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01.
arXiv (CS.AI) 2026-06-11

Graph2Idea:Retrieval-Augmented Scientific Idea Generation with Graph-Structured Contexts

arXiv:2606.09105v3 Announce Type: replace Abstract: Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific discovery. Recent Large Language Model (LLM)-based methods often ground idea generation with retrieved literature, but the retrieved evidence is usually provided as flat text, such as titles, abstracts, or summaries. Such flat contexts may contain redundant or weakly relevant information, while making cross-paper relations among problems, methods, mechanisms, and findings difficult to identify and trace. To address this challenge, we propose Graph2Idea, a knowledge graph-guided framework for retrieval-augmented scientific idea generation.Graph2Idea first retrieves papers according to the input topic, transforms them into structured knowledge triples, and dynamically constructs a target-centered knowledge graph to make literature relations explicit. It then extracts compact graph-derived contexts that retain target-relevant relational evidence while reducing noisy textual input. Based on these contexts, a two-stage generation process first identifies promising research directions and then guides the LLM to synthesize candidate ideas from graph-grounded evidence. Experiments on a scientific idea generation benchmark show that Graph2Idea outperforms representative baselines under the automatic evaluation protocol. Compared with the strongest baseline scores, it improves Novelty from 0.45 to 0.52, Quality from 0.24 to 0.29, and Feasibility from 0.22 to 0.28. These results suggest that graph-structured evidence helps LLMs generate research ideas through more explicit, compact, and traceable recombination of prior scientific knowledge.

02.
arXiv (CS.CV) 2026-06-17

MM++: Unsupervised Scale-Invariant Multilayer OOD Detection via Top-K Gated Feature Fusion

We introduce MM++ (Multilayer Mahalanobis++), a fully unsupervised, strictly post-hoc, and scale-invariant framework for Out-of-Distribution (OOD) detection. To address the trade-off between scale invariance and hierarchical expressivity, MM++ constructs a principled joint feature space. It first identifies discriminative intermediate layers by measuring entropy density drops, which mark the boundaries of sharp semantic compression. By fusing these selected layers with the terminal representation, the framework captures latent cross-layer correlations while mitigating early-layer noise. Crucially, a Ledoit-Wolf regularized tied covariance matrix stabilizes this unified space, enabling reliable distance estimation. Requiring no auxiliary OOD data, classifier fine-tuning, or architectural modifications, MM++ delivers robust performance across distinct architectures for both near- and far-OOD detection.

03.
arXiv (CS.CV) 2026-06-16

MMLongEmbed: Benchmarking Multimodal Embedding Models in Long-Context Scenarios

Recent advancements have significantly expanded the theoretical context windows of Multimodal Embedding Models (MEMs). However, larger context windows do not necessarily translate into effective comprehension and representation of long-context multimodal inputs, which remains a critical bottleneck for real-world deployment. To address the lack of systematic evaluation in this setting, we introduce MMLongEmbed, the first comprehensive benchmark for evaluating MEMs in long-context scenarios. MMLongEmbed comprises four retrieval tasks spanning multiple context-length ranges, covering text, document, and video modalities. Through extensive evaluation of state-of-the-art models, we find that current architectures rely heavily on superficial feature matching and struggle to capture deep semantic and structural dependencies. We further observe that performance degradation varies systematically with context length and key information placement. Moreover, models exhibit substantially different robustness to redundant contextual information across modalities. For reproducibility, the benchmark and code are publicly available.

04.
arXiv (CS.CV) 2026-06-16

Efficient Reinforcement for Visual-Textual Thinking with Discrete Diffusion Model

RL-based post-training has been widely adopted to enable interleaved visual and textual reasoning in unified multimodal models capable of both text and image generation. However, most existing approaches are built upon autoregressive (AR) unified models, which require full image regeneration during visual reasoning. In this work, we demonstrate that multimodal discrete diffusion models are effective alternatives to AR models for reinforcement learning in interleaved reasoning, owing to their ability to perform efficient visual rollouts via localized visual editing rather than full image-token regeneration. This reduces rollout computation during GRPO by 26.9\% compared to AR baselines, with minimal performance drop. Despite the improved efficiency, we find that joint reward assignment, which employs a shared reward signal across modalities, introduces cross-modal interference between unrelated image and text token sequences during RL updates. To address this issue, we propose factorized reward assignment, a strategy that assigns rewards independently to text and vision segments. With factorized reward assignment, our RL approach achieves an 11.2% improvement over joint reward assignment and a 38.04% improvement over the base model.

05.
arXiv (CS.AI) 2026-06-11

MODF-SIR: A Multi-agent Omni-modal Distilled Framework for Social Intelligence Reasoning

arXiv:2606.12018v1 Announce Type: new Abstract: We propose a multi-agent collaborative framework built upon a lightweight Multimodal Large Language Model (MLLM), specifically designed for social intelligence reasoning. A key feature of our approach is that both the training and inference phases are augmented via knowledge distillation. Within this architecture, multi-modal data pertinent to social intelligence is precisely localized. Furthermore, relevant long-tail events are identified, extracted, and rendered as formatted, explicit text. This formatting strategy prevents critical long-tail information from being overshadowed by head events and environmental noise during the tokenization process. Specifically, we integrate Test-Time Adaptation (TTA) across the entire reasoning pipeline, encompassing the extraction and representation of long-tail events, Chain-of-Thought (CoT) prompting, and self-reflection. This TTA mechanism is also distillation-enhanced, utilizing Low-Rank Adaptation (LoRA) to fine-tune the foundation model exclusively for instance-level reasoning. Extensive evaluations against various open-source and proprietary AI models across multiple benchmarks demonstrate the effectiveness of the proposed framework. With around 30% of training data from IntentTrain, we achieve state-of-the-art results. Codes are available at https://github.com/eeee-sys/MODF-SIR, demo is available at https://huggingface.co/spaces/Harry-1234/MODF-SIR, LoRA is available at https://huggingface.co/Harry-1234/MODF-SIR and the dataset for training router is available at https://huggingface.co/datasets/Harry-1234/IntentRouterTrain.

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

GOOSE-M2F: Adapting Mask2Former for High-Fidelity, Long-Tailed Fine-Grained Semantic Segmentation in Unstructured Outdoor Terrain

We present GOOSE-M2F, a task-specific adaptation of Mask2Former for the GOOSE 2D Fine-Grained Semantic Segmentation (FGSS) Challenge at ICRA~2026. The GOOSE benchmark spans 64 fine-grained classes across unstructured outdoor terrain with a severely long-tailed distribution, where rare classes occupy fewer than 50 pixels per image. We extend the Swin-Large Mask2Former baseline with three targeted contributions: (1)200 Object Queries to eliminate representational saturation; (2)a Feature Refinement Module (FRM) combining ASPP-lite and CBAM dual-attention; and (3)an Auxiliary Supervision Head that delivers direct per-pixel gradients for rare classes. A multi-stage training strategy pairs Distribution-Balanced loss, Rare-Class Copy-Paste augmentation, dynamic IoU-aware re-weighting, and EMA. At inference, a dense sliding-window engine with 2D Gaussian kernel blending and 4-scale TTA adds +10.57\%. GOOSE-M2F achieves 70.08\% Official Composite mIoU (63.55\% fine, 76.61\% coarse), placing 3rd on the GOOSE 2D FGSS leaderboard. Code and trained models are publicly available at: \href{https://github.com/Aditya-Lingam-9000/GOOSE-M2F}{Github GOOSE-M2F Code} and \href{https://huggingface.co/XYZ9843/GOOSE-M2F}{Hugging Face GOOSE-M2F}.

07.
arXiv (quant-ph) 2026-06-17

Coherent Control of an Embedded Bound State Without a Spectral Gap

Authors:

arXiv:2606.17685v1 Announce Type: new Abstract: Bound states in the continuum (BICs) can confine photonic excitations in open systems without conventional cavities or band gaps, making them natural candidates for long-lived quantum storage and single-photon control. Their use is limited, however, by two obstacles: they are dark to incident photons, and they lack spectral-gap protection from the surrounding continuum. We overcome both limitations in a giant atom coupled to a one-dimensional waveguide using two temporal control knobs. Atomic-frequency modulation breaks and restores the destructive-interference condition, enabling deterministic capture and release of mode-matched single photons. Coupling modulation instead preserves the BIC condition while tuning the atomic and photonic weights of the stored state. A key result is that this embedded state can nevertheless be controlled adiabatically despite the absence of a spectral gap, with an intrinsic leakage probability linear in the ramp rate. By separating radiative access from BIC-preserving deformation, the protocol turns a dark BIC into a single-photon memory whose fidelity is set by the intrinsic continuum-induced leakage law, providing a route to embedded-state control in open photonic platforms.

08.
arXiv (CS.AI) 2026-06-15

Quantized Evolution Strategies: High-precision Fine-tuning of Quantized LLMs at Low-precision Cost

arXiv:2602.03120v2 Announce Type: replace-cross Abstract: Post-Training Quantization (PTQ) is essential for deploying Large Language Models (LLMs) on memory-constrained devices, yet it renders models static and difficult to fine-tune. Standard fine-tuning paradigms, including Reinforcement Learning (RL), fundamentally rely on backpropagation and continuous weights to compute gradients. Thus they cannot be used on quantized models, where the parameter space is discrete and non-differentiable. While Evolution Strategies (ES) offer a backpropagation-free alternative, optimization of the quantized parameters can still fail due to vanishing or inaccurate gradient estimation. This paper introduces Quantized Evolution Strategies (QES), an optimization paradigm that performs full-parameter fine-tuning directly in the quantized space. QES is based on two innovations: (1) it integrates accumulated error feedback to preserve high-precision weight updating signals, and (2) it utilizes a stateless seed replay to reduce memory usage to low-precision inference levels. QES significantly outperforms the state-of-the-art zeroth-order fine-tuning methods on a variety of tasks, making direct fine-tuning for quantized models possible. It therefore opens up the possibility for scaling up LLMs entirely in the quantized space. The source code is available at https://github.com/dibbla/Quantized-Evolution-Strategies .

09.
arXiv (quant-ph) 2026-06-16

Weak continuous measurements require more work than strong ones

arXiv:2502.09732v4 Announce Type: replace Abstract: Understanding the energy cost of quantum measurement process and its connection to the measurement performance faces the challenge of modeling the objectification process. The latter, turns the measurement result into an objective fact, available to independent observers, and is responsible for the measurement irreversibility. To address this issue, we propose and analyze a dynamical model of quantum measurement, able to capture nonideal (weak and inefficient) measurements. In this model, the objectification is induced by a contact with a macroscopic reservoir at equilibrium which is responsible for the redundant broadcast of the measurement outcome (producing a Spectrum Broadcast Structure (SBS) state) while inducing decoherence in the pointer basis, in the line of the theory of quantum Darwinism. We analyze the performance of the obtained measurement process by introducing figures of merit to quantify the strength of the measurement and its efficiency. We also derive and a lower bound on the measurement work cost that we can relate to the measurement quality. We take as an illustration the readout of a qubit via its coupling to a harmonic oscillator. We investigate the long sequences of extremely short and weak measurements (a.k.a continuous measurements), to find under which conditions they converge to an ideal (projective) measurement and analyze their work cost. Surprisingly, we find that a sequence converging to projective measurement has a much larger work cost than an equivalent strong measurement obtained from a single intense interaction with the apparatus. We extend this result to a large class of models owing to scaling arguments. Our analysis offers new insights into the trade-offs between measurement strength, energy consumption, and information extraction in quantum measurement protocols.

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

How Linear Is a Transformer Feed-Forward Block? Per-Block Linear Recoverability Is Learned, Not Architectural

Authors:

Transformer feed-forward networks (FFNs) are often treated as nonlinear stores of computation, yet how nonlinear a trained FFN block actually is has rarely been measured. We treat each FFN as a position-wise input-to-output map and split it into the exact least-squares linear approximation plus a residual. The held-out variance the closed-form linear map explains defines a block's linear recoverability (R^2_lin), an optimiser-free measure of its linearity. Across all twelve blocks of GPT-2, Pythia-160m, and llama-160m, R^2_lin is highly heterogeneous and non-monotone with depth, ranging from near-linear (>0.99) to strongly nonlinear (

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

Co-PLNet: A Collaborative Point-Line Network for Prompt-Guided Wireframe Parsing

Wireframe parsing aims to recover line segments and their junctions to form a structured geometric representation useful for downstream tasks such as Simultaneous Localization and Mapping (SLAM). Existing methods predict lines and junctions separately and reconcile them post-hoc, causing mismatches and reduced robustness. We present Co-PLNet, a point-line collaborative framework that exchanges spatial cues between the two tasks, where early detections are converted into spatial prompts via a Point-Line Prompt Encoder (PLP-Encoder), which encodes geometric attributes into compact and spatially aligned maps. A Cross-Guidance Line Decoder (CGL-Decoder) then refines predictions with sparse attention conditioned on complementary prompts, enforcing point-line consistency and efficiency. Experiments on Wireframe and YorkUrban show consistent improvements in accuracy and robustness, together with favorable real-time efficiency, demonstrating our effectiveness for structured geometry perception. Our code is available at https://github.com/GalacticHogrider/Co-PLNet.

12.
arXiv (math.PR) 2026-06-16

The distribution of the de Moivre experiment

arXiv:2606.15178v1 Announce Type: new Abstract: In this paper, we focus on de Moivre random experience which allows us to introduce the $ s- $Bernoulli distribution and the bi$ ^s $nomial distribution. We present some probabilistic properties such as the expectation, the variance, the skewness and kurtosis coefficients, the moments and the generating functions. Then we establish that for $ s\in\mathbb{N} $, the bi$ ^s $nomial distribution converges to a limiting Poisson and normal distributions when $ n\rightarrow\infty. $

13.
arXiv (CS.CL) 2026-06-15

Reward-SQL: Boosting Text-to-SQL via Stepwise Execution-Aware Reasoning and Process-Supervised Rewards

Recent advances in large language models (LLMs) trained with reinforcement learning (RL) have improved Text-to-SQL performance. However, RL-based approaches still struggle with complex queries due to two key limitations: insufficient stepwise execution-aware reasoning grounded in database feedback, and the lack of process-level rewards for guiding reasoning optimization. To address these issues, we propose CoCTE, a divide-and-conquer and execution-aware reasoning framework that progressively composes SQL queries through intermediate view validation and structured Common Table Expressions (CTEs), improving both accuracy and interpretability. To realize a CoCTE reasoning process, we develop Reward-SQL, a unified approach with three stages: (1) model initialization, which equips LLMs with structured CoCTE reasoning capabilities; (2) process reward design, which delivers fine-grained, execution-aware supervision; and (3) process-supervised RL and inference, which integrates process rewards into training and guides the inference stage by process rewards. This paper addresses the core challenges in Reward-SQL and makes the following contributions. We introduce a process reward model (PRM) that combines execution-aware trajectory scoring with entropy-based step weighting, providing dense and interpretable supervision across reasoning steps. We integrate PRM into both RL training and inference stages, stabilizing optimization and improving trajectory exploration with process-level signals. Experiments show that Reward-SQL significantly outperforms baselines with comparable model sizes, and exhibits strong cross-domain generalization.

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

Reconfigurable Computing Challenge: Transformer for Jet Tagging on Versal AI Engines

arXiv:2606.17500v1 Announce Type: new Abstract: Transformer-based models achieve strong performance for jet tagging at the CERN LHC, but deploying them in low-latency, resource-constrained trigger systems is challenging. We present an initial implementation of a quantized, integer-only transformer for jet tagging on the AMD Versal AI Engine (AIE), mapping dense and multi-head attention (MHA) layers to AIE tiles. The main contribution is a reusable software framework that represents transformer layers as composable AIE building blocks and automatically generates the corresponding Vitis graph code from a high-level Python model description. This framework provides a foundation for future research and is released as open-source software at https://github.com/KastnerRG/particle_transformer_aie.

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

EM-NeSy: Expectation Maximization for Neurosymbolic Learning

arXiv:2606.14463v1 Announce Type: new Abstract: Neurosymbolic (NeSy) models integrate neural networks and symbolic reasoning for robust and interpretable AI. State-of-the-art NeSy models require that the symbolic component is expressed in a differentiable way, often complicating the use of approximate inference. We propose EM-NeSy which casts probabilistic NeSy learning as an instance of the Expectation-Maximization (EM) algorithm. In the expectation step, we compute the posterior over the neurally predicted symbols conditioned on the label via probabilistic inference. In the maximization step, we update the neural parameters based on this posterior using gradient descent only through the neural component. This formulation unlocks the full potential of the EM algorithm for NeSy learning. It allows NeSy to extend naturally to approximate reasoning without any additional modifications or differentiability requirements of the symbolic component. Furthermore, it recovers the standard end-to-end gradient-based NeSy setting under exact inference. Our experimental results demonstrate the scalability and computational efficiency of EM-NeSy.

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

MVAD: A Benchmark Dataset for Multimodal AI-Generated Video-Audio Detection

The rapid advancement of AI-generated multimodal video-audio content has raised significant concerns regarding information security and content authenticity. Existing synthetic video datasets predominantly focus on the visual modality alone, while the few incorporating audio are largely confined to facial deepfakes–a limitation that fails to address the expanding landscape of general multimodal AI-generated content and substantially impedes the development of trustworthy detection systems. To bridge this critical gap, we introduce the Multimodal Video-Audio Dataset (MVAD), the first comprehensive dataset specifically designed for detecting AI-generated multimodal video-audio content. Our dataset exhibits three key characteristics: (1) genuine multimodality with samples generated according to three realistic video-audio forgery patterns; (2) high perceptual quality achieved through diverse state-of-the-art generative models; and (3) comprehensive diversity spanning realistic and anime visual styles, four content categories (humans, animals, objects, and scenes), and four video-audio multimodal data types. Our dataset will be available at https://github.com/HuMengXue0104/MVAD.

17.
arXiv (CS.LG) 2026-06-19

Low-Energy Reduced RISC-V Instruction Subset Processor for Tsetlin Machine Inference at the Edge

arXiv:2606.19964v1 Announce Type: new Abstract: Tsetlin Machine (TM) is a logic-based machine learning approach that relies on simple bitwise operations and finite-state automata, which makes it attractive for edge AI deployments. Recent work has focused on co-processor and accelerator designs based on Tsetlin Machines (TMs). Although these designs achieve high performance, they typically depend on tightly coupled interfaces, microcode-style programming, and external host processors, limiting flexibility and ease of programming. In this work, we present a domain-specific RISC-V microprocessor architecture and design flow tailored for TM inference. Leveraging the modular structure of RISC-V, we design a reduced instruction subset processor that retains programmability while targeting improved performance and lower energy consumption for TM workloads. Instruction profiling is employed to guide instruction reduction, followed by datapath and control path simplifications tailored to TM inference. Both the baseline RV32IM core and the proposed reduced core are evaluated across multiple datasets and compared with Binarized Neural Networks (BNNs), which serve as a hardware-efficient baseline due to their reliance on bitwise operations during inference. Results show that TM achieves comparable or higher accuracy (e.g., up to 88.18% on CIFAR-2 compared to 60.0% for BNN) while reducing execution time by up to 98% across multiple datasets. Furthermore, the proposed design achieves an average $29.7\times$ reduction in energy consumption, demonstrating its effectiveness for programmable and efficient edge AI systems.

18.
arXiv (math.PR) 2026-06-16

The existence of invariant sublinear expectations for $G$-SDEs

arXiv:2606.15203v1 Announce Type: new Abstract: In this paper, we study the existence of invariant sublinear expectations of Markovian semigroups on sublinear expectation spaces. To achieve this, we establish a complete metric space of sublinear expectations, on which we extend Harris' method to the nonlinear setting on the convergence of sublinear semigroups. We then explore two cases of $G-$diffusions by studying the Lyapunov function and the local Doeblin condition. One is the $G-$Brownian motion on the unit circle which is the case studied in Feng and Zhao [Zhaonon], but with the new method. Another is the multidimensional $G-$SDEs on the whole space $\mathbb{R}^d$. We establish, for the first time in the literature, the existence of the invariant sublinear expectation for $G-$SDEs under the non-degenerate and weakly dissipative assumption. For this, we prove that for a class of $G-$SDEs, the $G-$expectation can be represented as the supremum of the semigroup of a family of SDEs, of which the regularity is obtained by considering the Bismut-Elworthy-Li formula and the Denis-Hu-Peng representation for the distribution of $G-$Brownian motions.

19.
arXiv (quant-ph) 2026-06-15

Dynamically frozen long-distance entanglement via non-Hermitian PT-symmetric systems

arXiv:2606.14177v1 Announce Type: new Abstract: In distributed quantum networks, interacting spin systems can mediate the generation of highly entangled links between distant nodes. We investigate the role of effective parity-time (PT)-symmetric non-Hermitian spin-1/2 bulks weakly coupled to two quantum links, obtained due to the environmental interactions affecting both the bulk and the links. Focusing on effective non-Hermitian nearest-neighbor (NN) Su-Schrieffer-Heeger (SSH) models, we analyze how non-Hermiticity influences the dynamical formation of long-distance entanglement (LDE). For a paradigmatic model consisting of a quantum XX bulk subjected to imaginary staggered magnetic fields, we analytically determine the exceptional points arising from the resulting bulk-mediated interactions between the links. Combining analytical and numerical methods, we demonstrate that an initially fully separable state can dynamically evolve into highly entangled link states near these exceptional points in the broken regime. Further, after optimizing over time and system parameters, near-unit time-averaged entanglement between the links emerges under weak imaginary magnetic fields and bulk-link couplings, which cannot be attained in the corresponding Hermitian systems. Moreover, the non-Hermitian dynamics exhibit a freezing of high entanglement in the vicinity of exceptional points, a feature absent in Hermitian counterparts. We also identify regimes of long-range interaction strengths that yield a higher time-averaged entanglement than the corresponding NN models. Furthermore, we establish that LDE persists in the stationary regime, highlighting the promise of engineered non-Hermitian dynamics for realizing robust and frozen entangled links in quantum networks.

20.
arXiv (CS.AI) 2026-06-18

Mechanism-Guided Selective Unlearning for RLVR-Induced Reasoning

arXiv:2606.19222v1 Announce Type: cross Abstract: We propose MAST (Mechanism-Aligned Selective Targeting), a mechanism-guided method for unlearning RLVR-induced reasoning with substantially lower collateral damage than standard full-parameter updates. In matched SFT/RLVR checkpoints on Qwen2.5-Math-1.5B and Qwen3-1.7B-Base, the SFT-to-RLVR increment differs sharply from the SFT update in token-level delta-log-probability, and full-parameter gradient ascent forgets only by damaging retain MATH and GSM8K. MAST ranks attention-projection tensors by off-principal energy, update magnitude, and forget-gradient coupling magnitude, then updates only the top-ranked subset. On the primary model, MAST induces statistically significant target forgetting (MATH forget 45/150 to 37/150; McNemar p=0.0078) while preserving GSM8K (+0.8 pp) and MATH retain (-0.5 pp). The advantage reproduces across seeds, NPO/SimNPO objectives, and Qwen3, where MAST preserves GSM8K while full-parameter unlearning collapses it.

21.
arXiv (CS.CL) 2026-06-12

Why Sampling Is Not Choosing: Intentionality, Agency, and Moral Responsibility in Large Language Models

Authors:

Recent advances in large language models (LLMs) have prompted claims that such systems exhibit agency or qualify as moral agents. This paper argues that these attributions are misguided. We maintain that moral responsibility requires commitment-bearing agency grounded in intrinsic intentionality and self-attributed action, and that such agency constitutes the form of free will relevant to responsibility. Although LLMs generate coherent and normatively evaluable outputs, their operation is fully characterized by probabilistic input-output mappings learned from data. Their apparent intentionality is derived rather than intrinsic, and their outputs are neither owned as commitments nor guided by reasons. Variability introduced by stochastic sampling does not amount to choice or authorship. We address objections from the intentional stance, functionalism, compatibilism, and the presence of moral reasoning in model outputs, arguing that none suffice to establish genuine agency.

22.
arXiv (CS.LG) 2026-06-11

Persistent Homology as a Theory of Emergent Structure

Authors:

arXiv:2507.03065v2 Announce Type: replace Abstract: Why do some macroscopic structures remain identifiable even though their microscopic constituents continually change? Vortices persist while fluid parcels turn over, neural memories persist while spikes and synapses fluctuate, and institutions persist while individuals enter and leave. We propose a scale-relative answer: an emergent property is a persistent nontrivial homology class $[z]\in H_p=\ker\partial_p/\im\partial_{p+1}$, a macro-feature that is closed but not exact across a filtration of descriptions. This identification turns emergence into a measurement problem. Persistent bars detect stable macro-features, and we introduce a contractive-similarity (CS) graph operator to supply scaffold spectral gaps that predict robustness. Hodge decomposition separates harmonic macro-scaffold from exact and co-exact micro-flow; and functorial condensation explains when one level's emergent class becomes a unit for the next. The resulting scaffold-flow framework expresses six familiar signatures of emergence (i.e., inevitability, coherence, irreducibility, complementarity, robustness, and hierarchy) within one mathematical language. It also yields falsifiable predictions across atmospheric, neural, and social systems: genuine emergent structures should persist across filtrations, remain spectrally stable, respond disproportionately to harmonic interventions, and require timescale separation for hierarchical autonomy.

23.
arXiv (CS.AI) 2026-06-15

A Fixed-Point Neural Operator for Size- and Functional-Transferable Hamiltonian Prediction

arXiv:2606.14498v1 Announce Type: cross Abstract: Predicting the Kohn-Sham Hamiltonian with machine learning can accelerate density functional theory while retaining access to molecular orbitals, energy levels, and electronic-structure observables that energy-only surrogates cannot resolve. Yet element-wise agreement with the converged Hamiltonian, an implicit fixed point of the self-consistent field iteration, does not determine the occupied subspace that governs orbital energies and densities. Here we present HamEvo, a neural operator that learns the single-step self-consistent update and returns the converged Hamiltonian as its fixed point. HamEvo is pre-trained on intermediate self-consistent trajectories and calibrated at equilibrium with density-matrix supervision. Across benchmarks from MD17 to drug-like QMugs, HamEvo lowers Hamiltonian errors by 35-49% over direct-regression and deep-equilibrium baselines, and predicts QMugs HOMO and LUMO energies with mean absolute errors of 0.036 and 0.053 eV, near the 1 kcal/mol chemical-accuracy scale. Few-shot fine-tuning with only 20 reference conformations extends HamEvo to molecules of up to 122 atoms, well beyond the size range covered by pre-training. With thermal molecular-dynamics sampling, HamEvo captures temperature-dependent HOMO-LUMO gap renormalization beyond the harmonic approximation. Inference is up to 242 times faster than conventional DFT.

24.
bioRxiv (Bioinfo) 2026-06-11

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individual cells, offering new opportunities to characterize cellular states as integrated biological systems. However, developing a unified framework that can seamlessly integrate diverse omics modalities and remain robust to heterogeneous modality missingness remains challenging. Here we present HoloCell, to our knowledge the first generative foundation model for joint representation learning and generative modeling across all three major single-cell omics modalities, i.e., epigenomics, transcriptomics, and proteomics. HoloCell contains over 860 million parameters and is pretrained on the Human-Multi-Omics-Corpus, which comprises approximately 468 million single-cell profiles across these three omics layers, corresponding to over 425 billion tokens. HoloCell introduces a simple yet biologically grounded hierarchical tokenization strategy that encodes cis-regulatory elements, genes, and proteins as structured tokens within a shared modeling framework. We evaluated HoloCell across single-omics representation learning, paired multi-omics integration, unpaired multi-omics alignment, and cross-modal generation via iterative diffusion and remasking, demonstrating its superior performance and flexibility across diverse omics tasks. From a representation perspective, HoloCell provides a unified digital mapping of cellular states across multiple omics layers, capturing cell heterogeneity as an integrated system. From a generation perspective, its iterative diffusion and remasking framework accounts for the inherently unordered nature of biological features, enabling in silico simulation of multi-omics information flow. Together, these capabilities position HoloCell as a versatile foundation model toward the emerging concept of a virtual cell, offering both systematic characterization and generative simulation of cellular systems within a unified framework.

25.
arXiv (CS.AI) 2026-06-18

IPSL-AID: Generative Diffusion Models for Climate Downscaling from Global to Regional Scales

arXiv:2604.03275v2 Announce Type: replace-cross Abstract: Effective adaptation and mitigation strategies for climate change require high-resolution projections to inform strategic decision-making. Conventional global climate models, which typically operate at resolutions of 150 to 200 kilometers, lack the capacity to represent essential regional processes. IPSL-AID is a global to regional downscaling tool based on a denoising diffusion probabilistic model designed to address this limitation. Trained on ERA5 reanalysis data, it generates 0.25 degree resolution fields for temperature, wind, and precipitation using coarse inputs and their spatiotemporal context. It also models probability distributions of fine-scale features to produce plausible scenarios for uncertainty quantification. The model accurately reconstructs statistical distributions, including extreme events, power spectra, and spatial structures. This work highlights the potential of generative diffusion models for efficient climate downscaling with uncertainty