Statistics Theory · Cross-listed from math-ph
When Stein-Type Test Detects Equilibrium Distributions of Finite N-Body Systems
Jae Wan Shim
Starting from the probability distribution of finite N-body systems, which maximises the Havrda–Charvát
entropy, we build a Stein-type goodness-of-fit test. The Maxwell–Boltzmann distribution is exact only in the thermodynamic limit, where the system is composed of infinitely many particles as N approaches infinity. For an isolated system with a finite number of particles, the
equilibrium velocity distribution is compact and markedly non-Gaussian, being restricted by the fixed total energy. Using Stein's method, we first obtain a differential operator that characterises the target density. Its eigenfunctions are symmetric Jacobi
polynomials, whose orthogonality yields a simple, parameter-free statistic. Under the null hypothesis that the data follows the finite-N distribution, the statistic converges to a chi-squared law, so critical values are available in closed form. Large-scale Monte Carlo experiments confirm exact size control and give a clear picture of the power. These findings quantify how quickly a finite system approaches the classical limit and provide a practical tool for testing kinetic models in regimes where normality cannot be assumed.
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Statistical Methodology
Conformal changepoint localization
Rohan Hore and Aaditya Ramdas
We study the problem of offline changepoint localization in a distribution-free setting. One observes a vector of data with a single changepoint, assuming that the data before and after the changepoint are i.i.d. (or more generally exchangeable) from arbitrary and unknown distributions. The goal is to produce a finite-sample confidence set for the index at which the change occurs without making any other assumptions. Existing methods often rely on parametric assumptions, tail conditions, or asymptotic approximations, or only produce point estimates. In contrast, our distribution-free
algorithm, CONformal CHangepoint localization (CONCH), only leverages exchangeability arguments to construct confidence sets with finite sample coverage. By proving a conformal Neyman–Pearson lemma, we derive principled score functions that yield informative (small) sets. Moreover, with such score functions, the normalized length of the confidence set shrinks to zero under weak assumptions. We also establish a universality result showing that any distribution-free changepoint localization method must be an instance of CONCH. Experiments suggest that CONCH delivers precise confidence sets even in challenging settings involving images or text.
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Statistical Methodology
Latent variation in pathogen strain-specific effects under multiple-versions-of-treatment theory
Bronner P. Gonçalves
Evidence-informed policy on infections requires estimates of their effects on health. However, pathogenic variation, whereby occurrence of adverse outcomes depends on the infecting strain, might complicate the study of many infectious
agents. Here, we consider the interpretation of epidemiologic studies on effects of infections on health when there is heterogeneity in strain-specific effects and information on strain composition is unavailable. We use potential outcomes and causal inference theory for analyses in the presence of multiple versions of treatment to argue that oft-reported quantities in these studies have a causal interpretation that depends on population frequencies of infecting strains. Moreover, as in other contexts where the treatment-variation-irrelevance assumption might be violated, transportability requires additional considerations, beyond those needed for non-compound exposures. This discussion, that considers potential heterogeneity in strain-specific effects, will facilitate interpretation of these studies, and for the reasons mentioned above, also highlights the value of pathogen subtype data.
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Machine Learning (Statistics)
Inheritance Between Feedforward and Convolutional Networks via Model Projection
Nicolas Ewen, Jairo Diaz-Rodriguez and Kelly Ramsay
Neural-network techniques are often transferred across architecture families by analogy, but such transfer is valid only when the assumptions required by a technique are preserved. We introduce this idea as inheritance between model classes. Using a unified node-level framework with tensor-valued activations, we prove that generalized feedforward networks (GFFNs) form a strict subset of generalized convolutional networks (GCNNs), so GCNN properties transfer directly to GFFNs. The reverse direction is not automatic: standard CNN nodes use spatial kernels, while FFN nodes use one scalar weight per input contribution. We introduce model projection to recover a restricted reverse inheritance path. Projection freezes each convolutional input-channel sub-function and learns one scalar coefficient for each input-output channel contribution, giving projected CNN nodes the GFFN-style trainable structure of scalar-weighted input recombination. This inherited structure leads naturally to parameter-efficient transfer learning. Across multiple ImageNet-pretrained CNN backbones and downstream image-classification
datasets, model projection is competitive with standard and PEFT baselines and provides an effective initialization for subsequent full fine-tuning.
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Statistics Applications
Evaluating Predictive Modeling Strategies for Predicting Individual Treatment Effects in Precision Medicine
Pamela M. Chiroque-Solano, M Lee Van Horn and Thomas Jaki
Precision medicine seeks to match patients with treatments that produce the greatest benefit. The Predicted Individual Treatment Effect (PITE)-the difference between predicted outcomes under treatment and control-quantifies this benefit but is difficult to estimate due to unobserved counterfactuals, high dimensionality, and complex interactions. We compared 30+ modeling strategies, including penalized and projection-based methods, flexible learners, and tree-ensembles, using a structured simulation framework varying sample size, dimensionality, multicollinearity, and interaction complexity. Performance was measured using root mean squared error (RMSE) for prediction accuracy and directional accuracy (DIR) for correctly classifying benefit versus harm. Internal validation produced optimistic estimates, whereas external validation with distributional shifts and higher-order interactions more clearly revealed model weaknesses. Penalized and projection-based approaches-ridge, lasso, elastic net, partial least squares (PLS), and principal components regression (PCR)-consistently achieved strong RMSE and DIR performance. Flexible learners excelled only under strong signals and sufficient sample sizes. Results highlight robust linear/projection defaults and the necessity of rigorous external validation.
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Statistics Theory
Optimal rates for density and mode estimation with expand-and-sparsify representations
Kaushik Sinha and Christopher Tosh
Expand-and-sparsify representations are a class of theoretical models that capture sparse representation phenomena observed in the sensory systems of many animals. At a high level, these representations map an input $x \in \mathbb{R}^d$ to a much higher dimension $m \gg d$ via random linear projections before zeroing out all but the $k \ll m$ largest entries. The result is a $k$-sparse vector in $\{0,1\}^m$. We study the suitability of this representation for two fundamental statistical problems: density estimation and mode estimation. For density estimation, we show that a simple linear function of the expand-and-sparsify representation produces an
estimator with minimax-optimal $\ell_{\infty}$ convergence rates. In mode estimation, we provide simple
algorithms on top of our density
estimator that recover single or multiple modes at optimal rates up to logarithmic factors under mild conditions.
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Machine Learning (Statistics) · Cross-listed from cs.LG
From Seeds to Semantics: Measuring Semantic Accessibility in Deterministic Diffusion Models
Kuntian Chen, Wei Wei, Yizhou Zeng et al. (+3 more)
Diffusion models generate samples through a sequence of learned denoising steps, and recent work has studied how semantic structure appears along this sampling process. We study this question in deterministic samplers by measuring semantic accessibility: how much information about a final semantic property, such as an image class label or attribute, can be extracted from the seed and intermediate states along the trajectory that produces the sample. Using DDIM sampling, for which each initial noise seed determines a unique trajectory and final image, we train separate classifiers (probes) at several points along the trajectory to predict a semantic property of the final image. We measure how well such a property can be predicted from the state at a given point using top-1 accuracy and normalized mutual information. Across MNIST, Fashion-MNIST, CIFAR-10, and CelebA, class labels and image attributes can be predicted above chance from the initial noise seed, and along DDIM trajectories, this accessibility exceeds matched-noise forward baselines. We find that semantic accessibility is substantially higher along the trajectories whose final images are classified with high confidence than along those classified with low confidence. These measurements provide a quantitative view of when semantic properties can be recovered during deterministic generation.
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All authors Kuntian Chen, Wei Wei, Yizhou Zeng, Sophie Langer, Mariia Seleznova, Hung-Hsu Chou
Statistical Methodology
A Compound Logistic Regression Model for Binary Responses
Anthony Almudevar and Jacob Almudevar
Logistic regression is the most commonly used method for constructing predictive models for binary responses. One significant drawback to this approach, however, is that the asymptotes of the logistic response function are fixed at 0 and 1, and there are many applications for which this constraint is inappropriate. More flexible models have been proposed for this application, most proceeding by supplementing the logistic response function with additional parameters. In this article we extend these models to allow correlated responses and the inclusion of
covariates. This is achieved through the compound logistic regression model, for which the mean response is a function of several logistic regression functions. This permits a greater variety of models, while retaining the advantages of logistic regression.
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Statistics Applications
Non-Linear Drivers of Population Dynamics: a Nonparametric Coalescent Approach
Filippo Monti, Nuno R. Faria, Xiang Ji et al. (+3 more)
Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-based methods enable the inference of Ne(t) trajectories through time from phylogenies reconstructed from molecular sequence data. Understanding the ecological and environmental drivers of population dynamics requires linking Ne(t) to external
covariates. Existing approaches typically impose log-linear relationships between
covariates and Ne(t), which may fail to capture complex biological processes and can introduce bias when the true relationship is nonlinear. We present a flexible
Bayesian framework that integrates
covariates into coalescent models with piecewise-constant Ne(t) through a Gaussian process (GP) prior. The GP, a distribution over functions, naturally accommodates nonlinear
covariate effects without restrictive parametric assumptions. This formulation improves estimation of
covariate-Ne(t) relationships, mitigates bias under nonlinear associations, and yields interpretable uncertainty quantification that varies across the
covariate space. To balance global
covariate-driven patterns with local temporal dynamics, we couple the GP prior with a Gaussian Markov random field that enforces smoothness in Ne(t) trajectories. Through simulation studies and three empirical applications - yellow fever virus dynamics in Brazil (2016-2018), late-Quaternary musk ox demography, and HIV-1 CRF02-AG
evolution in Cameroon - we demonstrate that our method both confirms linear relationships where appropriate and reveals nonlinear
covariate effects that would otherwise be missed or mischaracterized. This framework advances phylodynamic inference by enabling more accurate and biologically realistic modeling of how environmental and epidemiological factors shape population size through time.
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All authors Filippo Monti, Nuno R. Faria, Xiang Ji, Philippe Lemey, Moritz U.G. Kraemer, Marc A. Suchard
Machine Learning (Statistics) · Cross-listed from cs.LG
Optimistic Training and Convergence of Q-Learning – Extended Version
Prashant Mehta and Sean Meyn
In recent work it is shown that Q-learning with linear function approximation is stable, in the sense of bounded parameter estimates, under the $(\varepsilon,\kappa)$-tamed Gibbs policy; $\kappa$ is inverse temperature, and $\varepsilon>0$ is introduced for additional exploration. Under these assumptions it also follows that there is a solution to the projected Bellman equation (PBE). Left open is uniqueness of the solution, and criteria for convergence outside of the standard tabular or linear MDP settings. The present work extends these results to other variants of Q-learning, and clarifies prior work: a one dimensional example shows that under an oblivious policy for training there may be no solution to the PBE, or multiple solutions, and in each case the
algorithm is not stable under oblivious training. The main contribution is that far more structure is required for convergence. An example is presented for which the basis is ideal, in the sense that the true Q-function is in the span of the basis. However, there are two solutions to the PBE under the greedy policy, and hence also for the $(\varepsilon,\kappa)$-tamed Gibbs policy for all sufficiently small $\varepsilon>0$ and $\kappa\ge 1$.
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Machine Learning (Statistics) · Cross-listed from quant-ph
Warm Starts, Cold States: Exploiting Adiabaticity for Variational Ground-States
Ricard Puig, Berta Casas, Alba Cervera-Lierta et al. (+2 more)
Reliable preparation of many-body ground states is an essential task in
quantum computing, with applications spanning areas from chemistry and materials modeling to
quantum optimization and benchmarking. A variety of approaches have been proposed to tackle this problem, including variational methods. However, variational training often struggle to navigate complex energy landscapes, frequently encountering suboptimal local minima or suffering from barren plateaus. In this work, we introduce an iterative strategy for ground-state preparation based on a stepwise (discretized)
Hamiltonian deformation. By complementing the Variational
Quantum Eigensolver (VQE) with adiabatic principles, we demonstrate that solving a sequence of intermediate problems facilitates tracking the ground-state
manifold toward the target system, even as we scale the system size. We provide a rigorous theoretical foundation for this approach, proving a lower bound on the loss variance that suggests trainability throughout the deformation, provided the system remains away from gap closings. Numerical simulations, including the effects of shot noise, confirm that this path-dependent tracking consistently converges to the target ground state.
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All authors Ricard Puig, Berta Casas, Alba Cervera-Lierta, Zoë Holmes, Adrián Pérez-Salinas
Statistics Applications
Early warning of Mpox outbreaks in U.S. jurisdictions using Lasso Vector Autoregression models with cross-jurisdictional lags
Hannah Craddock, Joel O. Wertheim, Eliah Aronoff-Spencer et al. (+8 more)
Mpox is an orthopoxvirus that infects humans and animals and is transmitted primarily through close physical contact. The episodic and spatially heterogeneous dynamics of Mpox transmission underscores the need for timely, area-specific forecasts to support targeted public health responses in the U.S. We develop a Vector Autoregression model with Lasso regularization (VAR-Lasso) to generate rolling two-week-ahead forecasts of weekly Mpox cases for eight high-incidence U.S. jurisdictions using national surveillance data from the Centers for Disease Control and Prevention (CDC). The VAR-Lasso model identifies significant long-lag, cross-jurisdictional predictors. For a case study in San Diego County (SDC), these statistical predictors align with phylogenetic analysis that traces a 2023 cluster in SDC to an outbreak in Illinois six months earlier. As the need for public health action is often greatest when incidence is increasing, our performance evaluation focuses on positive-slope weighted error metrics. Forecast performance of the VAR-Lasso model is compared to a uni-variate Auto-Regressive (AR) Lasso model and a naive moving-average estimate. The models are compared using slope-weighted Root Mean Squared Error (RMSE), slope-weighted Mean Absolute Error (MAE), and slope-weighted bias. Across all observations, the VAR-Lasso model reduces slope-weighted RMSE, MAE, and bias by 12%, 7%, and 66% relative to the AR model, and by 16%, 13%, and 76% relative to the naive
benchmark. Our findings highlight the value of sparse multivariate time-series models that leverage cross-jurisdictional case data for early
forecasting of Mpox outbreaks. Such
forecasting can aid health departments in proactively providing timely resources and messaging to mitigate the risks of a future outbreak.
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All authors Hannah Craddock, Joel O. Wertheim, Eliah Aronoff-Spencer, Mark Beatty, David Valentine, Rishi Graham, Jade C. Wang, Lior Rennert, Seema Shah, Ravi Goyal, Natasha K. Martin
Machine Learning (Statistics)
Robustness Verification of Polynomial Neural Networks
Yulia Alexandr, Hao Duan and Guido Montúfar
We study robustness verification of neural networks via metric algebraic geometry. For
polynomial neural networks, certifying a robustness radius amounts to computing the distance to the algebraic decision boundary. We use the Euclidean distance (ED) degree as an intrinsic measure of the complexity of this problem, analyze the associated ED discriminant, and introduce a parameter discriminant that detects parameter values at which the ED degree drops. We derive formulas for the ED degree for several network architectures and characterize the expected number of real critical points in the infinite-width limit. We develop symbolic elimination methods to compute these quantities and homotopy-continuation methods for exact robustness certification. Finally, experiments on lightning self-
attention modules reveal decision boundaries with strictly smaller ED degree than generic cubic hypersurfaces of the same ambient dimension.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Pragmatic Curiosity: A Unified Framework for Hybrid Learning and Optimization via Active Inference
Yingke Li, Anjali Parashar, Enlu Zhou et al. (+1 more)
Many engineering and scientific workflows rely on expensive black-box evaluations, requiring sequential decisions that must both improve task performance and reduce uncertainty.
Bayesian optimization (BO) and
Bayesian experimental design (BED) provide powerful but largely separate treatments of goal-directed optimization and information-seeking experimentation, leaving limited guidance for hybrid settings in which learning and optimization are intrinsically coupled. We propose Pragmatic Curiosity (PraC), a unified framework for hybrid learning and optimization via active inference. PraC evaluates candidate queries by trading information gain about a task-relevant latent symbol against an expected regret-based potential over outcomes. This formulation exposes three operational design choices: which latent quantity should be clarified, how task value is encoded as regret, and how strongly information gain should be exchanged against pragmatic value. We instantiate PraC across three regimes of increasing complexity: decision-oriented plume monitoring with fixed global symbols and known downstream losses, targeted active search with induced local symbols and evolving coverage goals, and composite
Bayesian optimization with hierarchical regret learning under unknown preferences. Across these regimes, PraC reduces downstream decision risk, improves coverage of critical outcome regions, and jointly learns predictive and preference structures without relying on task-specific staging rules.
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All authors Yingke Li, Anjali Parashar, Enlu Zhou, Chuchu Fan
Machine Learning (Statistics)
Diffusion Model's Generalization Can Be Characterized by Inductive Biases toward a Data-Dependent Ridge Manifold
Ye He, Yitong Qiu and Molei Tao
We study a data-dependent notion of
diffusion-model generalization: when a model does not memorize the training set, where do its generated samples go relative to the geometry induced by the data? To answer this, we introduce a time-dependent family of log-density ridge
manifolds constructed from the smoothed empirical distribution, and use it to characterize reverse-time inference. Our main result shows that generated samples evolve by a reach-align-slide mechanism: they first enter a neighborhood of the ridge, then their distance to the ridge is controlled by the normal component of training error, and finally their motion along the ridge is controlled by the tangential component. We further connect this
geometric picture to training dynamics through directional decompositions of the learned error, and make this link explicit for random feature models, where architectural bias and optimization error can be separated quantitatively. Experiments on synthetic
multimodal data and MNIST latent
diffusion support the predicted
geometric behavior in both low and high dimensions.
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Statistics Theory · Cross-listed from cs.LG
Optimism Stabilizes Thompson Sampling for Adaptive Inference
Shunxing Yan and Han Zhong
Thompson sampling (TS) is widely used for
stochastic multi-armed bandits, yet its inferential properties under adaptive data collection are subtle. Classical asymptotic theory for sample means can fail because arm-specific sample sizes are random and coupled with the rewards through the action-selection rule. We study adaptive inference for Thompson sampling with Gaussian randomized indices in $K$-armed
stochastic bandits with independent sub-Gaussian reward noises, and identify optimism as a key mechanism for restoring stability, meaning that each arm's pull count concentrates around a deterministic scale. This stability yields asymptotically valid Wald inference despite adaptive sampling. First, we prove that variance-inflated TS is stable for any $K \ge 2$, including the challenging regime where multiple arms are optimal, with asymptotically uniform allocation over optimal arms and sharp logarithmic pull-count asymptotics for suboptimal arms. This resolves the $K$-armed extension question raised by \citet{halder2025stable}, using new winner-map and Lyapunov-drift techniques to control allocation among multiple optimal arms. Second, we analyze an alternative optimistic modification that keeps the Gaussian index variance unchanged but adds an explicit mean bonus to the index center, and establish a similar stability conclusion. In summary, suitably implemented optimism stabilizes Thompson sampling and enables asymptotically valid Wald inference in multi-armed bandits, while incurring only a mild additional regret cost.
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Machine Learning (Statistics)
Causal Inference on Stopped Random Walks in Online Advertising
Jia Yuan Yu
We consider a causal inference problem frequently encountered in online advertising systems, where a publisher (e.g., Instagram, TikTok) interacts repeatedly with human users and advertisers by sporadically displaying to each user an advertisement selected through an auction. Each treatment corresponds to a parameter value of the advertising mechanism (e.g., auction reserve-price), and we want to estimate through experiments the corresponding long-term treatment effect (e.g., annual advertising revenue). In our setting, the treatment affects not only the instantaneous revenue from showing an ad, but also changes each user's interaction-trajectory, and each advertiser's bidding policy – as the latter is constrained by a finite budget. In particular, each a treatment may even affect the size of the population, since users interact longer with a tolerable advertising mechanism. We drop the classical i.i.d. assumption and model the experiment measurements (e.g., advertising revenue) as a stopped random walk, and use a budget-splitting experimental design, the Anscombe
Theorem, a Wald-like equation, and a Central Limit
Theorem to construct confidence intervals for the long-term treatment effect.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Leo Zhang and James Martens
Softmax Self-
Attention (SSA) is a key component of
Transformer architectures. However, when utilised within skipless architectures, which aim to improve representation learning, recent work has highlighted the inherent instability of SSA due to inducing rank collapse and poorly-conditioned Jacobians. In this work, we design a novel
attention mechanism: Orthogonal Self-
Attention (OSA), which aims to bypass these issues with SSA, in order to allow for (non-causal)
Transformers without skip connections and normalisation layers to be more easily trained. In particular, OSA parametrises the
attention matrix to be orthogonal via mapping a skew-symmetric
matrix, formed from query-key values, through the
matrix exponential. We show that this can be practically implemented, by exploiting the low-rank structure of our query-key values, resulting in the computational complexity and
memory cost of OSA scaling linearly with sequence length. Furthermore, we derive an initialisation scheme for which we prove ensures that the Jacobian of OSA is well-conditioned.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Inverse Depth Scaling From Most Layers Being Similar
Yizhou Liu, Sara Kangaslahti, Ziming Liu et al. (+1 more)
Neural scaling laws relate loss to model size in large
language models (LLMs), yet depth and width may contribute to performance differently, requiring more detailed studies. Here, we quantify how depth affects loss via analysis of LLMs and toy residual networks. We find loss scales inversely proportional to depth in LLMs, probably due to functionally similar layers reducing error through ensemble averaging rather than compositional learning or discretizing smooth dynamics. This regime is inefficient yet robust and may arise from the architectural bias of residual networks and target functions incompatible with smooth dynamics. The findings suggest that improving LLM efficiency may require architectural innovations to encourage compositional use of depth.
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All authors Yizhou Liu, Sara Kangaslahti, Ziming Liu, Jeff Gore
Machine Learning (Statistics) · Cross-listed from cs.LG
Discrete diffusion samplers and bridges: Off-policy algorithms and applications in latent spaces
Arran Carter, Sanghyeok Choi, Kirill Tamogashev et al. (+2 more)
Sampling from a distribution $p(x) \propto e^{-\mathcal{E}(x)}$ known up to a normalising constant is an important and challenging problem in statistics. Recent years have seen the rise of a new family of amortised sampling
algorithms, commonly referred to as
diffusion samplers, that enable fast and efficient sampling from an unnormalised density. Such
algorithms have been widely studied for continuous-space sampling tasks; however, their application to problems in discrete space remains largely unexplored. Although some progress has been made in this area, discrete
diffusion samplers do not take full advantage of ideas commonly used for continuous-space sampling. In this paper, we propose to bridge this gap by introducing off-policy training techniques for discrete
diffusion samplers. We show that these techniques improve the performance of discrete samplers on both established and new synthetic
benchmarks. Next, we generalise discrete
diffusion samplers to the task of bridging between two arbitrary distributions, introducing data-to-energy Schrödinger bridge training for the discrete domain for the first time. Lastly, we showcase the application of the proposed
diffusion samplers to data-free posterior sampling in the discrete latent spaces of image generative models.
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All authors Arran Carter, Sanghyeok Choi, Kirill Tamogashev, Víctor Elvira, Esmeralda S. Whitammer
Machine Learning (Statistics) · Cross-listed from cs.LG
f-GRPO and Beyond: Divergence-Based Reinforcement Learning Algorithms for General LLM Alignment
Rajdeep Haldar, Lantao Mei, Guang Lin et al. (+2 more)
Recent work shows that preference
alignment objectives can be interpreted as divergence
estimators between aligned (preferred) & unaligned (less-preferred) distributions, yielding a principled recipe for designing
alignment losses. However, this view has so far been limited to preference-based supervision. We extend it to general LLM
alignment, including reinforcement learning with verifiable rewards (RLVR), where
alignment feedback is given only as scalar rewards. We introduce $f$-Group Relative Policy Optimization ($f$-GRPO), a class of on-policy RL objectives, and $f$-Hybrid
Alignment Loss ($f$-HAL), which combines on-policy reward optimization with off-policy preference supervision. We show that these objectives estimate $f$-divergences between reward-aligned & reward-unaligned distributions induced by above- & below-average reward responses, and prove expected reward improvement after
alignment. Empirically, $f$-GRPO improves over GRPO on math-
reasoning RLVR tasks, while hybrid $f$-HAL mitigates reward hacking in on-policy safety
alignment when verifiable rewards are unavailable and learned reward models must be used.
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All authors Rajdeep Haldar, Lantao Mei, Guang Lin, Yue Xing, Qifan Song
Statistical Methodology
DiPPER: A Bayesian approach to differential prevalence analysis with applications in microbiome studies
Juho Pelto, Kari Auranen, Janne V. Kujala et al. (+1 more)
Recent evidence suggests that analyzing the presence/absence of taxonomic features can offer a compelling alternative to differential abundance analysis in microbiome studies. However, standard approaches to differential prevalence analysis face challenges with boundary cases and multiple testing. To address these limitations, we developed DiPPER (Differential Prevalence via Probabilistic Estimation in R), a method based on
Bayesian hierarchical modeling. We benchmarked our method against existing differential prevalence methods, along with two differential abundance tools, using publicly available data from 57 human gut microbiome studies. We observed considerable variation in performance across the evaluated methods. Importantly, DiPPER demonstrated high sensitivity to detect potentially differentially prevalent features while maintaining a well-calibrated family-wise error rate under the global null hypothesis. Most notably, it outperformed the alternatives in the replication of findings across independent studies. Furthermore, DiPPER provides differential prevalence estimates and uncertainty intervals that are inherently adjusted for multiple testing.
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All authors Juho Pelto, Kari Auranen, Janne V. Kujala, Leo Lahti
Machine Learning (Statistics)
Transformers Are Born Biased: Structural Inductive Biases at Random Initialization and Their Practical Consequences
Siquan Li, Yao Tong, Haonan Wang et al. (+1 more)
Transformers underpin modern large
language models (LLMs) and are commonly assumed to be behaviorally unstructured at random initialization, with all meaningful preferences emerging only through large-scale training. We challenge this assumption by showing that randomly initialized
transformers already exhibit strong and systematic structural biases. In particular, untrained models display extreme
token preferences: across random input sequences, certain
tokens are predicted with probabilities orders of magnitude larger. We provide a mechanistic explanation for this phenomenon by dissecting the
transformer architecture at initialization. We show that extreme
token preference arises from a contraction of
token representations along a random seed-dependent direction. This contraction is driven by two interacting forces: (i) asymmetric nonlinear activations in MLP sublayers induce global (inter-sequence) representation concentration, and (ii) self-
attention further amplifies this effect through local (intra-sequence) aggregation. Together, these mechanisms align hidden representations along a direction determined solely by the random initialization, producing highly non-uniform next-
token predictions. Beyond mechanistic insight, we demonstrate that these initialization-induced biases persist throughout training, forming a stable and intrinsic model identity. Leveraging this property, we introduce SeedPrint, a fingerprinting method that can reliably distinguish models that differ only in their random initialization, even after extensive training and under substantial distribution shift. Finally, we identify a fundamental positional discrepancy inherent to the
attention mechanism's intra-sequence contraction that is causally linked to the
attention-sink phenomenon. This discovery provides a principled explanation for the emergence of sinks and offers a pathway for their control.
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All authors Siquan Li, Yao Tong, Haonan Wang, Tianyang Hu
Machine Learning (Statistics)
Wedge Sampling: Efficient Tensor Completion with Nearly-Linear Sample Complexity
Hengrui Luo, Anna Ma, Ludovic Stephan et al. (+1 more)
We introduce Wedge Sampling, a new non-adaptive sampling scheme for low-rank tensor completion. We study recovery of an order-$k$ low-rank tensor of dimension $n\times\cdots\times n$ from structured observations of its entries. Unlike the standard uniform entry model (i.e., i.i.d. samples from $[n]^k$), wedge sampling allocates observations to structured length-two patterns (wedges) in an associated bipartite sampling graph. By directly promoting these length-two connections, the sampling design strengthens the spectral signal that underlies efficient initialization, in regimes where uniform sampling is too sparse to generate enough informative correlations. Our main result shows that this change in sampling paradigm enables
polynomial-time
algorithms to achieve both weak and exact recovery with nearly linear sample complexity in $n$. The approach is also plug-and-play: wedge-sampling-based spectral initialization can be combined with existing refinement procedures (e.g., spectral or gradient-based methods) using only an additional $\tilde O(n)$ uniformly sampled entries, substantially improving over the $\tilde O(n^{k/2})$ sample complexity typically required under uniform entry sampling for efficient methods. We also formulate a noisy wedge-sampling extension for additive Gaussian observations and analyze both the spectral and gradient-descent procedures under suitable signal-to-noise conditions. Thus, the computational barrier in tensor completion is sensitive to the observation model: while it persists under uniform entry sampling, it can be bypassed by non-adaptive structured designs that provide a stronger initialization.
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All authors Hengrui Luo, Anna Ma, Ludovic Stephan, Yizhe Zhu
Machine Learning (Statistics)
Distribution-free two-sample testing with blurred total variation distance
Rohan Hore and Rina Foygel Barber
Two-sample testing, where we aim to determine whether two distributions are equal or not equal based on samples from each one, is challenging if we cannot place assumptions on the properties of the two distributions. In particular, certifying equality of distributions, or even providing a tight upper bound on the total variation (TV) distance between the distributions, is impossible to achieve in a distribution-free regime. In this work, we examine the blurred TV distance, a relaxation of TV distance that enables us to perform inference without assumptions on the distributions. We provide theoretical guarantees for distribution-free upper and lower bounds on the blurred TV distance, and examine its properties in high dimensions.
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Machine Learning (Statistics) · Cross-listed from cs.LG
CFRecs: Counterfactual Recommendations on Real Estate User Listing Interaction Graphs
Seyedmasoud Mousavi, Ruomeng Xu and Xiaojing Zhu
Graph-structured data is ubiquitous and powerful in representing complex relationships in many online platforms. While graph neural networks (GNNs) are widely used to learn from such data, counterfactual graph learning has emerged as a promising approach to improve model interpretability. Counterfactual explanation research focuses on identifying a counterfactual graph that is similar to the original but leads to different predictions. These explanations optimize two objectives simultaneously: the sparsity of changes in the counterfactual graph and the validity of its predictions. Building on these qualitative optimization goals, this paper introduces CFRecs, a novel framework that transforms counterfactual explanations into actionable insights. CFRecs employs a two-stage architecture consisting of a graph neural network (GNN) and a graph variational auto-encoder (Graph-VAE) to strategically propose minimal yet high-impact changes in graph structure and node attributes to drive desirable outcomes in recommender systems. We apply CFRecs to Zillow's graph-structured data to deliver actionable recommendations for both home buyers and sellers with the goal of helping them navigate the competitive housing
market and achieve their homeownership goals. Experimental results on Zillow's user-listing interaction data demonstrate the effectiveness of CFRecs, which also provides a fresh perspective on recommendations using counterfactual
reasoning in graphs.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Exact Recovery in the Data Block Model
Amir R. Asadi, Akbar Davoodi, Ramin Javadi et al. (+1 more)
Community detection in networks is a fundamental problem in machine learning and statistical inference, with applications in social networks, biological systems, and communication networks. The
stochastic block model (SBM) serves as a canonical framework for studying community structure, and exact recovery, identifying the true communities with high probability, is a central theoretical question. While classical results characterize the phase transition for exact recovery based solely on graph connectivity, many real-world networks contain additional data, such as node attributes or labels. In this work, we study exact recovery in the Data Block Model (DBM), an SBM augmented with node-associated data, as formalized by Asadi, Abbe, and Verdú (2017). We introduce the Chernoff–TV divergence and use it to characterize a sharp exact recovery threshold for the DBM. We further provide an efficient
algorithm that achieves this threshold, along with a matching converse result showing impossibility below the threshold. Finally, simulations validate our findings and demonstrate the benefits of incorporating vertex data as side information in community detection.
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All authors Amir R. Asadi, Akbar Davoodi, Ramin Javadi, Farzad Parvaresh