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Sparse Network Inference under Imperfect Detection and its Application to Ecological Networks

Zhang, Aoran, Wei, Tianyao, Guerrero, Maria J., Uribe, César A.

arXiv.org Machine Learning

Abstract--Recovering latent structure from count data has received considerable attention in network inference, particularly when one seeks both cross-group interactions and within-group similarity patterns in bipartite networks, which is widely used in ecology research. Such networks are often sparse and inherently imperfect in their detection. Existing models mainly focus on interaction recovery, while the induced similarity graphs are much less studied. Moreover, sparsity is often not controlled, and scale is unbalanced, leading to oversparse or poorly rescaled estimates with degrading structural recovery. We impose nonconvex ℓ1/2 regularization on the latent similarity and connectivity structures to promote sparsity within-group similarity and cross-group connectivity with better relative scale. To solve it, we develop an ADMM-based algorithm with adaptive penalization and scale-aware initialization and establish its asymptotic feasibility and KKT stationarity of cluster points under mild regularity conditions. Experiments on synthetic and real-world ecological datasets demonstrate improved recovery of latent factors and similarity/connectivity structure relative to existing baselines. Index Terms--augmented Lagrangian, nonconvex nonsmooth optimization, nonnegative matrix factorization, link prediction, ecological network inference, structured sparse recovery I. INTRODUCTION This setting is inherent in sensing and monitoring applications [3], [4], where observations, such as counts, are obtained via an imperfect sampling process. In this paper, we are interested in ecological interaction networks describing how species associate with locations and how environments shape biodiversity patterns [5], [6].


What I've learned from 25 years of automated science, and what the future holds: an interview with Ross King

AIHub

What I've learned from 25 years of automated science, and what the future holds: an interview with Ross King We're excited to launch our new series, where we're speaking with leading researchers to explore the breakthroughs driving AI and the reality of the future promises - to give you an inside perspective on the headlines. Our first interviewee is Ross King, who created the first robot scientist back in 2009. He spoke to us about the nature of scientific discovery, the role AI has to play, and his recent work in DNA computing. Automated science is a really exciting area, and it feels like everyone's talking about it at the moment - e.g. But you've been working in this field for many years now. In 2009 you developed Adam, the first robot scientist to generate novel scientific knowledge. Could you tell me some more about that? So the history goes back to before Adam.


ALMAB-DC: Active Learning, Multi-Armed Bandits, and Distributed Computing for Sequential Experimental Design and Black-Box Optimization

Hui-Mean, Foo, Chang, Yuan-chin I

arXiv.org Machine Learning

Sequential experimental design under expensive, gradient-free objectives is a central challenge in computational statistics: evaluation budgets are tightly constrained and information must be extracted efficiently from each observation. We propose \textbf{ALMAB-DC}, a GP-based sequential design framework combining active learning, multi-armed bandits (MAB), and distributed asynchronous computing for expensive black-box experimentation. A Gaussian process surrogate with uncertainty-aware acquisition identifies informative query points; a UCB or Thompson-sampling bandit controller allocates evaluations across parallel workers; and an asynchronous scheduler handles heterogeneous runtimes. We present cumulative regret bounds for the bandit components and characterize parallel scalability via Amdahl's Law. We validate ALMAB-DC on five benchmarks. On the two statistical experimental-design tasks, ALMAB-DC achieves lower simple regret than Equal Spacing, Random, and D-optimal designs in dose--response optimization, and in adaptive spatial field estimation matches the Greedy Max-Variance benchmark while outperforming Latin Hypercube Sampling; at $K=4$ the distributed setting reaches target performance in one-quarter of sequential wall-clock rounds. On three ML/engineering tasks (CIFAR-10 HPO, CFD drag minimization, MuJoCo RL), ALMAB-DC achieves 93.4\% CIFAR-10 accuracy (outperforming BOHB by 1.7\,pp and Optuna by 1.1\,pp), reduces airfoil drag to $C_D = 0.059$ (36.9\% below Grid Search), and improves RL return by 50\% over Grid Search. All advantages over non-ALMAB baselines are statistically significant under Bonferroni-corrected Mann--Whitney $U$ tests. Distributed execution achieves $7.5\times$ speedup at $K = 16$ agents, consistent with Amdahl's Law.


Equivalence Testing Under Privacy Constraints

Pareek, Savita, Insolia, Luca, Molinari, Roberto, Guerrier, Stéphane

arXiv.org Machine Learning

Protecting individual privacy is essential across research domains, from socio-economic surveys to big-tech user data. This need is particularly acute in healthcare, where analyses often involve sensitive patient information. A typical example is comparing treatment efficacy across hospitals or ensuring consistency in diagnostic laboratory calibrations, both requiring privacy-preserving statistical procedures. However, standard equivalence testing procedures for differences in proportions or means, commonly used to assess average equivalence, can inadvertently disclose sensitive information. To address this problem, we develop differentially private equivalence testing procedures that rely on simulation-based calibration, as the finite-sample distribution is analytically intractable. Our approach introduces a unified framework, termed DP-TOST, for conducting differentially private equivalence testing of both means and proportions. Through numerical simulations and real-world applications, we demonstrate that the proposed method maintains type-I error control at the nominal level and achieves power comparable to its non-private counterpart as the privacy budget and/or sample size increases, while ensuring strong privacy guarantees. These findings establish a reliable and practical framework for privacy-preserving equivalence testing in high-stakes fields such as healthcare, among others.


Fast Uncertainty Quantification for Kernel-Based Estimators in Large-Scale Causal Inference

Kosko, Matthew, J, Falco, Bargagli-Stoffi, null, Wang, Lin, Santacatterina, Michele

arXiv.org Machine Learning

Kernel methods are widely used in causal inference for tasks such as treatment effect estimation, policy evaluation, and policy learning. The bootstrap is a standard tool for uncertainty quantification because of its broad applicability. As increasingly large datasets become available, such as the 2023 U.S. Natality data from the National Vital Statistics System (NVSS), which includes 3,596,017 registered births, the computational demands of these methods increase substantially. Kernel methods are known to scale poorly with sample size, and this limitation is further exacerbated by the repeated re-fitting required by the bootstrap. As a result, bootstrap-based inference for kernel-based estimators can become computationally infeasible in large-scale settings. In this paper, we address these challenges by extending the causal Bag of Little Bootstraps (cBLB) algorithm to kernel methods. Our approach achieves computational scalability by combining subsampling and resampling while preserving first-order uncertainty quantification and asymptotically correct coverage. We evaluate the method across three representative implementations: kernelized augmented outcome-weighted learning, kernel-based minimax weighting, and double machine learning with kernel support vector machines. We show in simulations that our method yields confidence intervals with nominal coverage at a fraction of the computational cost. We further demonstrate its utility in a real-world application by estimating the effect of any amount of smoking on birth weight, as well as the optimal treatment regime, using the NVSS dataset, where the standard bootstrap is prohibitively expensive computationally and effectively infeasible at this scale.





Supplementarymaterialfor DynamicCausalBayesianOptimisation

Neural Information Processing Systems

In this section we describe in detail the experiment conducted in 4.2. This example is based on theworkbyBlasiusetal.(2020). Inthisdemonstration wecontinuealongthatparadigm whenwe investigate a biological systems in which two species interact, one as a predator and the other as prey.