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Unsupervised learning of acquisition variability in structural connectomes via hybrid latent space modeling

arXiv.org Machine Learning

Acquisition differences across sites, scanners, and protocols in dMRI introduce variability that complicates structural connectome analysis. This motivates deep learning models that can represent high-dimensional connectomes in a low-dimensional space while explicitly separating acquisition-related effects from biological variation. Conventional dimensionality reduction methods model all variance as continuous, so acquisition effects often get absorbed into a continuous latent space. Recent hybrid latent-space models combine discrete and continuous components to address this, but typically require manual capacity tuning to ensure the discrete component captures the intended variability. We introduce an unsupervised framework that removes this manual tuning by architecturally annealing encoder outputs before decoding, allowing the model to adaptively balance discrete and continuous latent variables during training. To evaluate it, we curated a dataset of N=7,416 structural connectomes derived from dMRI, spanning ages 2 to 102 and 13 studies with 25 unique acquisition-parameter combinations. Of these, 5,900 are cognitively unimpaired, 877 have mild cognitive impairment (MCI), and 639 have Alzheimer's disease (AD). We compare against a standard VAE, PCA with k-means clustering, and hybrid models that anneal only through the loss function. Our architectural annealing produces stronger site learning (ARI=0.53, p<0.05) than these baselines. Results show that a hybrid continuous-discrete latent space, with architectural rather than loss-based annealing, provides a useful unsupervised mechanism for capturing acquisition variability in dMRI: by jointly modeling smooth and categorical structure, the Joint-VAE recovers clusters aligned with scanner and protocol differences.


Winning Lottery Tickets in Neural Networks via a Quantum-Inspired Classical Algorithm

arXiv.org Machine Learning

Quantum machine learning (QML) aims to accelerate machine learning tasks by exploiting quantum computation. Previous work studied a QML algorithm for selecting sparse subnetworks from large shallow neural networks. Instead of directly solving an optimization problem over a large-scale network, this algorithm constructs a sparse subnetwork by sampling hidden nodes from an optimized probability distribution defined using the ridgelet transform. The quantum algorithm performs this sampling in time $O(D)$ in the data dimension $D$, whereas a naive classical implementation relies on handling exponentially many candidate nodes and hence takes $\exp[O(D)]$ time. In this work, we construct and analyze a quantum-inspired fully classical algorithm for the same sampling task. We show that our algorithm runs in time $O(\operatorname{poly}(D))$, thereby removing the exponential dependence on $D$ from the previous classical approach. Numerical simulations show that the proposed sampler achieves empirical risk comparable to exact sampling from the optimized distribution and substantially lower than sampling from the non-optimized uniform distribution, while also exhibiting exponentially improved runtime scaling compared with the conventional classical implementation. These successful dequantization results show that sparse subnetwork selection via optimized sampling can be achieved classically with polynomial data-dimension scaling on conventional computers without quantum hardware, providing an alternative to the existing quantum algorithm.


TabPFN-3: Technical Report

arXiv.org Machine Learning

Tabular data underpins most high-value prediction problems in science and industry, and TabPFN has driven the foundation model revolution for this modality. Designed with feedback from our users, TabPFN-3 builds on this foundation to scale state-of-the-art performance to datasets with 1M training rows and substantially reduce training and inference time. Pretrained exclusively on synthetic data from our prior, TabPFN-3 dramatically pushes the frontier of tabular prediction and brings substantial gains on time series, relational, and tabular-text data. On the standard tabular benchmark TabArena, a forward pass of TabPFN-3 outperforms all other models, including tuned and ensembled baselines, by a significant margin, and pareto-dominates the speed/performance frontier. On more diverse datasets, TabPFN-3 ranks first on datasets with many classes, and beats 8-hour-tuned gradient-boosted-tree baselines on datasets up to 1M training rows and 200 features. TabPFN-3 introduces test-time compute scaling to tabular foundation models. Our API offering TabPFN-3-Plus (Thinking) exploits this to beat all non-TabPFN models by over 200 Elo on TabArena, rising to 420 Elo on the largest data subset, and outperforms AutoGluon 1.5 extreme while being 10x faster, without using LLMs, real data, internet search or any other model besides TabPFN. TabPFN-3 extends the capabilities of our models, enabling SOTA prediction on relational data (new SOTA foundation model on RelBenchV1) and tabular-text data (SOTA on TabSTAR via TabPFN-3-Plus); and improves existing integrations: a specialized checkpoint, TabPFN-TS-3, ranks 2nd on the time-series benchmark fev-bench, and SHAP-value computation is up to 120x faster. TabPFN-3 achieves this performance while being up to 20x faster than TabPFN-2.5. In addition, a reduced KV cache and row-chunking scale to 1M rows on one H100 with fast inference speed.


Finite-size scaling of hetero-associative retrieval in continuous-signal-driven Ising spin systems

arXiv.org Machine Learning

Kosko's Bidirectional Associative Memory [17] first formalised this idea for two layers, showing that stable recallContent-addressable memory--the recovery of a complete stored record from a partial or degraded cue--is aarises from the same energy-descent principle as in Hopcornerstone of neural computation and a paradigmaticfield networks but across two distinct pattern spaces: a problem in the statistical mechanics of disordered sys-cue presented to one layer drives the other toward the tems. The Hopfield model [1] demonstrated that binarymatching stored pattern, enabling cross-modal compleNtion. Multi-species spin-glass analyses [18] subsequentlypatterns in { 1,+1} can be stored as fixed-point attractors of an energy landscape shaped by Hebbian couplings, provided a rigorous thermodynamic foundation for arwhile Little's earlier stochastic formulation [2] cast thechitectures with an arbitrary number of interacting popsame architecture in the language of equilibrium statisti-ulations, generalising the classical single-species phase cal mechanics through parallel probabilistic updates.


Pause and Reflect: Conformal Aggregation for Chain-of-Thought Reasoning

arXiv.org Machine Learning

Chain-of-thought (CoT) reasoning with self-consistency improves performance by aggregating multiple sampled reasoning paths. In this setting, correctness is no longer tied to a single reasoning trace but to the aggregation rule over a pool of candidate paths, making aggregation uncertainty the central challenge. This issue is critical where confidently incorrect answers are far more costly than abstentions. We introduce a conformal procedure for CoT reasoning that directly addresses aggregation uncertainty. Our approach replaces majority voting with weighted score aggregation over reasoning paths and calibrates an abstention rule using conformal risk control. This approach leads to finite-sample guarantees on the confident-error rate--the probability that the system answers and is wrong. We further identify score separability as the key condition under which abstention provably improves selective accuracy, and derive closed-form expressions that predict accuracy gains from calibration data alone. The method is fully inference-time, and requires no retraining. Across four benchmarks, four open-source models, and three score classes, realized confident-error rates are consistent with the prescribed targets up to calibration-split and test-set variability. Our method achieves $90.1\%$ selective accuracy on GSM8K by abstaining on less than $5\%$ of problems, compared with $82\%$ accuracy under majority-voting baseline.


To discretize continually: Mean shift interacting particle systems for Bayesian inference

arXiv.org Machine Learning

Integration against a probability distribution given its unnormalized density is a central task in Bayesian inference and other fields. We introduce new methods for approximating such expectations with a small set of weighted samples -- i.e., a quadrature rule -- constructed via an interacting particle system that minimizes maximum mean discrepancy (MMD) to the target distribution. These methods extend the classical mean shift algorithm, as well as recent algorithms for optimal quantization of empirical distributions, to the case of continuous distributions. Crucially, our approach creates dynamics for MMD minimization that are invariant to the unknown normalizing constant; they also admit both gradient-free and gradient-informed implementations. The resulting mean shift interacting particle systems converge quickly, capture anisotropy and multi-modality, avoid mode collapse, and scale to high dimensions. We demonstrate their performance on a wide range of benchmark sampling problems, including multi-modal mixtures, Bayesian hierarchical models, PDE-constrained inverse problems, and beyond.


Finite Sample Bounds for Learning with Score Matching

arXiv.org Machine Learning

Learning of continuous exponential family distributions with unbounded support remains an important area of research for both theory and applications in high-dimensional statistics. In recent years, score matching has become a widely used method for learning exponential families with continuous variables due to its computational ease when compared against maximum likelihood estimation. However, theoretical understanding of the statistical properties of score matching is still lacking. In this work, we provide a non-asymptotic sample complexity analysis for learning the structure of exponential families of polynomials with score matching. The derived sample bounds show a polynomial dependence on the model dimension. These bounds are the first of its kind, as all prior work has shown only asymptotic bounds on the sample complexity.


How to Scale Mixture-of-Experts: From muP to the Maximally Scale-Stable Parameterization

arXiv.org Machine Learning

Recent frontier large language models predominantly rely on Mixture-of-Experts (MoE) architectures. Despite empirical progress, there is still no principled understanding of how hyperparameters should scale with network width $N$, expert width $N_e$, number of experts $M$, sparsity $K$, and depth $L$ to ensure both stability and optimal performance at scale. We take a principled step toward resolving this gap by analyzing three different scaling regimes: (I) co-scaling $N\asymp N_e$, (II) co-scaling $N\asymp M\asymp K$, and (III) full proportional scaling of $N, N_e, M$, and $K$. For each regime, we develop a novel Dynamical Mean Field Theory (DMFT) description of the limiting training dynamics of MoEs that provides a formal foundation for our analysis. Within this framework, we derive the unique parameterization for SGD and Adam satisfying all maximal-update ($ฮผ$) desiderata. We then show that the resulting $ฮผ$P prescription does not reliably induce monotonic improvement with scale or robust learning-rate transfer. We trace these pathologies to scale-dependent observables in the aggregation dynamics, which motivates a refined set of desiderata that we term maximal scale stability. Guided by this principle, we derive a Maximally Scale-Stable Parameterization (MSSP) for both SGD and Adam in all three scaling regimes, and characterize the corresponding limiting dynamics - qualitatively distinct from the $ฮผ$P limit - through a separate DMFT analysis. Experiments verify that MSSP robustly recovers learning rate transfer and monotonic improvement with scale across regimes. Combined with existing depth-scaling theory, these results provide a complete scaling prescription for MoE architectures as a function of width, depth, expert width, and number of experts.


Training-Free Generative Sampling via Moment-Matched Score Smoothing

arXiv.org Machine Learning

Diffusion models generate samples by denoising along the score of a perturbed target distribution. In practice, one trains a neural diffusion model, which is computationally expensive. Recent work suggests that score matching implicitly smooths the empirical score, and that this smoothing bias promotes generalization by capturing low-dimensional data geometry. We propose moment-matched score-smoothed overdamped Langevin dynamics (MM-SOLD), a training-free interacting particle sampler that enforces the target moments throughout the sampling trajectory. We prove that, in the large-particle limit, the empirical particle density converges to a deterministic limit whose one-particle stationary marginal is a Gibbs--Boltzmann density obtained by exponentially tilting a naive score-smoothed diffusion target. The mean and covariance of this distribution agree with the empirical moments of the training data. Experiments on 2D distributions and latent-space image generation show that MM-SOLD enables fast, robust, training-free sampling on CPUs, with sample fidelity and diversity competitive with neural diffusion baselines.


TILT: Target-induced loss tilting under covariate shift

arXiv.org Machine Learning

We introduce and analyze Target-Induced Loss Tilting (TILT) for unsupervised domain adaptation under covariate shift. It is based on a novel objective function that decomposes the source predictor as $f+b$, fits $f+b$ on labeled source data while simultaneously penalizing the auxiliary component $b$ on unlabeled target inputs. The resulting fit $f$ is deployed as the final target predictor. At the population level, we show that this target-side penalty implicitly induces relative importance weighting at the population level, but in terms of an estimand $b^*_f$ that is self-localized to the current error, and remains uniformly bounded for any source-target pair (even those with disjoint supports). We prove a general finite-sample oracle inequality on the excess risk, and use it to give an end-to-end guarantee for training with sparse ReLU networks. Experiments on controlled regression problems and shifted CIFAR-100 distillation show that TILT improves target-domain performance over source-only training, exact importance weighting, and relative density-ratio baselines, with a stable dependence on the regularization parameter.