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

Cross-lingual Embedding Clustering for Hierarchical Softmax in Low-Resource Multilingual Speech Recognition

We present a novel approach centered on the decoding stage of Automatic Speech Recognition (ASR) that enhances multilingual performance, especially for low-resource languages. It utilizes a cross-lingual embedding clustering method to construct a hierarchical Softmax (H-Softmax) decoder, which enables similar tokens across different languages to share similar decoder representations. It addresses the limitations of the previous Huffman-based H-Softmax method, which relied on shallow features in token similarity assessments. Through experiments on a downsampled dataset of 15 languages, we demonstrate the effectiveness of our approach in improving low-resource multilingual ASR accuracy.

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

Contextual Bandits for Maximizing Stimulated Word-of-Mouth Rewards

arXiv:2606.15146v1 Announce Type: new Abstract: Stimulated word-of-mouth is a strategy that promotes information sharing through prompts or incentives. Optimizing stimulated word-of-mouth through social networks requires identifying and targeting connected users who are most susceptible to spillover, a phenomenon where the influence of recommendations extends beyond the immediate audience to impact their connected users. The probability of spillover varies across individuals, and their connections, leading to heterogeneity. Understanding and accurately estimating the spillover probabilities among users in social networks is crucial for improving the effectiveness of stimulated word-of-mouth. To address this, we present a novel contextual multi-armed bandit framework that learns individual spillover probabilities and ranks connected users to maximize rewards from stimulated word-of-mouth. Experiments on real-world network datasets demonstrate that accounting for spillover heterogeneity enhances the targeting precision of top-$k$ connected users, boosting rewards and outperforming baseline methods that do not learn individual spillover effects.

03.
arXiv (CS.AI) 2026-06-24

OmniPath: A Multi-Modal Agentic Framework for Auditing Wheelchair Accessibility

arXiv:2606.24129v1 Announce Type: new Abstract: For a wheelchair user, a standard blue line on a map is often a broken promise. While platforms like OpenStreetMap (OSM) successfully capture where a path is, they frequently fail to convey how it physically feels to travel on it. This information barrier is problematic for wheelchair users. To solve this issue, we present OmniPath, a system that moves from passive mapping to proactive environmental auditing. Our framework fuses the network topology of OSM with the submeter precision of high-density aerial LiDAR (USGS 3DEP) to create a high-fidelity 3D model of the pedestrian environment. Rather than simply routing a user, our agent virtually traverses the network, analyzing the surface in 0.5 meter increments. It rigorously quantifies physical friction points specifically running slope, cross slope, and vertical discontinuities against ADA compliance standards, calculating a weighted severity score to categorize hazards from ``Mild'' to ``Critical.'' To ensure real world reliability, we validated the system against 200 physical ground truth field surveys across the National Mall using stratified random sampling. The framework demonstrated strong diagnostic reliability for high-severity hazards, achieving F1-scores of 0.60 for Severe and 0.58 for critical categories. By automating this micro-scale inspection, OmniPath identifies the ``invisible'' barriers that standard maps miss, effectively transforming a static dataset into accessibility data source that anticipates accessibility challenges before the user ever leaves home.

04.
arXiv (CS.AI) 2026-06-15

Large-scale semantic mapping of learner agency and autonomy reveals what measurement and generative AI research overlook

arXiv:2606.10881v2 Announce Type: replace Abstract: Learner agency and autonomy are foundational to personal development, yet a pervasive "jingle-jangle" fallacy (i.e. identical terms denoting different constructs, distinct terms denoting identical ones) has substantially hindered cumulative knowledge. Treating meaning as a phenomenon constituted through use in linguistic practice, we extracted 8,954 definitions and 2,700 scale items from over 14,000 publications, to investigate how researchers actually used learner agency and autonomy with a semantic analysis pipeline. The definitional landscape of two constructs resolves into three dimensions: regulation and control of learning (task), intrinsic motivation and internal decision-making (person), and social-relational action (sociocultural), thereby empirically quantifying the jingle-jangle fallacy. Existing scales, however, systematically underrepresent the sociocultural dimension. Critically, current generative AI research in education concentrates on learning regulation and control, narrowing the behavioral repertoire that AI-mediated learning environments are designed to cultivate. Beyond conceptual clarification, this work carries direct implications for conceptualization, measurement, and practice towards supporting the multidimensional learner agency and autonomy.

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

Towards Quantum Limited Spatial Resolution of NV-Diamond Magnetometry

arXiv:2508.13438v2 Announce Type: replace Abstract: Optically addressable ensembles of solid-state defects, such as nitrogen vacancy (NV) centers, are a leading modality for imaging-based magnetometry, thermometry and strain sensing. However, monitoring the fluorescence of individual defects within a sub-diffraction ensemble remains an outstanding challenge that currently limits access to atomic-scale features and dynamics. For compact clusters of NVs, we formulate imaging-based atomic sensing as a low-dimensional multiparameter estimation task in which one seeks to localize each defect and quantify the field strength in its immediate vicinity. In this work, we employ optical spatial mode demultiplexing (SPADE) to enhance localization and brightness estimation accuracy at sub-diffraction scales. Specifically, we develop a two-stage sensing protocol that augments direct imaging by projecting the incoming optical field onto point spread function (PSF)-adapted, i.e., PAD spatial modes and Yuen-Kennedy-Lax (YKL) spatial modes enabling efficient extraction of emitter positions and brightnesses. The YKL-SPADE measurement employed for brightness estimation is shown to be quantum-optimal in the case of two emitters and establishes a new connection between quantum detection and estimation theories. We numerically evaluate the statistical performance of our protocol for sub-diffraction optically detected magnetic resonance (ODMR) and Rabi sensing experiments. Compared to conventional focal plane intensity measurements, our protocol improves emitter localization accuracy by 6$\times$ and brightness estimation accuracy by 2$\times$ for tightly confined ensembles, residing well below the diffraction limit.

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

Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability

arXiv:2606.14245v1 Announce Type: new Abstract: Drug-target interaction (DTI) and affinity (DTA) predictors increasingly achieve strong benchmark scores, yet their internal use of sequence, fingerprint, and graph features often remains opaque. We present an interpretability audit of BridgeDPI architecture on three different datasets including Gao, Human, and C.elegans. This study combines gradient-based attributions – integrated gradients, saliency, layer-wise relevance propagation, SmoothGrad, and SmoothGrad-IG – with feature-wise occlusion ablation and strict intersection consensus across methods to reduce single-explainer bias. We summarize sensitivity and signed effects at raw inputs, at the bridge similarity scaffold, and through the graph convolution, including edge-level sensitivities and targeted edge removals. The results show that explainability is most informative when treated as model criticism: it reveals modality dominance, padding and special-token artifacts, dataset-dependent cooperative versus suppressive effects across layers, and chemistry-consistent fragment and composition motifs where methods agree. These analyses do not substitute for structural or experimental ground truth, yet they can provide testable hypotheses for downstream validation in computational drug discovery pipelines. More broadly, applying modern XAI to contemporary DTI/DTA models is still an early pass over the rich structure implicit in trained weights and data – yet even this first layer of scrutiny already helps researchers relate predictions to drug- and target-side representations and to prioritize external validation.

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

The Distribution Postulate in Algorithmic Bohmian Mechanics

arXiv:2606.16165v1 Announce Type: new Abstract: In order to make the right empirical predictions Bohmian mechanics requires a special statistical boundary condition – the distribution postulate – but it is unclear how best to understand this condition. We show how one might use the theory of algorithmic randomness to formulate the distribution postulate as an objective constraining law. The framework requires us to say something about admissible quantum-mechanical states and measurements. In return, algorithmic Bohmian mechanics (aBM) guarantees the standard Born statistics for a collection of canonical quantum experiments in the limit, not just with high probability. The algorithmic distribution postulate provides a sharp typicality condition, clarifies the status of quantum probabilities in the deterministic theory, and provides a concrete example of how notions provided by the theory of algorithmic randomness can aid in specifying the content of a physical law.

08.
arXiv (CS.AI) 2026-06-16

AgenticRec: A Recommendation-Oriented Agentic Framework with Progressive Tool-Integrated Reasoning Optimization

arXiv:2603.21613v2 Announce Type: replace-cross Abstract: Recommender agents built on Large Language Models offer a promising paradigm for personalized recommendation. However, existing agents typically suffer from a misalignment between their tool-integrated reasoning trajectories and recommendation feedback, limiting their ability to distinguish fine-grained user preferences. To address these challenges, we propose AgenticRec, an agentic recommendation framework that formulates recommendation as a tool-integrated reasoning process over a recommendation-oriented tool suite. Built upon this framework, we further develop a dedicated two-stage training paradigm tailored for recommender agents. In the first stage, we introduce Recommendation-Oriented Trajectory Activation, optimize the agentic recommendation ability under implicit feedback. In the second stage, Progressive Preference Refinement further refines the agent through bidirectional preference reasoning over self-bootstrapped hard pairs, progressively sharpening preference boundaries. Theoretical analysis and extensive experiments demonstrate the effectiveness of AgenticRec. Our code is available at https://anonymous.4open.science/r/AgenticRec-FB16.

09.
arXiv (CS.AI) 2026-06-15

AgentCyberRange: Benchmarking Frontier AI Systems in Realistic Cyber Ranges

arXiv:2606.14295v1 Announce Type: cross Abstract: Frontier AI systems are increasingly capable of cybersecurity tasks, including codebase inspection, vulnerability detection, and exploitation. However, evaluating their offensive capabilities remains constrained by limited access to open, reproducible, multi-host cyber ranges. Existing public benchmarks capture isolated skills such as CTF solving, vulnerability reproduction, and exploit generation, but often abstract away realistic intrusion workflows: discovering exposed services, gaining a foothold, collecting internal information, and expanding compromise across hosts. This gap makes it difficult to observe emerging risks early, because frontier AI systems are rarely evaluated under realistic attack conditions. We introduce AgentCyberRange, the first open, multi-range infrastructure for measuring autonomous cyber attack capability in realistic cyber ranges. It combines 110 vulnerabilities across 15 real web applications and 8 enterprise-like cyber ranges with 156 internal hosts, plus Cage, a toolchain for execution, orchestration, result collection, and verification. The benchmark covers two core stages: web exploitation, where agents explore exposed applications and validate vulnerabilities, and post exploitation, where agents turn an initial foothold into broader internal compromise. We evaluate six frontier AI systems under matched prompts and budgets. GPT-5.5 with Codex performs best, solving 16.1% of web exploitation tasks and 31.7% of post-exploitation tasks; with more concrete hints, these rates increase to 33.0% and 46.3%. We also observe out-of-benchmark findings, including unknown vulnerabilities in popular projects, and payload mutation that bypasses host defenses. These results show that open cyber-range evaluation is necessary for observing emerging offensive capabilities under realistic and reproducible conditions.

10.
arXiv (CS.CV) 2026-06-18

EDoF-NeRF: extended depth-of-field neural radiance fields using a coded aperture camera

We propose a method for extending the depth-of-field (DoF) to construct high-fidelity neural radiance fields (NeRF) – an emerging technique for rendering photorealistic novel views from a dataset of images captured at different viewpoints, based on implicit neural representations. The trade-off between DoF and light quantity is inherent not only in conventional cameras but also in NeRF, since the datasets used by NeRF are captured by these cameras. To address this issue, we introduce a coded aperture placed at the camera pupil, preserving spatial frequency components under defocused conditions. We develop a camera model incorporating coded apertures into NeRF, allowing direct input of coded images and enabling the generation of novel views with an extended DoF. We validate the proposed method, termed extended DoF-NeRF (EDoF-NeRF), through simulations and experiments, demonstrating its superior performance compared to conventional aperture cameras.

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

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

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

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

Geometry-Preserving Encoder/Decoder in Latent Generative Models

arXiv:2501.09876v4 Announce Type: replace-cross Abstract: Generative modeling aims to generate new data samples that resemble a given dataset. When using diffusion models for this task, one of the main challenges is solving the problem in the input space, which tends to be very high-dimensional. To address this, recent approaches solve diffusion models in the latent space through an encoder that maps from the data space to a lower-dimensional latent space, improving training efficiency and achieving state-of-the-art results. The variational autoencoder (VAE) is the most commonly used encoder/decoder framework in this domain, known for its ability to learn latent representations and generate data samples. In this paper, we introduce a novel encoder/decoder framework with theoretical properties distinct from those of the VAE, specifically designed to preserve the geometric structure of the data distribution. We demonstrate the significant advantages of this geometry-preserving encoder in the training process of both the encoder and decoder. Additionally, we provide theoretical results proving convergence of the training process, including convergence guarantees for encoder training, and results showing faster convergence of decoder training when using the geometry-preserving encoder.

13.
arXiv (CS.AI) 2026-06-19

Policy-Embedded Graph Expansion: Networked HIV Testing with Diffusion-Driven Network Samples

arXiv:2601.16233v2 Announce Type: replace-cross Abstract: HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and the University of Witwatersrand, we study how to improve the efficiency of HIV testing with the goal of eventual deployment, directly supporting progress toward UN Sustainable Development Goal 3.3. While prior work has demonstrated the promise of intelligent algorithms for sequential, network-based HIV testing, existing approaches rely on assumptions that are impractical in our real-world implementations. Here, we study sequential testing on incrementally revealed disease networks and introduce Policy-Embedded Graph Expansion (PEGE), a novel framework that directly embeds a generative distribution over graph expansions into the decision-making policy rather than attempting explicit topological reconstruction. We further propose Dynamics-Driven Branching (DDB), a diffusion-based graph expansion model that supports decision making in PEGE and is designed for data-limited settings where forest structures arise naturally, as in our real-world referral process. Experiments on real HIV transmission networks show that the combined approach (PEGE + DDB) consistently outperforms baselines (e.g., 17.3% improvement in discounted reward and 15.4% more HIV detections with 25% of the population tested) and explore key tradeoffs that drive solution quality.

14.
arXiv (CS.AI) 2026-06-16

The Initial Exploration Problem in Knowledge Graph Exploration

arXiv:2602.21066v2 Announce Type: replace Abstract: Knowledge Graphs (KGs) enable the integration and representation of complex information across domains, but their semantic richness and structural complexity create substantial barriers for lay users without expertise in semantic web technologies. When encountering an unfamiliar KG, such users face a distinct orientation challenge: they do not know what questions are possible, how the knowledge is structured, or how to begin exploration. This paper identifies and theorises this phenomenon as the Initial Exploration Problem (IEP). Drawing on theories from information behaviour and human-computer interaction, including ASK, exploratory search, information foraging, and cognitive load theory, we develop a conceptual framing of the IEP characterised by three interdependent barriers: scope uncertainty, ontology opacity, and query incapacity. We argue that these barriers converge at the moment of first contact, distinguishing the IEP from related concepts that presuppose an existing starting point or information goal. Analysing KG exploration interfaces at the level of interaction primitives, we suggest that many systems rely on epistemic assumptions that do not hold at first contact. This reveals a structural gap in the design space: the absence of interaction primitives for scope revelation, mechanisms that communicate what a KG contains without requiring users to formulate queries or interpret ontological structures. In articulating the IEP, this paper provides a theoretical lens for evaluating KG interfaces and for designing entry-point scaffolding that supports initial exploration.

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

Formalizing Numerical Analysis: An Agent Pipeline and Quality Audit Beyond Kernel Acceptance

arXiv:2606.14000v1 Announce Type: new Abstract: Recent work has demonstrated that coding agents can formalize entire advanced mathematics textbooks in Lean 4, yet existing efforts concentrate on branches of mathematics already well-represented in mathlib and measure success solely through kernel acceptance. We address both limitations by applying a coding agent to formalize Numerical Methods for Ordinary Differential Equations, a textbook in numerical analysis that is largely absent from mathlib, stressing the agent's capacity to develop new theory from scratch. We further introduce a systematic, reproducible three-dimensional framework for evaluating the quality of agent-produced formalizations beyond compilation: semantic correctness, Mathlib reuse, and cross-file reuse via LLM-as-judge methods. Applying this framework to our own formalization and to the released outputs of RepoProver and M2F, we uncover recurring unfaithful formalization patterns, including incomplete multi-part statements, added weakening hypotheses, and parameter restrictions, that kernel acceptance entirely obscures. Our results suggest that compilation-based metrics substantially overstate formalization quality, and we provide a reproducible audit methodology to support more rigorous evaluation of future autoformalization systems.

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

HiMPO: Hindsight-Informed Memory Policy Optimization for Less-Entangled Credit in Long-Horizon Agents

Long-horizon agents rely on memory mechanisms to compress interaction history, but optimizing memory writing faces a distinct credit assignment challenge: a memory update may be rewarded or penalized due to downstream tool failures, noisy observations, or reasoning errors rather than its own contribution. This causally entangled credit can lead agents to discard useful evidence or preserve irrelevant information. We propose HiMPO, a Hindsight-Informed Memory Policy Optimization framework for assigning less-entangled credit to memory-writing actions in long-horizon agents. HiMPO first estimates the local utility of a memory update by comparing the task-relevant information recoverable from the previous and updated memories under the same pre-write state. It then uses hindsight relevance as a bounded retrospective filter that attenuates memory credit when local utility is not supported by the target outcome. The resulting memory-specific advantage is applied only to memory tokens, while trajectory-level rewards optimize the rest of the agent behavior. Across judge-based open-domain tasks and objective compressive-memory QA, HiMPO improves over strong memory-based and RL-based baselines while preserving compressed-context efficiency. Controlled interventions further show that HiMPO reduces blame leakage from tool-induced errors and improves attribution fidelity of memory updates.

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

Automated Scoring of Arabic Text Using Large Language Models: A Literature Review

In modern educational systems, Automatic Text Scoring (ATS) plays a central role by enabling scalable and consistent evaluation of learner responses without human intervention. Recently, the increased accessibility of LLMs and Arabic-specific datasets has sparked renewed interest in this area. In this work, we investigate LLM-Based approaches for the automated evaluation of Arabic texts, focusing on both short answer grading (ASAG) and essay scoring (AES). We further introduce a structured taxonomy comprising five dimensions: application domain, feedback generation capability, LLM architecture deployed, alignment with competency referential frameworks, and prompt engineering strategy. By applying this taxonomy, we conduct a comparative analysis of existing studies, examining their methodological approaches, datasets, evaluation metrics, and reported performance. The findings highlight the need for sustained and pedagogically grounded research efforts in Arabic ATS, given its significance for improving educational quality across Arabic-speaking communities.

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

ReFoCUS: Reinforcement-guided Frame Optimization for Contextual Understanding

Recent progress in Large Multi-modal Models (LMMs) has enabled effective vision-language reasoning, yet the ability to video understanding remains constrained by suboptimal frame selection strategies, albeit with the rapid development of video-specialized LMMs. Prior works attempted to solve this with static heuristics or external retrieval modules to feed frame-level information, but these approaches often fail to capture visual cues grounded to the given user queries conflating raw visual dynamics with true semantic relevance. In this paper, we introduce ReFoCUS (Reinforcement-guided Frame Optimization for Contextual UnderStanding), the first framework to integrate online policy-gradient reinforcement learning into frame-level optimization for video-LLMs. ReFoCUS aims to learn a frame selection policy, leveraging reward signals derived from reference models to capture their underlying scoring behavior over frame combinations that best support temporally grounded responses. To efficiently explore the large combinatorial frame space, we employ an autoregressive and query-conditional selection architecture that ensures contextual consistency while reducing complexity. Our policy learning removes the need for explicit frame-level supervision, as it implicitly discovers optimal and semantically consistent frame compositions. ReFoCUS consistently improves reasoning accuracy across multiple video QA benchmarks, demonstrating the advantage of aligning frame selection with model-internal utility.

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

BLUEmed: Retrieval-Augmented Multi-Agent Debate for Clinical Error Detection

Terminology substitution errors in clinical notes, where one medical term is replaced by a linguistically valid but clinically different term, pose a persistent challenge for automated error detection in healthcare. We introduce BLUEmed, a multi-agent debate framework augmented with hybrid Retrieval-Augmented Generation (RAG) that combines evidence-grounded reasoning with multi-perspective verification for clinical error detection. BLUEmed decomposes each clinical note into focused sub-queries, retrieves source-partitioned evidence through dense, sparse, and online retrieval, and assigns two domain expert agents distinct knowledge bases to produce independent analyses; when the experts disagree, a structured counter-argumentation round and cross-source adjudication resolve the conflict, followed by a cascading safety layer that filters common false-positive patterns. We evaluate BLUEmed on a clinical terminology substitution detection benchmark under both zero-shot and few-shot prompting with multiple backbone models spanning proprietary and open-source families. Experimental results show that BLUEmed achieves the best accuracy (69.13%), ROC-AUC (74.45%), and PR-AUC (72.44%) under few-shot prompting, outperforming both single-agent RAG and debate-only baselines. Further analyses across six backbone models and two prompting strategies confirm that retrieval augmentation and structured debate are complementary, and that the framework benefits most from models with sufficient instruction-following and clinical language understanding.

20.
arXiv (CS.CL) 2026-06-12

LLMs Can Better Capture Human Judgments–With the Right Prompts

Are large language models (LLMs) bad at capturing human judgment? Two commonly stated limitations are that LLMs fail to capture full distributions of responses, and that their judgments are unstable across wording variations. We demonstrate simple prompting strategies that mitigate these limitations. Across two datasets–a U.S.-representative set of 144 moral scenarios and 38 moral beliefs from the International Social Survey Programme's Family and Changing Gender Roles module covering 32 countries–we show how simple elicitation techniques help improve AI-human alignment. First, prompting models to report standard deviations and response proportions recovers the full range of human responses better than common strategies. Second, ensuring scenarios are clear to human participants–as reflected in human confusion ratings–boosts model alignment, and LLMs can track human confusion ratings. At the same time, we find that LLMs' estimates of their own error are poorly calibrated, though they can predict human variability relatively well. These results suggest that asking better questions to LLMs can yield better answers.

21.
arXiv (quant-ph) 2026-06-11

Machine-learned, finite temperature Fermi-operator expansions suitable for GPUs and AI-hardware

arXiv:2605.08523v2 Announce Type: replace Abstract: We present several finite-temperature recursive Fermi-operator expansion schemes based on the second-order spectral projection (SP2) method. Our approach builds on a previous observation that the electronic structure problem, as formulated through a recursive SP2 expansion, can be mapped onto the architecture of a deep neural network. Using this perspective, we generalize SP2 to finite electronic temperatures by constructing machine learning models that determine optimized recursive expansion coefficients. The same approach is also applied to the prediction of the electronic entropy for fractional occupation numbers. The coefficients are trained for a specified chemical potential and electronic temperature and are not available in closed analytical form. However, by employing an appropriate affine rescaling strategy to the Hamiltonian matrix, we eliminate the need to retrain the model for different temperatures and chemical potentials. Our approach avoids explicit diagonalization and relies solely on highly optimized matrix-matrix multiplication kernels. Compared to state-of-the-art diagonalization, we achieve an order-of-magnitude speedup in the single-particle finite-temperature density matrix calculation for small and moderately sized matrices on modern GPUs and dense matrix multiply units.

22.
arXiv (CS.CL) 2026-06-24

A Synthetic Reliability-Aware PINN Benchmark for Offshore Wind Turbine Support-Structure Monitoring with Bayesian Inverse Identification

Reliable structural health monitoring (SHM) of offshore wind turbine (OWT) support structures requires fast state estimation from sparse measurements. Repeated high fidelity finite element or aeroelastic analyses are difficult to use directly in online monitoring loops, while purely data-driven surrogates can require large training sets. This paper presents Digi Turbine, a synthetic reliability-aware Physics Informed Neural Network (PINN) benchmark for OWT monopile support structure monitoring. The workflow embeds a simplified Euler Bernoulli beam equation with Winkler soil foundation in the training objective, couples it with Bayesian-prior-informed inverse identification, and adds First Order Reliability Method (FORM) screening. All validation uses synthetic configurations with analytical or finite-difference ground truth motivated by the NREL 5MW reference turbine context.

23.
bioRxiv (Bioinfo) 2026-06-17

DNA-binding specificity recognition from predicted homologous protein-DNA structures

Predicting protein DNA-binding specificity is essential for understanding gene regulation and disease mechanisms. Existing deep learning methods typically infer specificity from a single protein-DNA complex structure, which limits their ability to capture the diverse geometric patterns underlying protein-DNA recognition. Homologous protein-DNA interfaces provide complementary structural evidence and richer geometric features related to interatomic interactions. To address the limited diversity and coverage of experimentally determined complexes, we constructed a large-scale library of predicted homologous protein-DNA complex structures. Building on this resource, we propose HomoDSP, a template-retrieval-based framework for accurate DNA-binding specificity prediction. Benchmark evaluations and validation on newly released JASPAR 2026 samples indicate that HomoDSP outperforms existing methods in both accuracy and generalization, with particularly substantial gains on high-error samples. Moreover, this performance is largely retained when AlphaFold3-predicted complex structures are used as input. Template- and residue-level interpretability analyses suggest that HomoDSP improves prediction by focusing on DNA-affinity residues across multiple homologous templates. Finally, universal Protein Binding Microarrays evaluations on AI-designed DNA-binding proteins show that HomoDSP rescues a baseline failure mode in which the baseline method produces incorrect predictions because of training-set bias. Together, these results support the use of homologous template interfaces as informative structural priors for decoding protein DNA-binding specificity.

24.
bioRxiv (Bioinfo) 2026-06-12

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

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

25.
arXiv (CS.CV) 2026-06-24

ForensicsTok: Forensics-Guided Tokenized Modeling for Image Tampering Localization

Multi-modal Large Language Models (MLLMs) offer powerful reasoning for forensic tasks, yet existing approaches utilizing exogenous segmentation decoders often suffer from suboptimal localization. The reliance on stitched pipelines introduces information bottlenecks during backpropagation, which dilutes spatial signals and is limited by semantic priors of the segmentor. To address these limitations, we propose ForensicsTok, which reformulates image manipulation localization as an autoregressive sequence generation task. ForensicsTok directly generates spatially grounded token sequences, enabling precise mask prediction without intermediary supervision. Specifically, we introduce a Token Splatting Decoder (TSD) to map tokens to binary masks via codebook-aware code smoothing, which mitigates sharp gradients from deterministic detokenizers. Furthermore, to capture diverse tampering clues, we propose a Hierarchical Expert Fusion (HEF) module that injects multi-scale features from a forensic expert model. This unified architecture effectively compensates for the lack of forensic priors in standard MLLMs. Extensive experiments on six benchmarks show that ForensicsTok substantially improves over existing MLLM-based baselines and slightly improves over strong forensic expert baselines, while exhibiting stronger robustness to perturbations.