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01.
arXiv (CS.AI) 2026-06-12

PolyFlow: Safe and Efficient Polytope-Constrained Flow Matching with Constraint Embedding and Projection-free Update

arXiv:2606.13400v1 Announce Type: cross Abstract: While flow-based generative models have demonstrated strong performance across a wide range of domains, deploying them in safety-critical physical systems remains challenging due to strict constraint requirements. Existing approaches typically enforce safety through post-hoc corrections, which incur substantial computational overhead and may distort the learned distribution. We propose PolyFlow, a polytope-constrained flow matching framework that embeds constraints directly into the model and flow dynamics. PolyFlow introduces a discrete-time flow formulation and a projection-free architecture, which eliminate the discretization error and guarantee strict satisfaction of arbitrary polyhedral constraints, without the need for expensive iterative solvers. Experimental results show that PolyFlow achieves zero constraint violation while maintaining high distributional fidelity across a range of planning and control tasks. Compared to state-of-the-art constrained generation baselines, PolyFlow significantly reduces inference latency and demonstrates a favorable trade-off between safety, efficiency, and generative quality. Code is available on https://github.com/MJianM/PolyFlow.

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

WorkflowPerturb: Calibrated Stress Tests for Evaluating Multi-Agent Workflow Metrics

arXiv:2602.17990v2 Announce Type: replace Abstract: Multi-agent LLM systems that generate structured workflows from natural-language requests are now deployed in production across cloud automation, DevOps, and enterprise process orchestration. Operating such systems exposes a recurring change-management problem. Routine updates, such as re-running the same input, swapping the underlying LLM, or refactoring an agent's prompt or orchestration code, frequently produce workflows that differ substantially from previously validated references. Engineers are then left without a principled way to decide whether a change is safe to ship. Automatic workflow evaluation is the natural tool for answering this question. In practice, however, metric scores are poorly calibrated, and a numeric change rarely communicates the severity of the underlying degradation. We introduce WorkflowPerturb, a controlled benchmark for studying workflow evaluation metrics by applying realistic, graded perturbations to golden workflows. WorkflowPerturb contains 4,973 golden workflows and 44,757 perturbed variants across three perturbation types (Missing Steps, Compressed Steps, and Description Changes), each applied at severity levels of 10%, 30%, and 50%. We benchmark multiple metric families and analyze their sensitivity and calibration using expected score trajectories and residuals. Our results characterize systematic differences across metric families and support severity-aware interpretation of workflow evaluation scores in change-management settings. Our dataset will be released upon acceptance.

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

DCP-Prune: Ultra-Low Token Pruning with Distribution Consistency Preservation

Recent vision token pruning methods effectively preserve model performance under moderate token budgets but become unstable under ultra-low token budget. Our analysis shows that as the pruning budget decreases, accuracy degradation is often accompanied by larger feature distribution shifts. Critically, the degree of this distribution shift strongly correlates with performance degradation. To better characterize this phenomenon, we introduce a lightweight distribution consistency metric to estimate the distribution shift between retained and full tokens. Motivated by these observations, we propose a two-stage pruning framework consisting of Anchor-Context Graph Recovery (ACGR) and Text-Aware Token Cluster Selection (TATCS). Specifically, ACGR transfers contextual information before token removal, while TATCS dynamically re-selects representative tokens when severe distribution shift is detected. Extensive experiments demonstrate that our method achieves superior and more stable performance under ultra-low token budget. Notably, it retains 92.1% of the upper-bound average performance on LLaVA-1.5-7B with only 16 visual tokens.

04.
arXiv (CS.AI) 2026-06-19

Triangular Consistency as a Universal Constraint for Learning Optical Flow

arXiv:2606.19938v1 Announce Type: cross Abstract: We propose triangular consistency as a first-principled constraint for optical flow, which is agnostic to network architecture, supervision type, and dataset, and applies to both image-pair and multi-frame settings. This simple but powerful constraint is to compose two flows to induce a third flow and enforce consistency among the three. The composed flows may arise from (i) image pairs, yielding cycle consistency; (ii) multiple video frames, producing longer-range motion through temporal chaining; or (iii) image pairs combined with controlled synthetic transformations, which becomes data augmentation. This triangular consistency introduces negligible computational overhead and requires no additional annotations. Since it is derived directly from the geometry of optical flow, it does not rely on model-specific assumptions and serves as a ``universal'' plug-and-play component for optical flow training. Experiments show consistent improvement across supervised, unsupervised, and transfer learning settings.

05.
arXiv (CS.CV) 2026-06-16

Parameter-Efficient Adaptation of SAM 3 for Automated ITV Generation from 4DCT Images

Four-dimensional computed tomography (4DCT) captures the full respiratory cycle of thoracic anatomy, yet current Internal Target Volume contouring workflows process each phase in isolation, discarding temporal coherence and leaving contours vulnerable to phase-specific artifacts. We present a lightweight framework that applies parameter-efficient fine-tuning to the Segment Anything Model 3 (SAM 3) via low-rank adaptation (LoRA) to align its text-prompted segmentation with the medical domain using only seven annotated 3D CT volumes. Furthermore, the framework incorporates a hard negative mining strategy to improve boundary discrimination in low-contrast thoracic regions. At inference, phase-wise predictions are refined through phase-coherent temporal filtering and spatial connectivity analysis. Since respiratory motion is continuous and periodic, genuine anatomy appears in contiguous blocks of phases, whereas transient artifacts appear sporadically and are thus effectively suppressed. Experiments on pulmonary and cardiac structures yield median Dice scores of 0.968 and 0.910 with 95th-percentile Hausdorff distances of 0.998 mm and 2.931 mm, respectively. The proposed framework effectively eliminates the severe false-positive predictions inherent in the zero-shot inference of the unadapted SAM 3. With only seven annotated volumes, the framework retains over 95% of full-data accuracy, and the entire pipeline is trainable on a single consumer-grade GPU, demonstrating a scalable, data-efficient solution for adaptive radiotherapy.

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

Entropy-Aware On-Policy Distillation of Language Models

On-policy distillation is a promising approach for transferring knowledge between language models, where a student learns from dense token-level signals along its own trajectories. This framework typically uses reverse KL divergence, encouraging the student to match the teacher's high-confidence predictions. However, we show that the mode-seeking property of reverse KL reduces generation diversity and yields unstable learning signals when the teacher distribution has high entropy. To address this, we introduce Entropy-Aware On-Policy Distillation. Our key idea is augmenting the standard reverse KL objective with forward KL when teacher entropy is high, capturing the full range of plausible outputs while retaining precise imitation elsewhere. It balances mode-seeking precision with mode-covering robustness without sacrificing on-policy training efficiency. Experiments show that our method maintains generation diversity (sustained token-level entropy) and improves student-teacher alignment (lower forward KL on high-entropy tokens). Across six math reasoning benchmarks, this yields Pass@8 accuracy gains of +1.37 for Qwen3-0.6B-Base, +2.39 for Qwen3-1.7B-Base, and +5.05 for Qwen3-4B-Base compared to baseline on-policy distillation methods. These results demonstrate that accounting for teacher uncertainty is essential for maintaining diversity and achieving effective knowledge transfer.

07.
arXiv (CS.CV) 2026-06-16

Multi-HMR 2: Multi-Person Camera-Centric Human Detection, Mesh Recovery and Tracking

Most advances in human mesh recovery (HMR) have focused on pelvis-centered recovery, overlooking metric 3D localization and detection accuracy in the camera coordinate system - two key factors for real-world applications such as human-robot interaction and social scene understanding. Current evaluation protocols often ignore these aspects, emphasizing per-person, root-centered recovery rather than camera-space perception. As a result, existing approaches rely on fixed camera assumptions or handcrafted post-processing, limiting their robustness and practical deployment. We introduce Multi-HMR 2, a simple yet robust DETR-based framework for Multi-person Camera-centric Human detection, mesh Recovery, and tracking. Multi-HMR 2 predicts a scene-consistent camera together with human meshes, enabling metric 3D localization without ground-truth intrinsics. Moreover, by distilling image-based memory features from SAM2, Multi-HMR 2 extends to tracking, achieving consistent identity association without video supervision. Despite its conceptual simplicity - no handcrafted components, no video input, and no ground-truth cameras - Multi-HMR 2 achieves state-of-the-art pelvis-centered performance while substantially improving detection accuracy and metric 3D localization.

08.
medRxiv (Medicine) 2026-06-18

The relationship between serotonin transporter occupancy and extracellular serotonin concentration is hyperbolic, not linear: implications for safely tapering antidepressants

Background: Hyperbolic tapering is an increasingly recognized approach for discontinuing serotonin reuptake inhibitor (SRI) antidepressants that involves non-linear dose reductions with equal stepwise reductions in serotonin transporter (SERT) occupancy to mitigate withdrawal symptoms. Its theoretical basis is the hyperbolic relationship between SRI dose and SERT occupancy reported in radioligand imaging studies. Hyperbolic tapering implicitly assumes that changes in SERT occupancy approximate changes in biologic effect and withdrawal risk. Because SERT occupancy plateaus across the therapeutic dose range of SRIs, this framework predicts relatively small biologic effects and withdrawal risk within this range. However, SERT occupancy influences serotonergic activity only indirectly via its effects on extracellular serotonin concentrations, and the relationship between these two variables is poorly characterized. Methods: We developed a two-pathway clearance model derived from mass-action kinetics to evaluate the steady-state relationship between SERT occupancy and extracellular serotonin concentrations under chronic SRI treatment. Results: Our analysis indicates that serotonin concentrations increase hyperbolically as transporter occupancy increases, suggesting that biologically meaningful differences in serotonergic signaling persist across the therapeutic dose range of SRIs despite plateauing occupancy. Conclusions: Our model predicts a hyperbolic relationship between SERT occupancy and extracellular serotonin concentrations, suggesting that changes in occupancy may not map proportionally onto serotonergic effect. These findings provide a potential mechanistic explanation for dose-dependent clinical effects of SRIs despite plateauing transporter occupancy and generate testable hypotheses regarding antidepressant tapering strategies. Empirical validation is warranted.

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

Learning Topological Representations for Molecular Dynamics

arXiv:2606.14737v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings. Designing descriptors that are both expressive and broadly applicable, however, remains challenging. We study persistent homology (PH) as a general-purpose representation for MD and introduce the masked Flood complex, a protein-tailored modification of a recently introduced simplicial complex construction that emphasizes inter-residue structure at low computational cost. Vectorized persistence diagrams then provide information-rich, geometry-aware summaries of protein conformations, which we evaluate on protein class prediction, frame-level observable regression, and Markov state model (MSM) estimation from learned low-dimensional coordinates in a single shared representation space. Results on the mdCATH dataset show that PH-based descriptors are competitive across tasks, with masked Flood PH yielding the most consistent overall performance. Further, when using topologically-informed MSMs as a drop-in replacement within the recent MarS-FM framework for generative modeling of protein conformations, we obtain consistently better ensemble statistics than MSMs based on physical observables. Finally, we explore the transferability of the generative model to qualitatively different, fast folding, proteins.

10.
arXiv (quant-ph) 2026-06-15

On-site interactions in quantum thermal machines: efficiency, rectification and entanglement beyond local and global master equations

arXiv:2606.14593v1 Announce Type: new Abstract: Advances in experimental techniques have opened new routes for harnessing non-equilibrium dynamics in mesoscopic quantum systems. In this context, we study the impact of on-site interactions on the transport properties of a continuous quantum thermal machine composed of two coupled oscillators connected to two thermal reservoirs. In the weak system-reservoir coupling regime, where a long-standing debate concerns which reduced description should be preferred, we first show that the Redfield master equation (RME) provides an accurate and unifying framework that interpolates between two well-known limits: the local and global master equations. By relying on the Hierarchy of Pure States (HOPS), a numerically exact stochastic method, we then explore the full parameter space and show that interactions can be leveraged to tune the efficiency of the thermal machine at high temperatures (while leaving it essentially unchanged at low temperatures), induce non-reciprocal transport under asymmetric reservoir couplings, and generate steady-state entanglement within the junction. We derive expressions for system-bath correlators, such as heat and particle currents, consistently across different frameworks. Our work features on-site interactions to enhance the versatility of quantum thermodynamic junctions and clarifies the role of non-Markovianity and non-linearities in quantum transport.

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

Ultra Flash: Scaling Real-Time Streaming Video Generation to High Resolutions

While recent autoregressive video diffusion models achieve remarkable streaming quality, they remain confined to low resolutions (e.g., 480P), leaving efficient, scalable, real-time high-resolution video generation a fundamental open challenge. To bridge this gap, we present Ultra Flash, a cascaded streaming framework capable of real-time high-resolution video generation. Ultra Flash achieves ~30 FPS at 1K resolution and ~18 FPS at 2K resolution on a single GPU through three key contributions: (1) an architecture-preserving T2V-to-TV2V super-resolution training paradigm coupled with an AIGC-oriented data degradation pipeline that effectively preserves the generative capability of the base model, enabling enhanced high-resolution detail when cascaded after mainstream low-resolution generative models; (2) a causal streaming latent upsampler paired with a high-resolution decoder, which enhances spatiotemporal coherence while enabling efficient latent spatial scaling and precise high-resolution decoding with negligible computational overhead; and (3) a cascade high-resolution streaming video generation optimization scheme that first performs hybrid-reward-enhanced sparse causalization and single-step distillation of the super-resolution model, then introduces cascaded streaming self-forcing preference optimization with dynamic cache management, jointly enhancing overall coherence, improving quality, and enabling real-time high-resolution streaming video generation. Extensive experiments demonstrate that Ultra Flash reliably produces ultra-high-resolution streaming video while maintaining state-of-the-art visual quality and superior efficiency. Project Page: https://xin1u.github.io/UltraFlash/

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

Structural Role Injection in Handlebars-Templated LLM Prompts: Triple-Brace Interpolation, Delimiter Family, and the Limits of HTML Auto-Escaping

Large language model applications build prompts from templates, and Handlebars is a widely used templating engine and the default prompt-template format in Microsoft Semantic Kernel. Its double-brace {{x}} expression HTML-escapes the interpolated value and is documented as the safe default; its triple-brace {{{x}}} expression inserts the value raw. We show that this choice silently governs an application's exposure to structural role injection, where attacker-controlled data carries chat role delimiters that forge a higher-privilege turn. A model-free analysis establishes the mechanism: Handlebars escaping rewrites angle brackets but not square brackets, colons, or Markdown hashes, so it neutralises ChatML, Llama-3, and XML role delimiters (survival rate 0.00) while leaving Llama-2 [INST], legacy Human:/Assistant:, and Markdown ### delimiters intact (survival rate 1.00 for the last two). We then run 5760 trials across seven delimiter families, two attack objectives, and four models (GPT-3.5 Turbo, GPT-4o mini, GPT-4.1 mini, Claude Haiku 4.5) at a combined API cost of 1.63 USD. GPT-3.5 Turbo follows the task-hijack instruction in 97% of raw and 91% of escaped trials, with the escaping protection concentrated in the angle-bracket families and absent for the colon- and Markdown-based families; the harder secret-exfiltration objective, which does not saturate, exposes the same family interaction more cleanly. Claude Haiku 4.5 resists both objectives almost entirely. The escaped default protects only the delimiter schemes whose characters HTML escaping happens to cover, gives no protection for the rest, and cannot substitute for a structural separation of instruction and data.

13.
arXiv (CS.AI) 2026-06-12

APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization

arXiv:2606.12991v1 Announce Type: new Abstract: Cyclic peptides represent a promising class of therapeutic compounds in modern drug discovery, often offering improved stability and binding affinity. However, the de novo design of cyclic peptides remains challenging because methods must identify pocket-adaptive cyclization patterns and linkage sites while simultaneously controlling drug-relevant properties. This challenge is particularly pronounced for recent generative models trained predominantly on linear peptide data, which may fail to capture cyclization-specific constraints. To address the limitation, we introduce APCyc, a target-aware de novo cyclic peptide generation framework that explicitly models cyclization and jointly optimizes multiple essential physicochemical properties. By using an expanded residue vocabulary and explicitly encoding cyclization-site and linkage-type information, APCyc learns cyclization-aware representations and leverages Bayesian posterior guidance to steer sampling toward cyclic peptides satisfying multiple property objectives. Experimental results demonstrate that our model learns target-dependent cyclization preferences, and enables effective and controllable multi-property optimization for cyclic peptide design. The source code of this paper is available at https://github.com/HKUSTGZ-ML4Health-Lab/APCyc.

14.
arXiv (quant-ph) 2026-06-16

Quantum-classical hybrid models based on error correction for time series forecasting

arXiv:2606.15213v1 Announce Type: new Abstract: Time series forecasting largely benefits from combining the strengths of different models, especially using a scheme where a model corrects another model by capturing supplementary patterns from forecasting errors. Concurrently, quantum models are providing a means to augment the classical capacity, including in time series forecasting, by acting alongside classical models in hybrid architectures. In this work, we propose the first forecasting system based on error correction that jointly uses quantum and classical models. Here, quantum models first extract patterns by exploring quantum phenomena, and classical models capture the remaining patterns from the quantum errors. Compared to classical single models and classical-classical hybrid models based on error correction, the complementary capacity that emerges from this quantum-classical system provided the best results in most of the addressed problems. Therefore, this work paves the way to introduce quantum models in established hybridization schemes for time series forecasting.

15.
medRxiv (Medicine) 2026-06-22

The circulating blood proteome of childhood acute leukemia

The circulating blood proteome provides a systemic readout of disease biology and holds promise for advancing diagnostics and disease monitoring in pediatric leukemia. Here, we profiled 3072 proteins in diagnostic serum from 54 children with acute lymphoblastic leukemia (ALL), 21 with acute myeloid leukemia (AML), and 12 healthy controls using the Olink Proximity Extension Assay. We observed profound alterations in circulating protein levels in leukemia patients compared with controls and identified immunophenotype-specific proteins, including SIGLEC15 in B-cell precursor ALL (BCP-ALL), NOTCH1 in T-ALL, and CEBPA in AML, all which remained high even in patients with low (

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

Planning with the Views via Scene Self-Exploration

Can VLMs predict how each camera move changes the view, and plan many such moves ahead? We call this capability view planning, requiring (1)understanding how a single action transforms the view, and (2)composing many such transformations across multi-turn plans to identify a target view. We probe both abilities in our proposed ViewSuite, a 3D point-cloud environment on real ScanNet scenes. Across 13 frontier VLMs, a critical planning gap emerges: they possess basic view-action knowledge but fail to compose it across multi-turn plans, with the gap widening as viewpoint distance grows. To close this gap, we propose an iterative framework that alternates self-exploration with view graph distillation. The key insight is that all exploration trajectories, regardless of their outcome, collectively form a view graph that compactly captures how viewpoints connect across a scene. Distilling this graph into diverse supervised tasks reshapes the policy distribution and overcomes the sparse rewards that stall pure RL. This improves Qwen2.5-VL-7B from 2.5% to 47.8% on interactive view planning, surpassing GPT-5.4 Pro (18.5%) and Gemini 3.1 Pro (21.4%). Self-exploration emerges as a promising path toward VLMs that can actively reason and plan in 3D space. Code and Data are at https://viewsuite.github.io.

17.
arXiv (quant-ph) 2026-06-16

Decoherence-free algebras in quantum dynamics

arXiv:2403.12926v2 Announce Type: replace Abstract: In this Article we analyze the algebraic properties of the asymptotic dynamics of finite-dimensional open quantum systems in the Heisenberg picture. In particular, a natural product (Choi-Effros product) can be defined in the asymptotic regime. Motivated by this structure, we introduce a new space called the Choi-Effros decoherence-free algebra. Interestingly, this space is both a C*-algebra with respect to the composition product, and a B*-algebra with respect to the Choi-Effros product. Moreover, such space admits a direct-sum decomposition revealing a clear relationship with the attractor subspace of the dynamics. In particular, the equality between the attractor subspace and the Choi-Effros decoherence-free algebra is a necessary and sufficient condition for a faithful dynamics. Finally, we show how all the findings do not rely on complete positivity but on the much weaker Schwarz property.

18.
medRxiv (Medicine) 2026-06-12

An integrative multi-omics framework identifies epigenetic dysregulation of HAND2 as a potential primary driver of impaired enteric neural crest cell differentiation in Hirschsprung Disease

Hirschsprung disease (HSCR) is a congenital neurodevelopmental disorder characterized by segmental aganglionosis due to impaired developmental processes of enteric neural crest cells (NCCs). Despite being the leading genetic cause of functional intestinal obstruction in early childhood, HSCR represents a paradigmatic challenge in precision medicine: its multifactorial etiology, complex gene-environment interactions and limited resolution of single-modality analyses have long hindered mechanistic understanding and therapeutic translation. Here, we applied an integrative multi-omics approach combining genetic, phenotypic, epigenomic and transcriptomic analyses of matched ganglionic and aganglionic formalin-fixed paraffin-embedded (FFPE) patient tissues, complemented by patient-specific in vitro models. Beyond established genetic contributors, our integrative approach reveals novel regulatory pathways predominantly affecting enteric NCC differentiation, with convergent evidence pointing to epigenetic dysregulation as a primary disease mechanism. Notably, we identified over 1,300 differentially methylated positions between ganglionic and aganglionic FFPE samples, with HAND2 emerging as a key candidate due to multiple hypermethylated sites and consistently reduced expression levels in aganglionic tissues and in vitro models, suggesting a potential role in HSCR pathophysiology. We propose that our multi-omics approach offers a powerful and comprehensive framework for dissecting disease mechanisms. Beyond advancing biological understanding, this strategy holds promise for paving the way for molecularly informed patient stratification and supporting the development of personalized treatment and postoperative management strategies.

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

Discrete optimal transport is a strong audio adversarial attack

arXiv:2509.14959v3 Announce Type: replace-cross Abstract: In this paper, we investigate discrete optimal transport (DOT) as a black-box attack against modern automatic speaker verification (ASV) and anti-spoofing countermeasure (CM) systems. Our attack operates as a post-processing distribution-alignment step. Frame-level WavLM embeddings of generated speech (or another person speech) are aligned to an unpaired bona fide speech pool using entropic optimal transport and a top-k barycentric projection, followed by neural vocoding. Unlike gradient-based attacks, the proposed method requires no access to model parameters, gradients, or training data. Experiments on ASVspoof2019 and ASVspoof5 demonstrate that DOT attack substantially increases CM EER and substantially degrades ASV performance across multiple spoofing attacks. The attack transfers across datasets and remains effective after CM fine-tuning. Analysis using speaker similarity, Fréchet Audio Distance, and visualization of embedding distributions suggests that DOT succeeds by shifting source speech toward bona fide regions of the representation space rather than by maximizing speaker similarity. These results indicate that optimal-transport-based distribution alignment represents a previously underexplored attack vector for contemporary ASV and anti-spoofing systems.

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

Generativism: Toward a Learning Theory for the Age of Generative Artificial Intelligence

arXiv:2606.12441v1 Announce Type: cross Abstract: The four dominant learning theories of behaviorism, cognitivism, constructivism, and connectivism show significant conceptual limitations as generative artificial intelligence (AI) proliferates in educational settings. These frameworks were formulated before the emergence of AI systems capable of generating, synthesizing, and reasoning about knowledge. This article critically examines each learning theory and identifies assumptions challenged by generative AI's affordances. Drawing on research in distributed cognition, extended mind, human-AI collaboration, AI literacy, cognitive offloading, and metacognition, the article proposes Generativism as a learning theory for the generative AI age. Generativism posits that learning increasingly occurs through the iterative co-construction of knowledge between human learners and AI systems. The proposed framework is organized around four principles: epistemic partnership, distributed agency, generative literacy, and adaptive metacognition. The framework offers a foundation for rethinking instructional design, learning, assessment, and expertise development in contexts where generative AI plays an integral role in cognition.

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

Quest for quantum advantage: Monte Carlo wave-function simulations of the Coherent Ising Machine

arXiv:2501.02681v2 Announce Type: replace Abstract: The Coherent Ising Machine (CIM) is a quantum network of optical parametric oscillators (OPOs) intended to find ground states of the Ising model. This is an NP-hard problem, related to several important minimization problems, including the max-cut graph problem. In order to enhance its potential performance, we analyze the coherent coupling strategy for the CIM in a highly quantum regime. To explore this limit, without assuming gaussianity, we employ accurate numerical simulations. Due to the inherent complexity of the system, the maximum network size is limited. While master equation methods can be used, their scalability diminishes rapidly for larger systems. Instead, we use Monte Carlo wave-function methods, which scale as the wave-function dimension, and use large numbers of samples. These simulations involve Hilbert spaces exceeding $10^{7}$ dimensions. To evaluate success probabilities, we use quadrature probabilities. We demonstrate the potential for quantum computational advantage by reducing the time required to reach maximum success probability in a low-dissipation regime enabled by initial quantum superpositions and entanglement. Furthermore, we demonstrate that tailored time-dependent couplings can amplify these quantum effects. Comparisons with classical CIM models give evidence that quantum tunneling effects in this strong coupling limit can overcome trapping in false minima. This can greatly increase success rates, indicating a potential for quantum advantage. Finally, we perform a coherence analysis based on the state purity to examine the role of quantum coherence in CIM performance and to determine how state purity correlates with improved optimization outcomes.

22.
bioRxiv (Bioinfo) 2026-06-11

DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics

De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides without relying on protein sequence databases. Recent advances in deep learning have substantially improved the performance of de novo sequencing methods, but the rapid emergence of new models has led to heterogeneous evaluation practices and limited comparability. To address this, we introduce DLDN-Bench, a benchmark framework including a set of benchmark datasets derived from human muscle biopsy mass spectrometry data retrieved from PRIDE and annotated through consensus across multiple widely used database search engines. Using these datasets, we systematically benchmark recent deep learning-based de novo sequencing tools alongside traditional approaches. Performance is assessed using established metrics, including precision and coverage relative to a pseudo-ground truth defined by cross-engine agreement. To demonstrate the utility of DLDN-Bench, we benchmark four recent deep learning models and make all results publicly available. This benchmark framework provides a standardized basis for comparing state-of-the-art methods and offers an extensible resource for evaluating future tools in de novo peptide sequencing.

23.
arXiv (quant-ph) 2026-06-19

Propagating Collective Spin-valley Modes in Twisted WSe2

arXiv:2507.18770v2 Announce Type: replace-cross Abstract: The emergence of neutral collective modes is a hallmark of correlated quantum phases but is often challenging to probe experimentally. In two-dimensional flatband systems, charge responses have been intensively investigated yet neutral excitations remain largely unexplored. In particular, intervalley coherent state (IVC) features a neutral Goldstone mode due to spontaneously broken valley U(1) symmetry. While IVC state has been proposed as a unifying theme across graphene and semiconductor based systems, its defining feature, the neutral Goldstone mode, remains elusive in experiment. Here we investigate space and time resolved transport of neutral modes in twisted WSe2 moire superlattices through a novel ultrafast imaging technique. We uncover two new propagating collective modes with very different velocities, which emerge near the van Hove singularity (VHS) in both intermediate (3.5 to 4 degree) and large (around 5 degree) angle twisted WSe2. The fast-propagating mode has a large speed of about 3 km/s and is consistent with a Goldstone mode for an IVC state, while the slow-moving mode is likely a gapped amplitude mode. They can be understood as the spin-valley analogues of collective modes of a superfluid, whose propagation is imaged for the first time in a condensed matter system. Our study demonstrates a powerful new approach for probing charge-neutral modes in quantum materials and offers key insights into the interplay between charge and spin-valley physics in moire superlattices.

24.
arXiv (CS.AI) 2026-06-15

When the Tool Decides: LLM Agents Defer Blindly to Graph Neural Network Tools, and Stronger Backbones Defer More

arXiv:2606.14476v1 Announce Type: new Abstract: A growing line of work equips large language model (LLM) agents with graph neural networks (GNNs) as callable tools, assuming the agent exercises judgment over when and how much to rely on such a tool. We test this directly. We expose a frozen GNN to a ReAct-style LLM agent as an explicit tool and measure, on node classification over a text-attributed graph (ogbn-arxiv, replicated on WikiCS), whether the agent uses the tool or merely obeys it. We find the agent does not exercise judgment: its predictions agree with the raw GNN's 97.6-99.2% of the time (5 seeds), collapsing into a GNN parrot that adopts the tool's output wholesale and bypasses its own reasoning. Sweeping backbone capability (Qwen2.5 0.5B-7B), the deference is not a weak-model artifact: among models able to invoke the tool, agreement rises with capability (0.60 to 0.98 from 1.5B to 7B). Crucially, the cost of deference does not shrink as capability grows and grows where alternatives emerge: a per-node oracle over the available actions beats the parrot by 0.09-0.18 at 3B and 0.12-0.22 at 7B, roughly doubling at high homophily, because the parrot is pinned to the frozen GNN while the agent's alternatives improve; at 7B a simple neighbour-label tool overtakes the GNN at high homophily (0.81 vs 0.71) yet the agent still defers. A simple selective-invocation gate recovers about half of that high-homophily gap (0.71 to 0.83) but yields no net global gain, and held-out estimates bound the best achievable gate over standard test-time features to at most a third of the oracle headroom: reliable selective invocation looks limited by available information, not merely router design. Our results are a cautionary measurement: evaluations of agent+tool systems cannot assume the agent adds judgment on top of the tool, and selective invocation must be designed in rather than expected to emerge from scale.