Panel data methods are widely used in empirical analysis to address unobserved heterogeneity, but causal inference remains challenging when treatments are endogenous and confounding variables high-dimensional and potentially nonlinear. Standard instrumental variables (IV) estimators, such as two-stage least squares (2SLS), become unreliable when instrument validity requires flexibly conditioning on many covariates with potentially non-linear effects. This paper develops a Double Machine Learning estimator for static panel models with endogenous treatments (panel IV DML), and introduces weak-identification diagnostics for it. We revisit three influential migration studies that use shift-share instruments. In these settings, instrument validity depends on a rich covariate adjustment. In one application, panel IV DML strengthens the predictive power of the instrument and broadly confirms 2SLS results. In the other cases, flexible adjustment makes the instruments weak, leading to substantially more cautious causal inference than conventional 2SLS. Monte Carlo evidence supports these findings, showing that panel IV DML improves estimation accuracy under strong instruments and delivers more reliable inference under weak identification.

For what purpose was the dataset created?

When training deep neural networks, a model's generalization error is often observed to follow a power scaling law dependent both on the model size and the

We thank all the reviewers for the helpful comments. Here, we address the main concerns raised by the reviewers. While the traditional method (e.g., Lasso) can find important individual The motivations and application are discussed in [1.1.] When the sparse assumption doesn't hold] Theoretically, the sparsity assumption is commonly Motivations] The motivations and one real application where sparsity holds are discussed in [1.1.]

While practitioners often employ variable importance methods that rely on this impurity-based information, these methods remain poorly characterized from a theoretical perspective.

Biological data sets are often high-dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions in genomics exemplify these difficulties, as only a small subset of biologically relevant features (e.g., motifs) are typically active, and their effects are often non-linear and context-dependent. While statistical approaches often result in more interpretable models, deep learning models have proven effective in modeling complex interactions and prediction accuracy, yet their black-box nature limits interpretability. We introduce BaGGLS, a flexible and interpretable probabilistic binary regression model designed for high-dimensional biological inference involving feature interactions. BaGGLS incorporates a Bayesian group global-local shrinkage prior, aligned with the group structure introduced by interaction terms. This prior encourages sparsity while retaining interpretability, helping to isolate meaningful signals and suppress noise. To enable scalable inference, we employ a partially factorized variational approximation that captures posterior skewness and supports efficient learning even in large feature spaces. In extensive simulations, we can show that BaGGLS outperforms the other methods with regard to interaction detection and is many times faster than MCMC sampling under the horseshoe prior. We also demonstrate the usefulness of BaGGLS in the context of interaction discovery from motif scanner outputs and noisy attribution scores from deep learning models. This shows that BaGGLS is a promising approach for uncovering biologically relevant interaction patterns, with potential applicability across a range of high-dimensional tasks in computational biology.

Modeling the dynamics from sparsely time-resolved snapshot data is crucial for understanding complex cellular processes and behavior. Existing methods leverage optimal transport, Schrödinger bridge theory, or their variants to simultaneously infer stochastic, unbalanced dynamics from snapshot data. However, these approaches remain limited in their ability to account for cell-cell interactions. This integration is essential in real-world scenarios since intercellular communications are fundamental life processes and can influence cell state-transition dynamics. To address this challenge, we formulate the Unbalanced Mean-Field Schrödinger Bridge (UMFSB) framework to model unbalanced stochastic interaction dynamics from snapshot data. Inspired by this framework, we further propose CytoBridge, a deep learning algorithm designed to approximate the UMFSB problem. By explicitly modeling cellular transitions, proliferation, and interactions through neural networks, CytoBridge offers the flexibility to learn these processes directly from data. The effectiveness of our method has been extensively validated using both synthetic gene regulatory data and real scRNA-seq datasets. Compared to existing methods, CytoBridge identifies growth, transition, and interaction patterns, eliminates false transitions, and reconstructs the developmental landscape with greater accuracy. Code is available at: https://github.com/zhenyiizhang/CytoBridge-NeurIPS.

When training deep neural networks, a model's generalization error is often observed to follow a power scaling law dependent both on the model size and the