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01.
arXiv (CS.CV) 2026-06-15

Gefen: Optimized Stochastic Optimizer

AdamW is a default optimizer for modern deep learning, but its first and second moment states add roughly two parameter-sized buffers to training memory. We propose Gefen, a memory-efficient optimizer that automatically shares second-moment estimates across parameter blocks and quantizes the first moment using a learned codebook, thereby reducing AdamW's memory footprint by ~8x while maintaining the same performance, corresponding to a reduction of 6.5 GiB per billion parameters. The method is motivated by a theoretical result showing that large mixed Hessian entries constrain the ratio of squared gradients toward one, suggesting that Hessian-aligned parameters are natural candidates for sharing second-moment statistics. Since computing Hessians is impractical at scale, Gefen infers block structure from the initial squared gradients, requiring no architecture-specific metadata or hyperparameters beyond AdamW defaults. Gefen learns an exact histogram-based dynamic-programming quantization codebook and reuses the same blocks for first-moment scaling. Across diverse experiments, Gefen achieves the lowest peak optimizer memory among the compared AdamW-like methods while maintaining AdamW-level performance. In FSDP and DDP training, the reduced memory footprint enables larger microbatches and improves throughput significantly over AdamW, providing a practical drop-in replacement with lower memory usage that can increase throughput and enable training larger models or using larger batch sizes. We provide the complete Python implementation, including fused CUDA kernels at https://github.com/ndvbd/Gefen

02.
arXiv (CS.AI) 2026-06-19

Optimal Order of Multi-Agent and General Many-Body Systems

作者:

arXiv:2606.20485v1 Announce Type: cross Abstract: This paper develops a general framework for analyzing multi-agent systems with feedback loops between agents actions and collective observations. The framework is built on two fundamental agent-level variables: power, which measures agent influence on collective outcomes, and response functions, which determine how agents react to observations. We derive how macroscopic properties, including total power, useful power, entropy, order, fragility, and mobility, emerge from these two variables of heterogeneous agents. To study the trade off between growth and resilience, we introduce a system-level utility function parameterized by a risk-appetite coefficient and derive an optimal degree of order that balances productivity, stability, and adaptability. The analysis suggests that stronger synchronization can increase collective output but may also increase systemic fragility and reduce mobility. We further argue that order, entropy, information, and useful energy are task-dependent and system-relative concepts whose meanings depend on the objectives of the system. By measuring and designing agent power distributions and response functions, it may be possible to better understand, predict, and optimize collective behavior and identify the conditions under which collective intelligence and optimal order emerge.

03.
arXiv (quant-ph) 2026-06-16

Entangled states are typically incomparable

arXiv:2406.03335v2 Announce Type: replace Abstract: Consider a bipartite quantum system, where Alice and Bob jointly possess a pure state $|\psi\rangle$. Using local quantum operations on their respective subsystems, and unlimited classical communication, Alice and Bob may be able to transform $|\psi\rangle$ into another state $|\phi\rangle$. Famously, Nielsen's theorem [Phys. Rev. Lett., 1999] provides a necessary and sufficient algebraic criterion for such a transformation to be possible (namely, the local spectrum of $|\phi\rangle$ should majorise the local spectrum of $|\psi\rangle$). In the paper where Nielsen proved this theorem, he conjectured that in the limit of large dimensionality, for almost all pairs of states $|\psi\rangle, |\phi\rangle$ (according to the natural unitary invariant measure) such a transformation is not possible. That is to say, typical pairs of quantum states $|\psi\rangle, |\phi\rangle$ are entangled in fundamentally different ways, that cannot be converted to each other via local operations and classical communication. Via Nielsen's theorem, this conjecture can be equivalently stated as a conjecture about majorisation of spectra of random matrices from the so-called trace-normalised complex Wishart-Laguerre ensemble. Concretely, let $X$ and $Y$ be independent $n \times m$ random matrices whose entries are i.i.d. standard complex Gaussians; then Nielsen's conjecture says that the probability that the spectrum of $X X^\dagger / \operatorname{tr}(X X^\dagger)$ majorises the spectrum of $Y Y^\dagger / \operatorname{tr}(Y Y^\dagger)$ tends to zero as both $n$ and $m$ grow large. We prove this conjecture, and we also confirm some related predictions of Cunden, Facchi, Florio and Gramegna [J. Phys. A., 2020; Phys. Rev. A., 2021].

04.
arXiv (CS.CV) 2026-06-19

Contour-Constrained Deformable Registration with Parameter Characterization for Head and Neck Surgical Guidance

With 890,000 annual new cases globally, head and neck squamous cell carcinoma has one of the highest recurrence rates among solid malignancies. Although frozen section analysis is the standard of care for intraoperative margin assessment, accurately relocating detected positive margins on the resection bed remains challenging due to imprecise alignment between resected specimens and their resection bed, compounded by post-resection mucosal tissue shrinkage. We present a biomechanics-driven deformable registration framework that corrects post-resection tissue deformation to provide intraoperative guidance. Our approach registers 3D specimen meshes to intraoperative resection bed point clouds using a deformable registration approach based on regularized Kelvinlet basis functions. The registration matches surface point clouds, fiducial landmarks, and boundary contour constraints that directly penalize perpendicular distance-to-agreement between specimen and resection bed boundaries. Across nine specimens from skin, buccal mucosa, and tongue sites, the overall mean target registration error was $11.11 \pm 4.07$ mm using rigid registration, which decreased to $8.20 \pm 2.68$ mm (26.19\% reduction) using deformable registration without contour constraint. The proposed contour-constrained deformable registration further reduced the error to $5.62 \pm 2.28$ mm, a 49.41\% reduction relative to rigid registration. We observed the largest reduction in the most clinically challenging tongue specimens. We also performed a systematic two-stage parameter search to characterize the relative importance of surface alignment, fiducial correspondences, contour constraint, and strain energy regularization. This search revealed that contour weighting dominates registration accuracy for tissue types with large lateral deformation, while the algorithm operates over a broad range of parameter combinations.

05.
arXiv (CS.LG) 2026-06-16

DP-Hype: Federated Differentially Private Hyperparameter Search

arXiv:2510.04902v3 Announce Type: replace Abstract: Tuning hyperparameters in federated machine learning can substantially impact model performance. When hyperparameters are tuned on sensitive data, privacy becomes an important challenge and to this end, differential privacy has emerged as the de facto standard for provable privacy. A standard setting in federated learning is that clients agree on a shared setup, i.e., find a compromise from a set of hyperparameters, like a model's learning rate. Yet, prior work on privacy-preserving hyperparameter tuning is tailored to specific learning tasks, does not account for the privacy leakage of aggregated results, or offers a sub-optimal privacy-utility trade-off. In this work, we present our algorithm DP-Hype, which performs a federated and privacy-preserving hyperparameter search by conducting a federated voting based on local hyperparameter evaluations of clients. In this way, DP-Hype selects hyperparameters that lead to a compromise supported by a majority of clients, while maintaining scalability and independence from specific learning tasks. We prove that DP-Hype preserves the strong notion of differential privacy called client-level differential privacy and, importantly, show that its privacy guarantees do not depend on the number of hyperparameters. We also provide bounds on its utility guarantees, that is, the probability of finding good hyperparameters, and implement DP-Hype as a submodule in the popular Flower framework for federated machine learning. In addition, we evaluate performance on multiple benchmark data sets in iid as well as multiple non-iid settings and demonstrate high utility of DP-Hype even under small privacy budgets.

06.
arXiv (CS.LG) 2026-06-11

Counterexample Guided Learning in the Large using Reasoning Agents

arXiv:2606.11521v1 Announce Type: new Abstract: LLMs and LLM agents should improve when given feedback, but identifying when they are able to do so is difficult: feedback is heterogeneous, domain-specific, and difficult to control. We approach this challenge by asking LLMs to perform regular-expression induction, a classical symbolic learning problem where precise mechanisms for feedback exist in the form of counterexamples. In counterexample-guided learning, a learner (LLM) proposes candidate regular expressions from positive/negative-labeled strings, and the teacher (verifier) returns counterexamples showcasing the difference between the candidate and target languages. We identify novel counterexample-guided refinement strategies that enable effective regex learning, such as regularization and symbolic counterexample clusters. We also explore agentic strategies such as reflection and repair loops. Empirically, we find that verifier feedback substantially improves sample efficiency on challenging regex-induction tasks, reducing the number of labeled examples required and enabling learning of complex target expressions where standard prompting fails. For example, on the hardest task groups, our counterexample-guided framework improves success from 3.2% to 38.1% and from 38.9% to 74.1% on two different regex domains. These results suggest that LLMs can benefit from rich feedback beyond treating it as additional data, opening the door for robust verifier-guided methods for LLM-based program synthesis and formal reasoning.

07.
arXiv (CS.CL) 2026-06-11

Quantifying Subliminal Behavioral Transfer Ratios in Language Model Distillation

Distillation of a language model intended to transfer benign behavior to a student model may also transfer undesirable characteristics, if they are present in the teacher model, a phenomenon known as subliminal learning. While qualitative evidence supports the existence of this effect, its magnitude has not been systematically characterized. This study quantifies subliminal behavioral transfer ratios by steering two teacher models (Llama-2-7B-Chat and Qwen2.5-7B-Instruct) at varying steering strengths and distilling student models using only benign data. Evaluation on 100 JailbreakBench prompts with GPT-4.1, serving as the evaluator, indicates that transfer is robust but exhibits distinct scaling behaviors. Llama-2 demonstrates a sharp threshold ($\tau = {0.25,0.32} \ beyond \ \alpha = -0.15$), whereas Qwen2.5 displays continuous and higher levels of transfer ($\tau$ up to $0.61$).

08.
arXiv (math.PR) 2026-06-16

Plateau Gaps of Poisson Correctors Encode Metastable Reaction Rates

arXiv:2606.14789v1 Announce Type: cross Abstract: Metastable reaction rates are commonly inferred from transition-state fluxes, mean first-passage times, or fitted kinetic models. We show that they are directly encoded in the plateau gap of an occupation-time Poisson corrector. For a centered basin-occupation observable, the Poisson corrector develops metastable plateaus in the reactant and product basins, and their separation determines the forward and backward transition rates. This construction requires only the generator, stationary measure, and metastable partition, and therefore does not rely on a predefined transition-state surface. In overdamped and underdamped double-well dynamics, the plateau-gap rate recovers the Kramers, Grote-Hynes, and Pollak-Grabert-Hänggi hierarchy. The same corrector-martingale decomposition yields a reactive-noise density, revealing where stochastic forcing contributes to transitions in configuration or phase space. Thus, reaction rates and their fluctuation sources emerge from a single corrector field.

09.
arXiv (CS.CV) 2026-06-16

Trusted Multi-View Deep Learning Classification of Fetal Congenital Heart Disease with Feature-level and Decision-level Fusion

Congenital heart disease (CHD) refers to the abnormal anatomical structure caused by the abnormal development of the heart and great vessels during embryonic development. Traditional diagnostics often fail to achieve high accuracy and efficiency, especially given the complexity of cardiac anatomy. This study presents a specialized multi-view deep learning framework for CHD binary classification using echocardiographic images. A large-scale CHD dataset, including five views, was used to train the model, enabling it to integrate multi-angle image data. The framework utilizes advanced feature extraction and attention mechanisms to improve diagnostic precision and reliability. An uncertainty-based decision-making component is also integrated to handle low-quality images, enhancing diagnostic outcomes. Experimental results show that this method achieves top-tier performance on our dataset and provides a robust tool for early CHD detection, underscoring its potential for clinical use. The dataset and source code will be released upon paper acceptance.

10.
arXiv (CS.LG) 2026-06-19

Self-Adaptive Scale Handling for Forecasting Time Series with Scale Heterogeneity

arXiv:2606.20010v1 Announce Type: new Abstract: Current time series forecasting (TSF) research predominantly focuses on scale-homogeneous data, where different time series share similar numerical magnitude ranges. However, in real-world industrial scenarios such as financial product sales, different time series often differ by orders of magnitude (scale heterogeneity). Since these series share similar temporal patterns, joint modeling is desirable for better data utilization, yet existing scaling methods either compress low-scale signals (global normalization) or destroy semantic discriminability and amplify inverse-scaling errors (window-based scaling). This paper proposes a self-Adaptive Scale-handling (AS) module that learns adaptive scale factors tailored to each input, preserving semantic discriminability while reducing inverse-scaling errors. AS consists of Scale Calibrating (SC), which calibrates prior mean scaling factors through neural networks, and Scaling Selection (SS), which decides whether to apply calibration or retain the original factor, avoiding over-calibration. Experiments on real-world fund sales datasets from Ant Fortune and Alipay show that AS seamlessly integrates into popular TSF models and consistently improves their performance. The code and dataset are available at the link https://github.com/Meteor-Stars/ASTSF.

11.
medRxiv (Medicine) 2026-06-15

Quantitative insights into the role of phages and plasmids in the persistence of nontuberculous mycobacteria in chloraminated drinking water

Nontuberculous mycobacteria (NTM) are opportunistic pathogens that persist in chloraminated drinking water systems, yet the roles of phages and plasmids in their persistence remain largely unexplored. Using genome-resolved and quantitative metagenomics, we characterized NTM, phages, prophages, and plasmids in a chloraminated building plumbing system. Bacterial metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) were quantified at mean concentrations of 8.41 * 10^7 and 8.00 * 10^8 copies/L, respectively, including seven NTM MAGs at a mean total concentration of 4.01 * 10^5 copies/L. NTM concentrations were highest at the site with the lowest bacterial and viral diversity. Predicted NTM-infecting virus concentrations were inversely related to NTM concentrations across sites, suggesting complex phage-host dynamics that warrant direct experimental investigation. NTM, putative phages, prophages, and plasmids encoded functions related to disinfectant tolerance, stress response, metal resistance, and secretion. These findings identify phage interactions, prophages, and plasmids as overlooked genomic and ecological dimensions of NTM persistence in engineered water systems.

12.
arXiv (CS.LG) 2026-06-17

Geometry-Preserving Encoder/Decoder in Latent Generative Models

arXiv:2501.09876v4 Announce Type: replace-cross Abstract: Generative modeling aims to generate new data samples that resemble a given dataset. When using diffusion models for this task, one of the main challenges is solving the problem in the input space, which tends to be very high-dimensional. To address this, recent approaches solve diffusion models in the latent space through an encoder that maps from the data space to a lower-dimensional latent space, improving training efficiency and achieving state-of-the-art results. The variational autoencoder (VAE) is the most commonly used encoder/decoder framework in this domain, known for its ability to learn latent representations and generate data samples. In this paper, we introduce a novel encoder/decoder framework with theoretical properties distinct from those of the VAE, specifically designed to preserve the geometric structure of the data distribution. We demonstrate the significant advantages of this geometry-preserving encoder in the training process of both the encoder and decoder. Additionally, we provide theoretical results proving convergence of the training process, including convergence guarantees for encoder training, and results showing faster convergence of decoder training when using the geometry-preserving encoder.

13.
arXiv (CS.AI) 2026-06-16

Ranking Abuse via Strategic Pairwise Data Perturbations

arXiv:2604.17805v2 Announce Type: replace-cross Abstract: Pairwise ranking systems based on Maximum Likelihood Estimation (MLE), such as the Bradley-Terry model, are widely used to aggregate preferences from pairwise comparisons. However, their robustness under strategic data manipulation remains insufficiently understood. In this paper, we study the vulnerability of MLE-based ranking systems to adversarial perturbations. We formulate the manipulation task as a constrained combinatorial optimization problem and propose an Adaptive Subset Selection Attack (ASSA) to efficiently identify high-impact perturbations. Experimental results on both synthetic data and real-world election datasets show that MLE-based rankings exhibit a sharp phase-transition behavior: beyond a small perturbation budget, a limited number of strategic voters can significantly alter the global ranking. In particular, our method consistently outperforms random and greedy baselines under constrained budgets. These findings reveal a fundamental sensitivity of MLE-based ranking mechanisms to structured perturbations and highlight the need for more robust aggregation methods in collective decision-making systems.

14.
arXiv (CS.LG) 2026-06-17

Non-negative Matrix Factorisation with Topological Regularisation

arXiv:2606.17531v1 Announce Type: new Abstract: We investigate the learning of interpretable bases in non-negative matrix factorisation (NMF) by regularising the topology of the learned basis functions. Our approach is motivated by the observation that many data modalities can be viewed as non-negative functions on a structured domain, where the quality of a basis is intrinsically linked to its topology. However, naive methods for incorporating the topology of the support are often hindered by discreteness and threshold dependence, rendering them unsuitable for continuous optimisation. We address these challenges by employing persistent homology as a stable, threshold-free topological quantifier and by designing topological scores that integrate into the NMF objective as regularisers. The resulting framework encompasses spatially coherent image components, periodic time-series structures, and clique-like graph signals within a unified modelling language.

15.
arXiv (CS.CV) 2026-06-15

UniversalRAG: Retrieval-Augmented Generation over Corpora of Diverse Modalities and Granularities

Retrieval-Augmented Generation (RAG) has shown substantial promise in improving factual accuracy by grounding model responses with external knowledge relevant to queries. However, most existing approaches are limited to a text-only corpus, and while recent efforts have extended RAG to other modalities such as images and videos, they typically operate over a single modality-specific corpus. In contrast, real-world queries vary widely in the type of knowledge they require, which a single type of knowledge source cannot address. To address this, we introduce UniversalRAG, an any-to-any RAG framework designed to retrieve and integrate knowledge from heterogeneous sources with diverse modalities and granularities. Specifically, motivated by the observation that forcing all modalities into a unified representation space derived from a single aggregated corpus causes a modality gap, where the retrieval tends to favor items from the same modality as the query, we propose modality-aware routing, which dynamically identifies the most appropriate modality-specific corpus and performs targeted retrieval within it, and further justify its effectiveness with a theoretical analysis. Moreover, beyond modality, we organize each modality into multiple granularity levels, enabling fine-tuned retrieval tailored to the complexity and scope of the query. We validate UniversalRAG on 10 benchmarks of multiple modalities, showing its superiority over various modality-specific and unified baselines.

16.
arXiv (quant-ph) 2026-06-15

Simultaneous Estimation of Partial-Transpose Moments with Active Memory Independent of the Moment Order

arXiv:2606.14204v1 Announce Type: new Abstract: We study the simultaneous estimation of partial-transpose moments $p_j(\rho_{AB})=\mathrm{Tr}[(\rho_{AB}^{T_B})^j]$, $j=2,\ldots,K$, of an unknown bipartite $n$-qubit state from independent copies under an explicit active-memory constraint. We give a sequential qubit-reuse realization of the partial-transpose permutation that uses at most $2n+1$ active qubits, independent of $K$, and estimates all moments $p_2,\ldots,p_K$ to uniform additive error $\epsilon$ with total copy complexity $O(K\log K/\epsilon^2)$. We also prove two converse bounds. First, any uniformly accurate simultaneous estimator requires $\Omega(K/\epsilon^2)$ copies in the worst case. Second, the same scaling holds on an explicit isospectral two-qubit negative-partial-transpose (NPT) family whose ordinary moments are constant while the partial-transpose moments vary. These results characterize the copy complexity of the partial-transpose moment hierarchy up to a logarithmic factor and extend simultaneous nonlinear-functional estimation from ordinary state powers to partial-transpose spectral data under active quantum memory independent of the target moment order.

17.
arXiv (CS.CV) 2026-06-18

Where Will They Go? Modelling Multimodal Pedestrian Manoeuvres from Ego-centric Videos

Pedestrian trajectory prediction from an ego-centric camera is challenging since it depends on complex interactions with vehicles and scene context, as well as the intention of the pedestrian. By modelling correlation and intent from the historical and future trajectories of the pedestrian, it will usually result in a multimodal (i.e. multiple modes) distribution. Existing stochastic predictors often sample multiple futures from a single unimodal distribution, which can yield sub-optimal 'mixed-mode' trajectories that lie between distinct motion patterns and become implausible in real scenes. In this paper, we propose MMPM, a mode-aware framework that separately models future trajectory distributions into semantically meaningful modes based on the pedestrian's crossing behavior. MMPM consists of two modules: behavior-aware Pedestrian Interaction Module (PIM) that jointly captures pedestrian-vehicle and pedestrian-environment interactions by introducing gaze, head and hand gesture, and a CVAE-based Mode-aware Trajectory Predictor (MTP) module to model the future trajectory distributions on two modes, crossing and non-crossing the road, separately. A query-based decoder further enforces mode consistency during decoding. Experiments on PIE and JAAD datasets show that our method surpasses state-of-the-art baselines. Our proposed MTP is model-agnostic, which can be integrated into existing frameworks such as BiTrap-NP and SGNet-ED to further improve future trajectory prediction performance. We additionally introduce a data-driven validation protocol that matches predictions to spatio-temporally consistent ground-truth trajectories, demonstrating improved frame-wise displacement errors over previous work.

18.
arXiv (CS.CV) 2026-06-18

Learned Radius Estimation for UDF-Based Point Cloud Reconstruction

Surface reconstruction from point clouds is important for consumer-grade 3D capture, including AR/VR and indoor scanning. Local-patch Unsigned Distance Field (UDF) methods are lightweight and generalizable, but their accuracy depends on the support radius, traditionally fixed or selected by a one-dimensional curvature heuristic that cannot capture heterogeneous local geometry. We propose a learned per-query radius selector that predicts a continuous support radius and plugs into a frozen LoSF-UDF backbone. The selector is trained using off-grid target radii obtained by parabolic interpolation of cached UDF error curves. Experiments show improved fine-scale reconstruction accuracy.

19.
arXiv (CS.LG) 2026-06-16

Identification and Inference for Algorithmic Frontiers with Selective Labels

arXiv:2606.14977v1 Announce Type: cross Abstract: This paper provides identification results to characterize a fairness-accuracy (FA) frontier, and statistical inference tools to test hypotheses and build a confidence set for the FA-frontier, when outcomes are observed only for selected individuals. When the selection process is unrestricted but loss is measured in specific ways, we provide a characterization of the sharp identification region of the FA-frontier. Under an assumption of unconfoundedness conditional on observables (and unrestricted loss functions), we obtain point identification and propose a debiased machine learning estimator, derive its asymptotic distribution, and show how this can be used to carry out inference for the FA-frontier. In work in progress, we extend the partial identification results to a broader class of loss functions.

20.
arXiv (math.PR) 2026-06-24

On the convergence of doubly stochastic Markov chains

arXiv:2606.24584v1 Announce Type: new Abstract: We characterize the asymptotic behavior of time-homogeneous doubly stochastic Markov chains. Our investigation revolves around understanding the dynamics of products of doubly stochastic matrices, which in turn allows us to fully characterize three distinct behaviors: cyclicity, convergence towards a special equilibrium matrix, and divergence. Notably, we introduce a novel and comprehensive sufficient condition for the convergence of an infinite product of doubly stochastic matrices.

21.
medRxiv (Medicine) 2026-06-12

Genomic wastewater surveillance of seasonal and zoonotic influenza A viruses in California during the 2024-2025 flu season

Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples.

22.
arXiv (CS.CV) 2026-06-19

S-Agent: Spatial Tool-Use Elicits Reasoning for Spatial Intelligence

Real-world spatial intelligence requires reasoning over a continuous and evolving 3D world, yet existing VLMs and tool-augmented agents largely remain tied to static, stateless inference from isolated visual observations. We introduce \textsc{S-Agent}, a spatial tool-use agentic paradigm for understanding and reasoning over continuous multi-view images and videos. By formulating spatial reasoning as spatio-temporal evidence accumulation rather than isolated frame-level prediction, \textsc{S-Agent} reshapes spatial perception into scene-centric understanding beyond frame-centric recognition. Specifically, \textsc{S-Agent} casts the VLM as a semantic planner that decides what evidence is needed, while a hierarchy of spatial tools and experts grounds objects in 2D, lifts them into 3D geometric evidence, and aggregates this evidence into high-level spatial knowledge (e.g., counting, measurement, orientation, and relative position). Additionally, a temporal memory mechanism, including Scene Memory for maintaining the evolving scene state and Agent Memory for accumulating reasoning context, enables evidence integration across frames and reasoning steps. Comprehensive experiments on multi-view and video spatial reasoning benchmarks show that \textsc{S-Agent} consistently improves both open-source and closed-source VLMs in a training-free manner. Beyond inference-time augmentation, supervised fine-tuning (SFT) on \textsc{S-Agent}-generated spatial trajectories \textsc{S-300K} yields \textsc{S-Agent-8B}, a compact spatial agent that significantly surpasses similar-scale baselines (e.g., Qwen3-VL-8B) and performs comparably to advanced closed-source models (e.g., GPT-5.4 and Gemini 3).

23.
Nature Biotechnology 2026-06-05

Structural motif search across the protein universe with Folddisco

作者:

Detecting similar protein structural motifs in large structure collections is computationally expensive. We developed Folddisco, a fast structural motif search tool that uses an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco is 20-fold faster in querying and fourfold more storage-efficient than existing methods while improving accuracy. Folddisco is freely available online ( https://folddisco.foldseek.com ), along with a webserver ( https://search.foldseek.com/folddisco ). Folddisco enables protein structural motif search in million scale databases.

24.
medRxiv (Medicine) 2026-06-15

Scalable estimation of temporal clustering in accelerometry: a kernel-independent dispersion index grounded in the Hawkes process

Background. Self-exciting (Hawkes) point processes are a natural model for the temporal clustering of human physical activity (PA) recorded by accelerometers, yet they have seldom been used in this setting—in part because the usual maximum-likelihood fitting is challenging due to potential estimation bias and convergence failures on these data. A moment-based alternative—estimating the Hawkes branching ratio from the dispersion index, the variance-to-mean ratio of event counts—is kernel-independent and computationally trivial, but it has not been evaluated for accelerometry or adapted to the intensity-marked recordings accelerometers provide. Methods. Treating each minute above a sedentary threshold as an event, we estimated the Hawkes branching ratio $n$ by maximum likelihood and, as a kernel-independent and far cheaper alternative, from the dispersion index. We compared four dispersion-based estimators—event-count-based, intensity-mark-weighted using the mark-moment ratio, and time-of-day (TOD) adjusted variants of each—against the marked and unmarked maximum-likelihood estimates. Estimators were evaluated for mutual agreement, goodness of fit, and finite-window results in two National Health and Nutrition Examination Survey (NHANES) accelerometry cohorts (hip-worn, $n=2{,}560$; wrist-worn, $n=3{,}132$). We related the resulting temporal clustering measures to all-cause mortality using survey-weighted Cox models, adjusting for PA frequency, Peak30 (the average of the 30 highest PA values), and demographic covariates. Results. Event-count-based dispersion estimates agreed strongly with maximum-likelihood branching ratios ($rapprox0.74$ in both cohorts); the intensity-marked variant incorporating PA intensity variability agreed less well. Marked and unmarked Hawkes models yielded similar excitation and decay parameters, suggesting PA intensity added little clustering information beyond event timing. In the survival analysis, temporal clustering was associated with all-cause mortality independently of PA frequency and Peak30; the direction of association differed between the hip- and wrist-worn cohorts. Conclusions. A scalable dispersion-index estimator recovers the Hawkes branching ratio and matches maximum-likelihood estimates without requiring kernel specification or iterative optimization. It offers a practical tool for quantifying temporal clustering in accelerometry, enabling decomposition of temporal PA patterns into its exogenous initiation and endogenous persistence. Such temporal patterns carry health-relevant information beyond PA intensity and volume. Keywords: dispersion index; Hawkes process; branching ratio; temporal clustering; point process estimation; accelerometry; mortality

25.
arXiv (CS.LG) 2026-06-15

Identifiable Markov Switching Models with Instantaneous Effects and Exponential Families

arXiv:2606.02231v2 Announce Type: replace-cross Abstract: Temporal systems often exhibit non-stationary behaviour, such as seasonal climate variation or glucose fluctuations in patients with type-1 diabetes. One way to model non-stationarity is through discrete latent regimes, i.e., stationary segments of time. Such systems induce a Markov Switching Model (MSM), a class of Hidden Markov Models with autoregressive dependencies among latent regimes and observed variables. Identifying latent regimes is challenging in the presence of frequent regime switches and nonlinear and non-Gaussian dynamics, particularly when there are instantaneous effects between the variables, e.g., due to slow rates of measurements. In this work, we establish the identifiability of both latent regimes and regime-dependent causal structures under temporal regime dependencies, nonlinear lagged and instantaneous effects, and independent noise from the exponential family. Our identifiability theory subsumes non-temporal mixtures of causal models. Furthermore, we introduce FlowMSM, a regime detection framework that can be paired with any stationary causal discovery method to recover regime-dependent causal structures. Experiments on synthetic benchmarks and a financial economics dataset demonstrate the effectiveness of our approach to detect latent regimes and discover causal structures from non-stationary time series.