Estimating the governing equation parameter values is essential for integrating experimental data with scientific theory to understand, validate, and predict the dynamics of complex systems. In this work, we propose a new method for structural system identification (SI), uncertainty quantification, and validation directly from data. Inspired by generative modeling frameworks, a neural network maps random noise to physically meaningful parameters. These parameters are then used in the known equation of motion to obtain fake accelerations, which are compared to real training data via a mean square error loss. To simultaneously validate the learned parameters, we use independent validation datasets. The generated accelerations from these datasets are evaluated by a discriminator network, which determines whether the output is real or fake, and guides the parameter-generator network. Analytical and real experiments show the parameter estimation accuracy and model validation for different nonlinear structural systems.

This tutorial provides a concise introduction to modern causal modeling by integrating potential outcomes and graphical methods. We motivate causal questions such as counterfactual reasoning under interventions and define binary treatments and potential outcomes. We discuss causal effect measures-including average treatment effects on the treated and on the untreated-and choices of effect scales for binary outcomes. We derive identification in randomized experiments under exchangeability and consistency, and extend to stratification and blocking designs. We present inverse probability weighting with propensity score estimation and robust inference via sandwich estimators. Finally, we introduce causal graphs, d-separation, the backdoor criterion, single-world intervention graphs, and structural equation models, showing how graphical and potential-outcome approaches complement each other. Emphasis is placed on clear notation, intuitive explanations, and practical examples for applied researchers.

We study the implicit bias of flatness / low (loss) curvature and its effects on generalization in two-layer overparameterized ReLU networks with multivariate inputs -- a problem well motivated by the minima stability and edge-of-stability phenomena in gradient-descent training. Existing work either requires interpolation or focuses only on univariate inputs. This paper presents new and somewhat surprising theoretical results for multivariate inputs. On two natural settings (1) generalization gap for flat solutions, and (2) mean-squared error (MSE) in nonparametric function estimation by stable minima, we prove upper and lower bounds, which establish that while flatness does imply generalization, the resulting rates of convergence necessarily deteriorate exponentially as the input dimension grows. This gives an exponential separation between the flat solutions vis-à-vis low-norm solutions (i.e., weight decay), which knowingly do not suffer from the curse of dimensionality. In particular, our minimax lower bound construction, based on a novel packing argument with boundary-localized ReLU neurons, reveals how flat solutions can exploit a kind of ''neural shattering'' where neurons rarely activate, but with high weight magnitudes. This leads to poor performance in high dimensions. We corroborate these theoretical findings with extensive numerical simulations. To the best of our knowledge, our analysis provides the first systematic explanation for why flat minima may fail to generalize in high dimensions.

We examine the concentration of uniform generalization errors around their expectation in binary linear classification problems via an isoperimetric argument. In particular, we establish Poincar e and log-Sobolev inequalities for the joint distribution of the output labels and the label-weighted input vectors, which we apply to derive concentration bounds. The derived concentration bounds are sharp up to moderate multiplicative constants by those under well-balanced labels. In asymptotic analysis, we also show that almost sure convergence of uniform generalization errors to their expectation occurs in very broad settings, such as proportionally high-dimensional regimes. Using this convergence, we establish uniform laws of large numbers under dimension-free conditions.

This paper introduces an active learning framework for manifold Gaussian Process (GP) regression, combining manifold learning with strategic data selection to improve accuracy in high-dimensional spaces. Our method jointly optimizes a neural network for dimensionality reduction and a Gaussian process regressor in the latent space, supervised by an active learning criterion that minimizes global prediction error. Experiments on synthetic data demonstrate superior performance over randomly sequential learning. The framework efficiently handles complex, discontinuous functions while preserving computational tractability, offering practical value for scientific and engineering applications. Future work will focus on scalability and uncertainty-aware manifold learning.

We develop sampling methods, which consist of Gaussian invariant versions of random walk Metropolis (RWM), Metropolis adjusted Langevin algorithm (MALA) and second order Hessian or Manifold MALA. Unlike standard RWM and MALA we show that Gaussian invariant sampling can lead to ergodic estimators with improved statistical efficiency. This is due to a remarkable property of Gaussian invariance that allows us to obtain exact analytical solutions to the Poisson equation for Gaussian targets. These solutions can be used to construct efficient and easy to use control variates for variance reduction of estimators under any intractable target. We demonstrate the new samplers and estimators in several examples, including high dimensional targets in latent Gaussian models where we compare against several advanced methods and obtain state-of-the-art results. We also provide theoretical results regarding geometric ergodicity, and an optimal scaling analysis that shows the dependence of the optimal acceptance rate on the Gaussianity of the target.

The advent of single-cell multi-omics technologies has enabled the simultaneous profiling of diverse omics layers within individual cells. Integrating such multimodal data provides unprecedented insights into cellular identity, regulatory processes, and disease mechanisms. However, it remains challenging, as current methods often rely on selecting highly variable genes or peaks during preprocessing, which may inadvertently discard crucial biological information. Here, we present scMamba, a foundation model designed to integrate single-cell multi-omics data without the need for prior feature selection while preserving genomic positional information. scMamba introduces a patch-based cell tokenization strategy that treats genomics regions as words (tokens) and cells as sentences. Building upon the concept of state space duality, scMamba distills rich biological insights from high-dimensional, sparse single-cell multi-omics data. Additionally, our novel contrastive learning approach, enhanced with cosine similarity regularization, enables superior alignment across omics layers compared to traditional methods. Systematic benchmarking across multiple datasets demonstrates that scMamba significantly outperforms state-of-the-art methods in preserving biological variation, aligning omics layers, and enhancing key downstream tasks such as clustering, cell type annotation, and trajectory inference. Our findings position scMamba as a powerful tool for large-scale single-cell multi-omics integration, capable of handling large-scale atlases and advancing biological discovery.

Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches use expensive, task-specific, and data-free training procedures, limiting their ability to benefit from high-quality datasets and large-scale pre-trained models. In this work, we address TPS by interpreting candidate paths as trajectories sampled from stochastic dynamics induced by the learned score function of pre-trained generative models, specifically denoising diffusion and flow matching. Under these dynamics, finding high-likelihood transition paths becomes equivalent to minimizing the Onsager-Machlup (OM) action functional. This enables us to repurpose pre-trained generative models for TPS in a zero-shot manner, in contrast with bespoke, task-specific approaches in previous work. We demonstrate our approach on varied molecular systems, obtaining diverse, physically realistic transition pathways and generalizing beyond the pre-trained model's original training dataset. Our method can be easily incorporated into new generative models, making it practically relevant as models continue to scale and improve with increased data availability. Code is available at github.com/ASK-Berkeley/OM-TPS.

Discrete latent factor models (DLFMs) are widely used in various domains such as machine learning, economics, neuroscience, psychology, etc. Currently, fitting a DLFM to some dataset relies on a customized solver for individual models, which requires lots of effort to implement and is limited to the targeted specific instance of DLFMs. In this paper, we propose a generic framework based on CVXPY, which allows users to specify and solve the fitting problem of a wide range of DLFMs, including both regression and classification models, within a very short script. Our framework is flexible and inherently supports the integration of regularization terms and constraints on the DLFM parameters and latent factors, such that the users can easily prototype the DLFM structure according to their dataset and application scenario. We introduce our open-source Python implementation and illustrate the framework in several examples.

The real world naturally has dimensions of time and space. Therefore, estimating the counterfactual outcomes with spatial-temporal attributes is a crucial problem. However, previous methods are based on classical statistical models, which still have limitations in performance and generalization. This paper proposes a novel framework for estimating counterfactual outcomes with spatial-temporal attributes using the Transformer, exhibiting stronger estimation ability. Under mild assumptions, the proposed estimator within this framework is consistent and asymptotically normal. To validate the effectiveness of our approach, we conduct simulation experiments and real data experiments. Simulation experiments show that our estimator has a stronger estimation capability than baseline methods. Real data experiments provide a valuable conclusion to the causal effect of conflicts on forest loss in Colombia. The source code is available at https://github.com/lihe-maxsize/DeppSTCI_Release_Version-master.