In this paper, we study the data-dependent convergence and generalization behavior of gradient methods for neural networks with smooth activation. Our first result is a novel bound on the excess risk of deep networks trained by the logistic loss, via an alogirthmic stability analysis. Compared to previous works, our results improve upon the shortcomings of the well-established Rademacher complexity-based bounds. Importantly, the bounds we derive in this paper are tighter, hold even for neural networks of small width, do not scale unfavorably with width, are algorithm-dependent, and consequently capture the role of initialization on the sample complexity of gradient descent for deep nets. Specialized to noiseless data separable with margin $\gamma$ by neural tangent kernel (NTK) features of a network of width $\Omega(\text{poly}(\log(n)))$, we show the test-error rate to be $e^{O(L)}/{\gamma^2 n}$, where $n$ is the training set size and $L$ denotes the number of hidden layers. This is an improvement in the test loss bound compared to previous works while maintaining the poly-logarithmic width conditions. We further investigate excess risk bounds for deep nets trained with noisy data, establishing that under a polynomial condition on the network width, gradient descent can achieve the optimal excess risk. Finally, we show that a large step-size significantly improves upon the NTK regime's results in classifying the XOR distribution. In particular, we show for a one-hidden-layer neural network of constant width $m$ with quadratic activation and standard Gaussian initialization that mini-batch SGD with linear sample complexity and with a large step-size $\eta=m$ reaches the perfect test accuracy after only $\ceil{\log(d)}$ iterations, where $d$ is the data dimension.

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

Medical image reconstruction with pre-trained score-based generative models (SGMs) has advantages over other existing state-of-the-art deep-learned reconstruction methods, including improved resilience to different scanner setups and advanced image distribution modeling. SGM-based reconstruction has recently been applied to simulated positron emission tomography (PET) datasets, showing improved contrast recovery for out-of-distribution lesions relative to the state-of-the-art. However, existing methods for SGM-based reconstruction from PET data suffer from slow reconstruction, burdensome hyperparameter tuning and slice inconsistency effects (in 3D). In this work, we propose a practical methodology for fully 3D reconstruction that accelerates reconstruction and reduces the number of critical hyperparameters by matching the likelihood of an SGM's reverse diffusion process to a current iterate of the maximum-likelihood expectation maximization algorithm. Using the example of low-count reconstruction from simulated $[^{18}$F]DPA-714 datasets, we show our methodology can match or improve on the NRMSE and SSIM of existing state-of-the-art SGM-based PET reconstruction while reducing reconstruction time and the need for hyperparameter tuning. We evaluate our methodology against state-of-the-art supervised and conventional reconstruction algorithms. Finally, we demonstrate a first-ever implementation of SGM-based reconstruction for real 3D PET data, specifically $[^{18}$F]DPA-714 data, where we integrate perpendicular pre-trained SGMs to eliminate slice inconsistency issues.

Multiphysics simulation, which models the interactions between multiple physical processes, and multi-component simulation of complex structures are critical in fields like nuclear and aerospace engineering. Previous studies often rely on numerical solvers or machine learning-based surrogate models to solve or accelerate these simulations. However, multiphysics simulations typically require integrating multiple specialized solvers-each responsible for evolving a specific physical process-into a coupled program, which introduces significant development challenges. Furthermore, no universal algorithm exists for multi-component simulations, which adds to the complexity. Here we propose compositional Multiphysics and Multi-component Simulation with Diffusion models (MultiSimDiff) to overcome these challenges. During diffusion-based training, MultiSimDiff learns energy functions modeling the conditional probability of one physical process/component conditioned on other processes/components. In inference, MultiSimDiff generates coupled multiphysics solutions and multi-component structures by sampling from the joint probability distribution, achieved by composing the learned energy functions in a structured way. We test our method in three tasks. In the reaction-diffusion and nuclear thermal coupling problems, MultiSimDiff successfully predicts the coupling solution using decoupled data, while the surrogate model fails in the more complex second problem. For the thermal and mechanical analysis of the prismatic fuel element, MultiSimDiff trained for single component prediction accurately predicts a larger structure with 64 components, reducing the relative error by 40.3% compared to the surrogate model.

A central goal of machine learning is generalization. While the No Free Lunch Theorem states that we cannot obtain theoretical guarantees for generalization without further assumptions, in practice we observe that simple models which explain the training data generalize best: a principle called Occam's razor. Despite the need for simple models, most current approaches in machine learning only minimize the training error, and at best indirectly promote simplicity through regularization or architecture design. Here, we draw a connection between Occam's razor and in-context learning: an emergent ability of certain sequence models like Transformers to learn at inference time from past observations in a sequence. In particular, we show that the next-token prediction loss used to train in-context learners is directly equivalent to a data compression technique called prequential coding, and that minimizing this loss amounts to jointly minimizing both the training error and the complexity of the model that was implicitly learned from context. Our theory and the empirical experiments we use to support it not only provide a normative account of in-context learning, but also elucidate the shortcomings of current in-context learning methods, suggesting ways in which they can be improved. We make our code available at https://github.com/3rdCore/PrequentialCode.

Recently, there has been an increasing interest in performing post-hoc uncertainty estimation about the predictions of pre-trained deep neural networks (DNNs). Given a pre-trained DNN via back-propagation, these methods enhance the original network by adding output confidence measures, such as error bars, without compromising its initial accuracy. In this context, we introduce a novel family of sparse variational Gaussian processes (GPs), where the posterior mean is fixed to any continuous function when using a universal kernel. Specifically, we fix the mean of this GP to the output of the pre-trained DNN, allowing our approach to effectively fit the GP's predictive variances to estimate the DNN prediction uncertainty. Our approach leverages variational inference (VI) for efficient stochastic optimization, with training costs that remain independent of the number of training points, scaling efficiently to large datasets such as ImageNet. The proposed method, called fixed mean GP (FMGP), is architecture-agnostic, relying solely on the pre-trained model's outputs to adjust the predictive variances. Experimental results demonstrate that FMGP improves both uncertainty estimation and computational efficiency when compared to state-of-the-art methods.

Logistic regression is a classical model for describing the probabilistic dependence of binary responses to multivariate covariates. We consider the predictive performance of the maximum likelihood estimator (MLE) for logistic regression, assessed in terms of logistic risk. We consider two questions: first, that of the existence of the MLE (which occurs when the dataset is not linearly separated), and second that of its accuracy when it exists. These properties depend on both the dimension of covariates and on the signal strength. In the case of Gaussian covariates and a well-specified logistic model, we obtain sharp non-asymptotic guarantees for the existence and excess logistic risk of the MLE. We then generalize these results in two ways: first, to non-Gaussian covariates satisfying a certain two-dimensional margin condition, and second to the general case of statistical learning with a possibly misspecified logistic model. Finally, we consider the case of a Bernoulli design, where the behavior of the MLE is highly sensitive to the parameter direction.

Dynamic Mode Decomposition (DMD) has received increasing research attention due to its capability to analyze and model complex dynamical systems. However, it faces challenges in computational efficiency, noise sensitivity, and difficulty adhering to physical laws, which negatively affect its performance. Addressing these issues, we present Online Physics-informed DMD (OPIDMD), a novel adaptation of DMD into a convex optimization framework. This approach not only ensures convergence to a unique global optimum, but also enhances the efficiency and accuracy of modeling dynamical systems in an online setting. Leveraging the Bayesian DMD framework, we propose a probabilistic interpretation of Physics-informed DMD (piDMD), examining the impact of physical constraints on the DMD linear operator. Further, we implement online proximal gradient descent and formulate specific algorithms to tackle problems with different physical constraints, enabling real-time solutions across various scenarios. Compared with existing algorithms such as Exact DMD, Online DMD, and piDMD, OPIDMD achieves the best prediction performance in short-term forecasting, e.g. an $R^2$ value of 0.991 for noisy Lorenz system. The proposed method employs a time-varying linear operator, offering a promising solution for the real-time simulation and control of complex dynamical systems.

Particle-based Bayesian inference methods by sampling from a partition-free target (posterior) distribution, e.g., Stein variational gradient descent (SVGD), have attracted significant attention. We propose a path-guided particle-based sampling~(PGPS) method based on a novel Log-weighted Shrinkage (LwS) density path linking an initial distribution to the target distribution. We propose to utilize a Neural network to learn a vector field motivated by the Fokker-Planck equation of the designed density path. Particles, initiated from the initial distribution, evolve according to the ordinary differential equation defined by the vector field. The distribution of these particles is guided along a density path from the initial distribution to the target distribution. The proposed LwS density path allows for an efficient search of modes of the target distribution while canonical methods fail. We theoretically analyze the Wasserstein distance of the distribution of the PGPS-generated samples and the target distribution due to approximation and discretization errors. Practically, the proposed PGPS-LwS method demonstrates higher Bayesian inference accuracy and better calibration ability in experiments conducted on both synthetic and real-world Bayesian learning tasks, compared to baselines, such as SVGD and Langevin dynamics, etc.

Relying on the representation power of neural networks, most recent works have often neglected several factors involved in haze degradation, such as transmission (the amount of light reaching an observer from a scene over distance) and atmospheric light. These factors are generally unknown, making dehazing problems ill-posed and creating inherent uncertainties. To account for such uncertainties and factors involved in haze degradation, we introduce a variational Bayesian framework for single image dehazing. We propose to take not only a clean image and but also transmission map as latent variables, the posterior distributions of which are parameterized by corresponding neural networks: dehazing and transmission networks, respectively. Based on a physical model for haze degradation, our variational Bayesian framework leads to a new objective function that encourages the cooperation between them, facilitating the joint training of and thereby boosting the performance of each other. In our framework, a dehazing network can estimate a clean image independently of a transmission map estimation during inference, introducing no overhead. Furthermore, our model-agnostic framework can be seamlessly incorporated with other existing dehazing networks, greatly enhancing the performance consistently across datasets and models.