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A Mathematical Optimization Approach for Expert-Informed Bayesian Best Subset Selection

arXiv.org Machine Learning

A central challenge in statistical modeling is identifying the subset of features that belong in the true regression model. The classical best subset selection problem, recently made tractable via mixed-integer optimization (MIO), finds the globally optimal sparse solution. It does not, however, make use of any information beyond the observed data. In many applied settings, domain experts can meaningfully rank or score the relevance of candidate predictors, yet no existing framework integrates such probabilistic expert assessments directly into the best-subsets objective. This paper presents Expert-Implied Bayesian Best Subsets (EBBS), a method that incorporates domain-expert probability estimates of feature relevance into the MIO best-subsets problem through a maximum a posteriori (MAP) framework. Expert views from multiple respondents are aggregated into a single prior probability per feature using the Poisson binomial distribution for marginal probability estimates, the pairwise win rate for pairwise comparisons, or the normalized mean rank for ordinal rankings. This probability enters the objective function as a log-odds penalty term that smoothly encourages or discourages the selection of each feature consistent with the expert consensus. This paper provides analytic derivations of the MAP formulation and characterizes its theoretical properties. The proposed model reduces to Best Subsets when experts all have no views. Empirical results on synthetic and real datasets are forthcoming.


Extrapolating from Regularised Solutions for Solving Ill-Conditioned Linear Systems in Machine Learning

arXiv.org Machine Learning

Rapid prototyping of algorithms is a critical step in modern machine learning. Most algorithms exploit linear algebra, creating a need for lightweight numerical routines which -- while potentially sub-optimal for the task at hand -- can be rapidly implemented. For the numerical solution of ill-conditioned linear systems of equations, the standard solution for prototyping is Tikhonov-regularised inversion using a nugget. However, selection of the size of nugget is often difficult, and the use of data-adaptive procedures precludes automatic differentiation, introducing instabilities into end-to-end training. Further, while data-adaptive procedures perform multiple linear solves to select the size of nugget, only the result of one such solve is returned, which we argue is wasteful. This paper aims to circumvent the above difficulties, presenting autonugget; a Python package for automatic and stable numerical solution of linear systems suitable for rapid prototyping, and fully compatible with automatic differentiation using JAX. autonugget combines multiple linear solves using Richardson extrapolation to determine the solution of the ill-conditioned system, improving in accuracy over approximations based on a single nugget.


Perspectives on Latent Factor Indeterminacy and its Implications for Data Representation

arXiv.org Machine Learning

The common factor analytic model is related to Helmholtz and Boltzmann machines, can be conceived as a linear autoencoder, or can be thought of as a single-hidden-layer generative neural network. We thus consider it a basal generative representation learner that can be used as a minimal model for studying the foundational characteristics of (deep) generative model architectures. We focus on the fundamental problem of indeterminacy in latent factor projections. This indeterminacy implies that, even when the intrinsic dimension of the latent vector is known, regularity conditions are met, and rotational indeterminacy is resolved, an inherent indefiniteness in the retrieval of causative latent sources remains: they will be uncertain, distributionally deviant, and non-unique. This can have major implications for data representation but remains an elusive issue, even to practitioners and theorists well-versed in the factor model. Moreover, this classic psychometric problem is intricately related to the modern issue of latent variable collapse in the variational autoencoder framework for deep generative modeling. Here, we assess this indeterminacy from various perspectives and show how these are mathematically and conceptually related and we discuss subsequent implications for the Psychometrics, Statistics, and Artificial Intelligence communities. We show that one has latent factor determinacy across all its facets when the feature-dimension grows to infinity. This feeds into an essentially distribution-free estimation approach in the sample case when the number of features grows very large. We conclude, as these are emergent properties at scale, that the factor model is suited for representation learning of very-high-dimensional data.


Variance or Standard Deviation? Shell Geometry and Global-Scale Priors in High-Dimensional Shrinkage

arXiv.org Machine Learning

We study how the choice of default prior for a common Gaussian scale affects high-dimensional shrinkage risk, highlighting the role played by high-dimensional geometry. Formally, we consider a high-dimensional setting in which the near-zero behavior of the common scale prior has first-order consequences for shrinkage risk, and show that priors that are flat on the variance and those flat on the standard deviation allocate markedly different mass near the zero-scale boundary, leading to distinct shrinkage behavior and informing principled default prior selection. Specifically, under a radial-power benchmark, we establish that the SD-flat benchmark has a one-unit asymptotic risk advantage near the origin, crosses over in the critical regime, and is second-order equivalent to the variance-flat benchmark for strong signals. Proper single global-scale hyperpriors and bounded coordinate-multiplier mixtures inherit these limits through the near-zero exponent of their SD-scale density. For heavier-tailed or sparse priors, that exponent still classifies the common global-scale component, while local-scale tails, model-size priors, or allocation priors can also affect risk.


OMiSO: Adaptive optimization of state-dependent brain stimulation to shape neural population states

Neural Information Processing Systems

The coordinated activity of neural populations underlies myriad brain functions. Manipulating this activity using brain stimulation techniques has great potential for scientific and clinical applications, as they causally influence the nervous system. To improve the accuracy by which one can manipulate neural activity, it is important to (1) take into account the pre-stimulation brain state, which can influence the brain's response to stimulation, and (2) adaptively update stimulation parameters over time to compensate for changes in the brain's response to stimulation. In this work, we propose Online MicroStimulation Optimization (OMiSO), a brain stimulation framework that leverages brain state information to find stimulation parameters that can drive neural population activity toward specified states. OMiSO includes two key advances: i) training a stimulation-response model that leverages the pre-stimulation brain state, and inverting this model to choose the stimulation parameters, and ii) updating this inverse model online using newly-observed responses to stimulation. We tested OMiSO using intracortical microstimulation with a "Utah" array and found that it outperformed competing methods that do not incorporate these advances. Taken together, OMiSO provides greater accuracy in achieving specified activity states, thereby advancing neuromodulation technologies for understanding the brain and for treating brain disorders.


Non-convex entropic mean-field optimization via Best Response flow

Neural Information Processing Systems

We study the problem of minimizing non-convex functionals on the space of probability measures, regularized by the relative entropy (KL divergence) with respect to a fixed reference measure, as well as the corresponding problem of solving entropy-regularized non-convex-non-concave min-max problems. We utilize the Best Response flow (also known in the literature as the fictitious play flow) and study how its convergence is influenced by the relation between the degree of non-convexity of the functional under consideration, the regularization parameter and the tail behaviour of the reference measure. In particular, we demonstrate how to choose the regularizer, given the non-convex functional, so that the Best Response operator becomes a contraction with respect to the L1Wasserstein distance, which ensures the existence of its unique fixed point that is then shown to be the unique global minimizer for our optimization problem. This extends recent results where the Best Response flow was applied to solve convex optimization problems regularized by the relative entropy with respect to arbitrary reference measures, and with arbitrary values of the regularization parameter. Our results explain precisely how the assumption of convexity can be relaxed, at the expense of making a specific choice of the regularizer. Additionally, we demonstrate how these results can be applied in reinforcement learning in the context of policy optimization for Markov Decision Processes and Markov games with softmax parametrized policies in the mean-field regime.


Non-asymptotic Tail Bounds for the Kostlan--Shub--Smale Field: Tensor PCA and Spherical $k$-Spin Complexity

arXiv.org Machine Learning

This paper builds a hierarchy of explicit, non-asymptotic tail bounds for the supremum of the Kostlan--Shub--Smale (KSS) random field on the sphere, and applies it to two problems: Spiked Tensor PCA and the landscape of the spherical $k$-spin model. For Tensor PCA, we study the non-asymptotic statistical limits of estimating a rank-$R$ symmetric signal tensor of order~$k\ge 3$ and dimension~$d\ge 3$ from a single Gaussian observation at signal-to-noise ratio~$ฮป$, through the \emph{profile maximum likelihood estimator}, the MLE restricted to normalized rank-$R$ tensors of coherence at least~$ฮบ$. Our analysis uses a single reduction: a deterministic geometric inequality (the Tube Method) and a rank-reduction step bound the estimation error by the supremum of the canonical KSS field, which the Kac--Rice formula turns into a Gaussian integral against the expected absolute characteristic polynomial of a shifted Gaussian Orthogonal Ensemble, controlled in turn by the four explicit tail bounds of our hierarchy (three from a Mehta--Fyodorov representation, one from a Ben Arous--Dembo--Guionnet large deviation). The same reduction yields two results, each with explicit constants. For estimation, a finite-$(k,d)$ error bound recovers the asymptotically optimal rate~$\sqrt{d\log k}$ of Perry, Wein and Bandeira, with explicit dependence on the rank~$R$ and the coherence~$ฮบ$. For the landscape, a two-sided non-asymptotic bracketing of the annealed complexity of the spherical $k$-spin Hamiltonian recovers the Auffinger--Ben Arous--ฤŒernรฝ complexity function in the high-dimensional limit.


On the necessity of adaptive regularisation: Optimal anytime online learning on โ„“p-balls

Neural Information Processing Systems

We study online convex optimisation on โ„“p-balls in Rd for p > 2. While always sub-linear, the optimal regret exhibits a shift between the high-dimensional setting (d > T), when the dimension d is greater than the time horizon T and the low-dimensional setting (d T). We show that Follow-the-Regularised-Leader (FTRL) with time-varying regularisation which is adaptive to the dimension regime is anytime optimal for all dimension regimes. Motivated by this, we ask whether it is possible to obtain anytime optimality of FTRL with fixed non-adaptive regularisation. Our main result establishes that for separable regularisers, adaptivity in the regulariser is necessary, and that any fixed regulariser will be sub-optimal in one of the two dimension regimes. Finally, we provide lower bounds which rule out sublinear regret bounds for the linear bandit problem in sufficiently high-dimension for all โ„“p-balls with p 1.


A Two-Parameter Weibull Framework for Diagnosing Transformer Weight Distributions

arXiv.org Machine Learning

We apply the Weibull distribution -- a two-parameter family from extreme-value theory -- as a diagnostic framework for element-wise weight magnitude distributions in transformers. At initialization, i.i.d. Gaussian weights give |w| ~ HalfNormal, yielding k ~ 1.20 via middle-80% probability-plot fit (the protocol used throughout this work). This anchor makes k a principled, architecture-independent measuring stick for training dynamics; fitting each weight matrix independently at every layer at every checkpoint enables per-component, per-layer, and per-step diagnostics that aggregate statistics cannot resolve. Applying this framework to 12 model entries spanning 7 architectural families (Pythia, OLMo-1/2, LLaMA-3, Mistral, Qwen2.5/3) reveals three findings. First, FFN modules and the attention output projection W_o -- the Transmission Class -- fall in a narrow k band: median terminal k in [1.186, 1.204] across 12 entries (cross-family CV = 0.51%), shared across SwiGLU/GeLU activations, Pre-LN/QK-Norm placements, and 70M-14B sizes. Second, the attention input projections W_q, W_k -- the Selection Class -- depart from the Weibull family, with severity shaped by storage: separately-stored Q/K (OLMo-1, OLMo-2) yields k in [0.76, 0.99] (deep); GQA models yield k in [1.10, 1.16] (mild); Pythia's merged W_qkv occupies a transitional zone tracking training budget T/tau monotonically. Third, lambda grows substantially during training and scales with sqrt(eta/lambda_wd) within the Pythia family (Pearson r = 0.94, three Transmission kinds), directionally consistent with Fan et al. (2025). The two parameters carry independent information: k labels the functional class, lambda labels training progress. We release npm-weibull-py v0.4 (Python library) and DATABASE_v9_1 at https://github.com/tiexinding/NPM-Weibull-public .


GraphGP: Scalable Gaussian Processes with Vecchia's Approximation

arXiv.org Machine Learning

Gaussian processes are a powerful tool for modeling continuous fields, but their naive $\mathcal{O}(N^3)$ computational cost and $\mathcal{O}(N^2)$ memory requirement often limit their practical use. Vecchia's approximation is a sparse precision matrix approximation for stationary, decaying kernels that conditions each point only on its $k$ nearest neighbors. We present GraphGP, a GPU algorithm for Vecchia's approximation that scales to nearly a billion parameters with linear time and memory requirements, handling arbitrary point distributions over a large dynamic range. Our key contributions are (1) a bit-reversed k-d tree ordering that allows efficient neighbor searches while also maximizing batch parallelism, and (2) a differentiable CUDA implementation, which is substantially faster and more memory efficient than our pure JAX baseline. GraphGP provides the building blocks for inference, including forward generation, inverse application, log-determinant, and kernel parameter derivatives.