currently considered very demanding in practice. Extensive numerical experiments demonstrate that our method often greatly outperforms its predecessors, including algorithms specifically designed for those particular problems.
We study the large-width asymptotics of random fully connected neural networks with weights drawn from $\alpha$-stable distributions, a family of heavy-tailed distributions arising as the limiting distributions in the Gnedenko-Kolmogorov heavy-tailed central limit theorem. We show that in an arbitrary bounded Euclidean domain $\mathcal{U}$ with smooth boundary, the random field at the infinite-width limit, characterized in previous literature in terms of finite-dimensional distributions, has sample functions in the fractional Sobolev-Slobodeckij-type quasi-Banach function space $W^{s,p}(\mathcal{U})$ for integrability indices $p < \alpha$ and suitable smoothness indices $s$ depending on the activation function of the neural network, and establish the functional convergence of the processes in $\mathcal{P}(W^{s,p}(\mathcal{U}))$. This convergence result is leveraged in the study of functional posteriors for edge-preserving Bayesian inverse problems with stable neural network priors.
Homogenisation empowers the efficient macroscale system level prediction of physical problems with intricate microscale structures. Here we develop an innovative powerful, rigorous and flexible framework for asymptotic homogenisation of dynamics at the finite scale separation of real physics, with proven results underpinned by modern dynamical systems theory. The novel systematic approach removes most of the usual assumptions, whether implicit or explicit, of other methodologies. By no longer assuming averages the methodology constructs so-called multi-continuum or micromorphic homogenisations systematically based upon the microscale physics. The developed framework and approach enables a user to straightforwardly choose and create such homogenisations with clear physical and theoretical support, and of highly controllable accuracy and fidelity.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.