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01.
arXiv (CS.AI) 2026-06-17

FacProcessTwin: An LLM-Based System for Process Twin Development

arXiv:2606.17666v1 Announce Type: cross Abstract: Process twins provide real-time representations of entire production processes. By capturing how process steps interact, rather than monitoring a single machine in isolation as an asset-based digital twin does, they have the potential to drive efficiency gains across the whole process. However, developing a process twin is costly. It requires accurately modelling the entire production process: its process steps, the equipment and product-specific settings each step uses, and its process variations. The resulting model must then be bound to live operational data. We present FacProcessTwin, a system that leverages a large language model (LLM) to reduce this development time, building a process twin from a plant's process documentation and natural-language input from an operator. FacProcessTwin generates this complete process model and then automatically binds its process steps to live operational data. The generated model and its data bindings are rendered as an interactive process diagram through which manufacturing personnel can monitor and correct the system's autonomous decisions, such as resolving uncertainty at safety-critical binding steps. We evaluate FacProcessTwin through a real-world case study of an Australian food manufacturer, covering 16 production process flows that span chilled, frozen, and aseptic shelf-stable product categories and include process variations within the same product. The results show that FacProcessTwin generates these process models accurately (a mean F1 of 95.2% against ground truth) and builds each twin in roughly a sixth of the manual time. Its human-in-the-loop governance then keeps the safety-critical bindings correct: at ambiguous tags where a single-pass baseline silently mis-binds 75.0% of the time, FacProcessTwin defers to the operator and mis-binds none.

02.
arXiv (quant-ph) 2026-06-19

Optimal multi-spectral squeezing via deterministic 2D-phase optimization

arXiv:2606.20192v1 Announce Type: new Abstract: Optimization routines are ubiquitous in quantum information technologies and essential to reach the resource levels required by quantum protocols. Specifically, multi-spectral squeezing for use in such protocols requires that losses be kept minimal at every stage, including coherent detection, which is performed by interfering the signal with a classical local-oscillator beam. This in turn requires control over all optical degrees of freedom of the beam in order to optimize the detection. The most general framework for this optimization relies on agnostic, off-the-shelf machine-learning techniques. Here we take the opposite approach: by focusing on a physical description of the specific optical process, we develop a deterministic sequential algorithm that provably reaches the global maximum of the visibility in a pixel basis and scales linearly with the number of pixels, thereby offering an efficient and theoretically grounded alternative to black-box optimization. In our waveguide-based setup, the optimized mask increases the visibility from 76% to 84%, corresponding to a 20% gain in mode-matching efficiency. Multi-spectral squeezing measurements confirm that this improvement translates directly into quantum readout: for the most squeezed spectral mode, the squeezing increases from $-2.08$ dB to $-2.64$ dB, consistent with the inferred efficiency gain. These results establish deterministic spatial phase shaping as an effective, interpretable route to enhanced multimode squeezing in waveguide platforms.

03.
arXiv (CS.CL) 2026-06-18

As Easy as Rocket Science: Assessing the Ability of Large Language Models to Interpret Negation in Figurative Language

Figurative language and negation are two areas that challenge current language models, however, both are widely used throughout written and spoken language. Large language models (LLMs) are also widely used in everyday contexts where they cannot necessarily be tuned for a specific dataset. It is therefore essential to understand the ability of LLMs to correctly interpret text that includes both negation and figurative language. To investigate this, we develop a set of new annotations to an existing dataset of figurative language, and test a range of language models on the dataset. We find that the combination of negation and figurativeness can present a particular challenge, and that performance overall and across different negation types is particularly dependent on the prompt style used.

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

Toward Calibrated Mixture-of-Experts Under Distribution Shift

arXiv:2606.20544v1 Announce Type: new Abstract: Calibration aligns a model's predictive uncertainty with the frequencies of its empirical outcomes and is important for understanding and trusting reported probabilities. Recent work shows that enforcing calibration at the level of individual predictors can improve ensemble accuracy and calibration, with mixture-of-experts (MoE) models showing strong empirical improvements in particular; however, the conditions under which calibration helps MoE are not well understood. In this work, we study how MoE models behave under distribution shift, focusing on how routing mechanisms interact with expert-level calibration. We show that expert calibration is sufficient to ensure calibration of the overall model under a broad class of distribution shifts in hard-routed models, but is insufficient for calibrating soft-routed models. To address this, we propose an adversarial reweighting that penalizes calibration errors of the routed aggregate under distribution shift, and we demonstrate that it improves the accuracy-calibration tradeoff both on average and on difficult subsets of the data, across model classes, prediction tasks, and distribution shifts.

05.
arXiv (CS.CV) 2026-06-18

Transformer Geometry Observatory TGO-I: Spectral Geometry Observatory

Despite the widespread adoption of Vision Transformers (ViTs) and their success across numerous computer vision applications, the fundamental understanding of their dimensional and representational geometry remains relatively underexplored. To address this gap, we introduce Transformer Geometry Observatory (TGO), a systematic framework of experiments and analysis pipelines designed to investigate the representational geometry and dynamics of Vision Transformers. TGO-I, the first installment of the framework, focuses on the spectral geometry of ViT representations. Using a ViT-Small/16 model trained on ImageNet-100, we analyze Effective Rank, Stable Rank, Participation Ratio, Spectral Entropy, Spectral Flatness, Spectral Anisotropy, covariance structure, eigenspectra, and singular value spectra throughout training. Our results reveal a consistent increase in dimensional utilization, accompanied by decreasing anisotropy, increasing spectral entropy, increasing participation ratio, and progressively flatter eigenspectra. Contrary to the common intuition that training should concentrate information into a small number of dominant directions, we observe a progressive redistribution of variance across representational dimensions. This phenomenon is particularly pronounced in the final CLS token representation, which exhibits the highest effective dimensionality and lowest anisotropy within the network.

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

Fourier Features Let Agents Learn High Precision Policies with Imitation Learning

arXiv:2606.12334v1 Announce Type: new Abstract: High-precision robotic manipulation requires fine-grained spatial reasoning that is often difficult to achieve with RGB-only policies due to depth ambiguity and perspective scale issues. Policies that leverage 3D information directly, such as those based on point clouds, offer a stronger geometric prior over purely image-based ones, yet their performance remains highly task-dependent. We hypothesize that this discrepancy may be due to the spectral bias of neural networks towards learning low frequency functions, which especially affects architectures conditioned on slow-moving Cartesian features. We thus propose to map point clouds from Cartesian space into high-dimensional Fourier space, effectively equipping the point cloud encoder with direct access to high-frequency features. We experimentally validate the use of Fourier features on challenging manipulation tasks from the RoboCasa and ManiSkill3 benchmarks and on a real robot setup. Despite their simplicity, we find that Fourier features provide significant benefits across diverse encoder architectures and benchmarks and are robust across hyperparameters. Our results indicate that Fourier features let policies leverage geometric details more effectively than Cartesian features, showing their potential as a general-purpose tool for point cloud-based imitation learning. We provide source code and videos on our project page: https://fourier-il.github.io/fourier-il

07.
arXiv (quant-ph) 2026-06-16

Quantum Algorithm for Open-System Battery Cathodes by Modeling Multiple Strongly Coupled Holstein Polarons with Chain-Mapped Caldeira-Leggett Dynamics

arXiv:2606.16017v1 Announce Type: new Abstract: Cathode lithiation occupies a chemical regime of tightly localized orbitals, narrow bandwidths, and strong electron-lattice coupling. The defining electrochemical observables (open-circuit voltage and differential capacity) are open-system, reservoir-equilibration quantities that closed-Hamiltonian quantum simulation cannot produce, set by exchange with electron, Li$^+$, and phonon baths. We present a fault-tolerant quantum algorithm that recovers them through a unitary chain-mapped Caldeira-Leggett embedding, rendering the baths Trotterizable. The resulting fourth-order Trotter step has a T-gate count polynomial in system size, validating its open-system dynamics against hierarchical equations of motion (HEOM) at strong coupling and the Lindblad limit at weak coupling. For single-carrier olivine LiFePO$_4$, a single voltage anchor on an otherwise DFT-fixed Hamiltonian places the differential-capacity peak within the $\pm5$ mV reproducibility of the experimental plateau. For multi-carrier spinel LiMn$_2$O$_4$, whose $1{:}1$ Mn$^{3+}$/Mn$^{4+}$ filling makes the inter-site Coulomb repulsion dynamically active, the same kernel yields a two-plateau voltage curve with a $125$ mV split, within $17\%$ of the observed $150$ mV. We deliver an end-to-end fault-tolerant resource estimate for such a multi-carrier, three-reservoir observable: $368$ logical qubits and $\sim3\times10^5$ T-gates per step, or $\sim1.7\times10^{12}$ T-gates for a full voltage curve (parallelizable over $\sim10^3$ trajectories), leaving the production-scale dynamical run as a milestone for future hardware. The same kernel reproduces macroscopic quantum coherence, two-band superconductivity, and the Mikheyev-Smirnov-Wolfenstein resonance without modification, placing dynamical battery chemistry and similar Hamiltonians within scope for fault-tolerant quantum simulation.

08.
arXiv (CS.AI) 2026-06-18

Dynamic In-Group Persona Generation for Enhancing Human-AI Rapport

arXiv:2606.18256v1 Announce Type: cross Abstract: LLM-based chatbots are increasingly applied in interpersonal domains such as counseling and peer support, where establishing human-AI rapport is crucial yet remains challenging. In this work, we introduce a novel approach for conditioning LLMs with in-group personas, which (i) first identifies a user's primary concern and brief personal context (e.g., a computer science undergraduate worried about future career prospects), and (ii) generates a synthetic in-group persona that shares a similar primary concern while differing in background and narrative details, such as age or profession (e.g., a junior researcher at an AI startup). Furthermore, we conduct a human-subject study to systematically evaluate the effectiveness of in-group persona agents in enhancing human-AI rapport. We compare our approach against two baseline conditions: a conventional agent without persona conditioning and an agent exhibiting minimal self-disclosure (e.g., "I've felt that too"). Results from post-task questionnaires assessing rapport and user experience indicate that the in-group persona agent significantly improves perceived rapport and personal relevance compared to the baselines, and also yields more positive user experience-most notably higher engagement.

09.
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.

10.
arXiv (quant-ph) 2026-06-16

Grid-state deformation in a no-jump non-Hermitian bosonic dimer

arXiv:2606.17036v1 Announce Type: new Abstract: We study the no-jump evolution of ideal grid states in a lossy bosonic dimer with differential decay. The effective non-Hermitian quadratic dynamics induces a complex symplectic flow in phase space that deforms both the primitive lattice vectors and the origin seed. The average decay rate controls common attenuation, while coherent hopping and differential decay control the reduced dimer deformation. The reduced sector contains elliptic, parabolic, and hyperbolic regimes with imaginary spectra, an exceptional point, and real spectra, producing oscillatory, linear, and exponential lattice deformations. Although projected lattice areas can change, the deformation comes from a determinant-one complex symplectic flow on the full four-dimensional phase space. For a Gaussian regularization of the origin seed, we derive the associated complex width matrix and identify the positivity conditions that preserve Gaussian form. For an initial two-mode qunaught product state, the lossless limit recovers the standard beam-splitter generation of a square GKP$+$ Bell pair, while the no-jump dynamics produces its non-Hermitian deformation with a postselection cost set by the no-jump probability.

11.
arXiv (CS.AI) 2026-06-15

Sensitivity Shaping for Latent Modeling

arXiv:2606.14585v1 Announce Type: cross Abstract: Generative dynamics models enable planning in challenging robotic systems, but safe deployment requires reliably detecting policy-induced out-of-distribution (OOD) transitions. Existing methods typically treat the learned dynamics as fixed and attach post hoc support surrogates. We show that these surrogates can fail when the dynamics are locally insensitive to critical action choices: unsupported control actions may produce latent predictions that resemble demonstrated transitions, suppressing OOD signals despite large true predictive errors. To address this, we introduce support-conditioned control-sensitivity regularization, which promotes sensitive local response to control input changes in learned dynamics in high-support training regions. This preserves control-induced variation while limiting unstable extrapolation due to weak empirical support. Experiments in vision-based obstacle avoidance, manipulation, and real-robot navigation show improved OOD detection and safer closed-loop planning.

12.
arXiv (CS.CV) 2026-06-15

PMOF: A Dataset and Benchmark for Passenger Monitoring Using Overhead Fisheye Cameras

Autonomous staff-free public transport requires reliable in-vehicle passenger monitoring. However, perception inside moving vehicles is challenged by confined spaces, variable illumination, motion-induced background variation, occlusion, and limited viewpoints. To mitigate these spatial constraints, ceiling-mounted fisheye cameras provide full-scene coverage from a single viewpoint. Yet existing public overhead fisheye datasets are recorded in static environments and do not capture the domain shift introduced by vehicle motion. To fill this gap, we introduce PMOF, Passenger Monitoring using Overhead Fisheye cameras, the first public dataset of top-view fisheye imagery captured inside a moving vehicle, comprising over 19k manually annotated frames. PMOF provides rotated bounding boxes, tracking identifiers, and action labels, supporting object detection, tracking, and action recognition. We benchmark PMOF using YOLO26m-obb models fine-tuned under multiple dataset configurations that combine PMOF with existing overhead fisheye datasets. Cross-domain fine-tuning with custom rotation-aware augmentation achieves 94.8% AP50 on PMOF and 96.5% AP50 on an unseen overhead fisheye dataset from a different domain. Our results highlight the domain gap between static and moving environments and show that incorporating PMOF improves detection performance and advances generalization beyond passenger monitoring to broader fisheye-based person detection tasks. The dataset and code are available at https://swermuth.github.io/pmof/.

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

PRISMR: Overcoming Parse Collapse in Multimodal Listwise Ranking via Parameterized Representation Internalization

arXiv:2606.12942v1 Announce Type: new Abstract: Generative listwise ranking with Large Multimodal Models (LMMs) aims to capture global list context in a single forward pass, but its effectiveness degrades in long-context multimodal scenarios. We identify a recurring failure mode, parse collapse, where the autoregressive decoder produces fluent yet incomplete rankings by silently omitting candidates and terminating early. This failure stems from limited context utilization rather than simple formatting mistakes, making prompt engineering and constrained decoding insufficient. We propose PRISMR (Parameterized Representation Internalization for Semantic Multimodal Ranking), a framework that replaces transient in-context list processing with parametric structural conditioning. PRISMR uses a lightweight hypernetwork to encode multimodal candidates in parallel and generate item-specific LoRA weights, which are synthesized into an instance-specific adapter for a LMM. This paradigm enables more robust internalization of list structure while preserving the base model. We further introduce a large-scale multimodal review-ranking benchmark for evaluation. Experiments demonstrate that PRISMR substantially reduces parse collapse, improves listwise ranking performance, and transfers effectively across domains and instruction-tuned backbones.

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

TextMesh4D: Zero-shot Text-to-4D Mesh Generation

Large-scale, high-quality dynamic 3D (4D) assets are essential for learning physically grounded representations, but remain costly to capture and annotate at scale. This limits the viability of supervised 4D learning and motivates zero-shot text-to-4D generation leveraging pretrained diffusion priors. To model complex dynamics, prior methods typically adopt implicit 3D representations (e.g., NeRFs or 3DGS) for their deformation capacity. However, their implicit nature provides limited control over surface topology, which hinders high-fidelity geometry and makes temporally coherent surface reconstruction challenging. To address these limitations, we explore zero-shot text-to-4D mesh generation. However, a structural mismatch arises when combining diffusion-based guidance with topology-constrained meshes: the guidance is noisy and spatially inconsistent, while meshes impose severe topological constraints, making direct vertex-level deformation unstable. In this paper, we introduce TextMesh4D, the first zero-shot framework for text-to-4D that directly generates dynamic meshes by addressing the above challenge at two complementary levels. Geometrically, we shift deformation modeling from vertices to faces via a Jacobian Deformation Field (JDF), enabling topology-aware surface reconstruction through an integrability-enforcing integration formulation. Semantically, we propose a Local-Global Semantic Regularizer (LGSR) that preserves identity over time by jointly constraining local deformation plausibility and global shape consistency. Extensive experiments demonstrate state-of-the-art temporal consistency, structural fidelity, and visual quality, while remaining efficient on a single 24GB GPU.

15.
arXiv (CS.CL) 2026-06-18

Dual Dimensionality for Local and Global Attention

Decoder-only Transformers compute attention over the KV cache of preceding tokens. Keys (and Values) are typically represented with the same dimensionality, regardless of its distance from the prediction target. In natural language, however, the next word is most strongly influenced by the immediately preceding tokens. We hypothesize that local and distant tokens impose asymmetric demands on representational capacity: local tokens are more critical for predicting immediate outputs and thus require richer representations, whereas distant tokens primarily serve as long-range memory, for which lower-dimensional representations may suffice. We formalize this idea as Distance-Adaptive Representation (DAR), implemented in a controlled setting that preserves full-dimensional representations within a local context window while assigning reduced-dimensional representations (e.g. 1/4 of the original dimensionality) to tokens beyond that window. Across multiple pretraining scales (70M to 410M parameters), as well as continued supervised fine-tuning on a 1B-scale model, this approach closely matches the performance of full-dimensional baselines. In contrast, uniformly reducing dimensionality across all token positions leads to worse performance. These results challenge the common assumption that key and value dimensionality should be uniform across token positions. Our findings suggest a new direction for designing attention architectures that adaptively allocate representational capacity across sequences, enabling further reductions in KV cache during inference.

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

DADP: Domain Adaptive Diffusion Policy

arXiv:2602.04037v3 Announce Type: replace Abstract: Learning domain adaptive policies that can generalize to unseen transition dynamics, remains a fundamental challenge in learning-based control. Substantial progress has been made through domain representation learning to capture domain-specific information, thus enabling domain-aware decision making. We analyze the process of learning domain representations through dynamical prediction and find that selecting contexts adjacent to the current step causes the learned representations to entangle static domain information with varying dynamical properties. Such mixture can confuse the conditioned policy, thereby constraining zero-shot adaptation. To tackle the challenge, we propose DADP (Domain Adaptive Diffusion Policy), which achieves robust adaptation through unsupervised disentanglement and domain-aware diffusion injection. First, we introduce Lagged Context Dynamical Prediction, a strategy that conditions future state estimation on a historical offset context; by increasing this temporal gap, we unsupervisedly disentangle static domain representations by filtering out transient properties. Second, we integrate the learned domain representations directly into the generative process by biasing the prior distribution and reformulating the diffusion target. Extensive experiments on challenging benchmarks across locomotion and manipulation demonstrate the superior performance, and the generalizability of DADP over prior methods. More visualization results are available on the https://outsider86.github.io/DomainAdaptiveDiffusionPolicy/.

17.
arXiv (quant-ph) 2026-06-16

Counterdiabatic Raman Atom Optics for Compact High-Sensitivity Gravimetry

arXiv:2606.16945v1 Announce Type: new Abstract: Large-momentum-transfer (LMT) atom interferometry provides a route toward enhanced inertial sensitivity in compact quantum sensors, but its scalability is limited by the accumulation of pulse-transfer errors across long Raman pulse sequences. We investigate theoretically the use of stimulated Raman shortcut-to-adiabatic passage (STIRSAP) for high-fidelity LMT atom optics in a Mach–Zehnder interferometer geometry. The counterdiabatic correction is encoded directly into the Raman pulse envelopes, eliminating the need for auxiliary microwave or radio-frequency control fields. Numerical simulations based on an effective Raman model show that $1~\mu\mathrm{s}$ STIRSAP pulses achieve single-pulse transfer fidelities of $F_\pi = 0.99902$ while maintaining negligible pulse-time overhead even at high momentum order. We analyze the resulting tradeoff between interferometric phase enhancement and compound contrast decay and identify an unconstrained shot-noise optimum near $n\approx270$. The analysis further shows that practical operation at extreme LMT order is constrained by wave-packet separation, vibration noise, Doppler detuning, and accumulated systematic effects rather than by pulse duration itself. These results establish superadiabatic Raman control as a promising approach for scalable high-fidelity atom optics and clarify the physical limitations governing compact high-order atom interferometers.

18.
arXiv (CS.LG) 2026-06-15

Detecting Lookahead Bias in LLM Forecasts

arXiv:2512.23847v2 Announce Type: replace-cross Abstract: We develop a statistical procedure to detect lookahead bias in economic forecasts generated by large language models (LLMs). Using a date-only recall query for a firm-date pair, we estimate the probability that the LLM has internalized information about the realized outcome, a statistic we term Lookahead Propensity (LAP). LAP is materially positive throughout the in-sample period and collapses essentially to zero right after the training-data cutoff. We show that a positive interaction between LAP and the LLM forecast in an accuracy regression indicates lookahead-bias contamination, and apply the test to two forecasting tasks: news headlines predicting stock returns and earnings call transcripts predicting capital expenditures. In both applications, the LLM forecast's predictive power is amplified on high-LAP firm-date pairs, and the interaction loses significance on post-training-cutoff samples. Our test provides a cost-efficient, diagnostic tool for assessing the validity and reliability of LLM-generated forecasts.

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

MetaResearcher: Scaling Deep Research via Self-Reflective Reinforcement Learning in Adversarial Virtual Environments

arXiv:2606.19893v1 Announce Type: new Abstract: Deep research agents have demonstrated remarkable capabilities in autonomous information gathering and synthesis, yet their training remains constrained by the static nature of simulated environments, the limits of fact-retrieval-only task designs, and the inefficiency of outcome-based reinforcement learning. In this work, we propose MetaResearcher, a novel framework that scales deep research agent training across four synergistic dimensions. First, we introduce an Evolving Virtual World that injects temporal dynamics and adversarial misinformation into the training environment, forcing agents to develop source credibility assessment and temporal conflict resolution skills. Second, we design Discovery-Oriented Tasks – including hypothesis generation and contradiction resolution – that transcend simple fact retrieval and push agents toward genuine research behaviors. Third, we propose a Self-Reflective Meta-Reward mechanism within the GRPO framework that jointly optimizes for answer correctness, search path efficiency, reflection depth, and tool call diversity, directly addressing the repetitive action loop problem observed in prior work. Fourth, we introduce a Heterogeneous Multi-Agent Swarm architecture comprising specialized Scout, Filter, and Synthesizer models that learn collaborative research strategies through coordinated reinforcement learning. Built upon the LiteResearcher infrastructure, MetaResearcher requires zero marginal API cost for training while targeting substantial improvements in both benchmark performance (GAIA, Xbench-DS) and epistemic robustness under adversarial conditions. We present the complete framework design, training methodology, and planned experimental validation.

20.
bioRxiv (Bioinfo) 2026-06-19

Evaluation of analysis modes for RNA coexpression in single-cell and bulk tissue

Coexpression of transcripts presents the most common means of computational inference of transcription factor regulation, and is often combined with other data types to infer regulatory networks. With the growing popularity of single-cell approaches, there are questions about how best to extract coexpression information from the data. Recently we reported a simulation study that explored the differences among coexpression performed at different levels: across single cells (xCell, per cell type), across subjects from pseudobulked single-cell data (xSubject, per cell type), or across subjects using bulk tissue samples (xBulk). Here we test predictions made by those models using real data. We consider both preservation (consistency of coexpression findings across different levels of analysis of the same data) and replicability across independent studies, as well as biological interpretability. We find that preservation across levels is limited, indicating the choice of analysis level will affect outcomes. We show that xCell coexpression is more replicable across studies compared to xSubject. xBulk coexpression is dominated by patterns driven by variability in cellular composition and fails to capture much coexpression that is reliably detected at finer resolutions. While all modes of analysis exhibit some enrichment for known regulatory relationships, it was highest with the xCell mode. Finally, we present a case study of the effect of analysis modes on a schizophrenia-associated pattern, reinforcing the importance of analytic choices in the interpretation and replicability of coexpression analyses. Together with our modeling study, this work emphasizes the importance of understanding sources of expression covariation as they relate to the goals of the analysis, and recommend single-cell-based data with biological replicates should be the focus of attempts to infer dynamic regulatory interactions that are more likely to be replicable by others.

21.
arXiv (quant-ph) 2026-06-12

Electric Field Distortions in Surface Ion Traps with Integrated Nanophotonics

arXiv:2503.20387v3 Announce Type: replace Abstract: The integration of photonic components into surface ion traps provides a scalable approach for trapped-ion quantum computing, sensing, and metrology, enabling compact systems with enhanced stability and precision. However, the introduction of optical apertures in the trap electrodes can distort the trapping electric field. This can lead to excess micromotion (EMM) and ion displacement which degrade the performance of quantum logic operations and optical clocks. In this work, we systematically investigate the electric field distortion in a surface ion trap with integrated waveguides and grating couplers using Finite Element Method (FEM) simulations. We analyze methods to reduce these distortions by exploiting symmetries and transparent conductive oxide materials.

22.
arXiv (CS.CV) 2026-06-16

Human Cognition in Machines: A Unified Perspective of World Models

This report of world models distinguishes prior works by the cognitive functions they innovate. Many works claim an almost human-like cognitive capability in their world models. To evaluate these claims requires a proper grounding in first principles from human and machine cognition theory. In moving towards human-like world models we present a conceptual unified framework for world models that fully incorporates all the cognitive functions (i.e., memory, perception, language, reasoning, imagining, motivation, and metacognition) and identify gaps in existing research as a guide for future states of the art. In particular, we find that motivation (especially intrinsic motivation) and metacognition remain drastically under-researched, and we propose concrete directions to address these gaps informed by active inference and global workspace theory. We also introduce epistemic world models, a new category encompassing agent frameworks for scientific discovery that operate over structured knowledge. Our taxonomy, applied to video, embodied, and epistemic world models, suggests research directions where prior taxonomies have not.

23.
arXiv (CS.CL) 2026-06-18

ToolGrad: Efficient Tool-use Dataset Generation with Textual "Gradients"

Prior work synthesizes tool-use LLM datasets by first generating a user query, followed by complex tool-use annotations like depth-first search (DFS). This leads to inevitable annotation failures and low efficiency in data generation. We introduce ToolGrad, an agentic framework that inverts this paradigm. ToolGrad first constructs valid tool-use chains through an iterative process guided by textual "gradients", and then synthesizes corresponding user queries. This "answer-first" approach led to ToolGrad-500, a dataset generated with more complex tool use, lower cost, and almost 100% pass rate. Experiments show that ToolGrad models outperform those trained on expensive baseline datasets and proprietary LLMs. The ToolGrad source code, dataset, and models are available at https://github.com/zhongyi-zhou/toolgrad.

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

No Accidental Software Agent First Canonical Code for Human Code Entropy Reduction and 30 to 500 times Lower Frontier Model Requirements

arXiv:2606.14357v1 Announce Type: cross Abstract: Frontier coding models may spend substantial capacity learning not only program behavior, but also accidental entropy in human repositories. Such repositories contain valuable signals: tests, incidents, migrations, edge cases, product judgment, and operational history. These signals are entangled with framework churn, naming drift, generated-source ambiguity, dependency rituals, CI dialects, weak proof routes, and human-oriented review customs. We propose agent-first canonical code, a proof-carrying substrate that rewrites routine product software into canonical behavior profiles, typed change algebra, proof lanes, constrained edit grammars, semantic patch cells, runtime negative memory, and proof-carrying change objects. The core hypothesis is that quotienting software by behavior equivalence under a declared oracle can collapse equivalent encodings into governed representatives with explicit evidence and proof obligations. The endpoint is amortized cost per verified correct change, including source, context, reasoning, tools, verification, security, provenance, review, failed loops, defects, and foundry cost under a common oracle. Reported reduction bands are hypotheses, not measured frontier results. The proposed limit is a No-Accident Horizon: removable accident decreases until residual novelty, evidence, governance, risk, and future optionality dominate. For supported routine-product distributions, this gives a defensible planning target near 100-fold all-in cost reduction, not a guarantee for all software. Preliminary QLoRA experiments on Qwen2.5-Coder-14B show that 64,088 canonical trajectories are learnable and suppress tested forbidden-language markers, but do not establish behavior preservation, scaling economics, or verified-change cost. The contribution is a falsifiable program centered on minimum functional description length and verified-change cost.

25.
arXiv (CS.AI) 2026-06-16

CoffeeBench: Benchmarking Long-Horizon LLM Agents in Heterogeneous Multi-Agent Economies

arXiv:2606.16613v1 Announce Type: new Abstract: As LLM agents become capable of increasingly long-horizon tasks, evaluating their performance in economic systems is becoming increasingly important. Unlike existing benchmarks that primarily evaluate a single agent interacting with a passive environment, economic systems are inherently multi-agent, requiring autonomous agents to communicate, negotiate, and transact while pursuing their own objectives over extended periods. We introduce CoffeeBench, a benchmark for evaluating LLM agents in a long-horizon multi-agent economy composed of heterogeneous firms. In CoffeeBench, two farmers, two roasters, and two retailers autonomously operate their businesses over a 90-day simulation, each seeking to maximize cumulative net income through communication and transactions while managing cash, inventory, and pricing. The evaluated model controls one coffee roaster, while the remaining firms are controlled by fixed reference agents. Across several recent open-weight and proprietary LLMs, all models outperform a passive baseline that takes no actions, with most achieving positive net income. Analysis of agent behavior reveals substantial differences in long-horizon economic interaction: higher-performing models communicate more actively with other firms, whereas Claude~Haiku~4.5 exhibits an idle-drift failure mode, repeatedly choosing inaction despite producing coherent assessments and plans. We release our code and agent trajectories to support future research.