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

Minim: Privacy-Aware Minimal View for Agents via Trusted Local Sanitization

arXiv:2606.13949v1 Announce Type: new Abstract: Modern LLM-powered autonomous agents increasingly rely on rich user interface (UI) state observations to achieve reliable action grounding in complex digital environments. However, many deployments transmit the full UI state to remote inference servers even when most elements are irrelevant to the current task, which can leak sensitive but unnecessary context such as authentication codes, private notifications, and background application states. We propose MINIM, a trusted local broker that performs privacy-aware minimization on the client side before any observation leaves the device. Grounded in Contextual Integrity (CI), MINIM learns a dual-score representation for each UI element by predicting an inherent sensitivity score (s) and a task-conditioned necessity score (n). These scores drive a ternary disclosure policy that keeps essential elements, abstracts sensitive attributes when needed, and removes task-irrelevant content. We optimize a CI-aware objective that penalizes necessity errors more strongly on high-risk content, enabling aggressive pruning while preserving task-critical information. Experiments on real-world UI observations derived from WebArena show that MINIM substantially reduces task-irrelevant sensitive leakage while preserving task-critical semantic context and the interactive affordances required for reliable agent actions.

02.
medRxiv (Medicine) 2026-06-22

Longitudinal multi-omics characterization of the malignant evolution in multirelapsing glioblastoma

Linking glioblastoma (GBM) evolution to clinical progression is challenged by multiple factors, including tumor location for repeated sample collection, and short patient survival. In a single individual, we collected and analysed samples from 11 operations distributed across 31 months of multi-relapsing and multifocal GBM, including terminal leptomeningeal progression. All samples shared genomic ancestry of the retinoblastoma protein 1 (RB1) and neurofibromin 1 (NF1) mutations while advanced progression and extracranial metastases featured mutations of tuberous sclerosis complex 2 (TSC2), PBRM1, CD22 and Fanconi anemia supplementation group I (FANCI), correlated with clinical resistance to immunotherapies and DNA-damaging agents. Single-cell analytics revealed distinct yet reversible shifts in response to the precision medicine arsenal. GBM parenchymal dissemination and extracranial progression were associated with strengthening of neuron-like cell phenotypes. Our multidimensional study describes GBM evolution over a rarely reported time scale, and provides a valuable resource linking genetic, molecular, cellular and clinical progressions.

03.
arXiv (math.PR) 2026-06-16

Sharp connectivity bounds for the vacant set of random interlacements

arXiv:2504.02777v2 Announce Type: replace Abstract: We consider percolation of the vacant set of random interlacements at intensity $u$ in dimensions three and higher, and derive lower bounds on the truncated two-point function for all values of $u>0$. These bounds are sharp up to principal exponential order for all $u$ in dimension three and all $u \neq u_\ast$ in higher dimensions, where $u_*$ refers to the critical parameter of the model, and they match the upper bounds derived in the article arXiv:2503.14497. In dimension three, our results further imply that the truncated two-point function grows at large distances $x$ at a rate that depends on $x$ only through its Euclidean norm, which offers a glimpse of the expected (Euclidean) invariance of the scaling limit at criticality. The rate function is atypical, it incurs a logarithmic correction and comes with an explicit pre-factor that converges to $0$ as the parameter $u$ approaches the critical point $u_*$ from either side. A particular challenge stems from the combined effects of lack of monotonicity due to the truncation in the super-critical phase, and the precise (rotationally invariant) controls we seek, that measure the effects of a certain "harmonic humpback" function. Among others, their derivation relies on rather fine estimates for hitting probabilities of the random walk in arbitrary direction $e$, which witness this invariance at the discrete level, and preclude straightforward applications of projection arguments.

04.
medRxiv (Medicine) 2026-06-16

Sleep regularity outweighs sleep duration as a predictor of disease

Sleep regularity, the consistency of sleep-wake timing from one day to the next, is more strongly associated with longevity than adequate sleep duration. Whether this relationship persists across common diseases is unknown. We compared sleep regularity vs. sleep duration as risk factors for 199 diseases and disorders, using ten million hours of objective sleep-wake data (N=60,998, age[mean{+/-}SD]=62.8{+/-}7.8, 55% female). Multivariable-adjusted risks of incident diseases/disorders for regular/irregular and short/adequate sleepers were compared across 9.5 years of follow-up. Irregular sleep predicted risks for 131 diseases/disorders, more than double the number predicted by short sleep duration (63). Irregular sleep was a superior predictor than short sleep duration for 90 diseases/disorders, including circulatory, metabolic, digestive, renal, infectious, neurological, and musculoskeletal conditions, and mental disorders, whereas short sleep duration was the superior predictor for only 9 diseases/disorders. For models where short sleep duration explained disease risks, 83% were improved by adding sleep regularity. Sleep regularity was a stronger predictor of diseases/disorders than sleep duration in this cohort and should be considered an essential dimension of sleep health.

05.
arXiv (quant-ph) 2026-06-24

The Quantum Split-Step Fourier Algorithm for Nonlinear Optical Waveguides

arXiv:2606.24643v1 Announce Type: cross Abstract: We introduce the Quantum Split-Step Fourier (QSSF) algorithm for nonlinear optical waveguides, a numerical framework that combines split-step propagation of the nonlinear Schrödinger equation with a commutator-preserving Bogoliubov evolution of Gaussian quantum fluctuations. The method propagates the classical mean field together with the Bogoliubov matrices $U$ and $V$, from which reduced second moments, covariance matrices, symplectic eigenvalues, and entropic measures are constructed for arbitrary spectral windows. Applied to soliton-driven resonant radiation, QSSF shows that the selected radiation band acquires a steadily increasing von Neumann entropy and a corresponding loss of purity, quantifying its entanglement with the rest of the spectrum in the lossless Gaussian setting. The analysis also reveals a surprisingly pronounced low-dimensional structure: although the radiation occupies many Fourier bins, its reduced Gaussian state is dominated by only a few Williamson modes. QSSF therefore provides a practical information-theoretic diagnostic for quantum correlations in nonlinear frequency conversion, supercontinuum generation, and multimode squeezed-light formation in ultrafast waveguide platforms.

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

A Hybrid GNN-FEM Framework for Phase-Field Fracture Simulation. Physics-Preserving Hybridization for Generalizable Surrogate Modeling

arXiv:2606.19378v1 Announce Type: new Abstract: Scientific machine learning (SciML) has emerged as a promising approach for accelerating simulations of complex physical systems, yet achieving physically consistent and generalizable predictions for nonlinear, history-dependent problems remains a central challenge. In this study, we propose a hybrid GNN–FEM framework for efficient and generalizable phase-field fracture modeling. While phase-field approaches provide a robust variational framework for simulating complex crack evolution, their high computational cost limits practical applications because they require solving coupled, nonlinear, and history-dependent systems within an incremental finite element procedure. To address this challenge, a graph neural network surrogate is integrated into the conventional staggered scheme, replacing the phase-field update at each load increment while retaining the FEM-based displacement solver to enforce mechanical equilibrium and boundary conditions. By preserving the incremental solution structure, the framework remains consistent with history-dependent fracture evolution without requiring the surrogate to approximate the full solution trajectory. This selective surrogate strategy emphasizes the identification of a physically meaningful and incrementally structured learning target, rather than relying on brute-force data generation to learn the full fracture process. The proposed framework achieves strong generalization across varying geometries, loading conditions, material properties, and discretizations through dimensionless feature design, a graph-based formulation on mesh-based domains, and a physics-informed loss derived from the governing phase-field equation. Numerical experiments demonstrate that the hybrid approach reduces computational cost while maintaining accuracy compared with conventional FEM, and exhibits robust predictive performance across diverse problem settings.

07.
arXiv (quant-ph) 2026-06-24

Suppressing Self-Discharging of Quantum Batteries by Cavity Interactions

arXiv:2606.23999v1 Announce Type: new Abstract: We analyse a two-cavity architecture, in which a lossy cavity hosting $N$ qubits is coherently coupled to an auxiliary cavity, as a resource for the storage phase of an open quantum battery at non-zero temperature. Within a local Lindblad treatment in the resonant configuration, we find that the inter-cavity coupling enhances the suppression of self-discharging across every initial preparation, battery size, and temperature we examine, with the protection degrading smoothly as the mean thermal occupation increases. For a single qubit, the energy-basis coherence of a pure superposition leads to better long-time retention than fully excited state, highlighting the beneficial role of quantum coherence in protecting stored energy against thermal degradation. For two-qubit batteries, Bell-state preparations exhibit enhanced long-time ergotropy retention compared with the fully excited state, while the inclusion of qubit-qubit interactions produces only a weak dependence on the interaction type and strength within the parameter regime considered. Extending the analysis to multi-qubit GHZ-charged batteries with all-to-all Heisenberg interactions, we find that the normalized retained ergotropy increases monotonically with the number of qubits. This behavior is consistent with the collective enhancement of the qubit-cavity coupling in the symmetric Dicke manifold, indicating that larger quantum batteries can benefit from improved protection against self-discharge. These findings establish cavity-assisted protection as a promising strategy for mitigating self-discharging and realizing of long-lived quantum batteries in experimentally accessible platforms.

08.
arXiv (CS.CL) 2026-06-12

Recursive Agent Harnesses

Recursive language models (RLMs) showed that recursion over model calls is an effective strategy for long-context reasoning, and production coding agents have begun to write code that spawns subagents at scale, most recently in Anthropic's dynamic workflows. We name and study the pattern between these two lines of work, where the recursive unit is a full agent harness with filesystem tools, code execution, and planning rather than a model call with no tools. We call this the Recursive Agent Harness (RAH) and frame it as harness recursion, the code-first extension to the model recursion of RLMs. A parent agent generates and runs an executable script that spawns subagent harnesses in parallel for fine-grained workloads and uses structured function calls for small subtasks. We provide a controlled evaluation on long-context reasoning. With the backbone held fixed at GPT-5 to match the published Codex and RLM baselines, RAH improves the Codex coding-agent baseline from 71.75% to 81.36% on Oolong-Synthetic (199 samples, 13 context-length buckets up to 4M tokens), a gain attributable to the harness rather than the model. With a stronger backbone, Claude Sonnet 4.5, the same design reaches 89.77%.

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

DreamX-World 1.0: A General-Purpose Interactive World Model

DreamX-World 1.0 is a general-purpose interactive text/image-to-video world model for controllable long-horizon generation. It supports camera navigation, revisits to previously observed regions, and promptable events across photorealistic, game-style, and stylized domains. Our data engine combines camera-accurate Unreal Engine rendering, action-rich gameplay recordings, and real-world videos with recovered camera geometry. For camera control, we introduce E-PRoPE, a lightweight variant of projective positional encoding that retains PRoPE's projective camera geometry while applying camera-aware attention to spatially reduced tokens. We convert a bidirectional video generator into a few-step autoregressive world model using causal forcing, DMD-style distillation, and long-rollout training. Training on self-generated long-horizon contexts exposes the model to its own generated history and reduces the style and color drift that accumulates across autoregressive chunks. Memory-Conditioned Scene Persistence retrieves earlier views through camera-geometry-based retrieval, while residual recycling makes the conditioning path less sensitive to imperfect memory latents. Event Instruction Tuning adds composable event control, and reinforcement learning alignment recovers camera control and visual quality after distillation. With mixed-precision DiT execution, residual reuse, 75\%-pruned VAE decoding, and asynchronous pipeline parallelism, DreamX-World 1.0 reaches up to 16\,FPS on eight RTX\,5090 GPUs. On our 5-second basic evaluation, DreamX-World 1.0 achieves a camera-control score of 73.75 and an overall score of 84.76, outperforming HY-WorldPlay 1.5 and LingBot-World in overall score, which achieve 80.79 and 80.45, respectively.

10.
arXiv (quant-ph) 2026-06-11

Super-Link Fragility in Asymmetric W-Class States under Quantum Noise

arXiv:2606.12307v1 Announce Type: new Abstract: The asymmetric three-qubit W-class state $|\overline{W_3^L}\rangle$ defines an isosceles entanglement-network geometry, (a) two vertex-base (VB) links form stronger bipartite connections, (b) while the base-base (BB) link is weaker. This suggests that concentrating entanglement into a super-link may be advantageous for quantum-network tasks. Here, we show that this intuition is incomplete. We analytically compare the bipartite concurrence dynamics of the symmetric |W> state and the asymmetric $|\overline{W_3^L}\rangle$ state, which differ both in entanglement-network geometry and excitation sector under standard noise models. In the absence of noise, the concurrence hierarchy is C_{VB} > C_W > C_{BB}$. Under phase damping, this hierarchy is preserved for all noise strengths and no entanglement sudden death occurs. Under amplitude damping, however, the hierarchy is reordered. The symmetric |W> state becomes the most robust, while the base-base concurrence of $|\overline{W_3^L}\rangle$ vanishes at the finite threshold of parameter $\gamma$. We term this reordering as the Super-Link Fragility Effect. The same structural asymmetry that produces a stronger vertex-base link also makes it more vulnerable to energy dissipation when coupled with multi-excitation amplitudes. Under depolarization, the asymmetry advantage is erased, with $C_W$ and $C_{VB}$ sharing the same sudden-death threshold for some value of the parameter p, while $C_{BB}$ disappears earlier at some other value of the parameter p. The generalized amplitude damping channel continuously connects the damping-dominated regime to the pure-excitation limit, where the initial hierarchy is restored. These results show that entanglement robustness in $W$-class resources is controlled not by initial concurrence alone, but by the joint structure of entanglement-network geometry, excitation sector, and noise symmetry.

11.
arXiv (CS.CL) 2026-06-18

Compact Geometric Representations of Hierarchies

Computing geometric representations of data is a cornerstone of modern machine learning, typically achieved by training dual encoders which map queries and documents into a shared embedding space. Recent work of You et al. [NeurIPS '25] has extended this approach to hierarchical retrieval, where relevance is determined by the ancestor-descendant relationships in a Directed Acyclic Graph (DAG). While previous work has shown that valid embeddings exist when the number of descendants is small, these bounds degrade significantly for deep hierarchies, requiring dimensions as large as the total number of nodes. In this paper, we investigate compact reachability embeddings for more general graph classes and provide theoretical guarantees for representing hierarchies using embeddings whose dimension depends on structural graph parameters. We prove that for any directed tree, there exists a reachability embedding in constant dimension 3, independent of the tree's size or depth. We generalize this result to graphs characterized by treewidth $t$, constructing embeddings of dimension $O(t \log n)$, where $n$ is the number of nodes. Complementing these upper bounds, we provide matching or near-matching lower bounds, showing that dimension $\Omega(n)$ is necessary for general DAGs and $\Omega(t/\log(n/t))$ is required for graphs of treewidth $t$. We also obtain upper and lower bounds parameterized by the number of cross-edges in the DAG. We additionally show that our embeddings can be constructed on real world datasets, and that they give much smaller dimensions in high recall regimes compared to prior embeddings with theoretical guarantees.

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

AAbAAC: An Annotated Corpus for Autoimmunity Information Extraction

arXiv:2606.13051v1 Announce Type: new Abstract: Despite advances in information extraction driven by deep learning and large language models, performance gaps remain in highly specialized biomedical fields, where domainspecific complexity poses challenges for generalist models. In this work, we focus on the domain of autoimmunity, where the main entities of interest are autoimmune diseases, autoantibodies (i.e., molecules that may mark or cause these diseases), their molecular targets, their location in the body, and their associated clinical signs. Herein, we present AAbAAC (AutoAntibodies and Autoimmunity Annotated Corpus), a corpus of 115 abstracts selected from PubMed, where we manually annotated entities and their relationships. First, AAbAAC was used to evaluate several methods on the task of named entity recognition (NER), and secondly, to fine-tune NER models. Our study demonstrates the utility of AAbAAC for information extraction in the domain of autoimmunity, showing expected improvement in NER performance after finetuning. This illustrates the value of small-scale annotation efforts for specialized domains and contributes to the computational study of autoimmunity. The AAbAAC corpus is available at https://github.com/f-maury/AAbAAC.

13.
arXiv (CS.CV) 2026-06-12

Improving Pre-trained Adult Glioma Segmentation Models Using only Post-processing Techniques

Gliomas are the most common malignant brain tumors in adults and are among the most lethal. Despite aggressive treatment, the median survival rate is less than 15 months. Accurate multiparametric MRI (mpMRI) tumor segmentation is critical for surgical planning, radiotherapy, and disease monitoring. While deep learning models have improved the accuracy of automated segmentation, large-scale pre-trained models generalize poorly and often underperform, producing systematic errors such as false positives, label swaps, and slice discontinuities in slices. These limitations are further compounded by unequal access to GPU resources and the growing environmental cost of large-scale model training. In this work, we propose adaptive post-processing techniques to refine the quality of glioma segmentations produced by large-scale pretrained models developed for various types of tumors. We demonstrated the techniques in multiple BraTS 2025 segmentation challenge tasks, with the ranking metric improving by 14.9 % for the sub-Saharan Africa challenge and 0.9% for the adult glioma challenge. This approach promotes a shift in brain tumor segmentation research from increasingly complex model architectures to efficient, clinically aligned post-processing strategies that are precise, computationally fair, and sustainable.

14.
arXiv (quant-ph) 2026-06-24

Quantum turbulence in the many-body regime

arXiv:2606.23822v1 Announce Type: cross Abstract: We discuss phenomenology associated with turbulent hydrodynamics in quantum fluids from a condensed-matter perspective. We begin with weakly-interacting superfluids, often modeled by a mean-field theory governed by the Gross-Pitaevskii equation. Considering the effect of quantum fluctuations beyond the mean-field approximation, we propose a study of many-body quantum effects in turbulent hydrodynamics, especially near zero temperature. We motivate examples of quantum many-body systems where such effects may be uncovered. These include bosons confined in a periodic potential in low spatial dimensions (one and two), and the associated quantum critical point of the superfluid-insulator transition, realized in present-day ultracold-atom and quantum computing platforms. We conclude by listing a set of (open) questions that may be answered using modern quantum many-body techniques. This article is part of the theme issue 'Frontiers of turbulence and statistical physics'.

15.
arXiv (CS.AI) 2026-06-24

Detecting AI Coding Agents in Open Source: A Validated Multi-Method Census of 180 Million Repositories

arXiv:2606.24429v1 Announce Type: cross Abstract: Generative AI coding agents are entering the open-source supply chain, yet their diverse and often invisible traces leave their prevalence poorly understood. We introduce a multi-layered detection framework that integrates configuration-file scanning, commit-message analysis, author-identity matching, and bot-signature lookup across World of Code (180M+ Git repositories), classifying agent traces into four behavioral types. No single method captures more than a fraction of activity: multi-method detection identifies 850,157 Claude Code commits in one snapshot, of which bot-account lookup_the signal most adoption studies rely on_recovers only 28,154 (3.3%), a 30x relative-recall gap, so single-signal prevalence estimates are biased low by at least this factor. Every detection pattern is hand-validated (495 labels) with per-cell precision and Wilson confidence intervals. Across snapshots from December 2024 to April 2026, commit-attributed agents generate over 320,000 commits per month; Claude Code leads (886,122 commits across 17,295 projects) and dominates silent, configuration-file-only adoption (21,078 projects). Compared against an independent pull-request census (AIDev), the two channels capture nearly disjoint agent populations_a PR census misses 79% of commit-detected Claude Code adopters and essentially all Codex adopters_and different kinds of work: PR-deployed cloud agents (Codex, Cursor) surface as feature work, while commit-deployed in-editor agents (Claude Code, OpenHands, Aider) surface as maintenance. The observed work profile follows deployment and detection mode rather than the tool itself, so no single channel is representative.

16.
bioRxiv (Bioinfo) 2026-06-15

Multiple Fault Analysis and Drug Therapy on Signaling Pathways Using Dynamic Bayesian Network-based Model

Cell growth is an intricate biological phenomenon that is closely regulated by the interplay between various growth factors and transcription factors. Signaling pathways are the main mediators in this event, which provide the driving force for mitosis or sometimes meiosis. However, when malfunctions occur within the biological network, they can cause uncontrolled cell division, regardless of external stimuli. By employing Dynamic Bayesian Networks (DBNs), these malfunctions can be explicitly simulated, offering insights into their effects on cellular behavior and growth regulation. To a significant extent, the resultant outcomes can be mitigated through the use of reduced drug combinations. This study delves into the intricacies of signaling pathway behavior under the influence of concurrent malfunctions. Initially, we replicate the effects of these dysfunctions within DBNs. Subsequently, drug therapy is applied to alleviate their impact. Our methodology introduces a parameter known as efficiency_score, enabling the identification of optimized drug combinations without prior knowledge of specific dysfunctions. Particularly relevant in the context of realistic cancer conditions, these tailored drug inhibition points demonstrate enhanced efficacy compared to conventional treatments. Leveraging GPU acceleration throughout the modeling process accelerates the analysis of multiple faults within the biological networks, rendering our approach notably faster and more efficient.

17.
arXiv (CS.CL) 2026-06-24

Exploring Academic Influence of Algorithms by Co-occurrence Network Based on Full-text of Academic Papers

Algorithms have become central to scientific research in the era of artificial intelligence (AI). Although algorithm mentions in papers are often used to indicate popularity and influence, existing studies usually evaluate individual algorithms in isolation and pay limited attention to the collective influence formed through their interconnections. This study constructs large-scale algorithm co-occurrence networks in natural language processing (NLP) based on the full text of academic papers and investigates algorithm influence from a network perspective. Using deep learning models, we extract algorithm entities and build overall, cumulative, and annual co-occurrence networks. We analyze their structural characteristics and apply multiple centrality measures to assess the group influence of algorithms across the whole field and over time. The results show that algorithm networks display typical features of complex networks, with increasingly dense connections developing over approximately two decades. Classic, high-performing algorithms and those located at the intersections of different research periods tend to have high popularity, control, centrality, and balanced influence. When the influence of an algorithm declines, it usually loses its core network position first, followed by weaker associations with other algorithms. This study is the first large-scale analysis of algorithm co-occurrence networks. Covering more than four decades of academic publications, it provides a temporal and structural view of algorithm influence and offers a foundation for future research on networks linking algorithms, scholars, and tasks.

18.
arXiv (CS.CV) 2026-06-12

Learning Visually Interpretable Oscillator Networks for Soft Continuum Robots from Video

Learning soft continuum robot (SCR) dynamics from video offers flexibility but existing methods lack interpretability or rely on prior assumptions. Model-based approaches require prior knowledge and manual design. We bridge this gap by introducing: (1) The Attention Broadcast Decoder (ABCD), a plug-and-play module for autoencoder-based latent dynamics learning that generates pixel-accurate attention maps localizing each latent dimension's contribution while filtering static backgrounds, enabling visual interpretability via spatially grounded latents and on-image overlays. (2) Visual Oscillator Networks (VONs), a 2D latent oscillator network coupled to ABCD attention maps for on-image visualization of learned masses, coupling stiffness, and forces, thereby enabling mechanical interpretability. We validate our approach on single- and double-segment SCRs, demonstrating that ABCD-based models significantly improve multi-step prediction accuracy with 5.8x error reduction for Koopman operators and 3.5x for oscillator networks on a two-segment robot. VONs autonomously discover a chain structure of oscillators. This fully data-driven approach yields compact, mechanically interpretable models with potential relevance for future control applications.

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

p-PSO: A Penalized Particle Swarm Optimization Technique for Finding D-Optimal Designs with Mixed Factors in Generalized Linear Models

arXiv:2606.15962v1 Announce Type: cross Abstract: Finding D-optimal designs for generalized linear models (GLMs) is challenging due to the dependence of the Fisher information matrix on unknown parameters and the lack of closed-form solutions, particularly when input factors include both discrete and continuous variables. Although classical algorithms and recent metaheuristic approaches have offered partial solutions, there remains a need for robust and computationally efficient methods. In this paper, we propose a penalized Particle Swarm Optimization (PSO) approach, named $p$-PSO. Here we introduce a new, general-purpose penalty formulation for constrained optimization and demonstrate its effectiveness in optimal design problems. The formulation is algorithm-agnostic and applicable to a broad class of black-box optimization methods. Results show that the method is highly efficient, with its primary contribution being a penalty formulation that enables the direct use of an off-the-shelf PSO algorithm and extends naturally to more general constrained optimization tasks.

20.
bioRxiv (Bioinfo) 2026-06-16

scIsoAgent enables autonomous isoform-resolved characterization and sequence-informed interpretation of long-read single-cell transcriptomes

Alternative isoform usage can alter gene function independently of total gene expression, creating a need to resolve transcript isoforms at single-cell resolution. Long-read single-cell RNA sequencing meets this need by linking cellular identity to transcript isoforms and sequence-level features. Realizing its full biological value requires reproducible workflows that connect specialized long-read analysis with biological interpretation. Existing large language model (LLM)-based biomedical agents support general omics analysis, but are not designed for isoform-resolved long-read single-cell workflows. Here, we present scIsoAgent, an autonomous LLM-powered scientific agent for long-read single-cell RNA-seq analysis. scIsoAgent turns heterogeneous long-read single-cell inputs into traceable isoform-resolved workflows, using stage-aware planning and persistent computational context to support both execution and interpretation. Across complementary evaluations, this design improved the continuity from analysis planning to executable, interactive workflows compared with general-purpose LLM baselines. In real-data reanalysis, scIsoAgent recovered major findings from published long-read single-cell resources and extended a representative differential transcript usage event into a sequence-informed functional hypothesis. By linking full-length isoform sequences with model-inferred transcript properties, scIsoAgent connects observed isoform usage with potential sequence-level functional consequences. These results demonstrate that autonomous scientific agents can transform fragmented long-read single-cell analysis into coherent, reproducible workflows for isoform-resolved discovery and biological interpretation.

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

It's About Time: Temporal References in Emergent Communication

Emergent communication enables agents to develop bespoke languages that improve communication efficiency. Despite the known importance of temporal structure in natural language, there is no existing evidence of temporal references in emergent communication. This paper addresses this gap, by exploring how agents communicate about temporal relationships. We analyse three potential factors for the emergence of temporal references: environmental, external, and architectural. Our experiments demonstrate that altering the loss function is insufficient for temporal references to emerge; rather, architectural changes are necessary. A minimal change in agent architecture, using a different batching method, allows the emergence of temporal references. This modified design is compared with the standard architecture in a temporal referential games environment, which emphasises temporal relationships. The analysis shows that over 95% of the agents with the modified batching method develop temporal references, without changes to their loss function. We consider temporal referencing necessary for future improvements to the agents' communication efficiency, enabling future agents to use a closer to optimal coding as compared to purely compositional languages. These insights provide the basis for incorporation of temporal references into other emergent communication settings, and investigation of other aspects of language.

22.
arXiv (math.PR) 2026-06-16

Free energy of non-convex multi-species spin glasses with centered Ising spins

arXiv:2606.16636v1 Announce Type: new Abstract: We identify the limit free energy of all multi-species spin glasses with centered $\pm 1$ spins. The result was previously known only under a convexity assumption on the covariance function of the Hamiltonian. We also obtain a one-species reduction of the formula for balanced multi-species models.

23.
arXiv (CS.AI) 2026-06-11

Model-Based and Data-Driven Hierarchical Control and Topology Co-Design for Robust Networked Systems

arXiv:2606.11596v1 Announce Type: cross Abstract: In this paper, we consider a class of networked systems comprising an interconnected set of linear subsystems, disturbance inputs, and performance outputs. Using dissipativity theory, we first propose a model-based hierarchical control design strategy to ensure the closed-loop networked system is dissipative from its disturbance inputs to performance outputs. This involves designing local controllers for each subsystem to enforce local dissipativity guarantees, which are then exploited to co-design distributed global controllers and the interconnection topology to enforce global dissipativity guarantees while optimizing interconnection topology costs. The overall design process requires only solving a sequence of linear matrix inequality (LMI) problems, thereby retaining compositionality and decentralizability while avoiding non-convex, iterative design processes that are inefficient and centralized. This model-based hierarchical control design strategy assumes the knowledge of the subsystem dynamics, which may not hold in many real-world networked systems. Motivated by this, we also propose a data-driven hierarchical control design strategy that assumes only the availability of rich input-state-output trajectory data from the subsystems. The proposed data-driven design process assumes that the unknown disturbances affecting the subsystem dynamics are bounded by a quadratic matrix inequality (relaxing conventional bounds) and accounts for this by using the matrix S-lemma. Finally, the effectiveness of the proposed model-based and data-driven hierarchical control designs is illustrated for a networked system representing a DC microgrid, with the aim of enforcing robust (dissipative) voltage regulation and current sharing.

24.
arXiv (CS.AI) 2026-06-24

Variational Model Merging for Pareto Front Estimation in Multitask Finetuning

arXiv:2412.08147v2 Announce Type: replace-cross Abstract: Pareto fronts are useful to find good task-mixing strategies for multitask finetuning, but they are also costly to compute. To reduce costs, recent works have used existing model merging methods to help train cheap surrogate models to estimate the Pareto fronts. However, no work has yet considered designing new model-merging methods to directly, and provably, improve the quality of Pareto fronts. Here, we fill this gap by proposing a new Bayesian approach called Variational Model Merging. In this approach, existing model-merging methods are obtained as special cases of "posterior-merging" when Gaussian posteriors are used and new model-merging strategies can be derived by using non-Gaussian posteriors. Our main theoretical result is to show that more flexible posteriors necessarily yield better estimates of Pareto fronts. For instance, a Pareto front estimate obtained by merging full-Gaussian posteriors is expected to be better than that obtained by using isotropic Gaussian posteriors. We validate the theory through extensive empirical results on vision and language transformers where better Gaussian families consistently yields better or comparable Pareto fronts. Our work is a rare instance where Bayesian ideas are used to improve Pareto analysis.

25.
arXiv (CS.LG) 2026-06-12

Deep Sleep Classification via EEG Signal Criticality: A Passive BCI Approach for Sleep-Improvement Neurofeedback

arXiv:2606.13017v1 Announce Type: cross Abstract: Automated sleep staging is a fundamental application of passive Brain-Computer Interfaces (pBCI), decoding spontaneous neural states to enable closed-loop interventions independent of user intent. This study evaluates criticality features derived from Detrended Fluctuation Analysis (DFA) for the specific identification of deep sleep (N3). We analyzed $347,232$ EEG epochs from $290$ older women using UMAP manifold learning to visualize state transitions. Subsequently, six classifiers were benchmarked via 10-fold cross-validation, using balanced accuracy to determine the optimal "state-sensing" engine for neurofeedback.Naive Bayes achieved the highest mean balanced accuracy ($87.17\% \pm 0.24\%$), significantly outperforming a fully connected deep neural network (FNN: $81.58\%$) and Random Forest ($80.97\%$). Linear models (LDA: $57.21\%$; SVM: $51.01\%$) performed poorly, indicating that DFA-derived criticality features reside on a distinct, non-linear manifold. Probabilistic decoding of EEG criticality provides a high-accuracy sensing mechanism for pBCIs. This robust classification pipeline supports the development of state-dependent neurofeedback, such as targeted auditory stimulation, to enhance cognitive recovery.