Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
arXiv (quant-ph) 2026-06-12

A refined thermodynamic analysis of nonsecular master equations

arXiv:2606.13504v1 Announce Type: new Abstract: We present a systematic thermodynamic analysis of nonsecular master equations. We consider master equations resulting either from the partial secular and the geometric-arithmetic approximations, two approximations ensuring the positivity of the system's dynamics when some of its transition frequencies are too small to enable the full secular approximation. Both cause the system to relax towards a steady state which is not the Gibbs state of its bare Hamiltonian. Nonetheless, we build a unified, consistent thermodynamic framework for those dynamics. Starting from a microscopic expression of the second law based on system-environment correlations, we employ a systematic perturbation theory to preserve the positivity of the second law despite the approximations done on the dynamics. We show that, in spite of the weak system-bath coupling, the system-bath interaction energy participates to the energy balance, as well as the Lamb-shift. Those extra contributions give rise to work performed by the system on the bath when the former is out of equilibrium. We compare this microscopic entropy production with the definition based on the contractivity of the reduced system dynamics (Spohn inequality). We show that, unlike for secular master equations, the two entropy production rates differ because of the presence of non-vanishing stationary coherences in the energy eigenbasis. However, in the case of a single thermal bath, the difference is purely transient, and no work can be cyclically extracted from the steady-state despite its non-Gibbs form. Finally, we illustrate our results with a simple example, clarifying and completing the thermodynamic picture of Markovian dynamics in the quantum regime.

02.
PLOS Computational Biology 2026-06-04

Cell differentiation can underpin the reproducibility of morphogenesis

by Dominic K. Devlin, Austen R. D. Ganley, Nobuto Takeuchi Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we ask how this reproducibility is achieved by evolving complex morphologies in a multi-scale, computational model. Each morphology consists of a population of cells on a two-dimensional grid using the Cellular Potts Model framework. Each cell contains a genome that encodes a gene regulatory network, morphogens for cell-cell signalling, and proteins that determine cell behaviours. By repeatedly simulating our model with different initial conditions under selection for shape complexity, we obtained a “zoo” of evolved morphologies. We find that these evolved, complex morphologies are reproducible in a sizeable fraction of simulations, despite no direct selection for reproducibility. We show that high reproducibility is caused by spatially segregating moving cells that “shape” morphologies from stationary cells that “maintain” morphologies during morphogenesis. Strikingly, most highly reproducible morphologies also evolved cell differentiation, where proliferative, moving progenitor cells irreversibly differentiate into non-dividing, stationary differentiated cells at tissue boundaries. These results suggest that cell differentiation observed in natural development plays a fundamental role in morphogenesis in addition to the production of specialised cell types. This previously unrecognised role of cell differentiation has major implications for our understanding of how morphologies are generated and regenerated.

03.
arXiv (CS.AI) 2026-06-15

LLM-Powered AI Agent Systems and Their Applications in Industry

arXiv:2505.16120v3 Announce Type: replace Abstract: The emergence of Large Language Models (LLMs) has reshaped agent systems. Unlike traditional rule-based agents with limited task scope, LLM-powered agents offer greater flexibility, cross-domain reasoning, and natural language interaction. Moreover, with the integration of multi-modal LLMs, current agent systems are highly capable of processing diverse data modalities, including text, images, audio, and structured tabular data, enabling richer and more adaptive real-world behavior. This paper comprehensively examines the evolution of agent systems from the pre-LLM era to current LLM-powered architectures. We categorize agent systems into software-based, physical, and adaptive hybrid systems, highlighting applications across customer service, software development, manufacturing automation, personalized education, financial trading, and healthcare. We further discuss the primary challenges posed by LLM-powered agents, including high inference latency, output uncertainty, lack of evaluation metrics, and security vulnerabilities, and propose potential solutions to mitigate these concerns.

04.
arXiv (CS.CL) 2026-06-12

ChiKhaPo: A Large-Scale Multilingual Benchmark for Evaluating Lexical Comprehension and Generation in Large Language Models

Existing benchmarks for large language models (LLMs) are largely restricted to high- or mid-resource languages, and often evaluate performance on higher-order tasks in reasoning and generation. However, plenty of evidence points to the fact that LLMs lack basic linguistic competence in the vast majority of the world's 3800+ written languages. We introduce ChiKhaPo, consisting of 8 subtasks of varying difficulty designed to evaluate the lexical comprehension and generation abilities of generative models. ChiKhaPo draws on existing lexicons, monolingual data, and bitext, and provides coverage for 2700+ languages for 2 subtasks, surpassing any existing benchmark in terms of language coverage. We further show that 6 SOTA models struggle on our benchmark, and discuss the factors contributing to performance scores, including language family, language resourcedness, task, and comprehension versus generation directions. With ChiKhaPo, we hope to enable and encourage the massively multilingual benchmarking of LLMs.

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

Seeing Below the Limit of Detection: A Censored-Poisson Bayesian Latent-Growth Change-Point Detector (the Span Detector) for Serial ctDNA in HR+/HER2- Metastatic Breast Cancer

arXiv:2606.11876v1 Announce Type: cross Abstract: Circulating-tumour DNA (ctDNA) carries evidence of drug resistance months before imaging shows it, but the earliest evidence lives below the assay's limit of detection (LoD): a nascent subclone is detected only intermittently, producing a flickering sequence of faint detects and non-detects. Commercial liquid biopsies treat each draw as an independent snapshot and a non-detect as nothing. We argue a non-detect is a left-censored observation, and the pattern of non-detects and faint detects over time carries actionable evidence of growth before any single value is trustworthy. We introduce Span, a censored-Poisson Bayesian latent-growth change-point detector that models the binary detection process, accumulates a sequential generalised-likelihood-ratio statistic for an upward change-point in the per-variant detection rate, and raises a competing-risks alarm with calibrated false-alarm control. Span has no learned weights, so there is nothing to overfit. On a synthetic cohort of HR+/HER2- metastatic breast cancer on first-line CDK4/6-inhibitor plus endocrine therapy, at a matched 10% false-alarm rate, Span roughly doubles the fraction of impending progressions caught three months ahead (indolent regime: 25% vs 11% for the snapshot), with a falsifiable dose-response: large for indolent emergence, vanishing for fast emergence. A value-trajectory baseline performs identically to the snapshot, isolating the gain to the censored detection model. The survival backbone matches a Cox baseline on real breast-cancer data (GBSG-2, n=686; C-index 0.67 vs 0.68), and on a real longitudinal cohort with clean biomarkers (PBC2, n=312) the same pipeline correctly declines to win, a falsifiable boundary test confirming the mechanism is regime-specific. All ctDNA trajectories are synthetic.

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

GENERIC-FNO: Embedding Energy Conservation and Entropy Production into Fourier Neural Operators

arXiv:2606.08343v2 Announce Type: replace Abstract: We introduce GENERIC-FNO, the first neural operator to embed the full GENERIC (metriplectic) structure of nonequilibrium thermodynamics – reversible, energy-conserving dynamics and irreversible, entropy-producing dynamics coupled through the degeneracy conditions – directly in function space. Existing structure-preserving neural operators enforce at most a single conservation law or reversible (Hamiltonian) structure, while thermodynamically consistent learning has been confined to finite-dimensional, graph, or particle systems. GENERIC-FNO closes this gap: it learns the energy and entropy functionals as neural operators and parameterizes the Poisson and friction operators as diagonal Fourier multipliers sandwiched between rank-one projections that enforce the degeneracy conditions exactly, by construction, with no penalty term, update projection, or residual. The degeneracy identities hold to machine precision (residuals ~10^-13) for any initialization, dimension, or resolution, so the continuous-time dynamics conserve the learned energy and produce entropy exactly; the explicit time stepping adds only a small O(dt^2) drift (per-step residual ~10^-6). We further note that the (E,S,L,M) decomposition of a given flow is not unique, and introduce a gauge-invariant dissipation diagnostic separating reversible from dissipative dynamics independently of the learned functionals. Across three operator backbones (1D/2D FNOs and DeepONet) and four PDEs spanning reversible, dissipative, and mixed regimes, GENERIC-FNO preserves its exact structural guarantees zero-shot across a 4x super-resolution range (64 to 256), recovers the ground-truth ordering of physical dissipation, and is competitive with strong unconstrained and energy-penalized baselines, outperforming them on several dissipative and mixed problems at comparable or fewer parameters.

07.
arXiv (CS.CV) 2026-06-17

SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology

Characterising the tumour microenvironment (TME) from routine H&E-stained histology images requires simultaneous cell segmentation, feature extraction, and interpretable clinical reporting. We present SEGTME-UNI2, a unified framework addressing these requirements. Its core is UNI2-UPERHOVER, a dual-head segmentation model pairing the UNI2-H pathology foundation model (ViT-Giant, pretrained on >100M tiles from 100K slides) with two parallel UperNet decoders: one for six-class semantic segmentation and one for horizontal-vertical gradient regression enabling watershed-based nuclear instance separation. To address the lack of pixel-level annotations in large real-world repositories, UNI2-UPERHOVER undergoes a three-stage progressive pseudo-label curriculum. Each stage trains a fresh model without weight transfer, driving improvement entirely via increased pseudo-label quality: Stage 1: Uses human-annotated PanNuke (7,901 images, 189,744 nuclei, 0.25 um/pixel). Stage 2: Uses entropy-filtered pseudo-labels from the Stage 1 model on 271,711 TCGA-UT scale-0 patches (0.5 um/pixel). Stage 3: Uses pseudo-labels from the Stage 2 model on all 1,608,060 TCGA-UT patches across six resolution scales (0.5-1.0 um/pixel). Segmentation outputs feed a structured TME feature extraction pipeline computing 20+ per-patch compositional, morphological, spatial entropy, and intercellular distance metrics. These are encoded as JSON and passed to a fine-tuned NVIDIA BioNeMo GPT model to generate clinically interpretable TME narratives. Preliminary validation on held-out PanNuke and TCGA-UT partitions demonstrates framework feasibility and internal consistency. The pseudo-labelled TCGA-UT dataset and UNI2-UPERHOVER checkpoint are publicly released to support large-scale TME profiling and spatial biology research.

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

Towards Efficient Large Language Reasoning Models via Extreme-Ratio Chain-of-Thought Compression

arXiv:2602.08324v5 Announce Type: replace Abstract: Chain-of-Thought (CoT) reasoning successfully enhances the reasoning capabilities of Large Language Models (LLMs), yet it incurs substantial computational overhead for inference. Existing CoT compression methods often suffer from a critical loss of logical fidelity at high compression ratios, resulting in significant performance degradation. To achieve high-fidelity, fast reasoning, we propose a novel EXTreme-RAtio Chain-of-Thought Compression framework, termed Extra-CoT, which aggressively reduces the token budget while preserving answer accuracy. To generate reliable, high-fidelity supervision, we first train a dedicated semantically-preserved compressor on mathematical CoT data with fine-grained annotations. An LLM is then fine-tuned on these compressed pairs via a mixed-ratio supervised fine-tuning (SFT), teaching it to follow a spectrum of compression budgets and providing a stable initialization for reinforcement learning (RL). We further propose Constrained and Hierarchical Ratio Policy Optimization (CHRPO) to explicitly incentivize question-solving ability under lower budgets by a hierarchical reward. Experiments on three mathematical reasoning benchmarks show the superiority of Extra-CoT. For example, on MATH-500 using Qwen3-1.7B, Extra-CoT achieves over 73\% token reduction with an accuracy improvement of 0.6\%, significantly outperforming state-of-the-art (SOTA) methods. Our source codes have been released at https://github.com/Mwie1024/Extra-CoT.

09.
arXiv (CS.AI) 2026-06-11

Geometric Erasure by Contrastive Velocity Matching in Rectified Flows

arXiv:2606.00140v2 Announce Type: replace-cross Abstract: While the rapid adoption of multimodal generative models offers immense potential, it has also increased the risks of harmful content synthesis, deepfakes, and copyright infringements. To address these challenges, concept erasure has emerged as a prospective safeguard. However, as the field gradually transitions from U-Net-based diffusion models to Rectified Flow Transformers, erasure research has struggled to keep pace. In this work, we introduce GEM, a simple but highly effective erasure framework for Rectified Flow models. As part of our contribution, we establish a principled bridge between trajectory-based unlearning grounded in Generative Flow Networks and classic teacher-guided erasure: we translate trajectory-based signals into a teacher-guided flow-matching setup that unifies the strengths of both paradigms. Concretely, a teacher provides complementary attraction and repulsion signals that we combine into a single geometric guidance objective, yielding targeted suppression of unwanted concepts while preserving benign generation.

10.
arXiv (CS.CV) 2026-06-16

Active Reference Acquisition in Few-Shot Font Generation

Few-shot font generation aims to synthesize the remaining glyphs of a font given one or a few reference glyphs while preserving stylistic consistency, thereby supporting font designers in efficiently completing a typeface. Existing methods primarily focus on improving generation quality given a fixed reference set. However, when the current reference glyphs are insufficient to represent the target style, few-shot font generation may fail to produce satisfactory results. In practical scenarios, additional reference glyphs can often be obtained from the designer when necessary. Accordingly, we propose a new framework, Active Reference Acquisition in Few-Shot Font Generation, in which the model sequentially decides which character to acquire next as an additional reference. Furthermore, we propose a reference part-coverage-based acquisition function to efficiently query the designer. Motivated by the observation that font styles are well characterized by local structural parts, we represent each glyph using a histogram of local features and select query characters that maximize the expected part coverage of the reference set. By prioritizing characters that contain parts not yet covered by the current references, the proposed method progressively expands the diversity of visual parts in the reference set. As a result, generation quality is improved with fewer queries. Experiments on the Google Fonts dataset demonstrate that the proposed method achieves higher generation quality than random querying and reference-agnostic baselines. The code is available at https://github.com/matsuo-shinnosuke/ActiveRef-FontGen.

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

HawkesNest: A Multi-Axis Synthetic Benchmark for Spatiotemporal Pattern Complexity

arXiv:2606.16863v1 Announce Type: new Abstract: Evaluation of spatiotemporal point process (STPP) models relies heavily on opaque real-world datasets, where latent generative structure is unknown and model failures are difficult to attribute. We introduce HawkesNest, a generator-aligned benchmark for controlled spatiotemporal pattern complexity built on a multivariate Hawkes backbone. HawkesNest defines four complexity axes: space–time entanglement, background heterogeneity, cross-type interaction, and domain topology. Each axis is associated with a deterministic index computed from the latent data-generating mechanism. By varying these axes while holding global rate, stability, and simulation budget fixed, HawkesNest enables diagnostic stress tests of STPP models under known structural difficulty. We verify that the indices are monotone and nearly orthogonal under controlled sweeps. We illustrate its use by showing that Hawkes-family baselines degrade under joint heterogeneity–entanglement complexity, even though they are structurally aligned with the Hawkes data-generating backbone. We further show that HawkesNest exposes neural-model sensitivity: AutoSTPP remains vulnerable under isolated increases in space–time entanglement. Code. Available at https://github.com/YahyaAalaila/HawkesNest

12.
medRxiv (Medicine) 2026-06-17

Low-Density Lipoprotein Cholesterol and Dementia Risk: Integrating Mendelian Randomization and Target Trial Emulation Within the Heart-Brain Axis

Background: The heart-brain axis links cardiovascular and neurodegenerative disease through shared vascular and inflammatory mechanisms. Although low-density lipoprotein cholesterol (LDL-C) is an established causal factor in atherosclerotic cardiovascular disease (ASCVD), its relationship with dementia remains uncertain, with midlife elevations associated with increased risk but late-life associations often appearing null or inverse. To address this cholesterol paradox, we integrated mendelian randomization (MR) with an active-comparator new-user target trial emulation. Methods: We applied a triangulated causal inference framework integrating two-sample MR with observational target trial emulation. Genetic variants associated with LDL-C were used as instrumental variables to evaluate Alzheimer disease (AD), dementia with Lewy bodies (DLB), frontotemporal dementia (FTD), and any dementia (AnyDem), with causal estimates derived using inverse-variance weighted models and sensitivity analyses for heterogeneity and pleiotropy. In parallel, an active-comparator new-user design compared statin versus ezetimibe initiation among adults aged 60 years or older using propensity score (PS) overlap weighting and Cox proportional hazards models to evaluate cardiovascular and dementia outcomes. Results: Genetically predicted LDL-C was associated with increased risk of DLB (OR 1.65, 95% CI 1.30-2.10; p

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

BLADE: Scalable Bi-level Adaptive Data Selection for LLM Training

arXiv:2606.18650v1 Announce Type: new Abstract: As Large Language Model (LLM) datasets scale to trillions of tokens, data selection has emerged as a critical frontier to filter out uninformative noise and construct adaptive learning trajectories. Beyond static heuristic filtering, advanced data selection methods for LLM training largely follow two paradigms, each with fundamental limitations. Influence-based methods provide principled bi-level objectives but require intractable inverse-Hessian computations, while excess-loss methods are computationally efficient but rely on a static reference model that becomes misaligned with the evolving proxy model during training. We propose BLADE (Bi-Level Adaptive Data sElection), a Hessian-free framework for data selection. BLADE reformulates the bi-level optimization problem underlying influence-based methods as a penalized single-level objective via Lagrange multipliers, avoiding inverse-Hessian computation while revealing a principled connection to excess-loss based data selection. The resulting objective recovers an excess-loss form but replaces the static reference model with a dynamic one that stays synchronized with training. Theoretically, we prove that this penalized formulation guarantees first-order convergence. For efficient online batch selection, we instantiate BLADE as a memoryless randomized block-coordinate Frank-Wolfe algorithm. Extensive experiments show that BLADE consistently outperforms state-of-the-art data selection baselines, providing a practical recipe for LLM training.

14.
medRxiv (Medicine) 2026-06-17

Deep learning for interactive and automated inner retinal layer segmentation in OCT images of patients with retinitis pigmentosa using limited training data

Purpose: New therapeutic strategies such as optogenetics have created a need for accurate tracking of inner retina degeneration in Retinitis pigmentosa (RP) patients. We introduce two tailored deep learning models to segment the RNFL (retinal nerve fibre layer), GCIPL (ganglion cell inner plexiform layer), INL (inner nuclear layer), CFT (central foveal thickness) and RPE (retinal pigment epithelium) in RP: The first is based on a Segment Anything Model (SAM), the second on nnU-Net. To our knowledge, SAM has not yet been applied to retinal layers in OCT data. Methods: SD-OCT images of a retrospective cohort of 37 RP patients were included. Data for four training cycles were prepared semi-automatically in MATLAB, then assessed and corrected by three expert graders. 1,700 segmented B-Scans from two open datasets were used for pretraining. For post-processing, semantic retinal boundary detection was developed. The final models, OCT-SAM and nnU-Net, were trained on 228 annotated RP scans. Detected layer thicknesses were validated against manual segmentation at 90 random points in 30 OCT B-Scans. Finally, OCT-SAM was tested on three RP cases with retrospective, longitudinal OCT data. Results: nnU-Net achieved a precision, recall and F-1 score of 0.96 while OCT-SAM performance resulted in slightly lower values of 0.93, 0.8 and 0.85, respectively. OCT-SAM measurements had low bias and good agreement with manual annotations, confirming reliability. Conclusions: OCT-SAM enabled fast data annotation and tool integration, whereas nnU-Net provided the best segmentation performance. OCT-SAM demonstrated longitudinal reproducibility and detected RP-characteristic pathologies and degenerative changes. Future work will extend OCT-SAM to 3D OCT segmentation.

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

Robin-Neumann Coupling of PINN and FEM Solvers: A Steklov-Poincaré View, with Application to Fluid-Structure Interaction with Contact

arXiv:2606.14181v1 Announce Type: cross Abstract: Physics-informed neural networks (PINNs) are meshless and carry moving geometry and topology change through resampling of collocation points; the finite-element method (FEM) is the workhorse for boundary-fitted discretisations. Coupling the two across a shared interface promises the best of both, yet existing PINN-FEM schemes are validated only empirically. We put the coupling on a domain-decomposition footing: viewing each solver as a Steklov-Poincaré (trace-to-flux) operator, we transfer the classical Dirichlet-Neumann (DN) divergence diagnosis and its Robin-Neumann (RN) cure, including a closed-form, sweep-free interface impedance, and prove a PINN-specific contraction theorem: a trained network realises only a perturbed Steklov operator with a per-step training residual, and RN still contracts, with no shared-eigenbasis hypothesis, to a floor set by the achieved training loss. Because a PINN has no stiffness matrix, we introduce a Fourier-mode interface probe that recovers the network's resolvable Steklov eigenvalues to within 0.5% and doubles as a diagnostic of the network's spectral cap. The theory predicts measured PINN-FEM contraction rates to within 7% on 1D and 2D Poisson couplings, and a two-slab analogue of the large-added-mass regime shows RN's per-mode impedance matching winning decisively where tuned scalar relaxation saturates. We demonstrate the framework on a Stokes/rigid-disc problem with Alart-Curnier contact: the meshless PINN fluid absorbs the topology change at contact by collocation exclusion alone, no remeshing and no cut cells, and the static-equilibrium contact reaction matches the submerged weight to 0.4% under mesh refinement. We quantify remaining limitations: the warm-started PINN drifts off the Stokes manifold over long horizons, and matched FEM-FEM benchmarks attribute pre-impact squeeze-film signatures to PINN under-resolution.

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

Momentum LMS Theory beyond Stationarity: Stability, Tracking, and Regret

arXiv:2602.11995v2 Announce Type: replace Abstract: In large-scale data processing scenarios, data often arrive in sequential streams generated by complex systems that exhibit drifting distributions and time-varying system parameters. This nonstationarity challenges theoretical analysis, as it violates classical assumptions of i.i.d. (independent and identically distributed) samples, necessitating algorithms capable of real-time updates without expensive retraining. An effective approach should process each sample in a single pass, while maintaining computational and memory complexities independent of the data stream length. Motivated by these challenges, this paper investigates the Momentum Least Mean Squares (MLMS) algorithm as an adaptive identification tool, leveraging its computational simplicity and online processing capabilities. Theoretically, we derive tracking performance and regret bounds for the MLMS in time-varying stochastic linear systems under various practical conditions. Unlike classical LMS, whose stability can be characterized by first-order random vector difference equations, MLMS introduces an additional dynamical state due to momentum, leading to second-order time-varying random vector difference equations whose stability analysis hinges on more complicated products of random matrices, which poses a substantially challenging problem to resolve. Experiments on synthetic and real-world data streams demonstrate that MLMS achieves rapid adaptation and robust tracking, in agreement with our theoretical results especially in nonstationary settings, highlighting its promise for modern streaming and online learning applications.

18.
arXiv (CS.CL) 2026-06-17

An expressivity analysis of hierarchical modelling in deep transformers via bounded-depth grammars

Deep neural networks are widely believed to derive their expressive power from their ability to form hierarchical representations, capturing progressively more abstract and compositional features across layers. In language modeling, transformers have emerged as the dominant architecture, with early layers capturing local syntactic patterns and later layers encoding more complex clause-level dependencies. While this intuition has shaped model design, there remains a lack of rigorous theoretical work demonstrating how deep transformers represent such hierarchical structures. In this work, we analyze the expressiveness of deep transformer models through the formal lens of bounded-depth, non-recursive context-free grammars. For this class of grammars, we explicitly construct transformers with positional attention whose depth grows linearly with grammar depth, while the neuron count scales with the number of derivation-tree shapes and quadratically with the number of production rules. Our theoretical results support the linear representation hypothesis by demonstrating that these architectures possess the structural capacity to encode abstract grammatical states into low-dimensional, linearly separable subspaces within the residual stream.

19.
bioRxiv (Bioinfo) 2026-06-23

Model-based inference of gene expression noise from single-cell RNA-sequencing data

The heterogeneity of expression levels among genetically identical cells, termed gene expression noise, is a property of the gene expression process whose importance in the biology of organisms and their evolution is increasingly recognized. Measuring gene expression noise requires single-cell expression data, as obtained from single-cell RNA sequencing (scRNASeq). Its estimation, however, is challenging owing to (i) the presence of technical noise in addition to biological noise, and (ii) the heterogeneity of cell types in the sampled population. We propose a maximum-likelihood framework to infer biological noise from scRNASeq data, while accounting for technical noise, dropout probabilities, and distinct cell sequencing depths. We demonstrate the parameter identifiability using simulations and that the resulting noise estimates are uncorrelated from the mean gene expression, and therefore do not need extra correction in downstream analyses, easing intra- and inter- genome comparisons. Using two technical replicates of scRNASeq data from the wild yeast *Saccharomyces paradoxus*, we show that expression noise can be inferred in a reproducible manner.

20.
Nature Biotechnology 2026-06-23

Efficient generation of epitope-targeted antibodies with Germinal

Obtaining antibodies to specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success rates that require resource-intensive screening. Here we introduce Germinal, a broadly enabling generative pipeline that designs antibodies against specific epitopes with nanomolar binding affinities while requiring only low-n experimental testing. Our method co-optimizes antibody structure and sequence by integrating a structure predictor with an antibody-specific protein language model to perform de novo design of functional complementarity-determining regions onto a user-specified structural framework. When tested against four diverse protein targets, Germinal designed functional antibodies across all targets and binder formats, testing only 43–101 designs for each antigen. Validated designs also exhibited robust expression in mammalian cells and high sequence and structural novelty. We provide open-source code and full computational and experimental protocols to facilitate wide adoption. Germinal achieves epitope-targeted, de novo complementarity-determining region design with high experimental success rates.

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

Exploring Exotic Spin-Dependent Interactions Beyond the Standard Model: Theoretical Foundations and Experimental Investigations

arXiv:2606.13318v1 Announce Type: cross Abstract: New interactions mediated by novel particles propose solutions to several important questions in modern physics. Axions serve as examples of such particles; they are lightweight and interact weakly with ordinary matter. This category of particles, including those similar to axions-termed Axion-Like Particles (ALPs)-arises from diverse theoretical frameworks, such as the Peccei-Quinn mechanism addressing the strong CP problem, string theory, and spontaneous supersymmetry breaking. Given their light mass and weak coupling, ALPs are also possible candidates for cold dark matter. Introducing these new interactions mediated by novel particles not only tackles several challenges in modern physics but also raises a crucial question: Are there undiscovered interactions beyond the Standard Model? Many of the interactions predicted by these theories are spin-dependent, which is the primary focus of this review. In this review, we first outline the theoretical foundations for investigating exotic spin-dependent interactions, highlighting their importance in various models beyond the Standard Model. We examine the potential roles of new lightweight particles in mediating these interactions, which may enhance our understanding of dark matter. Relevant formulas derived from theoretical models are included to support experimental investigations. Following this theoretical framework, we conduct a detailed review of recent experimental efforts to detect these exotic interactions. A systematic review of current constraints on these interactions is presented, along with an assessment of various detection approaches.

22.
arXiv (CS.CV) 2026-06-18

Motion-Focused Latent Action Enables Cross-Embodiment VLA Training from Human EgoVideos

Training generalist Vision-Language-Action(VLA) models typically requires massive, diverse robotic datasets with high-fidelity action annotations. While egocentric human manipulation videos are abundant and capture significant environmental diversity, the absence of action labels makes them difficult to use in conventional training paradigms. To address this, we propose a latent-action-based framework designed to extract general action priors from unlabeled human videos. The architecture features a Hybrid Disentangled VQ-VAE that decouples motion dynamics from environmental backgrounds through physical masks, enabling the construction of a cross-embodiment action codebook. By pre-training on human videos with the codebook, the VLM backbone learns deep representations of action intent. For adaptation to specific embodiments, we introduce an intent-perception decoupling strategy where the VLM predicts the action intent while a separate frozen visual encoder provides state-specific features to the action expert, thereby reducing action hallucinations. Results in simulation and real-world environments show that our method, pre-trained exclusively on unlabeled human videos, performs competitively with state-of-the-art VLA models trained on massive annotated datasets, requiring only 50 trajectories for downstream adaptation.

23.
arXiv (CS.LG) 2026-06-16

Using Reinforcement Learning to Optimize the Global and Local Crossing Number

arXiv:2509.06108v2 Announce Type: replace-cross Abstract: Graph drawing concerns the algorithmic visualization of graphs. A good drawing of a graph is easy to read and facilitates solving tasks on the graph. Several properties have been identified to occur in good drawings of graphs. Such properties include a low number of crossings, large angles between edges, short edges, and depicting symmetries. Many of these properties are explicitly measurable metrics. This brings us to the insight that graph drawing can be seen as a game. In this paper, we study a single-player optimization game in which the player iteratively moves vertices of a straight-line graph drawing to reduce edge crossings. This game arose naturally from the automatic track of the Graph Drawing Challenge, where solutions are obtained by repeatedly performing local vertex movements. We formalize this process as a game with full information and investigate whether reinforcement learning can discover effective strategies for playing it. Our reinforcement-learning agent observes the local geometric and structural context of a vertex and selects a movement direction with the goal of reducing either the global or the local crossing number, that is, the total number of crossings or the maximum number of crossings per edge. We compare the resulting strategies to existing methods and established crossing-minimization heuristics on standard benchmark graphs. While our approach does not out-compete state-of-the-art methods for minimizing the global crossing number, it is competitive and often superior for minimizing the local crossing number.

24.
arXiv (CS.AI) 2026-06-19

Hybrid Diffusion Transformer for Instruction-Guided Audio Editing via Rectified Flow

arXiv:2606.20101v1 Announce Type: cross Abstract: Audio editing aims to modify specific content in an existing audio clip according to a natural language instruction while preserving the remaining acoustic content. Despite the remarkable progress of diffusion models, existing training-based editing methods mainly rely on the local inductive biases and cross-attention interaction in convolutional U-Net backbones, which often hinder long-range semantic alignment and precise understanding and localization of instructions. In contrast, diffusion transformers provide stronger global modeling and multimodal fusion, but existing editing architectures usually adopt a simple stack of MMDiT and DiT blocks. Applying joint attention over concatenated audio and text tokens in all blocks results in quadratic complexity with respect to token length. To balance editing performance and efficiency, we propose a hybrid two-stage diffusion transformer architecture for instruction-guided audio editing based on rectified flow matching. It performs joint attention over audio and text tokens to establish coarse semantic alignment at low-resolution stage, then switches to alternating joint-attention and cross-attention blocks to refine editing details at high-resolution stage. This coarse-to-fine strategy enables efficient and accurate instruction-guided audio editing. Experiments show that the proposed framework achieves notable performance gains on challenging editing tasks involving overlapping audio events and complex instructions, while substantially improving editing efficiency with a compact model.

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

Space Is Intelligence: Neural Semigroup Superposition for Riemannian Metric Generation

作者:

arXiv:2606.18828v1 Announce Type: cross Abstract: Traditional approaches place intelligence in the agent, whether as a learned policy or a search procedure. We instead place intelligence in the space itself: a scene induces a Riemannian metric on the configuration manifold, and action reduces to following the geodesics of that metric rather than invoking a separate planner or collision checker. A single Encoder-Router network realizes this idea through three complementary parameter groups – frame parameters that orient the generators, modulation parameters that govern their spatial propagation, and basic coefficients that determine their strength. These groups combine through a shared semigroup-superposition mechanism to produce a single Riemannian metric field, yielding a compact architecture whose geometry scales naturally with scene complexity. Trained on a single two-obstacle scene, the model demonstrates robust zero-shot generalization across unseen obstacle configurations, with orders-of-magnitude separation between collision-free and obstacle-penetrating path costs.