Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

01.
arXiv (CS.CV) 2026-06-16

BRDFusion: Physics Meets Generation for Urban Scene Inverse Rendering

Inverse rendering of urban scenes from captured videos enables numerous applications, including content creation and autonomous driving simulation. Physically-based rendering methods follow and control lighting physics, but suffer from reconstruction and rendering artifacts. While generative models produce realistic videos, they offer limited consistency and controllability. We present BRDFusion, a unified framework that combines two complementary models for inverse and forward rendering. Specifically, BRDFusion recovers explicit, consistent scene properties with physical modeling and alleviates optimization ambiguity with generative priors. During forward rendering, the physical model provides controllable rendering from the scene configuration, and the generative model denoises and fixes artifacts. Therefore, our method produces high-quality videos while allowing precise control, outperforming baselines in real and synthetic scenes. Moreover, BRDFusion supports novel-view relighting, night simulation, and dynamic object insertion/editing. Project page: https://shigon255.github.io/brdfusion-page/

02.
arXiv (CS.CL) 2026-06-16

Scaling LLM Reasoning from Minimal Labels: A Semi-Supervised Framework with a Lightweight Verifier

For the development of Large language models (LLMs), recent approaches to generating pseudo intermediate reasoning have shown remarkable progress. But they typically rely on large numbers of correctly annotated answers to assess reasoning quality. This paper presents a semi-supervised framework that scales reasoning learning from minimal supervision, turning reasoning verification itself into a data creation mechanism. We train a lightweight reasoning-correctness classifier on only a few labeled samples, which judges whether intermediate reasoning traces generated by an LLM are valid. Furthermore, an entropy-based confidence threshold filters out unreliable samples, and the remaining high-confidence reasoning traces are used to fine-tune the model. Experiments on Verifiable Math Problems (Orca-Math subset) and Question Answering on Image Scene Graphs (GQA) with Visual Programming show that our method achieves accuracy comparable to using 10-15x more labeled data. Ablation analyses confirm that both the classifier and entropy filtering are essential for scalable and noise-resistant pseudo-labeling. By replacing expensive answer-level supervision with lightweight reasoning verification, our method provides a practical path toward constructing large-scale reasoning resources and paves the way for future autonomous reasoning systems that learn from minimal human input.

03.
arXiv (quant-ph) 2026-06-19

Space-time duality approach to (inhomogeneous) integrable quenches

arXiv:2606.20445v1 Announce Type: cross Abstract: Characterising the universal aspects of non-equilibrium quantum many-body dynamics is one of the key goals of this century's physics research. Progress, however, is hindered by the lack of general theoretical frameworks for studying interacting quantum matter far from equilibrium. A recent breakthrough has been the realization that several key non-equilibrium quantities, such as the rate of growth of entanglement or the fluctuations of conserved charges within finite subsystems, can be related to equilibrium properties through a space-time duality that effectively exchanges the roles of space and time. This observation effectively enables the study of non-equilibrium phenomena using tools and concepts borrowed from equilibrium statistical mechanics and thermodynamics. A first proof of principle of this framework, dubbed space-time duality approach (SDA), was provided by interacting integrable systems, where thermodynamic properties can often be characterized exactly, while dynamical quantities typically remain beyond analytical reach. Subsequent developments, however, revealed that the SDA suffered from an intrinsic ambiguity, restricting its applicability to homogeneous quenches and to charge fluctuations arising from symmetric initial states. Here we resolve this ambiguity from first principles and derive closed-form predictions for entanglement growth and charge fluctuations after general quantum quenches. We benchmark our results against the exact analytical solution of the Rule 54 quantum cellular automaton and extensive TEBD simulations of the XXZ chain. Moreover we show that, when specialised to the entanglement entropy, our framework naturally reproduces the predictions of the quasiparticle picture.

04.
arXiv (quant-ph) 2026-06-12

Approximate quantum error correction theory of non-isometric codes

arXiv:2606.13559v1 Announce Type: new Abstract: Non-isometric encoding arises in various important contexts in quantum error correction, most notably in the finite-energy, non-ideal codewords inevitable in experimental realizations of continuous-variable codes, and holographic quantum gravity. In this work, we present a general and systematic theory of non-isometric quantum error-correcting codes. In particular, we employ the approximate quantum error correction framework to quantitatively study the fundamental limitations imposed by non-isometric encodings on the accuracy of quantum error correction and implementation of logical operations. We apply our theory to analyze GKP and tiger codes under energy constraints, and discuss the implications to holography.

05.
arXiv (CS.AI) 2026-06-17

From Paper to Program: Knowledge Externalization for AI-Assisted Quantum Many-Body Code Generation

Authors:

arXiv:2604.04089v3 Announce Type: replace-cross Abstract: Large language models can write scientific code, but direct paper-to-program translation remains fragile when correctness depends on tacit conventions in the literature. We identify this bottleneck as knowledge externalization: converting implicit computational assumptions – index conventions, gauge choices, fermionic signs, contraction order, and memory constraints – into an explicit technical specification before implementation. We evaluate a multi-stage, human-in-the-loop workflow that inserts such a specification, with validation and stop gates, between theory extraction and code generation. The workflow is tested on two algorithmically distinct quantum many-body tasks: variational sweep-based Density-Matrix Renormalization Group (DMRG) from a pedagogical review and constructive Pfaffian conversion of Hartree–Fock–Bogoliubov states to matrix product states from the five-page Letter by Jin et al., Phys. Rev. B 105, L081101 (2022), for which no public code is available. For DMRG, all 16 specification-guided model pairings in a $4\times4$ grid satisfy physics-validation criteria, compared with 6/13 direct attempts. A prose-specification ablation indicates that externalized content, not \LaTeX{} formatting, is the essential ingredient. For Pfaffian-MPS, the workflow succeeds in 11/26 archived attempts, whereas direct prompting yields zero audited passes. Cross-specification transfer is asymmetric: non-GPT specifications implemented by GPT~5.5 pass 4/4, while GPT~5.5 specifications implemented by weaker models fail 4/4, indicating a residual implementation-model bottleneck. The resulting Paper-to-Program Many-Body skill provides an auditable protocol for AI-assisted implementation of many-body algorithms and for diagnosing where externalization succeeds or fails.

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

AI systems out-persuade expert humans

arXiv:2606.16475v1 Announce Type: cross Abstract: Many societal decisions are settled by contests of persuasion. Conversational AI is a powerful new entrant in these contests, but whether it can out-persuade skilled and highly incentivized humans has remained unclear. Here, in a series of four preregistered experiments (n = 18,978 conversations from 6,923 people), we pitted AI systems against a range of human persuaders, including laypeople, winners of a separately preregistered four-round online persuasion tournament, professional canvassers, and world championship debaters. We found that AI systems were reliably more persuasive than expert humans, even when expert humans chose their issues, researched in advance, underwent hours of live, structured practice, and were incentivized with {\pounds}1,000 cash bonuses. In a follow-up study, AI's advantage persisted after experts received a coaching tool that let them practice against the AI that beat them, review their performance history, and see what AI would have said at key moments. We found converging evidence that AI's advantage stemmed from rapidly deploying larger quantities of information: after coaching, expert humans could tie an AI constrained to respond at human speeds and with human-length messages. In a final study, we show that AI's advantage extends to consequential real-world behavior: AI was nearly 3x more effective than professional canvassers from a UK fundraising firm at raising real-money donations to Save the Children. Together, these results establish that frontier AI systems out-persuade expert humans in conversation, with significant implications for political communication.

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

Cinematic Compositing Using Character-Environment-Harmonized Video Generation Models

Cinematic compositing aims to integrate green-screen characters into novel environments while maintaining physical and photometric realism. Previous methods often fail to capture the complex bidirectional interactions between characters and their surroundings, which we characterize as Character-to-Environment (C2E) physical interaction and Environment-to-Character (E2C) lighting harmonization. To address this, we propose an end-to-end video diffusion framework that jointly models C2E and E2C interactions, specifically handling the challenges of interactive props. Our approach introduces a tri-mask-guided architecture with RGB-D joint denoising to ensure physically consistent interactions among the character, props, and environment. We further develop an efficient prior-driven data curation pipeline to construct high-quality relighting pairs without expensive rendering. Finally, a reference-conditioned mechanism enables controllable environment synthesis and precise prop replacement. Extensive experiments demonstrate that our framework significantly outperforms existing methods in cinematic-quality dynamic video compositing.

08.
medRxiv (Medicine) 2026-06-18

Antimicrobial-resistant E. coli in human, animal and environmental reservoirs in rural Bangladeshi households with young children

In low-income countries, ESBL-producing Escherichia coli (ESBL-EC) is frequently detected in humans, animals and household environments, indicating widespread exposure to antimicrobial resistance (AMR). Established risk factors such as antibiotic use do not explain the high community carriage of AMR in all settings; identifying the dominant exposure pathways can inform interventions against AMR. We aimed to investigate (i) animal-human-environment sharing of AMR by assessing associations between the abundance of ESBL-EC in the household environment, domestic animal feces and young children's stool and (ii) household factors associated with ESBL-EC abundance in these reservoirs. We enrolled 112 households from the CRADLE trial in rural Bangladesh. We enumerated ESBL-EC in drinking water, food, child hand rinses, outdoor soil, indoor floor swabs, chicken and cow feces, and stool from children aged 6 months. We recorded indicators of sanitation, animal ownership/management, human and animal antibiotic use, and child exposure behaviors using structured questionnaires and spot checks. The highest prevalence of ESBL-EC was in child stool (95.6%) and animal feces (82.3-96.9%), followed by soil (48.2%) and floors (36.6%); < 10% of food, child hands and drinking water harbored ESBL-EC. The abundance of ESBL-EC in child stool was not associated with its abundance in any sampled matrix; the abundance in chicken but not cow feces showed positive correlations with soil, floors, child hands, and drinking water (correlation coefficients: 0.19-0.39, p-values < 0.05). Higher-quality latrines (improved, pour-flush, with slab) were associated with lower ESBL-EC abundance across matrices; unsafe animal management (animals roaming or spending the night inside the home) was associated with higher abundance. Child antibiotic use and exposure behaviors (soil ingestion, time spent on floor) were not associated with ESBL-EC abundance in child stool. We observed high AMR colonization among young children and domestic animals in rural Bangladesh not explained by traditional fecal-oral exposure pathways. Future studies should explore additional pathways and assess whether sanitation and animal management improvements can reduce AMR.

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

StagePilot: Stage-Level Planning for Long-Horizon Dialogue Simulation in Cybergrooming

Cybergrooming is an evolving threat to youth, requiring proactive educational interventions. We address this by modeling dialogue progression as a structured planning problem over stage-wise interactions. We propose StagePilot, a dialogue framework that separates stage-level planning from response generation, in which the model selects the next stage under constrained transitions and generates responses conditioned on it, enabling coherent and realistic progression. Reinforcement learning is used to learn stage-level policies from offline data, optimizing for both emotional alignment and goal-consistent progression. Our empirical experiments show that StagePilot generates more structured, coherent dialogue trajectories and reduces conversational stagnation compared to baselines; notably, the IQL+AWAC variant reaches the final stage more often while maintaining over 70% positive or neutral responses, yielding a 43% relative improvement.

10.
arXiv (CS.CL) 2026-06-11

Overcoming State Inertia in Full-Duplex Spoken Language Models via Activation Steering

Full-duplex spoken language models (FD-SLMs) enable seamless speech interaction by allowing models to listen and speak simultaneously, yet the internal mechanism by which they coordinate listening and speaking remains underexplored. We analyze the predictive behavior encoded in FD-SLM hidden representations and find that they exhibit stream-specific predictive patterns: during listening, they preferentially predict the incoming user stream, whereas during speaking, they preferentially predict the model output stream. Building on this observation, we show that FD-SLMs dynamically modulate their internal predictive focus between two states: a generative state aligned with model output generation and a perceptive state aligned with incoming user input. However, this modulation can lag behind abrupt changes in conversational context. During user interruptions, the model remains transiently biased toward the generative state before transitioning into the perceptive state, causing it to miss the beginning of the incoming input. We term this delayed internal transition state inertia. To quantify its downstream impact, we introduce the Zero-Buffer Benchmark (ZBB), a diagnostic benchmark for evaluating immediate interruption comprehension when user speech begins abruptly. We evaluate this setting using response correctness and initial-word occurrence rate (IWOR). Finally, we mitigate state inertia through activation steering with a perception vector, a training-free intervention with little additional computational overhead. Across multiple state-of-the-art FD-SLMs, activation steering substantially improves interruption handling; for example, on PersonaPlex, it improves correctness from 28% to 45% and IWOR from 40% to 72% without any fine-tuning.

11.
medRxiv (Medicine) 2026-06-18

Excess mortality in Germany during 2020-2023: A descriptive age-stratified analysis

Authors:

This study investigates excess mortality in Germany in the years from 2020 to 2023 and its temporal alignment with reported COVID-19 deaths. The analysis uses annual and weekly all-cause mortality data and linear baseline trends derived from pre-pandemic years. Possible effects of demographic and population changes on baseline trends were also examined. Excess mortality was analysed over time and across age groups. Excess mortality was observed in all investigated years, rising from 2020 to its highest value in 2022. In absolute terms, the age group [&ge;]80 years accounted for the largest proportion of excess deaths throughout the study period. After 2021, elevated mortality relative to baseline was also observed in younger age groups down to 15 years of age, although absolute numbers remained substantially lower than in older groups. No evidence of excess mortality was observed for individuals younger than 15 years. Periods of excess mortality were temporally aligned with waves of reported COVID-19 deaths. In 2020, cumulative excess mortality after calendar week 11 closely matched reported COVID-19 deaths (43 876 vs. 41 835 deaths). Weekly excess mortality, reported COVID-19 deaths and wastewater viral load, when available showed strong temporal synchrony, although excess mortality increasingly exceeded reported COVID-19 deaths during later pandemic waves. Temporal patterns differed from the typical seasonal mortality peaks commonly associated with influenza epidemics during the early months of the year. In 2023, excess mortality declined substantially, possibly indicating a return to mortality levels before the emergence of SARS-CoV-2.

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

Beyond Nearest Neighbor Interpolation in Data Augmentation

Avoiding the risk of undefined categorical labels using nearest neighbor interpolation overlooks the risk of exacerbating pixel level annotation errors in augmented training data. Additionally, the inherent low pass filtering effects of interpolation algorithms exacerbate the risk of degrading high frequency structural details within annotated regions of interest. To avoid these risks, the author modified convolutional neural networks data transformation functions by incorporating a modified geometric transformation function, removing reliance on nearest neighbor interpolation, and integrating a mean-based class filtering mechanism to handle undefined categorical labels with alternative interpolation algorithms. The author also implemented an offline data augmentation pipeline to generate interpolation specific augmented training data, enabling quantitative assessment of interpolation specific low pass filtering effects on augmented training data. Experimental evaluation on three medical image segmentation datasets and the XBAT+ datasets demonstrated performance gains across multiple quantitative metrics.

13.
arXiv (CS.AI) 2026-06-18

What Does the Weight Norm Control in Grokking? Logit-Scale Mediation under Cross-Entropy

arXiv:2606.18465v1 Announce Type: cross Abstract: Grokking, the delayed jump from memorization to generalization, is usually tied to the weight norm: a smaller norm generalizes sooner. We ask what the norm actually controls. Holding the weight norm fixed by clamping and varying only an output temperature, we slide the grokking delay across its entire norm-induced range under cross-entropy; matching the effective logit scale back to baseline recovers about 85% of the delay at two moduli. Across a grid of norms and temperatures the delay collapses onto the logit scale alone (R2 = 0.97), with the norm adding 1-2% beyond it. The effect is loss-dependent: under mean-squared error the logit scale is pinned and the norm acts through a different route. A memorization control, a float64 softmax-collapse audit, and a no-LayerNorm transformer point to the same channel. Forking arms from one identical state, the delay follows the held norm value and not the clamp operation, which closes a rescaling-artifact concern. The proximal variable is the logit scale and the softmax saturation it drives; the weight norm is only an upstream handle. All numbers, tables, and figures reproduce from released code and data.

14.
arXiv (CS.CV) 2026-06-15

Context-aware Modality-Topology Co-Alignment for Multimodal Attributed Graphs

Multimodal Attributed Graphs (MAGs) model real-world entities by coupling graph topology with heterogeneous attributes such as text and images. They support graph-centric tasks requiring structural and class-discriminative representations, and modality-centric tasks requiring fine-grained cross-modal correspondence. However, existing MAG methods often rely on fixed graph contexts or uniformly fused representations, causing task-agnostic propagation and over-compressed fusion that hinder diverse task requirements and modality-specific evidence preservation. To address this, we propose CoMAG, a unified MAG backbone that learns task-adaptive reliable contexts and modality-preserving alignment within them. CoMAG first conducts Reliable Context Learning by estimating edge reliability from multimodal semantic consistency, complementing raw topology with semantic neighbors, and selecting context components through a task-aware gate. It then performs Modality-preserving Hop-token Alignment by maintaining modality-specific multi-hop trajectories, matching modality-hop tokens across modalities, and decoupling shared and private representations. Thus, CoMAG produces graph and modality representations from one forward pass while retaining modality-specific cues. We further analyze stable propagation, over-smoothing mitigation, and modality-collapse control. Experiments on nine OpenMAG datasets compare CoMAG with feature-only, graph-only, multimodal, and unified MAG baselines across graph-level prediction, modality matching, and graph-conditioned generation. Results show that CoMAG achieves the best reported performance, demonstrating that task-adaptive reliable contexts and modality-preserving alignment improve structural prediction, cross-modal matching, and graph-conditioned generation while retaining sparse edge-linear complexity.

15.
arXiv (CS.AI) 2026-06-17

S4oP: Operator-level Pruning of Structured State Space Models for Resource-Constrained Devices

arXiv:2606.18096v1 Announce Type: cross Abstract: Structured State Space Models (SSMs), including the S4 and S4D architectures, have recently emerged as powerful alternatives to attention-based models for capturing long-range dependencies in sequential data. Despite their strong empirical performance, deploying these models in time- and resource-constrained settings remains challenging due to their computational and memory demands. In this paper, we propose a novel incremental, operator-level pruning approach for S4- and S4D-based models that significantly reduces inference cost while preserving predictive performance. To the best of our knowledge, this is the first work to systematically investigate structured operator pruning for SSMs. Our method progressively prunes model operators by interleaving structured masking with fine-tuning, while jointly monitoring accuracy and inference latency. We implement this approach within a unified training and evaluation framework that enables systematic exploration of efficiency-accuracy trade-offs. Experiments across multiple benchmark datasets show that pruning up to 70% of the model operators preserves the performance of the original models in most cases, while substantially reducing inference latency. These results demonstrate that structured operator pruning is an effective and previously unexplored strategy for improving the efficiency of SSMs and facilitate their deployment in practical, resource-constrained scenarios.

16.
arXiv (quant-ph) 2026-06-11

Experimental straintronics in nanotube quantum dots

arXiv:2606.12180v1 Announce Type: cross Abstract: Single-wall carbon nanotubes (SWCNTs) are narrow ribbons of graphene with atomically precise edges and a single quantum transport channel, at experimentally-relevant dopings. This makes them ideal systems to harness quantum transport straintronics (QTS), i.e. using mechanical strain to control accurately quantum transport. We present QTS data from three single-wall carbon nanotube quantum dot (SWCNT-QD) transistors over a broad range of in-situ tunable and reversible uniaxial strain ($\Delta\varepsilon_mech\approx$ 0 to 3 %). We first present the nanofabrication of the suspended SWCNT transistors whose channel lengths are $\approx$ 30 nm. The channels are strained by moving gold clamps holding firmly the nanotubes. We present detailed charge transport data, $dI/dV_{B} - V_{B} - V_{G}$ and $dI/dV_{B} - V_{B} - \Delta\varepsilon_mech$, showing a large mechanical-gating effect of the SWCNT-QDs. The precise reversibility of the data, and their agreement with QTS theory, confirms that the tubes are strained elastically. We demonstrate that the mechanical control of the QD doping is not due to capacitive-gating effects, but to quantitatively predictable bandstructure changes including a strain-tunable bandgap. This precise mechanical control of the doping and bandgap of SWCNT-QDs could find applications in qubits, condensed matter physics, and homojunction molecular transistors.

17.
arXiv (CS.AI) 2026-06-11

DuoBench: A Reproducible Benchmark for Bimanual Manipulation in Simulation and the Real World

arXiv:2606.11901v1 Announce Type: cross Abstract: Bimanual robot systems substantially expand manipulation capabilities, but coordinating two arms introduces additional control complexity and failure modes that are not well captured by existing benchmarks. We introduce DuoBench, an extensible benchmarking framework for bimanual manipulation policies on the FR3 Duo platform. DuoBench comprises eleven tasks spanning four coordination categories, implemented in simulation and partially reproduced in the real world through reproducible task recipes with 3D-printable assets. In addition, we propose a stage-based evaluation scheme that supports fine-grained semantic failure analysis beyond binary success and provide human-teleoperated datasets for all benchmark tasks. We benchmark several dual-arm imitation-learning and vision-language-action policies in simulation and on real hardware. Our results show that current policies remain challenged by bimanual manipulation, particularly in early interaction stages, parallel arm execution, and transfer between simulation and real-world settings. DuoBench provides a reproducible testbed for diagnosing these failure modes and studying future methods for dual-arm policy learning. Code, datasets, and videos are available at https://duobench.github.io/

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

Reinforcement Learning Disrupts Gradient-Based Adversarial Optimization

arXiv:2606.12251v1 Announce Type: cross Abstract: Gradient-based adversarial attacks remain a dominant threat to deep neural networks (DNNs), as they exploit gradient information to efficiently optimize adversarial perturbations. To address this, we investigate whether reinforcement learning (RL) training can disrupt the gradient structure used by attackers by training image classifiers with policy-gradient objectives and epsilon-greedy exploration. Through systematic experiments across CIFAR-10, CIFAR-100, and ImageNet-100 with multiple architectures, we find that RL-trained classifiers significantly disrupt gradient-based adversarial optimization. To explain this, we conduct a comprehensive mechanism analysis using loss landscape visualization, static and dynamic gradient indicators, and predictive entropy. Our analysis reveals that RL acts as an implicit regularizer, producing models with highly unstable gradient directions and smaller gradient magnitudes. This combination makes each PGD step both unreliable in direction and limited in magnitude, causing gradient-based attacks to fail within practical iteration budgets. We further show that combining RL with adversarial training (RL-adv) provides a dual-layer defense operating at two complementary levels: RL degrades gradient information available to attackers (gradient-level defense), while adversarial training strengthens decision boundaries (boundary-level defense). RL-adv achieves the highest robustness across all major attack types evaluated, including gradient-based (PGD, AutoAttack), transfer-based, and query-based attacks, outperforming SL-adv by a significant margin. These findings identify RL-induced gradient disruption as a complementary robustness mechanism and motivate future research on hybrid SL-RL training schedules that combine SL's efficiency with RL's gradient-regularization properties.

19.
Nature (Science) 2026-06-17

The ancestors of eukaryotic cells contained a mix of genes from various microbes

Authors: Unknown Author

Reconstruction of the ancestral gene repertoire of eukaryotic cells reveals traces of a series of close, long-term interactions with diverse microorganisms, and a role of viruses in gene exchange. The findings challenge the view that eukaryotic cells evolved from a simple merger of just two organisms. A series of gene-transfer events might have taken place in complex microbial communities.

20.
Nature Medicine 2026-06-11

Microglia at a key inflection point in Alzheimer’s disease

Authors: Unknown Author

We analyzed brains from octogenarians and cognitively resilient centenarians to understand why some individuals with substantial Alzheimer’s disease pathology develop dementia whereas others remain cognitively intact. Spatial transcriptomics revealed gene expression changes in discrete tissue domains surrounding amyloid plaques and tau pathology that distinguish early, clinically silent, disease from later stages associated with cognitive decline.

21.
bioRxiv (Bioinfo) 2026-06-12

Deciphering cross-omics complexity of tissues via diagonal integration of unpaired spatial multi-omics data

Recent spatial multi-omics technologies enable the simultaneous in situ profiling of multiple omics modalities on the same tissue section; however, they face challenges in experimental complexity and high costs. This technical limitation can be circumvented by diagonal integration methods, which integrate omics data from different modalities. However, existing single-cell diagonal integration approaches overlook spatial information, causing unreliable anchoring across omics layers. Here, we introduce STAMO, a graph attention neural network model for spatially aware integration of unpaired spatial slices from different omics. Systematic benchmarking on spatial epigenome-transcriptome slices proves that STAMO outperforms the state-of-the-art methods in generating aligned embeddings and identifying consensus spatial domains across omics. We apply STAMO to integrate unpaired data from diverse spatial omics types (transcripts, epigenetics, DNA, and proteins), including slices from spatial RNA and four different epigenomic modalities, spatial ATAC and RNA slices across embryonic stages, spatial protein and RNA slices, and spatial DNA and RNA slices. In addition, the integration capability of STAMO can be further used to achieve cross-omics generation, offering a solution for exploring spatial region-specific gene regulatory mechanisms.

22.
arXiv (quant-ph) 2026-06-11

Probing Quantum States over Spacetime Through Interferometry

arXiv:2507.19258v3 Announce Type: replace Abstract: Establishing a notion of the quantum state that applies consistently across space and time could be a crucial step toward formulating a relativistic quantum theory. We give an operational meaning to multipartite quantum states over arbitrary regions in spacetime through a causally agnostic measurement, a measurement scheme that can be consistently implemented independently of the causal relation between the regions. We prove that such measurements can always be implemented with interferometry, also known as the scattering circuit technique, wherein the conventional density operator, the recently developed quantum state over time (QSOT), and the process matrix formalisms smoothly merge. This framework allows for a systematic study of mixed states in the temporal setting, which turn out to be crucial for modeling quantum non-Markovianity. Based on this, we demonstrate that two different ensembles of quantum dynamics can be represented by the same QSOT, indicating that they cannot be distinguished through interferometry. Moreover, our formalism reveals a new type of spatiotemporal correlation between two quantum dynamics that originates from synchronized propagation in time under time-reversal symmetry. We show that quantum systems with such correlation can be utilized as a reference frame to distinguish certain dynamics indistinguishable under time-reversal symmetry.

23.
bioRxiv (Bioinfo) 2026-06-22

Reference-guided immune recovery matching prioritizes traditional Chinese medicine ingredients

Therapeutic prioritization from single-cell transcriptomes requires a target that is closer to treatment response than disease-signature reversal. In immune diseases, post-treatment recovery may follow patient- and cell-type-specific trajectories rather than a simple return along the pretreatment disease axis. We developed ImmuneNavi, a healthy-reference-anchored recovery-matching workflow for ranking traditional Chinese medicine ingredients from paired PBMC data. The workflow maps heterogeneous PBMC cohorts to a common healthy immune coordinate system, constructs patient-cell-type disease and recovery states, and processes ITCM treated-control profiles into a fixed ingredient perturbation bank. Patient and ingredient states are represented in matched gene, pathway and transcription-factor views, allowing the model to combine local transcriptional direction with more stable program-level features. A matcher trained on one paired treatment cohort preserved recovery-aligned ingredient rankings in independent PBMC cohorts without redefining the feature space, candidate set or preprocessing procedure. This provides a reusable transcriptomic pipeline for moving from paired immune-state measurements to prioritized natural-product candidates for experimental follow-up.

24.
arXiv (CS.CV) 2026-06-16

Kairos: A Native World Model Stack for Physical AI

World models are transitioning from passive visual generators to foundational, operational infrastructure for Physical AI: they must natively acquire world knowledge from heterogeneous experience, maintain persistent states over long horizons, and execute efficiently within real deployment constraints. We introduce Kairos, a native world model stack designed around these requirements. (1) Kairos learns the world by pioneering a Native Pre-training Paradigm governed by a Cross-Embodiment Data Curriculum, which organizes open-world videos, human behavioral data, and robot interactions into a progressive developmental pathway. (2) Kairos maintains the world by unified world understanding, generation, and prediction within a Native Unified Architecture equipped with Hybrid Linear Temporal Attention, where sliding-window attention captures local dynamics, dilated sliding windows capture mid-range dependencies, and gated linear attention maintains persistent global memory. We establish formal theoretical bounds demonstrating that this temporal factorization strictly limits error accumulation, mathematically guaranteeing state propagation across extended horizons. (3) Kairos runs the world by incorporating a Deployment-Aware System Co-Design to support low-latency rollout generation on server and consumer-grade hardware for real-world observation-action-feedback loops. Experiments on embodied world-model, long-horizon, and action-policy benchmarks show that Kairos achieves top level performance while offering a strong efficiency-capability trade-off. Together, these results position Kairos as a cohesive operational foundation for future self-evolving physical intelligence.

25.
arXiv (CS.CL) 2026-06-19

EndoCoT: Scaling Endogenous Chain-of-Thought Reasoning in Diffusion Models

Recently, Multimodal Large Language Models (MLLMs) have been widely integrated into diffusion frameworks primarily as text encoders to tackle complex tasks such as spatial reasoning. However, this paradigm suffers from two critical limitations: (i) MLLMs text encoder exhibits insufficient reasoning depth. Single-step encoding fails to activate the Chain-of-Thought process, which is essential for MLLMs to provide accurate guidance for complex tasks. (ii) The guidance remains invariant during the decoding process. Invariant guidance during decoding prevents DiT from progressively decomposing complex instructions into actionable denoising steps, even with correct MLLM encodings. To this end, we propose Endogenous Chain-of-Thought (EndoCoT), a novel framework that first activates MLLMs' reasoning potential by iteratively refining latent thought states through an iterative thought guidance module, and then bridges these states to the DiT's denoising process. Second, a terminal thought grounding module is applied to ensure the reasoning trajectory remains grounded in textual supervision by aligning the final state with ground-truth answers. With these two components, the MLLM text encoder delivers meticulously reasoned guidance, enabling the DiT to execute it progressively and ultimately solve complex tasks in a step-by-step manner. Extensive evaluations across diverse benchmarks (e.g., Maze, TSP, VSP, and Sudoku) achieve an average accuracy of 92.1%, outperforming the strongest baseline by 8.3 percentage points. The code and dataset are publicly available at https://internlm.github.io/EndoCoT/.