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01.
arXiv (CS.LG) 2026-06-12

Epistemic Uncertainty Is Not the Reducible Kind

Authors:

arXiv:2606.12646v1 Announce Type: cross Abstract: The standard taxonomy of predictive uncertainty defines epistemic uncertainty as the part removable by collecting more data, while the standard measure identifies it with a mutual-information term. We prove the definition and the measure are extensionally inconsistent. On an explicit construction, the measure assigns all uncertainty to the epistemic class, yet no quantity of training data reduces it. Reducibility is instead a property of the pair (uncertainty, acquisition class), and the dichotomy resolves into three parts: aleatoric, sample-reducible epistemic, and mechanism-reducible epistemic uncertainty. An exact identity for the value of an observation shows that in-distribution data never reduces mechanism-irreducible uncertainty and generically increases it. Ensemble disagreement, the deployed epistemic estimate, tracks the training procedure rather than the epistemic term. It collapses to zero beneath a positive truth under consistent training, and equals hyperparameter-scaled initialization noise under interpolation. A finite-sample falsification test and seed-swept experiments confirm the theory.

02.
arXiv (math.PR) 2026-06-15

Limiting partition function for the Mallows model: a conjecture and partial evidence

Authors:

arXiv:2406.18855v2 Announce Type: replace Abstract: Let $S_n$ denote the set of permutations of $n$ labels. We consider a class of Gibbs probability models on $S_n$ that is a subfamily of the so-called Mallows model of random permutations. The Gibbs energy is given by a class of right invariant divergences on $S_n$ that includes common choices such as the Spearman foot rule and the Spearman rank correlation. Mukherjee in 2016 computed the limit of the (scaled) log partition function (i.e. normalizing factor) of such models as $n\rightarrow \infty$. Our objective is to compute the exact limit, as $n\rightarrow \infty$, without the log. We conjecture that this limit is given by the Fredholm determinant of an integral operator related to the so-called Schrödinger bridge probability distributions from optimal transport theory. We provide partial evidence for this conjecture, although the argument lacks a final error bound that is needed for it to become a complete proof.

03.
arXiv (quant-ph) 2026-06-12

Effective Geometry and Position-Dependent Mass in Dual-$q$ Quantum Mechanics

arXiv:2606.12444v1 Announce Type: new Abstract: This work investigates the deformed-derivative formalism introduced by Borges, with emphasis on the relation between the linear operator $D_{(q)}$ and its nonlinear dual counterpart $D^{(q)}$. Directly inserting the dual derivative into the kinetic term leads to a nonlinear Schrödinger equation and obscures the usual interpretation of superposition and probability. We show that this nonlinearity can be removed by a simultaneous transformation of the coordinate and of the wave function. The transformed problem is an ordinary linear Schrödinger equation in a deformed coordinate, and its representation in the physical coordinate is equivalent to a Hermitian position-dependent-mass (PDM) Hamiltonian. In this formulation, the deformation parameter $q$ determines both the effective mass profile and the associated metric. The formalism is applied to the free particle, the infinite square well, the rectangular barrier, and the harmonic oscillator in the weak-deformation regime. Comparison with the nonadditive-translation approach of Costa Filho et al. shows that the Borges dual-$q$ framework provides an alternative route to the same effective geometric structure. For $q1$, the effective length is increased, which lowers the spectrum and suppresses tunneling relative to the undeformed limit $q=1$.

04.
medRxiv (Medicine) 2026-06-20

EpiLink: a simulation-based compatibility model for genomic transmission clustering in infectious disease surveillance

Identifying recently linked infections from pathogen genome sequences is central to infectious disease surveillance, yet many clustering approaches rely on fixed genetic distance thresholds whose relationship to transmission is often unclear. This limitation is especially important in rapidly growing outbreaks and superspreading events, where many cases may be sampled close together in time and share little genetic variation, making true transmission links difficult to distinguish from other closely related infections. Supervised models can improve discrimination, but they require labelled transmission data that are rarely available during outbreak response. We developed EpiLink, a threshold-free method that estimates whether two cases are compatible with recent transmission. Here, compatibility means how well the observed genetic distance and sampling-time difference between two cases fit what would be expected if they were linked by defined recent transmission scenarios. EpiLink simulates plausible recent transmission histories while accounting for uncertainty in infection timing, testing delay, and mutation accumulation, then assigns higher scores to pairs whose observed differences are typical of those simulations. EpiLink was evaluated using both synthetic and empirical SARS-CoV-2 outbreak data from the 2020 Boston epidemic. Two EpiLink variants were compared to a logistic regression model trained on labelled transmission data. One EpiLink variant assumed deterministic mutation accumulation, with genetic differences proportional to elapsed evolutionary time; the other accounted for stochasticity by sampling mutation counts from a Poisson distribution. The logistic regression model performed better at distinguishing linked from unlinked pairs, but EpiLink achieved comparable clustering accuracy. In the Boston data, EpiLink recovered clusters enriched for documented conference and skilled nursing facility outbreaks. EpiLink thus provides an interpretable, simulation-based approach for identifying recent transmission clusters when fixed thresholds are difficult to justify and labelled transmission data are unavailable.

05.
arXiv (quant-ph) 2026-06-11

Power-law-graded Ising Interactions Stabilize Time Crystals Realizing Quantum Energy Storage and Sensing

arXiv:2508.14847v3 Announce Type: replace Abstract: We study discrete time-crystalline (DTC) phases in one-dimensional spin-1/2 chains with power-law-graded Ising interactions under periodic Floquet driving. By generalizing Stark localization to power-law-graded Ising interaction profiles, we identify robust period-doubled dynamics across a wide range of interaction exponents, stabilized by the interplay between coherent driving and spatially varying coupling. Within the DTC phase, the energy stored in the system, interpreted as a quantum battery, increases superlinearly with system size, although no scaling advantage persists in normalized power. Beyond energy storage, we demonstrate that the DTC phase supports enhanced quantum sensing. The quantum Fisher information associated with estimating timing deviations in the drive scales superextensively with system size, surpassing the Heisenberg limit. The degree of quantum advantage can be tuned by varying the interaction exponent, though DTC behavior remains robust throughout. Our results position power-law-graded Ising interacting Floquet systems as robust platforms for storing quantum energy and achieving metrological enhancement.

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

Aligned but Stereotypical? How System Prompts Shape Demographic Bias in LLM-Based Text-to-Image Models

Text-to-image (T2I) systems increasingly rely on Large Language Model (LLM)-based text conditioning to interpret and expand user prompts. While this improves prompt understanding and text-image alignment, we find that it can also introduce implicit demographic assumptions, even when demographic attributes are unspecified. To systematically investigate this behavior across varying levels of prompt ambiguity and complexity, we construct a comprehensive benchmark covering diverse prompt settings. Evaluations on eight recent T2I models show that LLM-based systems consistently exhibit stronger demographic skew than non-LLM-based baselines. We further analyze system prompts, a component unique to LLM-based T2I systems that guides prompt interpretation and expansion. Our analyses show that these instructions strongly influence text embeddings, which subsequently leads to biased image generations. Motivated by these findings, we propose FairPro, a training-free debiasing framework that adaptively generates fairness-aware instructions while preserving user intent. Experiments demonstrate that FairPro substantially reduces demographic disparities while maintaining prompt fidelity.

07.
arXiv (CS.AI) 2026-06-19

Rethinking Shrinkage Bias in LLM FP4 Pretraining: Geometric Origin, Systemic Impact, and UFP4 Recipe

arXiv:2606.20381v1 Announce Type: new Abstract: FP4 training promises substantial reductions in memory and computation cost for LLM pretraining, yet current FP4 hardware paths and recipes, including NVIDIA Blackwell/Rubin-class systems and AMD MI350-series GPUs, remain centered on E2M1 data elements. In this study, we identify a fundamental limitation of that choice: non-uniform formats such as E2M1 inherently suffer from Shrinkage Bias, a systematic negative rounding error caused by the geometric asymmetry of their representable bins. We show that this bias accumulates multiplicatively across layers and is amplified by the Random Hadamard Transform (RHT), providing a unified explanation for the training instability observed in existing E2M1-based FP4 recipes. In contrast, uniform grids (E1M2/INT4) bypass this grid-geometry error and better convert the improved bucket utilization from RHT into higher quantization quality. Based on this finding, we propose UFP4, a uniform 4-bit training recipe that applies RHT to all three training GEMMs while restricting stochastic rounding to dY alone. On Dense 1.5B, MoE 7.9B, and MoE 124B long-run pretraining, UFP4 consistently achieves lower BF16-relative loss degradation than strong E2M1-based baselines, supported by scaling-law analysis and ablation studies. Our results suggest that future accelerators should support E1M2/INT4-style uniform 4-bit grids as first-class training primitives alongside E2M1.

08.
arXiv (CS.LG) 2026-06-16

Single-Round Clustered Federated Learning via Data Collaboration Analysis for Non-IID Data

arXiv:2601.09304v2 Announce Type: replace Abstract: Federated Learning (FL) enables distributed learning across multiple clients without sharing raw data. When statistical heterogeneity across clients is severe, Clustered Federated Learning (CFL) can im-prove performance by grouping similar clients and training cluster-wise models. However, most CFL approaches rely on multiple communication rounds for cluster estimation and model updates, which limits their practicality under tight constraints on communication rounds. We propose Data Collaboration-based Clustered Federated Learning (DC-CFL), a single-round framework that completes both client clustering and cluster-wise learning, using only the information shared in DC analysis. DC-CFL quantifies inter-client similarity via total variation distance between label distributions, estimates clusters using hierarchical clustering, and performs cluster-wise learning via DC analysis. Experiments on multiple open datasets under representative non-IID conditions show that DC-CFL achieves accuracy comparable to multi-round baselines while requiring only one communication round. These results indicate that DC-CFL is a practical alternative for collaborative AI model development when multiple communication rounds are impractical. Our source code is publicly available at https://github.com/souta-suga/DC-CFL.

10.
bioRxiv (Bioinfo) 2026-06-20

Ribosomes are covered by a coat of flexible protein fragments

Ribosomal proteins contain flexible terminal regions that are averaged out during electron density reconstructions, rendering them absent from experimental models derived by X-ray crystallography or cryogenic electron microscopy. These flexible protein fragments (FPFs) collectively form an invisible coat on the ribosome surface whose presence has been systematically overlooked. Here we analysed FPFs from 36 ribosomes spanning bacteria, eukaryotes, and mitochondria. We found that mitoribosomes harbour the most numerous and longest FPFs. Structural predictions confirmed that FPFs are predominantly disordered across all ribosome classes. Comparison of FPF amino acid composition against proteome-wide background frequencies revealed strong and domain-specific compositional biases. The balance between arginine and lysine content tracks the cardiolipin content of the membrane each ribosome class contacts. The arginine enrichment in mitoribosomal FPFs may additionally reflect selection arising from the RNA-rich environment of mitochondrial RNA granules, membraneless condensates where mitoribosomes are assembled. FPFs are uniformly depleted in aromatic residues, arguing against protein-driven liquid–liquid phase separation propensity. Our findings suggest that the flexibly tethered coat is a highly functional intrinsic part of all ribosomes.

11.
arXiv (CS.AI) 2026-06-16

Critically Engaged Pragmatism: Scientific Norm and Social, Pragmatist Epistemology for AI Science Evaluation Tools

Authors:

arXiv:2601.09753v2 Announce Type: replace-cross Abstract: AI science evaluation tools aim to assess research credibility. As with traditional metrics such as impact factors, their edicts can be decontextualised and repurposed in problematic ways. To address this, I propose Critically-Engaged Pragmatism as a scientific norm enjoining scientific communities to scrutinise the purposes and purpose-specific reliability of AI science evaluation tools. To foster Critically Engaged Pragmatism, creators of AI science evaluation tools should transparently and fully report design, training, and benchmarking details to facilitate assessments of purpose-specific reliability, liability to different types of error, and bias. What count as best practices for the transparent reporting of AI science evaluation tools should be updated as new forms of error, bias, and gamesmanship are discovered. Under this framework, AI science evaluation tools are not objective arbiters of scientific credibility. Rather, they are the object of critical discursive practices that ultimately ground the credibility of scientific communities.

12.
arXiv (CS.AI) 2026-06-16

FlowState: Sampling-Rate-Equivariant Time-Series Forecasting

arXiv:2508.05287v3 Announce Type: replace-cross Abstract: Existing time series foundation models (TSFMs), often based on transformer variants, lack adaptability to different sampling rates, struggle with generalization across varying context and target lengths, and are computationally inefficient. We introduce FlowState, a novel TSFM architecture that achieves sampling-rate-equivariant forecasting through a unified design that pairs a state space model (SSM) encoder with a functional basis decoder (FBD). This design enables continuous-time modeling and dynamic time-scale adjustment, allowing FlowState to inherently generalize across all possible temporal resolutions, and dynamically adjust the forecasting horizons without retraining. We further propose an efficient pretraining strategy that improves robustness and accelerates training. Despite being one of the smallest TSFMs, FlowState achieves state-of-the-art results on the widely used GIFT-Eval benchmark, while demonstrating superior adaptability to unseen sampling rates. Our detailed analyses confirm the effectiveness of its components, and we demonstrate its unique ability to adapt to varying input sampling rates.

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

RoTRAG: Rule of Thumb Reasoning for Conversation Harm Detection with Retrieval-Augmented Generation

Detecting harmful content in multi turn dialogue requires reasoning over the full conversational context rather than isolated utterances. However, most existing methods rely mainly on models internal parametric knowledge, without explicit grounding in external normative principles. This often leads to inconsistent judgments in socially nuanced contexts, limited interpretability, and redundant reasoning across turns. To address this, we propose RoTRAG, a retrieval augmented framework that incorporates concise human written moral norms, called Rules of Thumb (RoTs), into LLM based harm assessment. For each turn, RoTRAG retrieves relevant RoTs from an external corpus and uses them as explicit normative evidence for turn level reasoning and final severity classification. To improve efficiency, we further introduce a lightweight binary routing classifier that decides whether a new turn requires retrieval grounded reasoning or can reuse existing context. Experiments on ProsocialDialog and Safety Reasoning Multi Turn Dialogue show that RoTRAG consistently improves both harm classification and severity estimation over competitive baselines, with an average relative gain of around 40% in F1 across benchmark datasets and an average relative reduction of 8.4% in distributional error, while reducing redundant computation without sacrificing performance.

14.
arXiv (CS.CV) 2026-06-16

MambaH-Fit: Rethinking Hyper-surface Fitting-based Point Cloud Normal Estimation via State Space Modelling

We present MambaH-Fit, a state space modelling framework tailored for hyper-surface fitting-based point cloud normal estimation. Existing normal estimation methods often fall short in modelling fine-grained geometric structures, thereby limiting the accuracy of the predicted normals. Recently, state space models (SSMs), particularly Mamba, have demonstrated strong modelling capability by capturing long-range dependencies with linear complexity and inspired adaptations to point cloud processing. However, existing Mamba-based approaches primarily focus on understanding global shape structures, leaving the modelling of local, fine-grained geometric details largely under-explored. To address the issues above, we first introduce an Attention-driven Hierarchical Feature Fusion (AHFF) scheme to adaptively fuse multi-scale point cloud patch features, significantly enhancing geometric context learning in local point cloud neighbourhoods. Building upon this, we further propose Patch-wise State Space Model (PSSM) that models point cloud patches as implicit hyper-surfaces via state dynamics, enabling effective fine-grained geometric understanding for normal prediction. Extensive experiments on benchmark datasets show that our method outperforms existing ones in terms of accuracy, robustness, and flexibility. Ablation studies further validate the contribution of the proposed components.

15.
arXiv (CS.CL) 2026-06-16

Can LLM Agents Infer World Models? Evidence from Agentic Automata Learning

We propose agentic automata learning to evaluate the extent to which tool-calling LLM agents can uncover hidden environments through interaction. In our setup, an agent should uncover a hidden deterministic finite automaton (DFA) by interacting with an oracle through (1) membership queries ("Does this string belong to the target language?") and (2) equivalence queries ("Is this the target DFA?"). This yields a scalable testbed with controlled task complexity, measurable interaction efficiency, and strong baselines (classic automata-learning algorithms). Evaluating state-of-the-art LLMs, we find that performance drops sharply as DFA size increases. Reasoning models are markedly stronger than non-reasoning models, yet trajectory analyses reveal recurring failures in query planning, evidence integration, and hypothesis construction. Overall, our results show that current LLM agents can sometimes perform non-trivial interactive discovery, but remain far less robust and efficient than classic algorithms for the task.

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

DiffMath: Symbol- and Graph-Aware Latent Diffusion Transformer for Handwritten Mathematical Expression Generation

Handwritten Mathematical Expression Generation (HMEG) is challenging due to the complex two-dimensional layouts and long-range structural dependencies of mathematical expressions. Existing methods typically rely on explicit spatial supervision, such as symbol-level bounding boxes, which incurs high annotation costs and limits scalability. In this work, we propose DiffMath, a symbol- and graph-aware latent diffusion framework that leverages the hierarchical structure inherent in LaTeX as a structural prior, eliminating the need for positional supervision. First, we design a Relational Abstract Syntax Tree (RelAST), a generation-oriented representation that distills MathML trees into compact triplet sequences [S, R, D], where each token directly encodes a symbol identity, spatial relation, or nesting depth. Second, we introduce MathVAE, which learns structure-preserving latent representations through symbol-aware and relation-aware perceptual regularization, ensuring that the latent space captures both character semantics and spatial topology. Third, MathDiT performs conditional denoising in this structured latent space, further guided by a global symbol-count prior via Adaptive Layer Normalization (AdaLN) to improve structural coherence. Experiments show that DiffMath produces structurally consistent handwritten expressions, achieves superior performance over existing methods, and improves the accuracy of downstream OCR models through synthetic data augmentation.

17.
arXiv (quant-ph) 2026-06-17

Practical Tests and Witnesses of Fermionic non-Gaussianity

arXiv:2605.26218v2 Announce Type: replace Abstract: Fermionic Gaussian states describe free fermions and underlie the mean-field picture of matter, from metals to superconductors; they are also efficiently simulable on classical computers. Departures from Gaussianity – the correlations produced by interactions – are therefore what make a fermionic system hard to simulate classically and useful for quantum computation, analogous to the role of magic in stabilizer-based quantum computation. Yet detecting and quantifying such non-Gaussianity at scale has remained challenging. Here we introduce practical tests and witnesses of fermionic non-Gaussianity built on fermionic antiflatness, a measure derived from the two-point covariance matrix. We estimate it with two protocols – a two-copy Bell measurement and a single-copy scheme using commuting Majorana bilinears – that determine whether a state is Gaussian or far from it at lower measurement cost than existing approaches, using only operations native to fault-tolerant hardware. For mixed states, a purity-corrected witness certifies non-Gaussianity and remains robust under strong noise; running it on the IQM quantum processor, we find that noise can both reduce and enhance non-Gaussianity. Finally, we show that preparing pseudorandom fermionic states requires extensive non-Gaussianity. Together, these tools enable the study and certification of non-Gaussian fermionic resources on present-day quantum devices.

18.
arXiv (quant-ph) 2026-06-12

Quantum Network Routing based on Surface Code Error Correction

arXiv:2606.12781v1 Announce Type: new Abstract: Quantum networks encounter unavoidable channel noises and erasure errors, presenting a huge obstacle in designing protocols that attain both high reliability and efficiency. Typically, quantum networks fall into two categories: those utilize quantum entanglements for quantum teleportation, and those directly transfer the actual quantum messages. In this paper, we present SurfNet, a quantum network that inherits the main advantages from both categories. It employs surface codes as logical qubits for encoding messages, and utilizes two parallel communication channels to fault-tolerantly transfer each surface code in a modular manner. Our approach of using surface codes can timely correct both operational and photon loss errors within the network, and the integration of the two channels within the network can greatly improve network throughput. For the implementation of SurfNet, we propose a novel network architecture, designed to better integrate surface codes into quantum networks. We also propose a novel error correction decoder, designed to fully utilize the modular characteristic of surface codes within our network. Simulation results demonstrate that SurfNet with its decoder significantly enhances the communication fidelity within quantum networks.

19.
medRxiv (Medicine) 2026-06-15

Excitation-Inhibition Balance in Schizophrenia Spectrum Disorders: EEG Criticality Reflects Frontal Metabolites and a Potential Compensatory Mechanism

Background The excitation-inhibition (E-I) balance is essential for normal brain functioning, while deviations from this balance have been implicated in several psychiatric disorders. However, the extent to which electroencephalography (EEG) and proton magnetic resonance spectroscopy (1H-MRS) E-I markers are altered in schizophrenia spectrum disorders (SSD), how they converge across modalities, and how they relate to cognitive performance and clinical symptoms remain insufficiently characterized. Methods We recruited 111 healthy controls (HC) and 113 individuals with SSD. All participants underwent resting-state EEG and 1H-MRS. Metabolites were measured either in the anterior cingulate cortex (ACC; NSSD = 63, NHC = 58) or in the left dorsolateral prefrontal cortex (lDLPFC; NSSD = 50, NHC = 53), from which gamma-aminobutyric acid (GABA), glutamate + glutamine (Glx), and the Glx/GABA ratio were extracted. Extracted EEG E-I markers included oscillatory activity, aperiodic activity, functional E-I, microstates, multiscale entropy, and neuronal avalanche criticality. Results MRS results showed no group differences in GABA, Glx, or the Glx/GABA ratio. In contrast, most EEG-derived E-I markers indicated increased cortical inhibition in SSD, including steeper aperiodic exponents, prolonged microstate durations, and greater prevalence of subcritical states. However, functional E-I showed a divergent pattern, suggesting balanced dynamics in SSD and relatively inhibition-weighted dynamics in HC. Across groups, higher ACC and lDLPFC GABA predicted a lower kappa index, whereas a higher lDLPFC Glx/GABA ratio was associated with a higher kappa index. In SSD, reduced avalanche criticality was associated with better cognition and less severe symptoms. Conclusion Several EEG-derived E-I proxies, but not MRS measures, indicate an increased cortical inhibition in SSD. Criticality indices best capture frontal neurochemical metabolites and improvements in clinical symptoms, potentially reflecting inhibitory compensation mechanisms in SSD.

20.
arXiv (CS.AI) 2026-06-16

XFlow: An Executable Protocol Programming System for Reliable Multi-Agent Workflows

arXiv:2606.14790v1 Announce Type: cross Abstract: LLM-based multi-agent systems increasingly coordinate planning, reasoning, tool use, and human interaction, yet their reliability remains limited. A central source of this limitation is the underspecified prompt–harness boundary. Current systems lack a principled way to decide which workflow commitments should remain in prompts and which should become harness structure. We present XFlow, an executable protocol programming system for reliable multi-agent workflows, and XPF (XFlow Protocol Format), its domain-specific protocol programming language. XFlow occupies a middle position between prompt-only orchestration and markup-like workflow descriptions. XPF remains readable as a literate protocol, but it is compiled and executed as a program. Its design keeps informal semantic work inside actors while moving selected commitments into harness structure that can be checked, preserved, and enforced. At runtime, XFlow stages uncertainty through lifecycle-governed symbols, which are typed state cells with validation and commit states. Actor outputs are mediated before they become shared state, instead of spreading through prompts, transcripts, or implicit memory. Our experiments cover Constrained Interaction, Long-Context Reasoning, and Agentic Software Engineering. They show that XFlow improves reliability by making constraints, evidence handling, and process requirements explicit and enforceable.

21.
arXiv (CS.LG) 2026-06-16

Hidden Degradation Costs in Energy-Cost-Only HEMS Optimisation: Study on Battery and PV Sensitivity

arXiv:2606.16051v1 Announce Type: cross Abstract: Residential battery energy storage systems (BESS) are increasingly deployed alongside photovoltaic (PV) generation to reduce household energy costs under volatile time-of-use (TOU) tariffs. Model predictive control (MPC) is a widely adopted optimisation strategy for home energy management systems (HEMS), typically formulated to minimise net energy cost, subject to physical and operational constraints. However, battery degradation is rarely embedded in the optimisation objective, meaning its cost is unquantified and aggressive; high-cycle-count strategies could incur significant losses once deployed to physical systems. This paper presents a receding-horizon mixed-integer linear programming (MILP) baseline for a UK residential HEMS, using demand data from the REFIT dataset. A 3 by 3 sensitivity study is conducted across three battery sizes and three PV array sizes, with post-hoc degradation cost estimated using the Naumann stress model and rainflow cycle counting. Results show that degradation remains constant for each battery size and can exceed energy cost savings by up to 1,060 %. These results demonstrate that energy-cost-only optimisation systematically underestimates the true system cost, motivating a degradation-aware control formulation.

22.
Nature Biotechnology 2026-06-09

Hybrid solid−liquid optics enable scalable, high-resolution light-sheet microscopy across diverse immersion media

Authors:

Many data-driven approaches rely on scalable and affordable three-dimensional (3D) imaging across subcellular to organ scales. Although advances in tissue clearing, expansion microscopy and light-sheet microscopy (LSM) have enabled high-resolution imaging of intact specimens, scalability in sample size, throughput and accessibility remains fundamentally limited by detection optics. Here we introduce hybrid solid−liquid optics (HySIL), a flexible refractive design framework in which a solid optical element and a refractive index (RI)-matched liquid function as a continuous optical system for wavefront correction and numerical aperture enhancement. We implement this framework as SCOPE and Super-SCOPE, enabling submicron-resolution, aberration-corrected LSM using long-working-distance air objectives. We demonstrate high-resolution volumetric imaging across diverse biological contexts, including cleared and expanded mouse, salamander and cavefish brains, human induced pluripotent stem cell (iPSC)-derived brain organoids and large intact human tissues for 3D histopathology. By combining enhanced optical performance with low-cost, long-working-distance and multi-immersion compatibility, HySIL provides an accessible and scalable foundation for next-generation volumetric imaging and data-driven biological discovery. Hybrid solid–liquid optics improve light-sheet imaging of intact biological samples.

23.
arXiv (math.PR) 2026-06-12

Data-driven subsampling rates for diffusion parameter estimation of SDEs

arXiv:2606.13615v1 Announce Type: new Abstract: We study the problem of diffusion parameter estimation for stochastic differential equation (SDE) models in scenarios where data and model are compatible only on specific scales that have yet to be determined. We introduce a simple and efficient method for selecting suitable rates at which given time series data should be subsampled in order to ensure that the statistical structure of the subsampled data is consistent with the behavior of the SDE model on an infinitesimal scale. Our approach is based on analyzing the statistics of the lengths of monotonically increasing or decreasing segments in the subsampled data sequence, which we refer to as monotone runs. As an analytical foundation, we prove for a large class of SDEs with additive noise that the lengths of monotone runs at an infinitesimal scale are approximately geometrically distributed with success probability $1/2$. This universal characterization is employed to derive an automated method for selecting appropriate subsampling rates for given time series data that is directly applicable in real-world scenarios and does not rely on an asymptotic framework of multiscale diffusions. The approach is demonstrated using an application from industrial mathematics concerning surrogate models for fiber lay-down curves in production processes of nonwoven textiles.

24.
arXiv (CS.LG) 2026-06-12

Deep Learning-based Algebraic Reynolds Stress Closures for RANS Simulations of Turbulent Flows

arXiv:2605.26358v2 Announce Type: replace-cross Abstract: Turbulence is ubiquitous in engineering and science, yet direct simulation is prohibitively expensive. The Reynolds-averaged Navier-Stokes (RANS) equations provide savings exceeding ten orders of magnitude but introduce unclosed terms (the closure problem). Offline-trained machine-learning (ML) closures suffer distribution shift in predictive simulations, while ML methods that bypass the governing equations struggle to generalise from scarce high-fidelity data. We develop a physics-derived deep learning closure model for RANS, the Deep Algebraic Reynolds Stress Model (DARSM), which can be trained on small datasets and accurately generalise across Reynolds numbers, to unseen geometries, and to different flow regimes. A neural network maps flow invariants to empirical parameters in an implicit algebraic Reynolds stress equation, derived from the Reynolds stress transport equations under the weak-equilibrium assumption, imposing physics-based structure on the ML closure. End-to-end optimisation through the governing PDEs and the coupled implicit closure eliminates distribution shift, but both unrolled and implicit automatic differentiation fail on the stiff coupled solver. We derive adjoint equations that exploit the solver's implicit-explicit structure for efficient optimisation. On canonical square-duct and periodic-hill benchmarks, DARSM reduces average test velocity error over baseline RANS by $2$-$4\times$ across Reynolds number, geometries, and flow regimes, with peak case-level reductions of $12\times$. The model trained on attached, anisotropy-dominated flows (square duct) accurately generalises without retraining to separated flows (periodic hills), a regime change in the underlying physics. DARSM also outperforms five established ML methods: offline training, tensor-basis neural networks, field-inversion machine learning, DeepONets, and physics-informed neural networks.

25.
arXiv (quant-ph) 2026-06-19

Matrix-product state skeletons in Onsager-integrable quantum chains

arXiv:2511.07212v2 Announce Type: replace Abstract: Matrix-product state (MPS) skeletons are connected networks of Hamiltonians with exact MPS ground states that underlie a phase diagram. Such skeletons have previously been found in classes of free-fermion models. For the translation-invariant BDI and AIII free-fermion classes, it has been shown that the underlying skeleton is dense, giving an analytic approach to MPS approximation of ground states anywhere in the class. In this paper, we partially expose the skeleton in certain interacting spin chains: the $N$-state Onsager-integrable chiral clock families. We construct MPS that form a dense MPS skeleton in the gapped regions surrounding a sequence of fixed-point Hamiltonians (the generators of the Onsager algebra). Outside these gapped regions, these MPS remain eigenstates, but no longer give the many-body ground state. Rather, they are ground states in particular sectors of the spectrum. Our methods also allow us to find further MPS eigenstates; these correspond to low-lying excited states within the aforementioned gapped regions. This set of MPS excited states goes beyond the previous analysis of ground states on the $N=2$ free-fermion MPS skeleton. As an application of our results, we find a closed form for the disorder parameter in a family of interacting models. Finally, we remark that many of our results use only the Onsager algebra and are not specific to the chiral clock model representation.