Daily Papers

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Deterministic inference is a comforting ideal in classical software: the same program on the same input should always produce the same output. As large language models move into real-world deployment, this ideal has been imported wholesale into inference stacks. Recent work from the Thinking Machines Lab has presented a detailed analysis of nondeterminism in LLM inference, showing how batch-invariant kernels and deterministic attention can enforce bitwise-identical outputs, positioning deterministic inference as a prerequisite for reproducibility and enterprise reliability. In this paper, we take the opposite stance. We argue that, for LLMs, deterministic inference kills. It kills the ability to model uncertainty, suppresses emergent abilities, collapses reasoning into a single brittle path, and weakens safety alignment by hiding tail risks. LLMs implement conditional distributions over outputs, not fixed functions. Collapsing these distributions to a single canonical completion may appear reassuring, but it systematically conceals properties central to artificial cognition. We instead advocate Stochastic CHAOS, treating distributional variability as a signal to be measured and controlled. Empirically, we show that deterministic inference is systematically misleading. Single-sample deterministic evaluation underestimates both capability and fragility, masking failure probability under paraphrases and noise. Phase-like transitions associated with emergent abilities disappear under greedy decoding. Multi-path reasoning degrades when forced onto deterministic backbones, reducing accuracy and diagnostic insight. Finally, deterministic evaluation underestimates safety risk by hiding rare but dangerous behaviors that appear only under multi-sample evaluation.

Tangles were originally introduced as a concept to formalize regions of high connectivity in graphs. In recent years, they have also been discovered as a link between structural graph theory and data science: when interpreting similarity in data sets as connectivity between points, finding clusters in the data essentially amounts to finding tangles in the underlying graphs. This paper further explores the potential of tangles in data sets as a means for a formal study of clusters. Real-world data often follow a normal distribution. Accounting for this, we develop a quantitative theory of tangles in data sets drawn from Gaussian mixtures. To this end, we equip the data with a graph structure that models similarity between the points and allows us to apply tangle theory to the data. We provide explicit conditions under which tangles associated with the marginal Gaussian distributions exist asymptotically almost surely. This can be considered as a sufficient formal criterion for the separabability of clusters in the data.

The analysis of parametric and non-parametric uncertainties of very large dynamical systems requires the construction of a stochastic model of said system. Linear approaches relying on random matrix theory and principal componant analysis can be used when systems undergo low-frequency vibrations. In the case of fast dynamics and wave propagation, we investigate a random generator of boundary conditions for fast submodels by using machine learning. We show that the use of non-linear techniques in machine learning and data-driven methods is highly relevant. Physics-informed neural networks is a possible choice for a data-driven method to replace linear modal analysis. An architecture that support a random component is necessary for the construction of the stochastic model of the physical system for non-parametric uncertainties, since the goal is to learn the underlying probabilistic distribution of uncertainty in the data. Generative Adversarial Networks (GANs) are suited for such applications, where the Wasserstein-GAN with gradient penalty variant offers improved convergence results for our problem. The objective of our approach is to train a GAN on data from a finite element method code (Fenics) so as to extract stochastic boundary conditions for faster finite element predictions on a submodel. The submodel and the training data have both the same geometrical support. It is a zone of interest for uncertainty quantification and relevant to engineering purposes. In the exploitation phase, the framework can be viewed as a randomized and parametrized simulation generator on the submodel, which can be used as a Monte Carlo estimator.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

Intelligent systems across physics, language and perception often exhibit factorisable structure, yet are typically modelled by monolithic neural architectures that do not explicitly exploit this structure. The separable neural architecture (SNA) addresses this by formalising a representational class that unifies additive, quadratic and tensor-decomposed neural models. By constraining interaction order and tensor rank, SNAs impose a structural inductive bias that factorises high-dimensional mappings into low-arity components. Separability need not be a property of the system itself: it often emerges in the coordinates or representations through which the system is expressed. Crucially, this coordinate-aware formulation reveals a structural analogy between chaotic spatiotemporal dynamics and linguistic autoregression. By treating continuous physical states as smooth, separable embeddings, SNAs enable distributional modelling of chaotic systems. This approach mitigates the nonphysical drift characteristics of deterministic operators whilst remaining applicable to discrete sequences. The compositional versatility of this approach is demonstrated across four domains: autonomous waypoint navigation via reinforcement learning, inverse generation of multifunctional microstructures, distributional modelling of turbulent flow and neural language modelling. These results establish the separable neural architecture as a domain-agnostic primitive for predictive and generative intelligence, capable of unifying both deterministic and distributional representations.

Vision-language models (VLMs) achieve strong multimodal performance, yet how computation is organized across populations of neurons remains poorly understood. In this work, we study VLMs through the lens of neural topology, representing each layer as a within-layer correlation graph derived from neuron-neuron co-activations. This view allows us to ask whether population-level structure is behaviorally meaningful, how it changes across modalities and depth, and whether it identifies causally influential internal components under intervention. We show that correlation topology carries recoverable behavioral signal; moreover, cross-modal structure progressively consolidates with depth around a compact set of recurrent hub neurons, whose targeted perturbation substantially alters model output. Neural topology thus emerges as a meaningful intermediate scale for VLM interpretability: richer than local attribution, more tractable than full circuit recovery, and empirically tied to multimodal behavior. Code is publicly available at https://github.com/he-h/vlm-graph-probing.

The success of deep learning is due in large part to our ability to solve certain massive non-convex optimization problems with relative ease. Though non-convex optimization is NP-hard, simple algorithms -- often variants of stochastic gradient descent -- exhibit surprising effectiveness in fitting large neural networks in practice. We argue that neural network loss landscapes often contain (nearly) a single basin after accounting for all possible permutation symmetries of hidden units a la Entezari et al. 2021. We introduce three algorithms to permute the units of one model to bring them into alignment with a reference model in order to merge the two models in weight space. This transformation produces a functionally equivalent set of weights that lie in an approximately convex basin near the reference model. Experimentally, we demonstrate the single basin phenomenon across a variety of model architectures and datasets, including the first (to our knowledge) demonstration of zero-barrier linear mode connectivity between independently trained ResNet models on CIFAR-10. Additionally, we identify intriguing phenomena relating model width and training time to mode connectivity. Finally, we discuss shortcomings of the linear mode connectivity hypothesis, including a counterexample to the single basin theory.

Markov categories are a novel framework to describe and treat problems in probability and information theory. In this work we combine the categorical formalism with the traditional quantitative notions of entropy, mutual information, and data processing inequalities. We show that several quantitative aspects of information theory can be captured by an enriched version of Markov categories, where the spaces of morphisms are equipped with a divergence or even a metric. As it is customary in information theory, mutual information can be defined as a measure of how far a joint source is from displaying independence of its components. More strikingly, Markov categories give a notion of determinism for sources and channels, and we can define entropy exactly by measuring how far a source or channel is from being deterministic. This recovers Shannon and R\'enyi entropies, as well as the Gini-Simpson index used in ecology to quantify diversity, and it can be used to give a conceptual definition of generalized entropy.

Structured state-space models (SSMs) such as S4, stemming from the seminal work of Gu et al., are gaining popularity as effective approaches for modeling sequential data. Deep SSMs demonstrate outstanding performance across a diverse set of domains, at a reduced training and inference cost compared to attention-based transformers. Recent developments show that if the linear recurrence powering SSMs allows for multiplicative interactions between inputs and hidden states (e.g. GateLoop, Mamba, GLA), then the resulting architecture can surpass in both in accuracy and efficiency attention-powered foundation models trained on text, at scales of billion parameters. In this paper, we give theoretical grounding to this recent finding using tools from Rough Path Theory: we show that when random linear recurrences are equipped with simple input-controlled transitions (selectivity mechanism), then the hidden state is provably a low-dimensional projection of a powerful mathematical object called the signature of the input -- capturing non-linear interactions between tokens at distinct timescales. Our theory not only motivates the success of modern selective state-space models such as Mamba but also provides a solid framework to understand the expressive power of future SSM variants.

The neural Hawkes process (Mei & Eisner, 2017) is a generative model of irregularly spaced sequences of discrete events. To handle complex domains with many event types, Mei et al. (2020a) further consider a setting in which each event in the sequence updates a deductive database of facts (via domain-specific pattern-matching rules); future events are then conditioned on the database contents. They show how to convert such a symbolic system into a neuro-symbolic continuous-time generative model, in which each database fact and the possible event has a time-varying embedding that is derived from its symbolic provenance. In this paper, we modify both models, replacing their recurrent LSTM-based architectures with flatter attention-based architectures (Vaswani et al., 2017), which are simpler and more parallelizable. This does not appear to hurt our accuracy, which is comparable to or better than that of the original models as well as (where applicable) previous attention-based methods (Zuo et al., 2020; Zhang et al., 2020a).

We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains - parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.

The striking fractal geometry of strange attractors underscores the generative nature of chaos: like probability distributions, chaotic systems can be repeatedly measured to produce arbitrarily-detailed information about the underlying attractor. Chaotic systems thus pose a unique challenge to modern statistical learning techniques, while retaining quantifiable mathematical properties that make them controllable and interpretable as benchmarks. Here, we present a growing database currently comprising 131 known chaotic dynamical systems spanning fields such as astrophysics, climatology, and biochemistry. Each system is paired with precomputed multivariate and univariate time series. Our dataset has comparable scale to existing static time series databases; however, our systems can be re-integrated to produce additional datasets of arbitrary length and granularity. Our dataset is annotated with known mathematical properties of each system, and we perform feature analysis to broadly categorize the diverse dynamics present across the collection. Chaotic systems inherently challenge forecasting models, and across extensive benchmarks we correlate forecasting performance with the degree of chaos present. We also exploit the unique generative properties of our dataset in several proof-of-concept experiments: surrogate transfer learning to improve time series classification, importance sampling to accelerate model training, and benchmarking symbolic regression algorithms.

We develop a framework for non-asymptotic analysis of deterministic samplers used for diffusion generative modeling. Several recent works have analyzed stochastic samplers using tools like Girsanov's theorem and a chain rule variant of the interpolation argument. Unfortunately, these techniques give vacuous bounds when applied to deterministic samplers. We give a new operational interpretation for deterministic sampling by showing that one step along the probability flow ODE can be expressed as two steps: 1) a restoration step that runs gradient ascent on the conditional log-likelihood at some infinitesimally previous time, and 2) a degradation step that runs the forward process using noise pointing back towards the current iterate. This perspective allows us to extend denoising diffusion implicit models to general, non-linear forward processes. We then develop the first polynomial convergence bounds for these samplers under mild conditions on the data distribution.

We examine the geometry of neural network training using the Jacobian of trained network parameters with respect to their initial values. Our analysis reveals low-dimensional structure in the training process which is dependent on the input data but largely independent of the labels. We find that the singular value spectrum of the Jacobian matrix consists of three distinctive regions: a "chaotic" region of values orders of magnitude greater than one, a large "bulk" region of values extremely close to one, and a "stable" region of values less than one. Along each bulk direction, the left and right singular vectors are nearly identical, indicating that perturbations to the initialization are carried through training almost unchanged. These perturbations have virtually no effect on the network's output in-distribution, yet do have an effect far out-of-distribution. While the Jacobian applies only locally around a single initialization, we find substantial overlap in bulk subspaces for different random seeds. Our code is available at https://github.com/EleutherAI/training-jacobian

Can we learn more from data than existed in the generating process itself? Can new and useful information be constructed from merely applying deterministic transformations to existing data? Can the learnable content in data be evaluated without considering a downstream task? On these questions, Shannon information and Kolmogorov complexity come up nearly empty-handed, in part because they assume observers with unlimited computational capacity and fail to target the useful information content. In this work, we identify and exemplify three seeming paradoxes in information theory: (1) information cannot be increased by deterministic transformations; (2) information is independent of the order of data; (3) likelihood modeling is merely distribution matching. To shed light on the tension between these results and modern practice, and to quantify the value of data, we introduce epiplexity, a formalization of information capturing what computationally bounded observers can learn from data. Epiplexity captures the structural content in data while excluding time-bounded entropy, the random unpredictable content exemplified by pseudorandom number generators and chaotic dynamical systems. With these concepts, we demonstrate how information can be created with computation, how it depends on the ordering of the data, and how likelihood modeling can produce more complex programs than present in the data generating process itself. We also present practical procedures to estimate epiplexity which we show capture differences across data sources, track with downstream performance, and highlight dataset interventions that improve out-of-distribution generalization. In contrast to principles of model selection, epiplexity provides a theoretical foundation for data selection, guiding how to select, generate, or transform data for learning systems.

The enduring legacy of Euclidean geometry underpins classical machine learning, which, for decades, has been primarily developed for data lying in Euclidean space. Yet, modern machine learning increasingly encounters richly structured data that is inherently nonEuclidean. This data can exhibit intricate geometric, topological and algebraic structure: from the geometry of the curvature of space-time, to topologically complex interactions between neurons in the brain, to the algebraic transformations describing symmetries of physical systems. Extracting knowledge from such non-Euclidean data necessitates a broader mathematical perspective. Echoing the 19th-century revolutions that gave rise to non-Euclidean geometry, an emerging line of research is redefining modern machine learning with non-Euclidean structures. Its goal: generalizing classical methods to unconventional data types with geometry, topology, and algebra. In this review, we provide an accessible gateway to this fast-growing field and propose a graphical taxonomy that integrates recent advances into an intuitive unified framework. We subsequently extract insights into current challenges and highlight exciting opportunities for future development in this field.

The input space of a neural network with ReLU-like activations is partitioned into multiple linear regions, each corresponding to a specific activation pattern of the included ReLU-like activations. We demonstrate that this partition exhibits the following encoding properties across a variety of deep learning models: (1) {\it determinism}: almost every linear region contains at most one training example. We can therefore represent almost every training example by a unique activation pattern, which is parameterized by a {\it neural code}; and (2) {\it categorization}: according to the neural code, simple algorithms, such as K-Means, K-NN, and logistic regression, can achieve fairly good performance on both training and test data. These encoding properties surprisingly suggest that {\it normal neural networks well-trained for classification behave as hash encoders without any extra efforts.} In addition, the encoding properties exhibit variability in different scenarios. {Further experiments demonstrate that {\it model size}, {\it training time}, {\it training sample size}, {\it regularization}, and {\it label noise} contribute in shaping the encoding properties, while the impacts of the first three are dominant.} We then define an {\it activation hash phase chart} to represent the space expanded by {model size}, training time, training sample size, and the encoding properties, which is divided into three canonical regions: {\it under-expressive regime}, {\it critically-expressive regime}, and {\it sufficiently-expressive regime}. The source code package is available at https://github.com/LeavesLei/activation-code.

We study the statistics of the local resolvent and non-ergodic properties of eigenvectors for a generalised Rosenzweig-Porter Ntimes N random matrix model, undergoing two transitions separated by a delocalised non-ergodic phase. Interpreting the model as the combination of on-site random energies {a_i} and a structurally disordered hopping, we found that each eigenstate is delocalised over N^{2-gamma} sites close in energy |a_j-a_i|leq N^{1-gamma} in agreement with Kravtsov et al, arXiv:1508.01714. Our other main result, obtained combining a recurrence relation for the resolvent matrix with insights from Dyson's Brownian motion, is to show that the properties of the non-ergodic delocalised phase can be probed studying the statistics of the local resolvent in a non-standard scaling limit.

In bipartite networks, community structures are restricted to being disassortative, in that nodes of one type are grouped according to common patterns of connection with nodes of the other type. This makes the stochastic block model (SBM), a highly flexible generative model for networks with block structure, an intuitive choice for bipartite community detection. However, typical formulations of the SBM do not make use of the special structure of bipartite networks. Here we introduce a Bayesian nonparametric formulation of the SBM and a corresponding algorithm to efficiently find communities in bipartite networks which parsimoniously chooses the number of communities. The biSBM improves community detection results over general SBMs when data are noisy, improves the model resolution limit by a factor of 2, and expands our understanding of the complicated optimization landscape associated with community detection tasks. A direct comparison of certain terms of the prior distributions in the biSBM and a related high-resolution hierarchical SBM also reveals a counterintuitive regime of community detection problems, populated by smaller and sparser networks, where nonhierarchical models outperform their more flexible counterpart.

Deep neural networks can approximate functions on different types of data, from images to graphs, with varied underlying structure. This underlying structure can be viewed as the geometry of the data manifold. By extending recent advances in the theoretical understanding of neural networks, we study how a randomly initialized neural network with piece-wise linear activation splits the data manifold into regions where the neural network behaves as a linear function. We derive bounds on the density of boundary of linear regions and the distance to these boundaries on the data manifold. This leads to insights into the expressivity of randomly initialized deep neural networks on non-Euclidean data sets. We empirically corroborate our theoretical results using a toy supervised learning problem. Our experiments demonstrate that number of linear regions varies across manifolds and the results hold with changing neural network architectures. We further demonstrate how the complexity of linear regions is different on the low dimensional manifold of images as compared to the Euclidean space, using the MetFaces dataset.

Recurrent neural networks (RNNs) provide a powerful approach in neuroscience to infer latent dynamics in neural populations and to generate hypotheses about the neural computations underlying behavior. However, past work has focused on relatively simple, input-driven, and largely deterministic behaviors - little is known about the mechanisms that would allow RNNs to generate the richer, spontaneous, and potentially stochastic behaviors observed in natural settings. Modeling with Hidden Markov Models (HMMs) has revealed a segmentation of natural behaviors into discrete latent states with stochastic transitions between them, a type of dynamics that may appear at odds with the continuous state spaces implemented by RNNs. Here we first show that RNNs can replicate HMM emission statistics and then reverse-engineer the trained networks to uncover the mechanisms they implement. In the absence of inputs, the activity of trained RNNs collapses towards a single fixed point. When driven by stochastic input, trajectories instead exhibit noise-sustained dynamics along closed orbits. Rotation along these orbits modulates the emission probabilities and is governed by transitions between regions of slow, noise-driven dynamics connected by fast, deterministic transitions. The trained RNNs develop highly structured connectivity, with a small set of "kick neurons" initiating transitions between these regions. This mechanism emerges during training as the network shifts into a regime of stochastic resonance, enabling it to perform probabilistic computations. Analyses across multiple HMM architectures - fully connected, cyclic, and linear-chain - reveal that this solution generalizes through the modular reuse of the same dynamical motif, suggesting a compositional principle by which RNNs can emulate complex discrete latent dynamics.

Many clustering schemes are defined by optimizing an objective function defined on the partitions of the underlying set of a finite metric space. In this paper, we construct a framework for studying what happens when we instead impose various structural conditions on the clustering schemes, under the general heading of functoriality. Functoriality refers to the idea that one should be able to compare the results of clustering algorithms as one varies the data set, for example by adding points or by applying functions to it. We show that within this framework, one can prove a theorems analogous to one of J. Kleinberg, in which for example one obtains an existence and uniqueness theorem instead of a non-existence result. We obtain a full classification of all clustering schemes satisfying a condition we refer to as excisiveness. The classification can be changed by varying the notion of maps of finite metric spaces. The conditions occur naturally when one considers clustering as the statistical version of the geometric notion of connected components. By varying the degree of functoriality that one requires from the schemes it is possible to construct richer families of clustering schemes that exhibit sensitivity to density.

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks that lack stochastic layers) or averaged responses (e.g., trial-averaged firing rates in biological data). However, these measures of _deterministic_ representational similarity ignore the scale and geometric structure of noise, both of which play important roles in neural computation. To rectify this, we generalize previously proposed shape metrics (Williams et al. 2021) to quantify differences in _stochastic_ representations. These new distances satisfy the triangle inequality, and thus can be used as a rigorous basis for many supervised and unsupervised analyses. Leveraging this novel framework, we find that the stochastic geometries of neurobiological representations of oriented visual gratings and naturalistic scenes respectively resemble untrained and trained deep network representations. Further, we are able to more accurately predict certain network attributes (e.g. training hyperparameters) from its position in stochastic (versus deterministic) shape space.

Dynamical systems (DS) theory is fundamental for many areas of science and engineering. It can provide deep insights into the behavior of systems evolving in time, as typically described by differential or recursive equations. A common approach to facilitate mathematical tractability and interpretability of DS models involves decomposing nonlinear DS into multiple linear DS separated by switching manifolds, i.e. piecewise linear (PWL) systems. PWL models are popular in engineering and a frequent choice in mathematics for analyzing the topological properties of DS. However, hand-crafting such models is tedious and only possible for very low-dimensional scenarios, while inferring them from data usually gives rise to unnecessarily complex representations with very many linear subregions. Here we introduce Almost-Linear Recurrent Neural Networks (AL-RNNs) which automatically and robustly produce most parsimonious PWL representations of DS from time series data, using as few PWL nonlinearities as possible. AL-RNNs can be efficiently trained with any SOTA algorithm for dynamical systems reconstruction (DSR), and naturally give rise to a symbolic encoding of the underlying DS that provably preserves important topological properties. We show that for the Lorenz and R\"ossler systems, AL-RNNs discover, in a purely data-driven way, the known topologically minimal PWL representations of the corresponding chaotic attractors. We further illustrate on two challenging empirical datasets that interpretable symbolic encodings of the dynamics can be achieved, tremendously facilitating mathematical and computational analysis of the underlying systems.

We develop a method to generate predictive regions that cover a multivariate response variable with a user-specified probability. Our work is composed of two components. First, we use a deep generative model to learn a representation of the response that has a unimodal distribution. Existing multiple-output quantile regression approaches are effective in such cases, so we apply them on the learned representation, and then transform the solution to the original space of the response. This process results in a flexible and informative region that can have an arbitrary shape, a property that existing methods lack. Second, we propose an extension of conformal prediction to the multivariate response setting that modifies any method to return sets with a pre-specified coverage level. The desired coverage is theoretically guaranteed in the finite-sample case for any distribution. Experiments conducted on both real and synthetic data show that our method constructs regions that are significantly smaller compared to existing techniques.

Recent large-scale neural autoregressive sequence models have shown impressive performances on a variety of natural language generation tasks. However, their generated sequences often exhibit degenerate properties such as non-termination, undesirable repetition, and premature termination, when generated with decoding algorithms such as greedy search, beam search, top-k sampling, and nucleus sampling. In this paper, we focus on the problem of non-terminating sequences resulting from an incomplete decoding algorithm. We first define an incomplete probable decoding algorithm which includes greedy search, top-k sampling, and nucleus sampling, beyond the incomplete decoding algorithm originally put forward by Welleck et al. (2020). We then propose a non-monotonic self-terminating language model, which significantly relaxes the constraint of monotonically increasing termination probability in the originally proposed self-terminating language model by Welleck et al. (2020), to address the issue of non-terminating sequences when using incomplete probable decoding algorithms. We prove that our proposed model prevents non-terminating sequences when using not only incomplete probable decoding algorithms but also beam search. We empirically validate our model on sequence completion tasks with various architectures.

In recent years, persistent homology (PH) has been successfully applied to real-world data in many different settings. Despite significant computational advances, PH algorithms do not yet scale to large datasets preventing interesting applications. One approach to address computational issues posed by PH is to select a set of landmarks by subsampling from the data. Currently, these landmark points are chosen either at random or using the maxmin algorithm. Neither is ideal as random selection tends to favour dense areas of the data while the maxmin algorithm is very sensitive to noise. Here, we propose a novel approach to select landmarks specifically for PH that preserves coarse topological information of the original dataset. Our method is motivated by the Mayer-Vietoris sequence and requires only local PH computation thus enabling efficient computation. We test our landmarks on artificial datasets which contain different levels of noise and compare them to standard landmark selection techniques. We demonstrate that our landmark selection outperforms standard methods as well as a subsampling technique based on an outlier-robust version of the k--means algorithm for low sampling densities in noisy data with respect to robustness to outliers.

The aim of this paper is to present an elementary computable theory of probability, random variables and stochastic processes. The probability theory is baed on existing approaches using valuations and lower integrals. Various approaches to random variables are discussed, including the approach based on completions in a Polish space. We apply the theory to the study of stochastic dynamical systems in discrete-time, and give a brief exposition of the Wiener process as a foundation for stochastic differential equations. The theory is based within the framework of type-two effectivity, so has an explicit direct link with Turing computation, and is expressed in a system of computable types and operations, so has a clean mathematical description.

We compare the (1,lambda)-EA and the (1 + lambda)-EA on the recently introduced benchmark DisOM, which is the OneMax function with randomly planted local optima. Previous work showed that if all local optima have the same relative height, then the plus strategy never loses more than a factor O(nlog n) compared to the comma strategy. Here we show that even small random fluctuations in the heights of the local optima have a devastating effect for the plus strategy and lead to super-polynomial runtimes. On the other hand, due to their ability to escape local optima, comma strategies are unaffected by the height of the local optima and remain efficient. Our results hold for a broad class of possible distortions and show that the plus strategy, but not the comma strategy, is generally deceived by sparse unstructured fluctuations of a smooth landscape.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

Real-world phenomena do not generate arbitrary variability: their signals concentrate on compact, low-variability subsets of functional space, enabling rapid generalization from few examples. A small child can recognize a dog after extremely limited exposure because the perceptual manifold of "dog" is compact, structured, and low-dimensional. We formalize this principle through a deterministic functional-topological framework in which the set of valid realizations produced by a physical process forms a compact subset of a Banach space, endowed with stable invariants, a finite Hausdorff radius, and an induced continuous perceptual functional. This geometry provides explicit limits on knowledge, conditions for identifiability, and guarantees for generalization from sparse evidence -- properties fundamental to both natural and artificial intelligence. Across electromechanical, electrochemical, and physiological domains, we show that real-world processes consistently generate compact perceptual manifolds with the same geometric characteristics. Their boundaries can be discovered in a fully self-supervised manner as the empirical radius saturates with increasing sampling, even when the governing equations are unknown. These results demonstrate that deterministic functional topology offers a unified mathematical foundation for perception, representation, and world-model construction. It provides a geometric explanation for why biological learners and self-supervised AI systems can generalize from few observations, and establishes compact perceptual manifolds as a fundamental building block for future AI architectures. Finally, this work unifies biological perception and modern self-supervised models under a single geometric principle: both derive their generalization ability from the compactness and invariants of real-world perceptual manifolds.

It is commonplace to encounter heterogeneous or nonstationary data, of which the underlying generating process changes across domains or over time. Such a distribution shift feature presents both challenges and opportunities for causal discovery. In this paper, we develop a framework for causal discovery from such data, called Constraint-based causal Discovery from heterogeneous/NOnstationary Data (CD-NOD), to find causal skeleton and directions and estimate the properties of mechanism changes. First, we propose an enhanced constraint-based procedure to detect variables whose local mechanisms change and recover the skeleton of the causal structure over observed variables. Second, we present a method to determine causal orientations by making use of independent changes in the data distribution implied by the underlying causal model, benefiting from information carried by changing distributions. After learning the causal structure, next, we investigate how to efficiently estimate the "driving force" of the nonstationarity of a causal mechanism. That is, we aim to extract from data a low-dimensional representation of changes. The proposed methods are nonparametric, with no hard restrictions on data distributions and causal mechanisms, and do not rely on window segmentation. Furthermore, we find that data heterogeneity benefits causal structure identification even with particular types of confounders. Finally, we show the connection between heterogeneity/nonstationarity and soft intervention in causal discovery. Experimental results on various synthetic and real-world data sets (task-fMRI and stock market data) are presented to demonstrate the efficacy of the proposed methods.

We introduce Minary, a computational framework designed as a candidate for the first formally provable autopoietic primitive. Minary represents interacting probabilistic events as multi-dimensional vectors and combines them via linear superposition rather than multiplicative scalar operations, thereby preserving uncertainty and enabling constructive and destructive interference in the range [-1,1]. A fixed set of ``perspectives'' evaluates ``semantic dimensions'' according to hidden competencies, and their interactions drive two discrete-time stochastic processes. We model this system as an iterated random affine map and use the theory of iterated random functions to prove that it converges in distribution to a unique stationary law; we moreover obtain an explicit closed form for the limiting expectation in terms of row, column, and global averages of the competency matrix. We then derive exact formulas for the mean and variance of the normalized consensus conditioned on the activation of a given semantic dimension, revealing how consensus depends on competency structure rather than raw input signals. Finally, we argue that Minary is organizationally closed yet operationally open in the sense of Maturana and Varela, and we discuss implications for building self-maintaining, distributed, and parallelizable computational systems that house a uniquely subjective notion of identity.

We are born with the ability to learn concepts by comparing diverse observations. This helps us to understand the new world in a compositional manner and facilitates extrapolation, as objects naturally consist of multiple concepts. In this work, we argue that the cognitive mechanism of comparison, fundamental to human learning, is also vital for machines to recover true concepts underlying the data. This offers correctness guarantees for the field of concept learning, which, despite its impressive empirical successes, still lacks general theoretical support. Specifically, we aim to develop a theoretical framework for the identifiability of concepts with multiple classes of observations. We show that with sufficient diversity across classes, hidden concepts can be identified without assuming specific concept types, functional relations, or parametric generative models. Interestingly, even when conditions are not globally satisfied, we can still provide alternative guarantees for as many concepts as possible based on local comparisons, thereby extending the applicability of our theory to more flexible scenarios. Moreover, the hidden structure between classes and concepts can also be identified nonparametrically. We validate our theoretical results in both synthetic and real-world settings.

Autoencoders have been proposed as a powerful tool for model-independent anomaly detection in high-energy physics. The operating principle is that events which do not belong to the space of training data will be reconstructed poorly, thus flagging them as anomalies. We point out that in a variety of examples of interest, the connection between large reconstruction error and anomalies is not so clear. In particular, for data sets with nontrivial topology, there will always be points that erroneously seem anomalous due to global issues. Conversely, neural networks typically have an inductive bias or prior to locally interpolate such that undersampled or rare events may be reconstructed with small error, despite actually being the desired anomalies. Taken together, these facts are in tension with the simple picture of the autoencoder as an anomaly detector. Using a series of illustrative low-dimensional examples, we show explicitly how the intrinsic and extrinsic topology of the dataset affects the behavior of an autoencoder and how this topology is manifested in the latent space representation during training. We ground this analysis in the discussion of a mock "bump hunt" in which the autoencoder fails to identify an anomalous "signal" for reasons tied to the intrinsic topology of n-particle phase space.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Straight line equation y=mx with slope m, when singularly perturbed as ay^3+y=mx with a positive parameter a, results in S-shaped curves or S-curves on a real plane. As arightarrow 0, we get back y=mx which is a cumulative distribution function of a continuous uniform distribution that describes the occurrence of every event in an interval to be equally probable. As arightarrowinfty, the derivative of y has finite support only at y=0 resembling a degenerate distribution. Based on these arguments, in this work, we propose that these S-curves can represent maximum entropy uniform distribution to a zero entropy single value. We also argue that these S-curves are superposable as they are only parametrically nonlinear but fundamentally linear. So far, the superposed forms have been used to capture the patterns of natural systems such as nonlinear dynamics of biological growth and kinetics of enzyme reactions. Here, we attempt to use the S-curve and its superposed form as statistical models. We fit the models on a classical dataset containing flower measurements of iris plants and analyze their usefulness in pattern recognition. Based on these models, we claim that any non-uniform pattern can be represented as a singular perturbation to uniform distribution. However, our parametric estimation procedure have some limitations such as sensitivity to initial conditions depending on the data at hand.

We consider dense, associative neural-networks trained by a teacher (i.e., with supervision) and we investigate their computational capabilities analytically, via statistical-mechanics of spin glasses, and numerically, via Monte Carlo simulations. In particular, we obtain a phase diagram summarizing their performance as a function of the control parameters such as quality and quantity of the training dataset, network storage and noise, that is valid in the limit of large network size and structureless datasets: these networks may work in a ultra-storage regime (where they can handle a huge amount of patterns, if compared with shallow neural networks) or in a ultra-detection regime (where they can perform pattern recognition at prohibitive signal-to-noise ratios, if compared with shallow neural networks). Guided by the random theory as a reference framework, we also test numerically learning, storing and retrieval capabilities shown by these networks on structured datasets as MNist and Fashion MNist. As technical remarks, from the analytic side, we implement large deviations and stability analysis within Guerra's interpolation to tackle the not-Gaussian distributions involved in the post-synaptic potentials while, from the computational counterpart, we insert Plefka approximation in the Monte Carlo scheme, to speed up the evaluation of the synaptic tensors, overall obtaining a novel and broad approach to investigate supervised learning in neural networks, beyond the shallow limit, in general.

Analysis of learned representations has a blind spot: it focuses on similarity, measuring how closely embeddings align with external references, but similarity reveals only what is represented, not whether that structure is robust. We introduce geometric stability, a distinct dimension that quantifies how reliably representational geometry holds under perturbation, and present Shesha, a framework for measuring it. Across 2,463 configurations in seven domains, we show that stability and similarity are empirically uncorrelated (ρapprox 0.01) and mechanistically distinct: similarity metrics collapse after removing the top principal components, while stability retains sensitivity to fine-grained manifold structure. This distinction yields actionable insights: for safety monitoring, stability acts as a functional geometric canary, detecting structural drift nearly 2times more sensitively than CKA while filtering out the non-functional noise that triggers false alarms in rigid distance metrics; for controllability, supervised stability predicts linear steerability (ρ= 0.89-0.96); for model selection, stability dissociates from transferability, revealing a geometric tax that transfer optimization incurs. Beyond machine learning, stability predicts CRISPR perturbation coherence and neural-behavioral coupling. By quantifying how reliably systems maintain structure, geometric stability provides a necessary complement to similarity for auditing representations across biological and computational systems.

The sampling of probability distributions specified up to a normalization constant is an important problem in both machine learning and statistical mechanics. While classical stochastic sampling methods such as Markov Chain Monte Carlo (MCMC) or Langevin Dynamics (LD) can suffer from slow mixing times there is a growing interest in using normalizing flows in order to learn the transformation of a simple prior distribution to the given target distribution. Here we propose a generalized and combined approach to sample target densities: Stochastic Normalizing Flows (SNF) -- an arbitrary sequence of deterministic invertible functions and stochastic sampling blocks. We show that stochasticity overcomes expressivity limitations of normalizing flows resulting from the invertibility constraint, whereas trainable transformations between sampling steps improve efficiency of pure MCMC/LD along the flow. By invoking ideas from non-equilibrium statistical mechanics we derive an efficient training procedure by which both the sampler's and the flow's parameters can be optimized end-to-end, and by which we can compute exact importance weights without having to marginalize out the randomness of the stochastic blocks. We illustrate the representational power, sampling efficiency and asymptotic correctness of SNFs on several benchmarks including applications to sampling molecular systems in equilibrium.

We introduce a theoretical framework for sampling from unnormalized densities based on a smoothing scheme that uses an isotropic Gaussian kernel with a single fixed noise scale. We prove one can decompose sampling from a density (minimal assumptions made on the density) into a sequence of sampling from log-concave conditional densities via accumulation of noisy measurements with equal noise levels. Our construction is unique in that it keeps track of a history of samples, making it non-Markovian as a whole, but it is lightweight algorithmically as the history only shows up in the form of a running empirical mean of samples. Our sampling algorithm generalizes walk-jump sampling (Saremi & Hyv\"arinen, 2019). The "walk" phase becomes a (non-Markovian) chain of (log-concave) Markov chains. The "jump" from the accumulated measurements is obtained by empirical Bayes. We study our sampling algorithm quantitatively using the 2-Wasserstein metric and compare it with various Langevin MCMC algorithms. We also report a remarkable capacity of our algorithm to "tunnel" between modes of a distribution.

This paper provides a non-asymptotic analysis of linear stochastic approximation (LSA) algorithms with fixed stepsize. This family of methods arises in many machine learning tasks and is used to obtain approximate solutions of a linear system Atheta = b for which A and b can only be accessed through random estimates {({bf A}_n, {bf b}_n): n in N^*}. Our analysis is based on new results regarding moments and high probability bounds for products of matrices which are shown to be tight. We derive high probability bounds on the performance of LSA under weaker conditions on the sequence {({bf A}_n, {bf b}_n): n in N^*} than previous works. However, in contrast, we establish polynomial concentration bounds with order depending on the stepsize. We show that our conclusions cannot be improved without additional assumptions on the sequence of random matrices {{bf A}_n: n in N^*}, and in particular that no Gaussian or exponential high probability bounds can hold. Finally, we pay a particular attention to establishing bounds with sharp order with respect to the number of iterations and the stepsize and whose leading terms contain the covariance matrices appearing in the central limit theorems.

We introduce rd-spiral, an open-source Python library for simulating 2D reaction-diffusion systems using pseudo-spectral methods. The framework combines FFT-based spatial discretization with adaptive Dormand-Prince time integration, achieving exponential convergence while maintaining pedagogical clarity. We analyze three dynamical regimes: stable spirals, spatiotemporal chaos, and pattern decay, revealing extreme non-Gaussian statistics (kurtosis >96) in stable states. Information-theoretic metrics show 10.7% reduction in activator-inhibitor coupling during turbulence versus 6.5% in stable regimes. The solver handles stiffness ratios >6:1 with features including automated equilibrium classification and checkpointing. Effect sizes (delta=0.37--0.78) distinguish regimes, with asymmetric field sensitivities to perturbations. By balancing computational rigor with educational transparency, rd-spiral bridges theoretical and practical nonlinear dynamics.

The problems of detecting and recovering planted structures/subgraphs in Erdős-Rényi random graphs, have received significant attention over the past three decades, leading to many exciting results and mathematical techniques. However, prior work has largely focused on specific ad hoc planted structures and inferential settings, while a general theory has remained elusive. In this paper, we bridge this gap by investigating the detection of an arbitrary planted subgraph Γ= Γ_n in an Erdős-Rényi random graph G(n, q_n), where the edge probability within Γ is p_n. We examine both the statistical and computational aspects of this problem and establish the following results. In the dense regime, where the edge probabilities p_n and q_n are fixed, we tightly characterize the information-theoretic and computational thresholds for detecting Γ, and provide conditions under which a computational-statistical gap arises. Most notably, these thresholds depend on Γ only through its number of edges, maximum degree, and maximum subgraph density. Our lower and upper bounds are general and apply to any value of p_n and q_n as functions of n. Accordingly, we also analyze the sparse regime where q_n = Θ(n^{-α}) and p_n-q_n =Θ(q_n), with αin[0,2], as well as the critical regime where p_n=1-o(1) and q_n = Θ(n^{-α}), both of which have been widely studied, for specific choices of Γ. For these regimes, we show that our bounds are tight for all planted subgraphs investigated in the literature thus farand many more. Finally, we identify conditions under which detection undergoes sharp phase transition, where the boundaries at which algorithms succeed or fail shift abruptly as a function of q_n.

Time series clustering promises to uncover hidden structural patterns in data with applications across healthcare, finance, industrial systems, and other critical domains. However, without validated ground truth information, researchers cannot objectively assess clustering quality or determine whether poor results stem from absent structures in the data, algorithmic limitations, or inappropriate validation methods, raising the question whether clustering is "more art than science" (Guyon et al., 2009). To address these challenges, we introduce CSTS (Correlation Structures in Time Series), a synthetic benchmark for evaluating the discovery of correlation structures in multivariate time series data. CSTS provides a clean benchmark that enables researchers to isolate and identify specific causes of clustering failures by differentiating between correlation structure deterioration and limitations of clustering algorithms and validation methods. Our contributions are: (1) a comprehensive benchmark for correlation structure discovery with distinct correlation structures, systematically varied data conditions, established performance thresholds, and recommended evaluation protocols; (2) empirical validation of correlation structure preservation showing moderate distortion from downsampling and minimal effects from distribution shifts and sparsification; and (3) an extensible data generation framework enabling structure-first clustering evaluation. A case study demonstrates CSTS's practical utility by identifying an algorithm's previously undocumented sensitivity to non-normal distributions, illustrating how the benchmark enables precise diagnosis of methodological limitations. CSTS advances rigorous evaluation standards for correlation-based time series clustering.

Foundation models have recently achieved impressive success in computational pathology, demonstrating strong generalization across diverse histopathology tasks. However, existing models overlook the heterogeneous and non-uniform organization of pathological regions of interest (ROIs) because they rely on natural image backbones not tailored for tissue morphology. Consequently, they often fail to capture the coherent tissue architecture beyond isolated patches, limiting interpretability and clinical relevance. To address these challenges, we present Cross-modal Adaptive Region Encoder (CARE), a foundation model for pathology that automatically partitions WSIs into several morphologically relevant regions. Specifically, CARE employs a two-stage pretraining strategy: (1) a self-supervised unimodal pretraining stage that learns morphological representations from 34,277 whole-slide images (WSIs) without segmentation annotations, and (2) a cross-modal alignment stage that leverages RNA and protein profiles to refine the construction and representation of adaptive regions. This molecular guidance enables CARE to identify biologically relevant patterns and generate irregular yet coherent tissue regions, selecting the most representative area as ROI. CARE supports a broad range of pathology-related tasks, using either the ROI feature or the slide-level feature obtained by aggregating adaptive regions. Based on only one-tenth of the pretraining data typically used by mainstream foundation models, CARE achieves superior average performance across 33 downstream benchmarks, including morphological classification, molecular prediction, and survival analysis, and outperforms other foundation model baselines overall.

Modern neural recording techniques allow neuroscientists to obtain spiking activity of multiple neurons from different brain regions over long time periods, which requires new statistical methods to be developed for understanding structure of the large-scale data. In this paper, we develop a bi-clustering method to cluster the neural spiking activity spatially and temporally, according to their low-dimensional latent structures. The spatial (neuron) clusters are defined by the latent trajectories within each neural population, while the temporal (state) clusters are defined by (populationally) synchronous local linear dynamics shared with different periods. To flexibly extract the bi-clustering structure, we build the model non-parametrically, and develop an efficient Markov chain Monte Carlo (MCMC) algorithm to sample the posterior distributions of model parameters. Validating our proposed MCMC algorithm through simulations, we find the method can recover unknown parameters and true bi-clustering structures successfully. We then apply the proposed bi-clustering method to multi-regional neural recordings under different experiment settings, where we find that simultaneously considering latent trajectories and spatial-temporal clustering structures can provide us with a more accurate and interpretable result. Overall, the proposed method provides scientific insights for large-scale (counting) time series with elongated recording periods, and it can potentially have application beyond neuroscience.

Neural network pruning serves as a critical technique for enhancing the efficiency of deep learning models. Unlike unstructured pruning, which only sets specific parameters to zero, structured pruning eliminates entire channels, thus yielding direct computational and storage benefits. However, the diverse patterns for coupling parameters, such as residual connections and group convolutions, the diverse deep learning frameworks, and the various time stages at which pruning can be performed make existing pruning methods less adaptable to different architectures, frameworks, and pruning criteria. To address this, we introduce Structurally Prune Anything (SPA), a versatile structured pruning framework that can prune neural networks with any architecture, from any framework, and at any stage of training. SPA leverages a standardized computational graph and ONNX representation to prune diverse neural network architectures without the need for manual intervention. SPA employs a group-level importance estimation method, which groups dependent computational operators, estimates their importance, and prunes unimportant coupled channels. This enables the transfer of various existing pruning criteria into a structured group style. As a result, SPA supports pruning at any time, either before training, after training with fine-tuning, or after training without fine-tuning. In the context of the latter, we introduce Optimal Brain SPA (OBSPA), an algorithm that achieves state-of-the-art pruning results needing neither fine-tuning nor calibration data. In extensive experiments, SPA shows competitive to state-of-the-art pruning performance across various architectures, from popular frameworks, at different pruning times.

We propose PROSE-FD, a zero-shot multimodal PDE foundational model for simultaneous prediction of heterogeneous two-dimensional physical systems related to distinct fluid dynamics settings. These systems include shallow water equations and the Navier-Stokes equations with incompressible and compressible flow, regular and complex geometries, and different buoyancy settings. This work presents a new transformer-based multi-operator learning approach that fuses symbolic information to perform operator-based data prediction, i.e. non-autoregressive. By incorporating multiple modalities in the inputs, the PDE foundation model builds in a pathway for including mathematical descriptions of the physical behavior. We pre-train our foundation model on 6 parametric families of equations collected from 13 datasets, including over 60K trajectories. Our model outperforms popular operator learning, computer vision, and multi-physics models, in benchmark forward prediction tasks. We test our architecture choices with ablation studies.

Partition logics -- non-Boolean event structures obtained by pasting Boolean algebras -- provide a natural language for situations in which a system has a definite latent state but can be accessed and resolved only through mutually incompatible coarse-grained modes of observation. We show that this structure arises in a range of social-science settings by constructing six explicit examples from personnel assessment, survey framing, clinical diagnosis, espionage coordination, legal pluralism, and organizational auditing. For each case we identify the latent state space, the observational contexts as partitions, and the shared atoms that intertwine contexts, yielding instances of the L_{12} bowtie, triangle, pentagon, and automaton partition logics. These examples make precise a notion of social complementarity: different modes of inquiry can be incompatible even though the underlying system remains fully value-definite. Complementarity in this sense does not entail contextuality or ontic indeterminacy. We further compare the classical probabilities generated by convex mixtures of dispersion-free states with the quantum-like Born probabilities available when the same exclusivity graph admits a faithful orthogonal representation. The framework thus separates logical structure from probabilistic realization and suggests empirically testable benchmarks for quantum-cognition models.

Autoregressive decoding is the only part of sequence-to-sequence models that prevents them from massive parallelization at inference time. Non-autoregressive models enable the decoder to generate all output symbols independently in parallel. We present a novel non-autoregressive architecture based on connectionist temporal classification and evaluate it on the task of neural machine translation. Unlike other non-autoregressive methods which operate in several steps, our model can be trained end-to-end. We conduct experiments on the WMT English-Romanian and English-German datasets. Our models achieve a significant speedup over the autoregressive models, keeping the translation quality comparable to other non-autoregressive models.

The integration of knowledge extracted from diverse models, whether described by domain experts or generated by machine learning algorithms, has historically been challenged by the absence of a suitable framework for specifying and integrating structures, learning processes, data transformations, and data models or rules. In this work, we extend algebraic specification methods to address these challenges within such a framework. In our work, we tackle the challenging task of developing a comprehensive framework for defining and analyzing deep learning architectures. We believe that previous efforts have fallen short by failing to establish a clear connection between the constraints a model must adhere to and its actual implementation. Our methodology employs graphical structures that resemble Ehresmann's sketches, interpreted within a universe of fuzzy sets. This approach offers a unified theory that elegantly encompasses both deterministic and non-deterministic neural network designs. Furthermore, we highlight how this theory naturally incorporates fundamental concepts from computer science and automata theory. Our extended algebraic specification framework, grounded in graphical structures akin to Ehresmann's sketches, offers a promising solution for integrating knowledge across disparate models and domains. By bridging the gap between domain-specific expertise and machine-generated insights, we pave the way for more comprehensive, collaborative, and effective approaches to knowledge integration and modeling.

The manifold hypothesis, which assumes that data lies on or close to an unknown manifold of low intrinsic dimension, is a staple of modern machine learning research. However, recent work has shown that real-world data exhibits distinct non-manifold structures, i.e. singularities, that can lead to erroneous findings. Detecting such singularities is therefore crucial as a precursor to interpolation and inference tasks. We address this issue by developing a topological framework that (i) quantifies the local intrinsic dimension, and (ii) yields a Euclidicity score for assessing the 'manifoldness' of a point along multiple scales. Our approach identifies singularities of complex spaces, while also capturing singular structures and local geometric complexity in image data.

We consider dense, associative neural-networks trained with no supervision and we investigate their computational capabilities analytically, via a statistical-mechanics approach, and numerically, via Monte Carlo simulations. In particular, we obtain a phase diagram summarizing their performance as a function of the control parameters such as the quality and quantity of the training dataset and the network storage, valid in the limit of large network size and structureless datasets. Moreover, we establish a bridge between macroscopic observables standardly used in statistical mechanics and loss functions typically used in the machine learning. As technical remarks, from the analytic side, we implement large deviations and stability analysis within Guerra's interpolation to tackle the not-Gaussian distributions involved in the post-synaptic potentials while, from the computational counterpart, we insert Plefka approximation in the Monte Carlo scheme, to speed up the evaluation of the synaptic tensors, overall obtaining a novel and broad approach to investigate neural networks in general.

Can evolving networks be inferred and modeled without directly observing their nodes and edges? In many applications, the edges of a dynamic network might not be observed, but one can observe the dynamics of stochastic cascading processes (e.g., information diffusion, virus propagation) occurring over the unobserved network. While there have been efforts to infer networks based on such data, providing a generative probabilistic model that is able to identify the underlying time-varying network remains an open question. Here we consider the problem of inferring generative dynamic network models based on network cascade diffusion data. We propose a novel framework for providing a non-parametric dynamic network model--based on a mixture of coupled hierarchical Dirichlet processes-- based on data capturing cascade node infection times. Our approach allows us to infer the evolving community structure in networks and to obtain an explicit predictive distribution over the edges of the underlying network--including those that were not involved in transmission of any cascade, or are likely to appear in the future. We show the effectiveness of our approach using extensive experiments on synthetic as well as real-world networks.

We explore the relations between the zeta distribution and algorithmic information theory via a new model of the transfer learning problem. The program distribution is approximated by a zeta distribution with parameter near 1. We model the training sequence as a stochastic process. We analyze the upper temporal bound for learning a training sequence and its entropy rates, assuming an oracle for the transfer learning problem. We argue from empirical evidence that power-law models are suitable for natural processes. Four sequence models are proposed. Random typing model is like no-free lunch where transfer learning does not work. Zeta process independently samples programs from the zeta distribution. A model of common sub-programs inspired by genetics uses a database of sub-programs. An evolutionary zeta process samples mutations from Zeta distribution. The analysis of stochastic processes inspired by evolution suggest that AI may be feasible in nature, countering no-free lunch sort of arguments.

Current evaluations of large language models (LLMs) often overlook non-determinism, typically focusing on a single output per example. This limits our understanding of LLM performance variability in real-world applications. Our study addresses this issue by exploring key questions about the performance differences between greedy decoding and sampling, identifying benchmarks' consistency regarding non-determinism, and examining unique model behaviors. Through extensive experiments, we observe that greedy decoding generally outperforms sampling methods for most evaluated tasks. We also observe consistent performance across different LLM sizes and alignment methods, noting that alignment can reduce sampling variance. Moreover, our best-of-N sampling approach demonstrates that smaller LLMs can match or surpass larger models such as GPT-4-Turbo, highlighting the untapped potential of smaller LLMs. This research shows the importance of considering non-determinism in LLM evaluations and provides insights for future LLM development and evaluation.

Bayes' rule tells us how to invert a causal process in order to update our beliefs in light of new evidence. If the process is believed to have a complex compositional structure, we may observe that the inversion of the whole can be computed piecewise in terms of the component processes. We study the structure of this compositional rule, noting that it relates to the lens pattern in functional programming. Working in a suitably general axiomatic presentation of a category of Markov kernels, we see how we can think of Bayesian inversion as a particular instance of a state-dependent morphism in a fibred category. We discuss the compositional nature of this, formulated as a functor on the underlying category and explore how this can used for a more type-driven approach to statistical inference.

Uncertainty is almost ubiquitous in safety-critical autonomous systems due to dynamic environments and the integration of learning-based components. Quantifying this uncertainty--particularly for time-series predictions in multi-stage optimization--is essential for safe control and verification tasks. Conformal Prediction (CP) is a distribution-free uncertainty quantification tool with rigorous finite-sample guarantees, but its performance relies on the design of the nonconformity measure, which remains challenging for time-series data. Existing methods either overfit on small datasets, or are computationally intensive on long-time-horizon problems and/or large datasets. To overcome these issues, we propose a new parameterization of the score functions and formulate an optimization program to compute the associated parameters. The optimal parameters directly lead to norm-ball regions that constitute minimal-average-radius conformal sets. We then provide a reformulation of the underlying optimization program to enable faster computation. We provide theoretical proofs on both the validity and efficiency of predictors constructed based on the proposed approach. Numerical results on various case studies demonstrate that our method outperforms state-of-the-art methods in terms of efficiency, with much lower computational requirements.

In this paper, we study the flow of signals through linear paths with the nonlinear condition that a node emits a signal when it receives external stimuli or when two incoming signals from other nodes arrive coincidentally with a combined amplitude above a fixed threshold. Sets of such nodes form a polychrony group and can sometimes lead to cascades. In the context of this work, cascades are polychrony groups in which the number of nodes activated as a consequence of other nodes is greater than the number of externally activated nodes. The difference between these two numbers is the so-called profit. Given the initial conditions, we predict the conditions for a vertex to activate at a prescribed time and provide an algorithm to efficiently reconstruct a cascade. We develop a dictionary between polychrony groups and graph theory. We call the graph corresponding to a cascade a chinampa. This link leads to a topological classification of chinampas. We enumerate the chinampas of profits zero and one and the description of a family of chinampas isomorphic to a family of partially ordered sets, which implies that the enumeration problem of this family is equivalent to computing the Stanley-order polynomials of those partially ordered sets.

A central problem in machine learning involves modeling complex data-sets using highly flexible families of probability distributions in which learning, sampling, inference, and evaluation are still analytically or computationally tractable. Here, we develop an approach that simultaneously achieves both flexibility and tractability. The essential idea, inspired by non-equilibrium statistical physics, is to systematically and slowly destroy structure in a data distribution through an iterative forward diffusion process. We then learn a reverse diffusion process that restores structure in data, yielding a highly flexible and tractable generative model of the data. This approach allows us to rapidly learn, sample from, and evaluate probabilities in deep generative models with thousands of layers or time steps, as well as to compute conditional and posterior probabilities under the learned model. We additionally release an open source reference implementation of the algorithm.

The K-core of a graph is the unique maximum subgraph within which each vertex connects to K or more other vertices. The optimal K-core attack problem asks to delete the minimum number of vertices from the K-core to induce its complete collapse. A hierarchical cycle-tree packing model is introduced here for this challenging combinatorial optimization problem. We convert the temporally long-range correlated K-core pruning dynamics into locally tree-like static patterns and analyze this model through the replica-symmetric cavity method of statistical physics. A set of coarse-grained belief propagation equations are derived to predict single vertex marginal probabilities efficiently. The associated hierarchical cycle-tree guided attack ({\tt hCTGA}) algorithm is able to construct nearly optimal attack solutions for regular random graphs and Erd\"os-R\'enyi random graphs. Our cycle-tree packing model may also be helpful for constructing optimal initial conditions for other irreversible dynamical processes on sparse random graphs.

Large Language Models achieve next-token prediction by transporting a vectorized piece of text (prompt) across an accompanying embedding space under the action of successive transformer layers. The resulting high-dimensional trajectories realize different contextualization, or 'thinking', steps, and fully determine the output probability distribution. We aim to characterize the statistical properties of ensembles of these 'lines of thought.' We observe that independent trajectories cluster along a low-dimensional, non-Euclidean manifold, and that their path can be well approximated by a stochastic equation with few parameters extracted from data. We find it remarkable that the vast complexity of such large models can be reduced to a much simpler form, and we reflect on implications.

Synchronization in one dimension displays generic scale invariance with universal properties previously observed in surface kinetic roughening and the wider context of the Kardar-Parisi-Zhang (KPZ) universality class. This has been established for phase oscillators and also for some limit-cycle oscillators, both in the presence of columnar (quenched) disorder and of time-dependent noise, by extensive numerical simulations, and has been analytically motivated by continuum approximations in the strong oscillator coupling limit. The robustness and the precise boundaries in parameter space for such critical behavior remain unclear, however, which may preclude further developments, including the extension of these results to higher dimensions and the experimental observation of nonequilibrium criticality in synchronizing (e.g.~electronic or chemical) oscillators. We here present complete numerical phase diagrams of one-dimensional synchronization, including saturation times and values, but, most importantly, also dynamical features giving insight into the gradual emergence of synchronous dynamics, based on systems of phase oscillators with either type of randomness. In the absence of synchronization, the dynamics evolves as expected for random deposition (for time-dependent noise) or linear growth (for columnar disorder), while a crossover from Edwards-Wilkinson to Kardar-Parisi-Zhang behavior (with the corresponding type of randomness) is observed as the randomness strength, or the nonoddity of the coupling among oscillators, is increased in the synchronous region -- their combined effect being partially captured by the so-called KPZ coupling. The distortion of scaling due to phase slips near the desynchronization boundary, a feature that is likely to play a role in experimental contexts, is also discussed.

With the development of large language models (LLMs), particularly with the introduction of the long reasoning chain technique, the reasoning ability of LLMs in complex problem-solving has been significantly enhanced. While acknowledging the power of long reasoning chains, we cannot help but wonder: Why do different reasoning chains perform differently in reasoning? What components of the reasoning chains play a key role? Existing studies mainly focus on evaluating reasoning chains from a functional perspective, with little attention paid to their structural mechanisms. To address this gap, this work is the first to analyze and evaluate the quality of the reasoning chain from a structural perspective. We apply persistent homology from Topological Data Analysis (TDA) to map reasoning steps into semantic space, extract topological features, and analyze structural changes. These changes reveal semantic coherence, logical redundancy, and identify logical breaks and gaps. By calculating homology groups, we assess connectivity and redundancy at various scales, using barcode and persistence diagrams to quantify stability and consistency. Our results show that the topological structural complexity of reasoning chains correlates positively with accuracy. More complex chains identify correct answers sooner, while successful reasoning exhibits simpler topologies, reducing redundancy and cycles, enhancing efficiency and interpretability. This work provides a new perspective on reasoning chain quality assessment and offers guidance for future optimization.

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

During the last decade, sampling-based path planning algorithms, such as Probabilistic RoadMaps (PRM) and Rapidly-exploring Random Trees (RRT), have been shown to work well in practice and possess theoretical guarantees such as probabilistic completeness. However, little effort has been devoted to the formal analysis of the quality of the solution returned by such algorithms, e.g., as a function of the number of samples. The purpose of this paper is to fill this gap, by rigorously analyzing the asymptotic behavior of the cost of the solution returned by stochastic sampling-based algorithms as the number of samples increases. A number of negative results are provided, characterizing existing algorithms, e.g., showing that, under mild technical conditions, the cost of the solution returned by broadly used sampling-based algorithms converges almost surely to a non-optimal value. The main contribution of the paper is the introduction of new algorithms, namely, PRM* and RRT*, which are provably asymptotically optimal, i.e., such that the cost of the returned solution converges almost surely to the optimum. Moreover, it is shown that the computational complexity of the new algorithms is within a constant factor of that of their probabilistically complete (but not asymptotically optimal) counterparts. The analysis in this paper hinges on novel connections between stochastic sampling-based path planning algorithms and the theory of random geometric graphs.

In this paper, we study a class of composite optimization problems whose objective function is given by the summation of a general smooth and nonsmooth component, together with a relatively simple nonsmooth term. While restart strategies are commonly employed in first-order methods to achieve optimal convergence under strong convexity, they introduce structural complexity and practical overhead, making algorithm design and nesting cumbersome. To address this, we propose a restart-free stochastic gradient sliding algorithm that eliminates the need for explicit restart phases when the simple nonsmooth component is strongly convex. Through a novel and carefully designed parameter selection strategy, we prove that the proposed algorithm achieves an ε-solution with only O(log(1ε)) gradient evaluations for the smooth component and O(1ε) stochastic subgradient evaluations for the nonsmooth component, matching the optimal complexity of existing multi-phase (restart-based) methods. Moreover, for the case where the nonsmooth component is structured, allowing the overall problem to be reformulated as a bilinear saddle-point problem, we develop a restart-free accelerated stochastic gradient sliding algorithm. We show that the resulting method requires only O(log(1ε)) gradient computations for the smooth component while preserving an overall iteration complexity of O(1{sqrtε}) for solving the corresponding saddle-point problems. Our work thus provides simpler, restart-f

The human brain is autonomously active, being characterized by a self-sustained neural activity which would be present even in the absence of external sensory stimuli. Here we study the interrelation between the self-sustained activity in autonomously active recurrent neural nets and external sensory stimuli. There is no a priori semantical relation between the influx of external stimuli and the patterns generated internally by the autonomous and ongoing brain dynamics. The question then arises when and how are semantic correlations between internal and external dynamical processes learned and built up? We study this problem within the paradigm of transient state dynamics for the neural activity in recurrent neural nets, i.e. for an autonomous neural activity characterized by an infinite time-series of transiently stable attractor states. We propose that external stimuli will be relevant during the sensitive periods, {\it viz} the transition period between one transient state and the subsequent semi-stable attractor. A diffusive learning signal is generated unsupervised whenever the stimulus influences the internal dynamics qualitatively. For testing we have presented to the model system stimuli corresponding to the bars and stripes problem. We found that the system performs a non-linear independent component analysis on its own, being continuously and autonomously active. This emergent cognitive capability results here from a general principle for the neural dynamics, the competition between neural ensembles.

Physics is based on probabilities as fundamental entities of a mathematical description. Expectation values of observables are computed according to the classical statistical rule. The overall probability distribution for one world covers all times. The quantum formalism arises once one focuses on the evolution of the time-local probabilistic information. Wave functions or the density matrix allow the formulation of a general linear evolution law for classical statistics. The quantum formalism for classical statistics is a powerful tool which allows us to implement for generalized Ising models the momentum observable with the associated Fourier representation. The association of operators to observables permits the computation of expectation values in terms of the density matrix by the usual quantum rule. We show that probabilistic cellular automata are quantum systems in a formulation with discrete time steps and real wave functions. With a complex structure the evolution operator for automata can be expressed in terms of a Hamiltonian involving fermionic creation and annihilation operators. The time-local probabilistic information amounts to a subsystem of the overall probabilistic system which is correlated with its environment consisting of the past and future. Such subsystems typically involve probabilistic observables for which only a probability distribution for their possible measurement values is available. Incomplete statistics does not permit to compute classical correlation functions for arbitrary subsystem-observables. Bell's inequalities are not generally applicable.

Conformal prediction is a widely used method to quantify the uncertainty of a classifier under the assumption of exchangeability (e.g., IID data). We generalize conformal prediction to the Hidden Markov Model (HMM) framework where the assumption of exchangeability is not valid. The key idea of the proposed method is to partition the non-exchangeable Markovian data from the HMM into exchangeable blocks by exploiting the de Finetti's Theorem for Markov Chains discovered by Diaconis and Freedman (1980). The permutations of the exchangeable blocks are viewed as randomizations of the observed Markovian data from the HMM. The proposed method provably retains all desirable theoretical guarantees offered by the classical conformal prediction framework in both exchangeable and Markovian settings. In particular, while the lack of exchangeability introduced by Markovian samples constitutes a violation of a crucial assumption for classical conformal prediction, the proposed method views it as an advantage that can be exploited to improve the performance further. Detailed numerical and empirical results that complement the theoretical conclusions are provided to illustrate the practical feasibility of the proposed method.

From a viewpoint of stochastic thermodynamics, we derive equations that describe the collective dynamics near the order-disorder transition in the globally coupled XY model and near the synchronization-desynchronization transition in the Kuramoto model. A new way of thinking is to interpret the deterministic time evolution of a macroscopic variable as an external operation to a thermodynamic system. We then find that the irreversible work determines the equation for the collective dynamics. When analyzing the Kuramoto model, we employ a generalized concept of irreversible work which originates from a non-equilibrium identity associated with steady state thermodynamics.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Recent advances in artificial intelligence reveal the limits of purely predictive systems and call for a shift toward causal and collaborative reasoning. Drawing inspiration from the revolution of Grothendieck in mathematics, we introduce the relativity of causal knowledge, which posits structural causal models (SCMs) are inherently imperfect, subjective representations embedded within networks of relationships. By leveraging category theory, we arrange SCMs into a functor category and show that their observational and interventional probability measures naturally form convex structures. This result allows us to encode non-intervened SCMs with convex spaces of probability measures. Next, using sheaf theory, we construct the network sheaf and cosheaf of causal knowledge. These structures enable the transfer of causal knowledge across the network while incorporating interventional consistency and the perspective of the subjects, ultimately leading to the formal, mathematical definition of relative causal knowledge.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

Consider a random uniform sample of n points in a compact region A of Euclidean d-space, d geq 2, with a smooth or (when d=2) polygonal boundary. Fix k bf N. Let T_{n,k} be the threshold r at which the geometric graph on these n vertices with distance parameter r becomes k-connected. We show that if d=2 then n (pi/|A|) T_{n,1}^2 - log n is asymptotically standard Gumbel. For (d,k) neq (2,1), it is n (theta_d/|A|) T_{n,k}^d - (2-2/d) log n - (4-2k-2/d) log log n that converges in distribution to a nondegenerate limit, where theta_d is the volume of the unit ball. The limit is Gumbel with scale parameter 2 except when (d,k)=(2,2) where the limit is two component extreme value distributed. The different cases reflect the fact that boundary effects are more more important in some cases than others. We also give similar results for the largest k-nearest neighbour link U_{n,k} in the sample, and show T_{n,k}=U_{n,k} with high probability. We provide estimates on rates of convergence and give similar results for Poisson samples in A. Finally, we give similar results even for non-uniform samples, with a less explicit sequence of centring constants.

Using a set of LambdaCDM simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams' development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web's hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.

We develop Markov categories as a framework for synthetic probability and statistics, following work of Golubtsov as well as Cho and Jacobs. This means that we treat the following concepts in purely abstract categorical terms: conditioning and disintegration; various versions of conditional independence and its standard properties; conditional products; almost surely; sufficient statistics; versions of theorems on sufficient statistics due to Fisher--Neyman, Basu, and Bahadur. Besides the conceptual clarity offered by our categorical setup, its main advantage is that it provides a uniform treatment of various types of probability theory, including discrete probability theory, measure-theoretic probability with general measurable spaces, Gaussian probability, stochastic processes of either of these kinds, and many others.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

We present a new distribution-free conformal prediction algorithm for sequential data (e.g., time series), called the sequential predictive conformal inference (SPCI). We specifically account for the nature that time series data are non-exchangeable, and thus many existing conformal prediction algorithms are not applicable. The main idea is to adaptively re-estimate the conditional quantile of non-conformity scores (e.g., prediction residuals), upon exploiting the temporal dependence among them. More precisely, we cast the problem of conformal prediction interval as predicting the quantile of a future residual, given a user-specified point prediction algorithm. Theoretically, we establish asymptotic valid conditional coverage upon extending consistency analyses in quantile regression. Using simulation and real-data experiments, we demonstrate a significant reduction in interval width of SPCI compared to other existing methods under the desired empirical coverage.

We study the properties of common loss surfaces through their Hessian matrix. In particular, in the context of deep learning, we empirically show that the spectrum of the Hessian is composed of two parts: (1) the bulk centered near zero, (2) and outliers away from the bulk. We present numerical evidence and mathematical justifications to the following conjectures laid out by Sagun et al. (2016): Fixing data, increasing the number of parameters merely scales the bulk of the spectrum; fixing the dimension and changing the data (for instance adding more clusters or making the data less separable) only affects the outliers. We believe that our observations have striking implications for non-convex optimization in high dimensions. First, the flatness of such landscapes (which can be measured by the singularity of the Hessian) implies that classical notions of basins of attraction may be quite misleading. And that the discussion of wide/narrow basins may be in need of a new perspective around over-parametrization and redundancy that are able to create large connected components at the bottom of the landscape. Second, the dependence of small number of large eigenvalues to the data distribution can be linked to the spectrum of the covariance matrix of gradients of model outputs. With this in mind, we may reevaluate the connections within the data-architecture-algorithm framework of a model, hoping that it would shed light into the geometry of high-dimensional and non-convex spaces in modern applications. In particular, we present a case that links the two observations: small and large batch gradient descent appear to converge to different basins of attraction but we show that they are in fact connected through their flat region and so belong to the same basin.

Non-convex optimization plays a key role in a growing number of machine learning applications. This motivates the identification of specialized structure that enables sharper theoretical analysis. One such identified structure is quasar-convexity, a non-convex generalization of convexity that subsumes convex functions. Existing algorithms for minimizing quasar-convex functions in the stochastic setting have either high complexity or slow convergence, which prompts us to derive a new class of stochastic methods for optimizing smooth quasar-convex functions. We demonstrate that our algorithms have fast convergence and outperform existing algorithms on several examples, including the classical problem of learning linear dynamical systems. We also present a unified analysis of our newly proposed algorithms and a previously studied deterministic algorithm.

We present new algorithms for optimizing non-smooth, non-convex stochastic objectives based on a novel analysis technique. This improves the current best-known complexity for finding a (delta,epsilon)-stationary point from O(epsilon^{-4}delta^{-1}) stochastic gradient queries to O(epsilon^{-3}delta^{-1}), which we also show to be optimal. Our primary technique is a reduction from non-smooth non-convex optimization to online learning, after which our results follow from standard regret bounds in online learning. For deterministic and second-order smooth objectives, applying more advanced optimistic online learning techniques enables a new complexity of O(epsilon^{-1.5}delta^{-0.5}). Our techniques also recover all optimal or best-known results for finding epsilon stationary points of smooth or second-order smooth objectives in both stochastic and deterministic settings.

RL training of multi-turn LLM agents is inherently unstable, and reasoning quality directly determines task performance. Entropy is widely used to track reasoning stability. However, entropy only measures diversity within the same input, and cannot tell whether reasoning actually responds to different inputs. In RAGEN-2, we find that even with stable entropy, models can rely on fixed templates that look diverse but are input-agnostic. We call this template collapse, a failure mode invisible to entropy and all existing metrics. To diagnose this failure, we decompose reasoning quality into within-input diversity (Entropy) and cross-input distinguishability (Mutual Information, MI), and introduce a family of mutual information proxies for online diagnosis. Across diverse tasks, mutual information correlates with final performance much more strongly than entropy, making it a more reliable proxy for reasoning quality. We further explain template collapse with a signal-to-noise ratio (SNR) mechanism. Low reward variance weakens task gradients, letting regularization terms dominate and erase cross-input reasoning differences. To address this, we propose SNR-Aware Filtering to select high-signal prompts per iteration using reward variance as a lightweight proxy. Across planning, math reasoning, web navigation, and code execution, the method consistently improves both input dependence and task performance.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

The presence of linear paths in parameter space between two different network solutions in certain cases, i.e., linear mode connectivity (LMC), has garnered interest from both theoretical and practical fronts. There has been significant research that either practically designs algorithms catered for connecting networks by adjusting for the permutation symmetries as well as some others that more theoretically construct paths through which networks can be connected. Yet, the core reasons for the occurrence of LMC, when in fact it does occur, in the highly non-convex loss landscapes of neural networks are far from clear. In this work, we take a step towards understanding it by providing a model of how the loss landscape needs to behave topographically for LMC (or the lack thereof) to manifest. Concretely, we present a `mountainside and ridge' perspective that helps to neatly tie together different geometric features that can be spotted in the loss landscape along the training runs. We also complement this perspective by providing a theoretical analysis of the barrier height, for which we provide empirical support, and which additionally extends as a faithful predictor of layer-wise LMC. We close with a toy example that provides further intuition on how barriers arise in the first place, all in all, showcasing the larger aim of the work -- to provide a working model of the landscape and its topography for the occurrence of LMC.

Large-scale land enclosure for speculative mega-development constitutes a non-equilibrium spatial process whose velocity, topology, and irreversibility remain poorly quantified. We study the Pantai Indah Kapuk 2 (PIK2) coastal mega-development north of Jakarta, Indonesia, using eight years (2017--2024) of Sentinel-2 land-use/land-cover (LULC) data at 10-meter resolution. The landscape is projected onto a Marxian probability simplex partitioning terrestrial pixels into Commons, Agrarian, and Capital fractions. Fisher-Rao (FR) geodesic distances on this simplex identify a transformation pulse of 0.405~rad/yr during 2019--2020, coinciding with major construction activity. Absorbing Markov chain analysis yields expected absorption times into the built environment of 46.0~years for cropland and 38.1~years for tree cover, with a pooled built-area self-retention rate of 96.4%. Percolation analysis reveals that a giant connected component containing 89--95% of all built pixels persists at occupation probabilities p in [0.096, 0.162], far below the random percolation threshold p_c approx 0.593, indicating planned rather than stochastic spatial growth. The box-counting fractal dimension of the urban boundary increases from d_f = 1.316 to 1.397, consistent with increasingly irregular frontier expansion. These results suggest that information-geometric and statistical-mechanical tools can characterize the kinematic and topological signatures of capitalist spatial accumulation with quantitative precision.

Machine learning models will often fail when deployed in an environment with a data distribution that is different than the training distribution. When multiple environments are available during training, many methods exist that learn representations which are invariant across the different distributions, with the hope that these representations will be transportable to unseen domains. In this work, we present a nonparametric strategy for learning invariant representations based on the recently-proposed Nadaraya-Watson (NW) head. The NW head makes a prediction by comparing the learned representations of the query to the elements of a support set that consists of labeled data. We demonstrate that by manipulating the support set, one can encode different causal assumptions. In particular, restricting the support set to a single environment encourages the model to learn invariant features that do not depend on the environment. We present a causally-motivated setup for our modeling and training strategy and validate on three challenging real-world domain generalization tasks in computer vision.

Hopfield attractor networks are robust distributed models of human memory, but lack a general mechanism for effecting state-dependent attractor transitions in response to input. We propose construction rules such that an attractor network may implement an arbitrary finite state machine (FSM), where states and stimuli are represented by high-dimensional random vectors, and all state transitions are enacted by the attractor network's dynamics. Numerical simulations show the capacity of the model, in terms of the maximum size of implementable FSM, to be linear in the size of the attractor network for dense bipolar state vectors, and approximately quadratic for sparse binary state vectors. We show that the model is robust to imprecise and noisy weights, and so a prime candidate for implementation with high-density but unreliable devices. By endowing attractor networks with the ability to emulate arbitrary FSMs, we propose a plausible path by which FSMs could exist as a distributed computational primitive in biological neural networks.

In statistics, independent, identically distributed random samples do not carry a natural ordering, and their statistics are typically invariant with respect to permutations of their order. Thus, an n-sample in a space M can be considered as an element of the quotient space of M^n modulo the permutation group. The present paper takes this definition of sample space and the related concept of orbit types as a starting point for developing a geometric perspective on statistics. We aim at deriving a general mathematical setting for studying the behavior of empirical and population means in spaces ranging from smooth Riemannian manifolds to general stratified spaces. We fully describe the orbifold and path-metric structure of the sample space when M is a manifold or path-metric space, respectively. These results are non-trivial even when M is Euclidean. We show that the infinite sample space exists in a Gromov-Hausdorff type sense and coincides with the Wasserstein space of probability distributions on M. We exhibit Fr\'echet means and k-means as metric projections onto 1-skeleta or k-skeleta in Wasserstein space, and we define a new and more general notion of polymeans. This geometric characterization via metric projections applies equally to sample and population means, and we use it to establish asymptotic properties of polymeans such as consistency and asymptotic normality.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

The statistical mechanics of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. In this paper, we follow the path set out by Jaynes, including elements added subsequently to that original work, to explore the consequences of the purely statistical point of view. We show how standard methods in the equilibrium theory could have been derived simply from a description of the available problem information. In addition, our presentation leads to novel insights into questions associated with symmetry and non-equilibrium statistical mechanics. Two surprising consequences to be explored in further work are that (in)distinguishability factors are automatically predicted from the problem formulation and that a quantity related to the thermodynamic entropy production is found by considering information loss in non-equilibrium processes. Using the problem of ion channel thermodynamics as an example, we illustrate the idea of building up complexity by successively adding information to create progressively more complex descriptions of a physical system. Our result is that such statistical mechanical descriptions can be used to create transparent, computable, experimentally-relevant models that may be informed by more detailed atomistic simulations. We also derive a theory for the kinetic behavior of this system, identifying the nonequilibrium `process' free energy functional. The Gibbs relation for this functional is a fluctuation-dissipation theorem applicable arbitrarily far from equilibrium, that captures the effect of non-local and time-dependent behavior from transient driving forces. Based on this work, it is clear that statistical mechanics is a general tool for constructing the relationships between constraints on system information.

Standard diffusion corrupts data using Gaussian noise whose Fourier coefficients have random magnitudes and random phases. While effective for unconditional or text-to-image generation, corrupting phase components destroys spatial structure, making it ill-suited for tasks requiring geometric consistency, such as re-rendering, simulation enhancement, and image-to-image translation. We introduce Phase-Preserving Diffusion φ-PD, a model-agnostic reformulation of the diffusion process that preserves input phase while randomizing magnitude, enabling structure-aligned generation without architectural changes or additional parameters. We further propose Frequency-Selective Structured (FSS) noise, which provides continuous control over structural rigidity via a single frequency-cutoff parameter. φ-PD adds no inference-time cost and is compatible with any diffusion model for images or videos. Across photorealistic and stylized re-rendering, as well as sim-to-real enhancement for driving planners, φ-PD produces controllable, spatially aligned results. When applied to the CARLA simulator, φ-PD improves CARLA-to-Waymo planner performance by 50\%. The method is complementary to existing conditioning approaches and broadly applicable to image-to-image and video-to-video generation. Videos, additional examples, and code are available on our https://yuzeng-at-tri.github.io/ppd-page/{project page}.

Stochastic processes have found numerous applications in science, as they are broadly used to model a variety of natural phenomena. Due to their intrinsic randomness and uncertainty, they are however difficult to characterize. Here, we introduce an unsupervised machine learning approach to determine the minimal set of parameters required to effectively describe the dynamics of a stochastic process. Our method builds upon an extended beta-variational autoencoder architecture. By means of simulated datasets corresponding to paradigmatic diffusion models, we showcase its effectiveness in extracting the minimal relevant parameters that accurately describe these dynamics. Furthermore, the method enables the generation of new trajectories that faithfully replicate the expected stochastic behavior. Overall, our approach enables for the autonomous discovery of unknown parameters describing stochastic processes, hence enhancing our comprehension of complex phenomena across various fields.

This paper presents a novel end-to-end framework for closed-form computation and visualization of critical point uncertainty in 2D uncertain scalar fields. Critical points are fundamental topological descriptors used in the visualization and analysis of scalar fields. The uncertainty inherent in data (e.g., observational and experimental data, approximations in simulations, and compression), however, creates uncertainty regarding critical point positions. Uncertainty in critical point positions, therefore, cannot be ignored, given their impact on downstream data analysis tasks. In this work, we study uncertainty in critical points as a function of uncertainty in data modeled with probability distributions. Although Monte Carlo (MC) sampling techniques have been used in prior studies to quantify critical point uncertainty, they are often expensive and are infrequently used in production-quality visualization software. We, therefore, propose a new end-to-end framework to address these challenges that comprises a threefold contribution. First, we derive the critical point uncertainty in closed form, which is more accurate and efficient than the conventional MC sampling methods. Specifically, we provide the closed-form and semianalytical (a mix of closed-form and MC methods) solutions for parametric (e.g., uniform, Epanechnikov) and nonparametric models (e.g., histograms) with finite support. Second, we accelerate critical point probability computations using a parallel implementation with the VTK-m library, which is platform portable. Finally, we demonstrate the integration of our implementation with the ParaView software system to demonstrate near-real-time results for real datasets.

The Wilson-Cowan model for metapopulation, a Neural Mass Network Model, treats different subcortical regions of the brain as connected nodes, with connections representing various types of structural, functional, or effective neuronal connectivity between these regions. Each region comprises interacting populations of excitatory and inhibitory cells, consistent with the standard Wilson-Cowan model. By incorporating stable attractors into such a metapopulation model's dynamics, we transform it into a learning algorithm capable of achieving high image and text classification accuracy. We test it on MNIST and Fashion MNIST, in combination with convolutional neural networks, on CIFAR-10 and TF-FLOWERS, and, in combination with a transformer architecture (BERT), on IMDB, always showing high classification accuracy. These numerical evaluations illustrate that minimal modifications to the Wilson-Cowan model for metapopulation can reveal unique and previously unobserved dynamics.

Precipitation nowcasting is a critical spatio-temporal prediction task for society to prevent severe damage owing to extreme weather events. Despite the advances in this field, the complex and stochastic nature of this task still poses challenges to existing approaches. Specifically, deterministic models tend to produce blurry predictions while generative models often struggle with poor accuracy. In this paper, we present a simple yet effective model architecture termed STLDM, a diffusion-based model that learns the latent representation from end to end alongside both the Variational Autoencoder and the conditioning network. STLDM decomposes this task into two stages: a deterministic forecasting stage handled by the conditioning network, and an enhancement stage performed by the latent diffusion model. Experimental results on multiple radar datasets demonstrate that STLDM achieves superior performance compared to the state of the art, while also improving inference efficiency. The code is available in https://github.com/sqfoo/stldm_official.

Understanding the galaxy-halo relationship is not only key for elucidating the interplay between baryonic and dark matter, it is essential for creating large mock galaxy catalogues from N-body simulations. High-resolution hydrodynamical simulations are limited to small volumes by their large computational demands, hindering their use for comparisons with wide-field observational surveys. We overcome this limitation by using the First Light and Reionisation Epoch Simulations (FLARES), a suite of high-resolution (M_gas = 1.8 x 10^6 M_Sun) zoom simulations drawn from a large, (3.2 cGpc)^3 box. We use an extremely randomised trees machine learning approach to model the relationship between galaxies and their subhaloes in a wide range of environments. This allows us to build mock catalogues with dynamic ranges that surpass those obtainable through periodic simulations. The low cost of the zoom simulations facilitates multiple runs of the same regions, differing only in the random number seed of the subgrid models; changing this seed introduces a butterfly effect, leading to random differences in the properties of matching galaxies. This randomness cannot be learnt by a deterministic machine learning model, but by sampling the noise and adding it post-facto to our predictions, we are able to recover the distributions of the galaxy properties we predict (stellar mass, star formation rate, metallicity, and size) remarkably well. We also explore the resolution-dependence of our models' performances and find minimal depreciation down to particle resolutions of order M_DM ~ 10^8 M_Sun, enabling the future application of our models to large dark matter-only boxes.

In computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown superior segmentation performances compared to classical machine learning and image processing techniques. However, these models need fully annotated datasets for training which is challenging to acquire, especially in the medical domain. In this work, we release one of the biggest fully manually annotated datasets of nuclei in Hematoxylin and Eosin (H&E)-stained histological images, called NuInsSeg. This dataset contains 665 image patches with more than 30,000 manually segmented nuclei from 31 human and mouse organs. Moreover, for the first time, we provide additional ambiguous area masks for the entire dataset. These vague areas represent the parts of the images where precise and deterministic manual annotations are impossible, even for human experts. The dataset and detailed step-by-step instructions to generate related segmentation masks are publicly available at https://www.kaggle.com/datasets/ipateam/nuinsseg and https://github.com/masih4/NuInsSeg, respectively.

Standard methods for detecting discontinuities in conditional means are not applicable to outcomes that are complex, non-Euclidean objects like distributions, networks, or covariance matrices. This article develops a nonparametric test for jumps in conditional means when outcomes lie in a non-Euclidean metric space. Using local Fr\'echet regressionx2014which generalizes standard regression to metric-space valued datax2014the method estimates a mean path on either side of a candidate cutoff, extending existing k-sample tests to a flexible regression setting. Key theoretical contributions include a central limit theorem for the local estimator of the conditional Fr\'echet variance and the asymptotic validity and consistency of the proposed test. Simulations confirm nominal size control and robust power in finite samples. Two applications demonstrate the method's value by revealing effects invisible to scalar-based tests. First, I detect a sharp change in work-from-home compositions at Washington State's income threshold for non-compete enforceability during COVID-19, highlighting remote work's role as a bargaining margin. Second, I find that countries restructure their input-output networks after losing preferential US trade access. These findings underscore that analyzing regression functions within their native metric spaces can reveal structural discontinuities that scalar summaries would miss.

The article explores an encoding and structural information processing approach using sparse bit vectors and fixed-length linear vectors. The following are presented: a discrete method of speculative stochastic dimensionality reduction of multidimensional code and linear spaces with linear asymptotic complexity; a geometric method for obtaining discrete embeddings of an organised code space that reflect the internal structure of a given modality. The structure and properties of a code space are investigated using three modalities as examples: morphology of Russian and English languages, and immunohistochemical markers. Parallels are drawn between the resulting map of the code space layout and so-called pinwheels appearing on the mammalian neocortex. A cautious assumption is made about similarities between neocortex organisation and processes happening in our models.

An established measure of the expressive power of a given ReLU neural network is the number of linear regions into which it partitions the input space. There exist many different, non-equivalent definitions of what a linear region actually is. We systematically assess which papers use which definitions and discuss how they relate to each other. We then analyze the computational complexity of counting the number of such regions for the various definitions. Generally, this turns out to be an intractable problem. We prove NP- and #P-hardness results already for networks with one hidden layer and strong hardness of approximation results for two or more hidden layers. Finally, on the algorithmic side, we demonstrate that counting linear regions can at least be achieved in polynomial space for some common definitions.

We improve the efficiency of algorithms for stochastic combinatorial semi-bandits. In most interesting problems, state-of-the-art algorithms take advantage of structural properties of rewards, such as independence. However, while being optimal in terms of asymptotic regret, these algorithms are inefficient. In our paper, we first reduce their implementation to a specific submodular maximization. Then, in case of matroid constraints, we design adapted approximation routines, thereby providing the first efficient algorithms that rely on reward structure to improve regret bound. In particular, we improve the state-of-the-art efficient gap-free regret bound by a factor m/log m, where m is the maximum action size. Finally, we show how our improvement translates to more general budgeted combinatorial semi-bandits.

We introduce a novel framework for efficient sampling from complex, unnormalised target distributions by exploiting multiscale dynamics. Traditional score-based sampling methods either rely on learned approximations of the score function or involve computationally expensive nested Markov chain Monte Carlo (MCMC) loops. In contrast, the proposed approach leverages stochastic averaging within a slow-fast system of stochastic differential equations (SDEs) to estimate intermediate scores along a diffusion path without training or inner-loop MCMC. Two algorithms are developed under this framework: MultALMC, which uses multiscale annealed Langevin dynamics, and MultCDiff, based on multiscale controlled diffusions for the reverse-time Ornstein-Uhlenbeck process. Both overdamped and underdamped variants are considered, with theoretical guarantees of convergence to the desired diffusion path. The framework is extended to handle heavy-tailed target distributions using Student's t-based noise models and tailored fast-process dynamics. Empirical results across synthetic and real-world benchmarks, including multimodal and high-dimensional distributions, demonstrate that the proposed methods are competitive with existing samplers in terms of accuracy and efficiency, without the need for learned models.

This paper introduces a continuous-time stochastic dynamical framework for understanding how large language models (LLMs) may self-amplify latent biases or toxicity through their own chain-of-thought reasoning. The model posits an instantaneous "severity" variable x(t) in [0,1] evolving under a stochastic differential equation (SDE) with a drift term μ(x) and diffusion σ(x). Crucially, such a process can be consistently analyzed via the Fokker--Planck approach if each incremental step behaves nearly Markovian in severity space. The analysis investigates critical phenomena, showing that certain parameter regimes create phase transitions from subcritical (self-correcting) to supercritical (runaway severity). The paper derives stationary distributions, first-passage times to harmful thresholds, and scaling laws near critical points. Finally, it highlights implications for agents and extended LLM reasoning models: in principle, these equations might serve as a basis for formal verification of whether a model remains stable or propagates bias over repeated inferences.

We describe nonparametric deconvolution models (NDMs), a family of Bayesian nonparametric models for collections of data in which each observation is the average over the features from heterogeneous particles. For example, these types of data are found in elections, where we observe precinct-level vote tallies (observations) of individual citizens' votes (particles) across each of the candidates or ballot measures (features), where each voter is part of a specific voter cohort or demographic (factor). Like the hierarchical Dirichlet process, NDMs rely on two tiers of Dirichlet processes to explain the data with an unknown number of latent factors; each observation is modeled as a weighted average of these latent factors. Unlike existing models, NDMs recover how factor distributions vary locally for each observation. This uniquely allows NDMs both to deconvolve each observation into its constituent factors, and also to describe how the factor distributions specific to each observation vary across observations and deviate from the corresponding global factors. We present variational inference techniques for this family of models and study its performance on simulated data and voting data from California. We show that including local factors improves estimates of global factors and provides a novel scaffold for exploring data.

We introduce a design strategy for neural network macro-architecture based on self-similarity. Repeated application of a simple expansion rule generates deep networks whose structural layouts are precisely truncated fractals. These networks contain interacting subpaths of different lengths, but do not include any pass-through or residual connections; every internal signal is transformed by a filter and nonlinearity before being seen by subsequent layers. In experiments, fractal networks match the excellent performance of standard residual networks on both CIFAR and ImageNet classification tasks, thereby demonstrating that residual representations may not be fundamental to the success of extremely deep convolutional neural networks. Rather, the key may be the ability to transition, during training, from effectively shallow to deep. We note similarities with student-teacher behavior and develop drop-path, a natural extension of dropout, to regularize co-adaptation of subpaths in fractal architectures. Such regularization allows extraction of high-performance fixed-depth subnetworks. Additionally, fractal networks exhibit an anytime property: shallow subnetworks provide a quick answer, while deeper subnetworks, with higher latency, provide a more accurate answer.

In this paper, we present a novel framework for the analysis of Riemann Hypothesis [27], which is composed of three key components: a) probabilistic modeling with cross entropy optimization and reasoning; b) the application of the law of large numbers; c) the application of mathematical inductions. The analysis is mainly conducted by virtue of probabilistic modeling of cross entropy optimization and reasoning with rare event simulation techniques. The application of the law of large numbers [2, 3, 6] and the application of mathematical inductions make the analysis of Riemann Hypothesis self-contained and complete to make sure that the whole complex plane is covered as conjectured in Riemann Hypothesis. We also discuss the method of enhanced top-p sampling with large language models (LLMs) for reasoning, where next token prediction is not just based on the estimated probabilities of each possible token in the current round but also based on accumulated path probabilities among multiple top-k chain of thoughts (CoTs) paths. The probabilistic modeling of cross entropy optimization and reasoning may suit well with the analysis of Riemann Hypothesis as Riemann Zeta functions are inherently dealing with the sums of infinite components of a complex number series. We hope that our analysis in this paper could shed some light on some of the insights of Riemann Hypothesis. The framework and techniques presented in this paper, coupled with recent developments with chain of thought (CoT) or diagram of thought (DoT) reasoning in large language models (LLMs) with reinforcement learning (RL) [1, 7, 18, 21, 24, 34, 39-41], could pave the way for eventual proof of Riemann Hypothesis [27].

A major challenge in structured prediction is to represent the interdependencies within output structures. When outputs are structured as sequences, linear-chain conditional random fields (CRFs) are a widely used model class which can learn local dependencies in the output. However, the CRF's Markov assumption makes it impossible for CRFs to represent distributions with nonlocal dependencies, and standard CRFs are unable to respect nonlocal constraints of the data (such as global arity constraints on output labels). We present a generalization of CRFs that can enforce a broad class of constraints, including nonlocal ones, by specifying the space of possible output structures as a regular language L. The resulting regular-constrained CRF (RegCCRF) has the same formal properties as a standard CRF, but assigns zero probability to all label sequences not in L. Notably, RegCCRFs can incorporate their constraints during training, while related models only enforce constraints during decoding. We prove that constrained training is never worse than constrained decoding, and show empirically that it can be substantially better in practice. Additionally, we demonstrate a practical benefit on downstream tasks by incorporating a RegCCRF into a deep neural model for semantic role labeling, exceeding state-of-the-art results on a standard dataset.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

There is a growing body of work that leverages features extracted via topological data analysis to train machine learning models. While this field, sometimes known as topological machine learning (TML), has seen some notable successes, an understanding of how the process of learning from topological features differs from the process of learning from raw data is still limited. In this work, we begin to address one component of this larger issue by asking whether a model trained with topological features learns internal representations of data that are fundamentally different than those learned by a model trained with the original raw data. To quantify ``different'', we exploit two popular metrics that can be used to measure the similarity of the hidden representations of data within neural networks, neural stitching and centered kernel alignment. From these we draw a range of conclusions about how training with topological features does and does not change the representations that a model learns. Perhaps unsurprisingly, we find that structurally, the hidden representations of models trained and evaluated on topological features differ substantially compared to those trained and evaluated on the corresponding raw data. On the other hand, our experiments show that in some cases, these representations can be reconciled (at least to the degree required to solve the corresponding task) using a simple affine transformation. We conjecture that this means that neural networks trained on raw data may extract some limited topological features in the process of making predictions.

In this study, we propose a multi branched network approach to predict the dynamics of a physics attractor characterized by intricate and chaotic behavior. We introduce a unique neural network architecture comprised of Radial Basis Function (RBF) layers combined with an attention mechanism designed to effectively capture nonlinear inter-dependencies inherent in the attractor's temporal evolution. Our results demonstrate successful prediction of the attractor's trajectory across 100 predictions made using a real-world dataset of 36,700 time-series observations encompassing approximately 28 minutes of activity. To further illustrate the performance of our proposed technique, we provide comprehensive visualizations depicting the attractor's original and predicted behaviors alongside quantitative measures comparing observed versus estimated outcomes. Overall, this work showcases the potential of advanced machine learning algorithms in elucidating hidden structures in complex physical systems while offering practical applications in various domains requiring accurate short-term forecasting capabilities.

Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and behaviour. Moreover, these hidden features can be directly manipulated to steer model behaviour. However, it remains an open question whether this phenomenon is unique to models trained on inherently structured data (ie. language, images) or if it is a general property of foundation models. In this work, we investigate the internal representations of a large physics-focused foundation model. Inspired by recent work identifying single directions in activation space for complex behaviours in LLMs, we extract activation vectors from the model during forward passes over simulation datasets for different physical regimes. We then compute "delta" representations between the two regimes. These delta tensors act as concept directions in activation space, encoding specific physical features. By injecting these concept directions back into the model during inference, we can steer its predictions, demonstrating causal control over physical behaviours, such as inducing or removing some particular physical feature from a simulation. These results suggest that scientific foundation models learn generalised representations of physical principles. They do not merely rely on superficial correlations and patterns in the simulations. Our findings open new avenues for understanding and controlling scientific foundation models and has implications for AI-enabled scientific discovery.

This paper develops a comprehensive theoretical framework that imports concepts from stochastic thermodynamics to model price impact and characterize the feasibility of round-trip arbitrage in financial markets. A trading cycle is treated as a non-equilibrium thermodynamic process, where price impact represents dissipative work and market noise plays the role of thermal fluctuations. The paper proves a Financial Second Law: under general convex impact functionals, any round-trip trading strategy yields non-positive expected profit. This structural constraint is complemented by a fluctuation theorem that bounds the probability of profitable cycles in terms of dissipated work and market volatility. The framework introduces a statistical ensemble of trading strategies governed by a Gibbs measure, leading to a free energy decomposition that connects expected cost, strategy entropy, and a market temperature parameter. The framework provides rigorous, testable inequalities linking microstructural impact to macroscopic no-arbitrage conditions, offering a novel physics-inspired perspective on market efficiency. The paper derives explicit analytical results for prototypical trading strategies and discusses empirical validation protocols.

Large language models (LLMs) have achieved unprecedented performance by leveraging vast pretraining corpora, yet their performance remains suboptimal in knowledge-intensive domains such as medicine and scientific research, where high factual precision is required. While synthetic data provides a promising avenue for augmenting domain knowledge, existing methods frequently generate redundant samples that do not align with the model's true knowledge gaps. To overcome this limitation, we propose a novel Structural Entropy-guided Knowledge Navigator (SENATOR) framework that addresses the intrinsic knowledge deficiencies of LLMs. Our approach employs the Structure Entropy (SE) metric to quantify uncertainty along knowledge graph paths and leverages Monte Carlo Tree Search (MCTS) to selectively explore regions where the model lacks domain-specific knowledge. Guided by these insights, the framework generates targeted synthetic data for supervised fine-tuning, enabling continuous self-improvement. Experimental results on LLaMA-3 and Qwen2 across multiple domain-specific benchmarks show that SENATOR effectively detects and repairs knowledge deficiencies, achieving notable performance improvements. The code and data for our methods and experiments are available at https://github.com/weiyifan1023/senator.

The solar wind is a medium characterized by strong turbulence and significant field fluctuations on various scales. Recent observations have revealed that magnetic turbulence exhibits a self-similar behavior. Similarly, high-resolution measurements of the proton density have shown comparable characteristics, prompting several studies into the multifractal properties of these density fluctuations. In this work, we show that low-resolution observations of the solar wind proton density over time, recorded by various spacecraft at Lagrange point L1, also exhibit non-linear and multifractal structures. The novelty of our study lies in the fact that this is the first systematic analysis of solar wind proton density using low-resolution (hourly) data collected by multiple spacecraft at the L1 Lagrange point over a span of 17 years. Furthermore, we interpret our results within the framework of non-extensive statistical mechanics, which appears to be consistent with the observed nonlinear behavior. Based on the data, we successfully validate the q-triplet predicted by non-extensive statistical theory. To the best of our knowledge, this represents the most rigorous and systematic validation to date of the q-triplet in the solar wind.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

Although recent methods have tried to introduce large multimodal models (LMMs) into industrial anomaly detection (IAD), their generalization in the IAD field is far inferior to that for general purposes. We summarize the main reasons for this gap into two aspects. On one hand, general-purpose LMMs lack cognition of defects in the visual modality, thereby failing to sufficiently focus on defect areas. Therefore, we propose to modify the AnyRes structure of the LLaVA model, providing the potential anomalous areas identified by existing IAD models to the LMMs. On the other hand, existing methods mainly focus on identifying defects by learning defect patterns or comparing with normal samples, yet they fall short of understanding the causes of these defects. Considering that the generation of defects is closely related to the manufacturing process, we propose a manufacturing-driven IAD paradigm. An instruction-tuning dataset for IAD (InstructIAD) and a data organization approach for Chain-of-Thought with manufacturing (CoT-M) are designed to leverage the manufacturing process for IAD. Based on the above two modifications, we present Triad, a novel LMM-based method incorporating an expert-guided region-of-interest tokenizer and manufacturing process for industrial anomaly detection. Extensive experiments show that our Triad not only demonstrates competitive performance against current LMMs but also achieves further improved accuracy when equipped with manufacturing processes. Source code, training data, and pre-trained models will be publicly available at https://github.com/tzjtatata/Triad.

We investigate statistical properties of a likelihood approach to nonparametric estimation of a singular distribution using deep generative models. More specifically, a deep generative model is used to model high-dimensional data that are assumed to concentrate around some low-dimensional structure. Estimating the distribution supported on this low-dimensional structure, such as a low-dimensional manifold, is challenging due to its singularity with respect to the Lebesgue measure in the ambient space. In the considered model, a usual likelihood approach can fail to estimate the target distribution consistently due to the singularity. We prove that a novel and effective solution exists by perturbing the data with an instance noise, which leads to consistent estimation of the underlying distribution with desirable convergence rates. We also characterize the class of distributions that can be efficiently estimated via deep generative models. This class is sufficiently general to contain various structured distributions such as product distributions, classically smooth distributions and distributions supported on a low-dimensional manifold. Our analysis provides some insights on how deep generative models can avoid the curse of dimensionality for nonparametric distribution estimation. We conduct a thorough simulation study and real data analysis to empirically demonstrate that the proposed data perturbation technique improves the estimation performance significantly.