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01.
arXiv (CS.AI) 2026-06-19

How Transparent is DiffusionGemma?

arXiv:2606.20560v1 Announce Type: cross Abstract: LLM reasoning transparency is a critical affordance for understanding model decisions, mitigating misuse and misalignment, and debugging surprising model behaviors. However, DiffusionGemma performs a larger fraction of its computation in a continuous latent space; does this make its reasoning less transparent? We study this question by decomposing transparency into two components: variable transparency, whether we understand intermediate snapshots of a model's computational state; and algorithmic transparency, whether we can use these snapshots to reconstruct the process by which the model arrived at its outputs. Naively, DiffusionGemma has poor variable transparency: its opaque serial depth, the amount of serial computation that occurs in between interpretable model states, seems at first 28.6X higher than the corresponding autoregressive Gemma 4 model. However, we show that we can map the information flowing between denoising steps through an interpretable token bottleneck with no decrease in downstream performance. Treating these intermediate states as interpretable reduces the opaque serial depth to just 1.1X that of Gemma 4. Algorithmic transparency is harder for diffusion models than for autoregressive models because all token predictions in the canvas can change at every denoising step, giving the model the power to implement complicated distributed algorithms during the denoising process. To begin bridging this gap, we conduct a suite of interpretability case studies, uncovering initial evidence of novel diffusion-specific phenomena such as non-chronological reasoning, token and sequence smearing, and intermediate-context reasoning. Finally, we test monitorability, a key application of transparency that measures whether model outputs are useful for downstream tasks. We find that DiffusionGemma is similarly monitorable to Gemma 4.

02.
arXiv (CS.AI) 2026-06-12

Proprioceptive-visual correspondence enables self-other distinction in humanoid robots

arXiv:2606.13222v1 Announce Type: cross Abstract: Distinguishing self from others is a prerequisite for social intelligence, yet humanoid robots that increasingly share workspaces with humans still lack this ability. Here we show that a humanoid robot can learn self-other distinction from proprioceptive-visual correspondence, without any identity labels or kinematic models. Once established, this distinction bootstraps a predictive self-model that maps joint configurations to three-dimensional body occupancy, capturing how the robot's body changes with action. In multi-agent scenes involving humans or morphologically identical robots, the system reliably identifies itself, learns a 3D self-model, and supports downstream tasks including target reaching, collision-aware motion planning, and human-to-robot motion retargeting. Together, these results outline a route toward bodily self-representation in robots that act and coordinate alongside others in shared physical environments. Project page: https://euron-zc.github.io/humanoid-self-model/.

03.
arXiv (CS.CV) 2026-06-11

Illumination-Robust Camera-Based Heart-Rate Estimation for Physiological Sensing in Robots

Physiological awareness is important for service, social, and assistive robots that interact with humans in everyday environments. Remote photoplethysmography (rPPG) enables non-contact heart-rate (HR) estimation from an RGB camera, making it a promising sensing modality for robot-mounted vision systems. However, illumination variation remains a major barrier to robust deployment. This paper presents an end-to-end spatial-temporal transformer framework for remote HR estimation on a new dataset with varied illumination. Our estimator integrates PRNet-based 3D face alignment, clip-level illumination augmentation, the Residual Temporal Standardization Module, and controlled hybrid temporal-frequency supervision. The training objective combines a Soft-Shifted Pearson waveform loss with a spectral Kullback-Leibler divergence loss, where a tuned weight ($\mathbf{\beta}$) controls the contribution of frequency-domain heart-rate guidance. Experiments on a static all-level mix protocol covering three illumination levels show that $\mathbf{\beta}=5$ provides the strongest result among the tested beta settings, achieving a best-run HR mean absolute error (MAE) of 0.79 bpm and an HR correlation of 0.982. Compared with the PhysFormer baseline evaluated on our dataset, our estimator reduces HR MAE by 93.6 %, while increasing HR correlation from 0.088 to 0.982, making it usable when illumination varies.

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

Training-Free Open-Vocabulary Visual Grounding for Remote Sensing Images and Videos

Remote sensing visual grounding (RSVG) aims to localize a referred target in a remote sensing image or video according to a natural language expression. Existing RSVG methods usually rely on task-specific manual annotations, which are costly to collect and inevitably limited in covering the diversity of real-world geospatial scenarios. As a result, they often struggle to generalize to open-vocabulary queries involving novel objects, fine-grained attributes, complex spatial relationships, and functional semantics. In this paper, we propose RSVG-ZeroOV, a training-free framework that leverages frozen generic foundation models for zero-shot open-vocabulary RSVG. RSVG-ZeroOV follows an Overview-Focus-Evolve paradigm, which exploits the distinct yet complementary attention patterns of vision-language models (VLMs) and diffusion models (DMs) to progressively generate precise grounding results. Specifically, (i) Overview utilizes a VLM to extract cross-attention maps that capture semantic correlations between the referring expression and visual regions; (ii) Focus leverages the fine-grained modeling priors of a DM to compensate for object structure and shape information often overlooked by VLM attention; and (iii) Evolve introduces a simple yet effective attention evolution module to suppress irrelevant activations, yielding purified object masks. To handle video inputs, we further present Video RSVG-ZeroOV, which extends image-level grounding to spatio-temporal grounding through a query-relevant key-frame selector and a temporal propagator, enabling efficient and temporally coherent video grounding without video annotations or fine-tuning. Extensive experiments on six image and video grounding benchmarks show that RSVG-ZeroOV consistently outperforms existing zero-shot baselines and achieves competitive or superior performance compared with weakly- and fully-supervised methods.

05.
arXiv (quant-ph) 2026-06-16

Sub-Poissonian Statistics and Quantum Non-Gaussianity from High-Harmonic Generation

arXiv:2602.10882v4 Announce Type: replace Abstract: Quantum technologies are powered by platforms to generate complex non-classical states of matter or light to realize applications. We investigate the non-classical properties of high-harmonic generation in semiconductors, an emerging photonic platform. Measuring the click statistics of three double-digit orders, we evaluate witness operators to certify the non-classicality of the generated states. We show that higher-order harmonics driven by a coherent laser are squeezed and entangled. The properties of the emission are well retrieved with an entangled Gaussian state model, obtained by numerical state optimization to multiple observables. Additionally, we perform inter-order heralded measurements to engineer the quantum state of the emission. The heralded states have distinct properties, showing sub-Poissonian photon statistics. Further, we witness the generation of a quantum non-Gaussian state, a resource highly relevant for quantum information. With this, we establish high-harmonic generation as a platform for generating quantum optical resources.

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

A Link between Shock-wave Theory and Symmetry-reduced Stochastic Gradient Descent for Artificial Neural Networks

arXiv:2606.18303v1 Announce Type: cross Abstract: We develop a mathematically explicit link between shock-wave theory and the symmetry-quotiented learning dynamics of stochastic gradient descent, drawing on differential geometry, Lie group theory, and fluid mechanics. Specifically, after quotienting parameter symmetries and applying local-entropy coarse-graining, the effective dynamics satisfy a viscous Hamilton–Jacobi equation on the quotient manifold. Moreover, under the assumption that the raw parameter dynamics can be summarized by a gradient field on the quotiented space, the gradient of the coarse-grained loss function obeys a Burgers-type equation, and shock formation can be established rigorously. We apply our theory to multilayer perceptrons, convolutional neural networks, Transformers, and mean-field networks, and show that they obey the Hamilton–Jacobi or Burgers-type equations. We conjecture that this framework also yields practical diagnostics for deep learning. In architectures such as Transformers, raw parameter norms are often distorted by symmetry redundancy and may therefore be misleading, whereas symmetry-corrected quotient observables provide a principled basis for monitoring, forecasting, and controlling training-phase transitions.

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

X-REFINE: XAI-based RElevance input-Filtering and archItecture fiNe-tuning for channel Estimation

arXiv:2602.22277v2 Announce Type: replace Abstract: AI-native architectures are vital for 6G wireless communications. The black-box nature and high complexity of deep learning models employed in critical applications, such as channel estimation, limit their practical deployment. While perturbation-based eXplainable Artificial Intelligence (XAI) solutions offer input filtering, they often neglect internal structural optimization. We propose X-REFINE, an XAI-based framework for joint input-filtering and architecture fine-tuning. By utilizing a decomposition-based, sign-stabilized LRP epsilon rule, X-REFINE backpropagates predictions to derive high-resolution relevance scores for both subcarriers and hidden neurons. This enables a reliable optimization that identifies the most reliable model components. Simulation results demonstrate that X-REFINE achieves a superior performance-complexity-interpretability trade-off compared to the external perturbation-based XAI frameworks, significantly reducing computational complexity while maintaining robust bit error rate (BER) performance.

08.
bioRxiv (Bioinfo) 2026-06-20

Ribosomes are covered by a coat of flexible protein fragments

Ribosomal proteins contain flexible terminal regions that are averaged out during electron density reconstructions, rendering them absent from experimental models derived by X-ray crystallography or cryogenic electron microscopy. These flexible protein fragments (FPFs) collectively form an invisible coat on the ribosome surface whose presence has been systematically overlooked. Here we analysed FPFs from 36 ribosomes spanning bacteria, eukaryotes, and mitochondria. We found that mitoribosomes harbour the most numerous and longest FPFs. Structural predictions confirmed that FPFs are predominantly disordered across all ribosome classes. Comparison of FPF amino acid composition against proteome-wide background frequencies revealed strong and domain-specific compositional biases. The balance between arginine and lysine content tracks the cardiolipin content of the membrane each ribosome class contacts. The arginine enrichment in mitoribosomal FPFs may additionally reflect selection arising from the RNA-rich environment of mitochondrial RNA granules, membraneless condensates where mitoribosomes are assembled. FPFs are uniformly depleted in aromatic residues, arguing against protein-driven liquid–liquid phase separation propensity. Our findings suggest that the flexibly tethered coat is a highly functional intrinsic part of all ribosomes.

09.
medRxiv (Medicine) 2026-06-12

Conversational Artificial Intelligence-Enabled Precision Oncology Reveals Context-Specific TGFβ and JAK/STAT Alterations in Pancreatic Cancer

Background: Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive molecular complexity, profound stromal remodeling, and limited responsiveness to systemic therapies. Although gemcitabine-based regimens remain widely utilized, the molecular pathways that influence treatment-associated biological variation are incompletely understood. The TGF{beta} and JAK/STAT signaling networks are recognized regulators of tumor progression, immune modulation, and therapeutic resistance; however, their genomic architecture in clinically stratified PDAC populations remains poorly defined. Methods: We employed a conversational artificial intelligence-driven analytical framework to investigate TGF{beta} and JAK/STAT pathway alterations in a cohort of 184 PDAC patients. Clinical and molecular data were integrated to generate age- and treatment-stratified cohorts, enabling pathway-level and gene-level analyses according to gemcitabine exposure. Findings generated through AI-assisted interrogation were subsequently evaluated using conventional statistical approaches. Results: TGF{beta} pathway alterations were identified in approximately one-quarter to one-third of tumors across clinical subgroups and demonstrated relatively stable frequencies regardless of age at diagnosis or gemcitabine treatment status. Gene-level analyses revealed that pathway disruption was predominantly driven by recurrent alterations in SMAD4, with additional low-frequency events involving TGFBR1 and TGFBR2. Notably, TGFBR2 mutations were significantly more frequent among late-onset PDAC patients receiving gemcitabine compared with untreated late-onset patients (8.8% vs. 1.4%; p = 0.04), suggesting a potential treatment-associated enrichment. In contrast, JAK/STAT pathway alterations were rare throughout the cohort, with only isolated mutations observed in pathway components including JAK1, JAK2, JAK3, STAT1, STAT3, and related regulatory genes. No significant differences in JAK/STAT alteration frequencies were identified according to age or treatment exposure. Conclusions: TGF{beta} and JAK/STAT pathways exhibit distinct genomic architectures in PDAC. TGF{beta} pathway disruption represents a recurrent feature of disease biology, largely driven by SMAD4 alterations, while TGFBR2 enrichment in gemcitabine-treated late-onset tumors suggests a potential context-specific association worthy of further investigation. Conversely, genomic alterations within the JAK/STAT pathway are uncommon, indicating that pathway activity may be regulated predominantly through non-genomic mechanisms. These findings demonstrate the utility of conversational artificial intelligence agents for rapid, scalable, and clinically contextualized pathway interrogation and support future studies integrating multi-omic data to refine precision medicine strategies in PDAC.

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

A Unified Definition of Hallucination: It's The World Model, Stupid!

Despite numerous attempts at mitigation since the inception of language models, hallucinations remain a persistent problem even in today's frontier LLMs. Why is this? We review existing definitions of hallucination and fold them into a single, unified definition wherein prior definitions are subsumed. We argue that hallucination can be unified by defining it as simply inaccurate (internal) world modeling, in a form where it is observable to the user. For example, stating a fact which contradicts a knowledge base OR producing a summary which contradicts the source. By varying the reference world model and conflict policy, our framework unifies prior definitions. We argue that this unified view is useful because it forces evaluations to clarify their assumed reference "world", distinguishes true hallucinations from planning or reward errors, and provides a common language for comparison across benchmarks and discussion of mitigation strategies. Building on this definition, we also connect our framework to HalluWorld, a complementary benchmark that instantiates fully specified reference world models for stress-testing model hallucinations.

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

CoBit: Language Modeling with Bitstream Diffusion

Diffusion language models (DLMs) promise parallel, order-agnostic generation, but on standard benchmarks they have historically lagged behind autoregressive models in sample quality and diversity. Recent continuous flow and diffusion approaches have narrowed this gap. In this work, we further close the autoregressive gap by modeling text as a continuous diffusion process over fixed-width binary bitstreams. We refer to the resulting model as CoBit (Continuous Bitstream Diffusion). Our approach represents semantic tokens as analog bit sequences and uses a matched-filter residual parameterization to isolate contextual learning from analytic independent-bit posteriors. Crucially, we adopt a stochastic sampler that applies Langevin-type corrections gated by the entropy-rate profile, concentrating stochasticity in high-information regions while remaining nearly deterministic elsewhere. On LM1B, our 130M-parameter model reaches a generative perplexity (GenPPL) of 59.76 at matched real-data entropy (4.31) using 256 neural function evaluations (NFEs), outperforming prior DLM baselines and reaching the autoregressive reference. On OpenWebText (OWT), our sampler establishes a new continuous-DLM Pareto frontier, achieving GenPPL 27.06 at entropy 5.26 using 4x fewer steps than previous 1024-NFE baselines. Scaling the same recipe to a 462M-parameter model (CoBit-M) further improves the OWT GenPPL-entropy frontier over the 130M model (CoBit-S) and over medium-scale continuous and discrete DLM baselines, reaching GenPPL 19.5 at entropy 5.40, near real-data entropy (5.44), and approaching pretrained GPT-2 Medium over the high-quality region. As an additional benefit, bitstream diffusion removes the O(V) vocabulary scaling bottleneck of standard DLMs: by predicting O(log V) bitwise logits via semantic bit-patching, it lowers memory and raises throughput, a scalable paradigm as vocabulary sizes grow.

12.
arXiv (CS.AI) 2026-06-19

Human Universal Grasping

arXiv:2606.17054v1 Announce Type: cross Abstract: Humans can grasp objects effortlessly, whereas multi-fingered robots are far from this level of generality. We argue that the most natural source of robot grasping data is from humans, who pick up thousands of objects every day. We present HUG, a flow-matching model that generates diverse human grasps for any user-specified object in a single RGB-D image captured from a stereo camera. Using smart glasses, we first collect 1M-HUGs, an egocentric dataset of human grasps spanning 1M frames (27.8 hrs) and 6,707 object instances across 41 buildings. Next, to model the distribution of natural human grasps, our novel flow-matching model fuses RGB and depth observations to output a grasp parameterized by wrist translation, wrist rotation, and MANO hand pose. Predicted grasps can be retargeted to various robot hands, enabling zero-shot grasping in everyday scenes. To standardize evaluation, we build a new simulated benchmark, HUG-Bench, of 90 unseen objects from five geometric categories and various sizes, with metric-scale 3D meshes. We evaluate HUG in the real world on the 30-object test set of HUG-Bench across multiple stereo cameras, robot embodiments, and household environments. HUG outperforms the state-of-the-art grasping baselines by +23% and +34% on our challenging object set. Code, data, benchmark, checkpoints, and an interactive demo are released on our website: https://grasping.io/

13.
arXiv (CS.LG) 2026-06-11

Space-sampled Value Decay: Forgetting Mechanisms for Non-stationary Deep Reinforcement Learning

arXiv:2606.11797v1 Announce Type: new Abstract: Studies on rodents such as mice have shown the capabilities to adapt their behavior when dealing with changing parameters (``drift'') of the environment even if no information about change is provided (uncertainty) – a behavior that can be modeled by forgetting mechanisms. Non-stationary Reinforcement Learning (NSRL) deals with adapting state-of-the-art RL methods to deal with changing environments: these however usually require (partially) perfect information about the drift such as ``task IDs'' or ``context''. To mitigate the effects of drift, this work develops Space-sampled Value Decay as an explicit forgetting mechanism for value-based deep RL architectures as a simple yet effective approach. In particular we demonstrate and discuss positive effects but also limitations in achieved returns for modifications of Deep Q-networks (DQN) and Soft Actor-Critic (SAC) when evaluated on non-stationary environments.

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

RAVA: Retrieval-Augmented Viewpoint Alignment for Subject-Driven Image Generation

Reference-driven image generation has made rapid progress on identity preservation, but reliable viewpoint control across different subjects remains poorly understood. The difficulty is not merely generating a new image of the target subject: the model must infer the implicit viewpoint of one subject and transfer it to another subject using only image-level evidence, without camera poses, depth, or ray-based conditions. In this setting, existing generators conditioned on multiple image references often rely on spurious semantic correlations, which lead to viewpoint drift, part-level structural mismatches, and missing or unsupported target-specific content. We formulate this challenge as cross-subject viewpoint alignment and propose RAVA, a retrieval-augmented framework that supplies explicit geometric evidence before generation. RAVA first learns a cross-instance viewpoint embedding that retrieves target-subject images aligned with the anchor viewpoint, then applies a LogDet-based subset selection strategy to retain a compact reference set that is both view-consistent and structurally complementary. The selected references are finally consumed by a fine-tuned multi-reference image generator. Experiments show that generic semantic embeddings are nearly random for this task, while the proposed retriever substantially improves viewpoint retrieval quality. On cross-subject generation, RAVA consistently outperforms zero-shot baselines and stronger retrieval alternatives under the same generation backbone. These results indicate that cross-subject viewpoint alignment benefits from retrieval-augmented geometric grounding rather than relying on end-to-end generation alone.

15.
arXiv (CS.AI) 2026-06-19

Cost-Optimal LLM Routing with Limited User Feedback under User Satisfaction Guarantees

arXiv:2606.19376v1 Announce Type: cross Abstract: Inference costs for large language model (LLM) applications are rapidly growing, driven by surging demand and rising infrastructure cost. Users expect high-quality responses, and in commercial settings this is formally codified in Service Level Agreements (SLAs), creating a fundamental tension between cost and quality. Recent progress on cost-aware LLM request routing has shown potential to resolve this tension, but existing approaches rely on complete feedback signals, offline training, extensive per-workload tuning, and most lack SLA guarantees or inference-time adaptivity. We introduce SLARouter, an online routing algorithm that learns a cost-optimal policy from the sparse, one-sided user feedback available in production systems. SLARouter provides theoretical guarantees for both cost optimality and strict SLA compliance. Experiments across a wide range of LLM benchmarks show that SLARouter satisfies SLA constraints without the need for per-benchmark tuning, reducing operating cost by up to 2.2x over existing baselines.

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

Flow Matching for Efficient and Scalable Data Assimilation

arXiv:2508.13313v4 Announce Type: replace-cross Abstract: Data assimilation (DA) estimates a dynamical system's state from noisy observations. Recent generative models like the ensemble score filter (EnSF) improve DA in high-dimensional nonlinear settings but are computationally expensive. We introduce the ensemble flow filter (EnFF), a training-free, flow matching (FM)-based framework that accelerates sampling and offers flexibility in flow design. EnFF uses Monte Carlo estimators for the marginal flow field, localized guidance for observation assimilation, and utilizes a novel flow path that exploits the Bayesian DA formulation. It generalizes classical filters such as the bootstrap particle filter and ensemble Kalman filter. Experiments on high-dimensional benchmarks demonstrate EnFF's improved cost-accuracy tradeoffs and scalability, highlighting FM's potential for efficient, scalable DA. Code is available at https://github.com/Utah-Math-Data-Science/Data-Assimilation-Flow-Matching.

17.
arXiv (CS.CV) 2026-06-12

World Tracing: Generative Pixel-Aligned Geometry Beyond the Visible

Image-to-3D methods often trade off faithfulness and completeness: depth estimators are anchored to input pixels but stop at the visible surface, while image-to-3D models generate complete shapes that are often misaligned with the input. We introduce World Tracing, a generative pixel-aligned geometry representation that predicts 3D points aligned with observed pixels while completing geometry beyond the visible surface. For each input pixel, World Tracing predicts an ordered stack of camera-space 3D points, where the first layer represents the visible surface and subsequent layers represent front-to-back intersections with occluded surfaces. We instantiate this representation with a world-tracing diffusion transformer, WT-DiT, which treats multiple geometry layers as separate denoising tokens coupled through factorized and global attention. WT-DiT is trained with pixel-space flow matching and a mixed noise schedule that balances visible-surface reconstruction with occluded-geometry generation. World Tracing achieves strong performance on visible-surface reconstruction and complete geometry generation across object, scene, and dynamic benchmarks, outperforming both depth predictors and image-to-3D generators. It also preserves 2D-to-3D correspondence, enabling text-driven 3D scene editing, geometry-conditioned novel-view video synthesis, and training-free integration with textured-mesh generators.

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

Efficient, Robust, and Anti-Collusion Fingerprinting of Image Diffusion Models

Model fingerprinting, embedding user-specific identifiers (fingerprints) into generated outputs, has recently emerged as a popular solution to protect the intellectual property rights (IPR) of generative text-to-image (T2I) models and prevent unauthorized redistribution. In this work, we reveal a previously unexplored systematic vulnerability in existing generative model fingerprinting methods: they lack robustness against collusion attacks, where multiple attackers combine their models to remove or obscure the fingerprints. To address this issue, we take the first step towards a robust fingerprinting method for T2I models with anti-collusion capabilities. The proposed method encodes strings of bits, namely fingerprints, into the coefficients of a personalized normalization module (PNM) incorporated into T2I models, so that fingerprints can be reliably recovered from any generated image. To defend against collusion attacks and prevent unauthorized model redistribution, we introduce an anti-collusion mechanism based on lossless function-invariant parameter transformations. This mechanism significantly degrades the image generation quality of colluded models, making them effectively unusable. Moreover, our method allows developers to efficiently create multiple copies of fingerprinted T2I models by reparameterizing the PNM without the need for retraining. We also introduce a worst-case optimization strategy to improve robustness against model-level attacks. Our experiments demonstrate that the proposed method achieves high fidelity and robustness across multiple T2I image generation and editing tasks, with fingerprint extraction accuracy exceeding 99.5%. Compared with existing methods, our method demonstrates, for the first time, a notable proactive robustness to collusion attacks by significantly increasing the FID of colluded models.

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

libhmm: A Modern C++20 Library for Hidden Markov Models with Correct MLE Emission M-Steps

作者:

arXiv:2605.29208v2 Announce Type: replace-cross Abstract: We describe libhmm, a C++20 library for Hidden Markov Model parameter estimation, sequence decoding, and model selection. libhmm addresses two gaps in existing software: the absence of a well-maintained, zero-dependency C++ HMM library suitable for embedding in production systems, and the widespread use of method-of-moments (MOM) approximations in the emission distribution M-step of the Baum-Welch algorithm. The library implements correct maximum likelihood estimators for sixteen scalar emission distributions, including an ECME algorithm for the location-scale Student-t distribution, Newton-Raphson maximization for Gamma, Beta, Weibull, and Negative Binomial distributions, and the von Mises distribution for circular data. All forward-backward and Viterbi calculations operate in full log-space. SIMD acceleration is provided for AVX-512, AVX2, SSE2, and ARM NEON via compile-time dispatch with scalar fallback. Version 4 adds multivariate observation support via the BasicHmm template, with three multivariate emission families (diagonal Gaussian, full-covariance Gaussian, and independent components) each with correct weighted MLE M-steps. Python bindings are available via the companion package pylibhmm. We compare libhmm against established C and C++ HMM libraries and against published R reference packages on seven real-data benchmarks, and discuss the architectural tradeoffs made in the design.

20.
arXiv (quant-ph) 2026-06-19

Matrix-product state skeletons in Onsager-integrable quantum chains

arXiv:2511.07212v2 Announce Type: replace Abstract: Matrix-product state (MPS) skeletons are connected networks of Hamiltonians with exact MPS ground states that underlie a phase diagram. Such skeletons have previously been found in classes of free-fermion models. For the translation-invariant BDI and AIII free-fermion classes, it has been shown that the underlying skeleton is dense, giving an analytic approach to MPS approximation of ground states anywhere in the class. In this paper, we partially expose the skeleton in certain interacting spin chains: the $N$-state Onsager-integrable chiral clock families. We construct MPS that form a dense MPS skeleton in the gapped regions surrounding a sequence of fixed-point Hamiltonians (the generators of the Onsager algebra). Outside these gapped regions, these MPS remain eigenstates, but no longer give the many-body ground state. Rather, they are ground states in particular sectors of the spectrum. Our methods also allow us to find further MPS eigenstates; these correspond to low-lying excited states within the aforementioned gapped regions. This set of MPS excited states goes beyond the previous analysis of ground states on the $N=2$ free-fermion MPS skeleton. As an application of our results, we find a closed form for the disorder parameter in a family of interacting models. Finally, we remark that many of our results use only the Onsager algebra and are not specific to the chiral clock model representation.

21.
arXiv (CS.CV) 2026-06-11

TextHOI-3D: Text-to-3D Hand-Object Interaction via Discrete Multi-View Generation and Joint Mesh Optimization

Text-conditioned 3D generation has progressed rapidly for images and isolated objects, but producing a hand-object mesh remains challenging: the output must preserve language semantics, cross-view consistency, object geometry, articulated hand shape, and physically plausible contact. We present TextHOI-3D, a staged framework that uses generated multi-view observations as an explicit interface between text-conditioned visual generation and geometry-aware hand-object recovery. TextHOI-3D learns a compact VQ token space for fixed-camera hand-object observations, predicts multi-view visual tokens from text with a CLIP-conditioned visual autoregressive model, and recovers a unified hand-object mesh through prior initialization, multi-view joint optimization, and anti-penetration refinement. The design separates semantic generation from geometric recovery while keeping both stages connected by a discrete multi-view representation. On HO3D-derived evaluations, the multi-view setting reduces object CD from 17.26 mm to 4.92 mm and penetration volume from 5.3721 cm^3 to 0.2193 cm^3 compared with a single-view counterpart, while improving hand errors and surface F-scores. These results support multi-view visual tokens as an effective intermediate representation for text-driven 3D hand-object mesh creation.

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

Prior-guided Fusion of Multimodal Features for Change Detection from Optical-SAR Images

Multimodal change detection (MMCD) identifies changed areas in multimodal remote sensing data, demonstrating significant application value in land use monitoring and urban sustainable development. However, literature MMCD approaches exhibit limitations in both cross-modal interaction and exploiting modality-specific characteristics. This leads to insufficient modeling of fine-grained change information, thus hindering the precise detection of semantic changes. To address these problems, we propose STSF-Net, a framework designed for MMCD between optical and SAR images. STSF-Net jointly models modality-specific and spatio-temporal common features to enhance change representations. Specifically, modality-specific features are exploited to capture genuine semantic change signals, while spatio-temporal common features are embedded to suppress pseudo-changes caused by differences in imaging mechanisms. Furthermore, we introduce an optical and SAR feature fusion strategy that adaptively adjusts multimodal feature importance based on semantic priors obtained from visual foundation models. Finally, we introduce the novel Delta-SN6 dataset, the first openly-accessible multiclass MMCD benchmark consisting of very-high-resolution fully polarimetric SAR and optical images. Experimental results on Delta-SN6, BRIGHT, and Wuhan datasets demonstrate that our method outperforms the state-of-the-art by 3.21%, 0.87%, and 1.32% in mIoU, respectively.

23.
bioRxiv (Bioinfo) 2026-06-18

Structure Bioinformatics of Eight Human ATP Synthase Fo Subunits and Their AlphaFold3-Predicted Water-Soluble QTY Analogs

Human mitochondrial ATP synthase is an essential rotary motor enzyme that produces most of the cellular ATP through oxidative phosphorylation. Its membrane-embedded Fo sector contains highly hydrophobic transmembrane subunits that are challenging to study in aqueous environments without detergents. This study explores whether applying the QTY code can reduce the hydrophobicity of selected ATP synthase Fo subunits while preserving their overall molecular structures. We applied the QTY code to eight human ATP synthase Fo subunits: ATP6, ATP8, ATPK, ATP68, ATPMK, AT5G1, AT5G2, and AT5G3. Hydrophobic amino acids leucine (L), isoleucine (I), valine (V), and phenylalanine (F) in transmembrane regions were systematically replaced with hydrophilic glutamine (Q), threonine (T), and tyrosine (Y). Four native subunits with available CryoEM structures from human ATP synthase (PDB: 8H9S) were superposed with their AlphaFold3-predicted QTY analogs. The native ATP synthase Fo subunits superposed well with their respective QTY analogs. For the CryoEM-native comparisons, RMSD values ranged from 0.565[A] to 2.546[A]. For the AlphaFold3-native comparisons of subunits without CryoEM structures, RMSD values ranged from 0.204[A] to 0.297[A]. Despite substantial QTY substitutions in the transmembrane regions, ranging from 38.89% to 50.79%, the QTY analogs retained similar overall folds, molecular weights, and isoelectric points. Hydrophobic surface analysis showed that the QTY analogs had reduced hydrophobic patches compared with their native counterparts, with average hydrophobicity decreasing from 0.2959 in native proteins to -1.1023 in QTY analogs. These structural bioinformatics studies suggest that the QTY code can be applied to ATP synthase Fo subunits to generate more hydrophilic, potentially water-soluble analogs while preserving overall structural similarity. These results extend the application of the QTY code to the membrane-embedded Fo sector of ATP synthase and provide a foundation for future experimental studies testing whether these QTY analogs can be expressed, purified, and evaluated for assembly or proton-transfer-related functions.

24.
bioRxiv (Bioinfo) 2026-06-11

A high-quality chromosome-scale reference genome assembly for Asparagus racemosus var. CIM-Shakti (Shatavari), a medicinal plant of Ayurvedic importance

Asparagus racemosus Wild., commonly known as Shatavari, is an important medicinal plant in Ayurveda and is valued for its steroidal saponins, particularly shatavarin compounds, which contribute to its adaptogenic, galactagogue, immunomodulatory, and therapeutic properties. Despite its medicinal and economic importance, genomic resources for this species have remained limited, restricting molecular breeding, pathway discovery, and comparative evolutionary studies within Asparagaceae. Here, we report a high quality chromosome scale reference genome assembly of A. racemosus var. CIM Shakti generated using PacBio HiFi long read sequencing and Omni C chromatin conformation scaffolding. The pseudo haploid assembly spans 817 Mb across 53 scaffolds, with a scaffold N50 of 98.50 Mb, L50 of 5, and a largest scaffold of 113.80 Mb. Ten major chromosome scale pseudomolecules were resolved, corresponding to the haploid chromosome complement of A. racemosus. The assembly showed high gene space completeness, with BUSCO completeness of 99.8% against the Eukaryota dataset and 98.0% against the Embryophyta dataset. BlobToolKit profiling further supported assembly quality, with GC content of approximately 39 to 40% and no major evidence of contamination. EDTA based repeat annotation identified 580.93 Mb of interspersed repetitive elements, accounting for 71.06% of the 817.57 Mb genome assembly. The repeat landscape was dominated by LTR retrotransposons, particularly Gypsy elements, which accounted for 25.01% of the assembly, followed by unclassified LTR elements at 26.58% and Copia elements at 4.84%. Structural and functional annotation identified 29,199 protein coding genes represented by 29,199 transcript models, 138,433 exons, and 125,201 CDS features. The annotation was structurally robust, with an average gene length of 4,605.1 bp, 4.74 exons per transcript, and 97.80% of transcripts containing multiple exons. The CIM Shakti reference genome provides a foundational genomic resource for investigating steroidal saponin biosynthesis, sex chromosome evolution, repeat driven genome expansion, and comparative genomics in Asparagaceae. This assembly will support future studies on medicinal trait improvement, conservation genomics, and genomics assisted breeding of climate resilient Shatavari cultivars.

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

Scribby: A Multi-Level LLM Framework for Semantic Video Analysis

As video content continues to expand across educational platforms, recorded lectures, and live-streamed entertainment, the need for efficient and structured analysis of long-form footage has increased [1]. Although many existing AI programs provide high-level video summaries based on AI-generated transcripts [2,3,4,5], these approaches are often limited to coarse overviews and lack detailed analysis of a video's structure, thematic progression, and semantic relationships, all of which are required for comprehensive video analysis. This paper proposes an LLM-based video summarization framework that balances macro-level comprehension with micro-level semantic analysis [6,12,13]. The first stage of the process indexes the video at a micro level by (1) analyzing the full transcript, (2) analyzing individual transcript sentences, and (3) grouping these sentences by semantic similarity using an LLM as a judge [6,13]. Contextual continuity is retained during sentence-level processing by incorporating both the global transcript analysis and adjacent sentence information into each evaluation prompt. This framework establishes a foundation for video analysis tools that visualize semantic chunking and semantic matching through relevance-based heatmaps. Limitations and future expansions of the framework are also discussed.