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01.
arXiv (CS.AI) 2026-06-18

AI Sandboxes: A Threat Model, Taxonomy, and Measurement Framework

arXiv:2606.18532v1 Announce Type: cross Abstract: AI systems are increasingly evaluated in bounded environments that combine isolation, simulation, instrumentation, supervision, and evidence capture. For physical AI, AIoT, and cyber-physical systems, this shift is not a matter of terminology: the system under test may sense, decide, actuate, communicate, and fail through physical processes, networked devices, and human operators. This article develops an assurance-oriented account of AI sandboxes as controlled environments for testing, evaluation, verification, and validation across digital AI, embodied autonomy, and cyber-physical deployments. We formalize the sandbox boundary and a weakest-link rule for composing per-dimension evidence into a bounded deployment claim; separate major sandbox archetypes; define a cyber-physical threat model that includes attacks on the assurance apparatus itself; and introduce a measurement framework spanning fidelity, controllability, observability, containment, reproducibility, and governance artifacts, instantiated on three worked case studies of real sandboxes. The resulting threat model, taxonomy, and measurement framework clarify what a sandbox can validly test, which risks it can contain, and what forms of evidence it can support for safety, security, and regulatory assurance.

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

Early Diagnosis of Wasted Computation in Multi-Agent LLM Systems via Failure-Aware Observability

arXiv:2606.01365v2 Announce Type: replace Abstract: Failure-aware observability diagnoses wasted computation in multi-agent LLM systems before final-answer evaluation can explain what went wrong. We propose a trace-based framework for a three-agent architecture – orchestrator, search agent, and execution agent – that converts structured events into online signals for loops, budget pressure, low information gain, and tool instability, then adds offline semantic grounding metrics and selective LLM-as-judge evaluation. On 165 GAIA validation traces under identical caps, 98 runs produce usable final answers and 67 fail or stop without one. Among warned failed runs, 58.1% of tokens are spent after the first warning on average, indicating substantial opportunity for intervention. A 10-task Level-2 pilot uses warnings to diversify search or require evidence, reducing post-warning token fraction from 0.638 in the baseline to 0.304. The results support a layered design: cheap online signals help the orchestrator redirect or halt redundant behavior, while deeper semantic checks identify whether completed answers are grounded enough to trust.

03.
arXiv (CS.LG) 2026-06-18

SCOPE-FL: A Strategy-proof Chain-based Optimal pareto efficient Federated Learning System

arXiv:2606.18384v1 Announce Type: new Abstract: Hierarchical Federated Learning (HFL) enables scalable collaborative model training across distributed devices while preserving data privacy. However, existing HFL client selection mechanisms suffer from a fundamental strategic inefficiency. By prioritizing stability over Pareto efficiency (PE), they produce suboptimal resource allocations, and without strategy proofness (SP), participants are incentivized to misrepresent their true preferences, both failures degrading system overall welfare in the Pareto sense in practice. To address it, we propose SCOPE-FL (Strategy-proof Chain-based Optimal pareto efficient Federated Learning), a synchronous HFL framework that formulates client selection as a two-sided school choice problem solved through the Top Trading Cycle (TTC) algorithm that simultaneously guarantees PE and SP. For reward distribution, SCOPE-FL employs a scalable Shapley value approximation based on One-Round Reconstruction (OR), ensuring compensation proportional to each client's contribution. The entire mechanism executes via blockchain smart contracts, providing the tamper-proof environment required for the SP guarantees to hold in practice. A comprehensive evaluation on MNIST, Fashion-MNIST, and CIFAR-10 demonstrates that SCOPE-FL outperforms state-of-the-art approaches, including DA, IAS, and other methods across model accuracy, convergence rate, and reward efficiency, while achieving communication latency comparable to DA and blockchain overhead significantly lower than DA at scale.

04.
arXiv (CS.AI) 2026-06-18

TMR-GGNN: Credit Card Fraud Detection based on Time-Aware Multi-Relational Guided Graph Neural Network

arXiv:2606.18444v1 Announce Type: cross Abstract: In recent years, credit card fraud detection has faced significant challenges due to highly imbalanced data, evolving fraud patterns, and complex relational structures among transaction entities. To address these issues, this research proposes a novel framework called Timeaware Multi Relational Guided Graph Neural Network (TMR GGNN). Particularly, the proposed TMR GGNN extends the encoder decoder Graph Neural Network GNN architecture by modeling heterogeneous interactions across customers, merchants, devices, and IPs over temporal windows. Subsequently, the proposed TMR GGNN approach constructs a dynamic, multi relational graph and incorporates a time aware relational attention mechanism within the encoder to adaptively weigh the transaction relevance based on temporal proximity and semantic context. Consequently, the decoder employs a contrastive learning module to distinguish between real and synthesized transaction patterns, while improving the models generalization of rare fraud cases. Additionally, to effectively manage severe class imbalances and emphasize discriminative learning, a composite loss function combining Information Noise Contrastive Estimation (InfoNCE) based contrastive loss with Focal Loss is introduced. This integration assists in improving fraud identification while mitigating false negatives.

05.
arXiv (CS.LG) 2026-06-17

Learning to Refine Hidden States for Reliable LLM Reasoning

arXiv:2606.17524v1 Announce Type: new Abstract: Large language models show strong reasoning ability, but their internal reasoning process can remain unstable in complex multi-step settings, where early hidden-state errors may propagate to incorrect predictions. We propose ReLAR, a reinforcement-guided latent refinement framework that iteratively updates hidden representations before decoding. ReLAR maintains a compact latent reasoning state and uses learned depth and action controllers to adaptively determine both the number and direction of refinement steps. The controllers are trained with a policy gradient objective based on step-wise likelihood improvement, enabling efficient input-dependent reasoning without explicit chain-of-thought generation. Experiments on medical, mathematical, multi-hop reasoning, and open-ended generation benchmarks show that ReLAR improves accuracy, generation quality, and reasoning stability with substantially lower inference overhead than explicit reasoning baselines.

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

Smooth time-dependent control of dipolar Bose-Einstein condensates

arXiv:2606.20507v1 Announce Type: cross Abstract: We consider protocols for control of dipolar Bose-Einstein condensates where the critical role is played by the long-range anisotropic interatomic magnetic dipole-dipole interaction. The phase diagram of such a condensate has been explored theoretically and experimentally with certain values of the interatomic scattering length corresponding to superfluid and supersolid phases, where supersolidity appears as a modulation in the ground state density. Preparation of this modulated ground state is challenging, since excitations appear as a result of a finite-time evolution required to produce qualitative changes in the wavefunction density. To solve this problem we consider the time-dependent control of a dipolar Bose-Einstein condensate using shortcuts to adiabaticity techniques, concentrating on design of the time-dependent scattering length, a parameter of the system easily tunable by contemporary experiments. The first technique is the variational approach based on the Euler-Lagrange equations for a separable ansatz describing the evolution of the superfluid state. Secondly, we study the transition from superfluid to supersolid using a direct optimization protocol. We discuss the fidelity of the developed protocols in terms of the evolution time.

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

Leptomeningeal Collateral Detection on DSA via Vessel-Graph Neural Networks

Leptomeningeal collaterals (LMCs) are an important prognostic factor in acute ischemic stroke. Existing automated methods rely on CT angiography (CTA), but individual LMCs are often too small to be resolved on CTA, limiting these methods to coarse collateral scoring. Digital subtraction angiography (DSA) visualizes individual collaterals at superior resolution, yet current assessment remains subjective, relying on manual grading scales that suffer from poor inter-rater agreement. We present a framework that formulates collateral detection as the classification of individual vessel segments on a graph derived from DSA. A hybrid graph-pixel architecture combines a topology-aware graph branch with a dense pixel branch, fused in a shared node-probability space. In a five-fold cross-validation setting, the fused model achieves a PR-AUC of 0.434, outperforming the graph-only (0.403) and pixel-only (0.362) baselines. To our knowledge, this is the first method to enable the individualization of LMCs in DSA, allowing for precise per-vessel quantitative assessment. This integration shifts DSA assessment toward objective evaluation, supporting future biomarker and pattern discovery for individual LMCs.

08.
arXiv (CS.LG) 2026-06-19

Score Approximation for Diffusion Models on Arbitrary Low-Dimensional Structures

arXiv:2606.19894v1 Announce Type: new Abstract: The remarkable success of score-based diffusion models has spurred significant efforts to establish their theoretical foundations. However, existing complexity bounds for score approximation rely heavily on restrictive assumptions like Lipschitz continuous densities or smooth manifold supports, which are routinely violated by the singularities, sharp boundaries, and disjoint clusters inherent to real-world perceptual data. This work establishes a universal score approximation theorem that works for any distribution supported on any compact set of upper Minkowski dimension $d$. Using a novel discrete-mixture formulation, we prove that the score function can be approximated with a ReLU network whose complexity grows exponentially only with $d$, thus breaking the exponential curse of ambient dimensionality. Combined with existing theories on accurately solving the backward diffusion SDE for arbitrary compact distributions, our work shows that diffusion models readily adapt to irregular, non-smooth data structures, explaining their competence in real-world generative tasks.

09.
arXiv (CS.CV) 2026-06-12

Budget-Constrained Step-Level Diffusion Caching

Step-level caching accelerates diffusion models by exploiting temporal redundancy across denoising steps. Existing methods make per-step cache decisions using threshold-based heuristics, without directly optimizing for final output quality. As a result, their inference latency varies across inputs and is difficult to control at deployment. In this work, we propose BudCache, which inverts this formulation: rather than letting per-step error thresholds dictate the runtime cost, we fix the compute budget in advance and search for the cache policy that best preserves the final output. To tackle the combinatorial complexity of step selection, we combine Simulated Annealing with deterministic Hill Climbing. This offline search identifies high-quality cache policies within minutes and introduces no online search or thresholding overhead during inference. When the compute budget is very tight, we further introduce cache-aware schedule alignment, which adapts the time discretization to the selected cache policy to reduce cache-induced trajectory mismatch. Experiments on FLUX.1-dev and Wan2.1 show that BudCache achieves better generation quality than heuristic caching baselines under the same inference budgets. Code is available at https://github.com/Westlake-AGI-Lab/BudCache

10.
arXiv (quant-ph) 2026-06-16

Improved Cryogenic Photodiode Optical Biasing for Low-Noise and Low-Jitter Superconducting Nanowire Single-Photon Detectors

arXiv:2606.07140v2 Announce Type: replace Abstract: We experimentally demonstrate an improved optical biasing scheme for superconducting nanowire single-photon detectors (SNSPDs), which employs a cryogenic InGaAs-InP photodiode (PD) as a local bias source. It is found that, under illumination from a stable external light source, this PD generates a stable photocurrent in a cryogenic environment (~2.3 K), with fluctuations in the photocurrent primarily attributed to fluctuations in the incident optical power. Furthermore, by screening and effectively blocking stray photons leaking from the PD, which give rise to background dark counts, we have achieved an SNSPD exhibiting an ultra-low intrinsic dark count rate of 1e-4 cps. Utilizing this improved optical biasing technique, our SNSPD achieved performance comparable to that obtained under conventional electrical biasing: a system detection efficiency of 80.7%, a background dark count rate of 32.6 cps, and a minimum timing jitter of 57.5 ps. These results indicate that cryogenic-PD-based optical biasing serves as a viable, low-noise, and low-jitter alternative to traditional electrical biasing. Moreover, this work offers useful design guidance for the future development of PD-based low-noise bias sources and for the construction of all-photonic SNSPD systems tailored for high-precision quantum photonics applications.

11.
bioRxiv (Bioinfo) 2026-06-11

EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

Inverse-folding models can rapidly generate protein sequences compatible with a supplied backbone, but unconstrained redesign is poorly suited to enzyme and genome-editor-associated domains, where catalytic, substrate-proximal, and conserved structural regions must remain protected. In this paper, we present EditorForge, a modular constraint-and-audit suite for editor-domain protein redesign that wraps fixed-backbone inverse folding with explicit design masks, fixed-position enforcement, active-site-proximity auditing, active-site-shielded regeneration, and downstream structural quality control. Using full-length Moloney murine leukemia virus reverse transcriptase structure 4MH8 (MMLV RT 4MH8) as a demonstration target, EditorForge first restricted redesign to a bounded 25-position envelope while fixing 428 residues. An initial audit detected active-site-proximal failure modes despite fixed-position integrity. Later, the Active Site Shield module then removed five unsafe design positions, replaced them with lower-contact alternatives, and regenerated candidates under stricter constraints. Post Shield Audit evaluated 24 regenerated candidates, all of which satisfied the hard sequence/mask and active-site-shield constraints. For the eight candidates that were selected or returned for structure-prediction/refolding quality control. Enhanced RefoldQC found that all 8 evaluated predicted structures passed the computational structure-QC screen. That said, the selected 8 candidates passed the computational structure-QC screen, with global C RMSD values of 1.2061–1.5555~[A], active-site C RMSD values of 0.4098–1.8397~[A], mutation-neighborhood C RMSD values of 1.3155-1.6848~[A], and average pLDDT-like confidence values of 94.87-95.11. In short, EditorForge provides a reproducible triage layer that converts general inverse-folding output into constrained and editor-specific candidate sets for downstream structural and biological review on top of existing structural prediction tools.

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

Visual Place Recognition in Forests with Depth-Aware Distillation

Visual place recognition in natural forest environments remains challenging due to repetitive vegetation, weak structural cues, and significant appearance variation across traversals. To address this limitation, this paper proposes a lightweight depth-aware distillation framework that injects geometric cues into a DINOv2-based place recognition model, while maintaining its pre-trained descriptor space. Evaluated on the recent WildCross benchmark, the proposed approach yields gains over an appearance-only counterpart, providing robustness to appearance variations. These results demonstrate the importance of depth as a strong complementary modality for place recognition in natural environments and identify depth-aware distillation as a promising direction for more robust forest perception.

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

HAARES Half-Split Residual Basis Routing for Deep Transformers

作者:

arXiv:2606.06564v2 Announce Type: replace-cross Abstract: Block-level residual routing makes learned residual aggregation practical by routing over block summaries, but each summary compresses an ordered sequence of attention and MLP updates into one cumulative vector. We propose \method{}, a lightweight residual basis router that keeps the cumulative block source and adds one half-split detail basis, computed as the difference between first-half and second-half residual updates. The detail basis is RMS-matched and updated online, exposing coarse intra-block trajectory information without dense sublayer-level routing. Across OpenWebText, cross-domain character-level benchmarks, and BPE-tokenized OpenWebText, the empirical pattern is depth-dependent: gains are small or mixed at shallow depth and most reliable in 48-layer models. In the 201M 48-layer setting, \method{} improves over Block AttnRes across all three seeds, while a 453M two-seed probe shows the same direction. Ablations rule out source duplication, random signed details, fixed detail-source biases, or block-count changes alone. Cost analysis shows that the method is FLOP-light but not wall-clock-free: it adds memory and routing overhead, yet its relative arithmetic cost is amortized as width grows and earlier convergence can reduce time-to-target.

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

Constraining the outputs of ReLU neural networks

arXiv:2508.03867v2 Announce Type: replace-cross Abstract: We introduce a class of algebraic varieties naturally associated with ReLU neural networks, arising from the piecewise linear structure of their outputs across activation regions in input space, and the piecewise multilinear structure in parameter space. By analyzing the rank constraints on the network outputs within each activation region, we derive polynomial equations that characterize the functions representable by the network. We further investigate conditions under which these varieties attain their expected dimension, providing insight into the expressive and structural properties of ReLU networks.

15.
arXiv (quant-ph) 2026-06-12

Trading symmetry for Hilbert-space dimension in Bell-inequality violation

arXiv:2601.02893v3 Announce Type: replace Abstract: In quantum information, asymmetry, i.e., the lack of symmetry, is a resource allowing one to accomplish certain tasks that are otherwise impossible. Similarly, in a Bell test using any given Bell inequality, the maximum violation achievable using quantum strategies respecting or disregarding a certain symmetry can be different. In this work, we focus on the symmetry involved in the exchange of parties and explore when we have to trade this symmetry for a lower-dimensional quantum strategy in achieving the maximal violation of given Bell inequalities. For the family of symmetric Collins-Gisin-Linden-Massar-Popescu inequalities, we provide evidence showing that there is no such trade-off. However, for several other Bell inequalities with a small number of dichotomic measurement settings, we show that symmetric quantum strategies in the minimal Hilbert space dimension can only lead to a suboptimal Bell violation. In other words, there exist symmetric Bell inequalities that can only be maximally violated by asymmetric quantum strategies of minimal dimension. In contrast, one can also find examples of asymmetric Bell inequalities that are maximally violated by symmetric correlations. The implications of these findings on the geometry of the set of quantum correlations and the possibility of performing self-testing therefrom are briefly discussed.

16.
arXiv (CS.CL) 2026-06-18

LLM Compression by Block Removal with Constrained Binary Optimization

In this paper, we formulate the compression of large language models (LLMs) by optimally deleting transformer blocks (``block removal'') as a constrained binary optimization (CBO) problem that can be mapped to a physical system (Ising glass), whose energies are a strong proxy for downstream model performance. This formulation enables an efficient ranking of a large number of candidate block-removal configurations yielding many high-quality, non-trivial solutions beyond those only removing consecutive regions. Our method performs strongly in the deep compression regime, such as for 50% compression of Llama-3.3-70B-Instruct, where we achieve an almost 23 percentage point increase on the MMLU benchmark compared to other state-of-the-art (SOTA) block-removal methods. For lighter compression, it performs on par with those methods across several benchmarks for Llama-3.1-8B-Instruct, Qwen3-14B (both before and after retraining), as well as Llama-3.3-70B-Instruct. The approach is computationally efficient and requires only forward and backward passes on a calibration dataset for a few active parameters. Additionally, we demonstrate that using good heuristic solvers for the CBO problem provides solutions that perform well on downstream tasks in negligible runtime when it is unfeasible to solve the problem exactly. The method can be readily applied to any architecture. We illustrate this generality on the recent NVIDIA-Nemotron-3-Nano-30B-A3B-FP8 model, which exhibits a highly inhomogeneous and challenging block structure, and where we outperform SOTA for AIME25 and GPQA when removing either 2 attention layers or 3 mixture-of-experts layers.

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

Multi-Bitwidth Quantization for LLMs Using Additive Codebooks

As large language models (LLMs) are increasingly deployed across heterogeneous hardware with varying resource constraints, the ability to adaptively manage the trade-off between performance and efficiency without retraining is critical. We propose Drop-by-Drop, a novel multi-bitwidth post-training quantization framework that enables inference-time precision control over LLM weights from a single trained model. Our method is theoretically grounded in information theory and successive refinement. We establish that LLM weights, which commonly follow a Gaussian distribution, can be optimally reconstructed with increasing fidelity as additional bits are incorporated, under a weighted mean squared error distortion motivated by LLM loss functions. To realize this in practice, Drop-by-Drop incorporates Matryoshka-style supervision into the loss function, exploiting the structure of additive codebooks. Drop-by-Drop produces a single model where ordered subsets of codebooks yield accurate partial reconstructions at each precision level. This approach significantly reduces storage and memory overhead by allowing a single checkpoint to serve multiple bitwidths, while maintaining competitive perplexity and accuracy across major architectures, such as Qwen, LLaMA, Gemma, and Mistral.

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

TerraBench: Can Agents Reason Over Heterogeneous Earth-System Data?

arXiv:2606.13148v1 Announce Type: new Abstract: Climate and environmental decision-making increasingly requires reasoning across heterogeneous inputs, including gridded physical data, satellite imagery, geospatial context, and simulator outputs. Weather and climate foundation models can forecast well, but do not reason interactively in language, while large language models (LLMs) reason in language but cannot operate directly on high-dimensional Earth-system data. As a result, real scientific workflows in Earth-science remain underserved. We introduce TerraBench, a benchmark for grounded Earth-science reasoning, built on TerraAgent, a ReAct-style executable framework that interleaves reasoning, tool calls, and observations to couple LLM planning with scientific tools for environmental retrieval, geospatial processing, simulation, and artifact-backed computation. TerraBench unifies analysis of Earth observation imagery, gridded data, GIS reasoning and simulation in a single executable interface, whereas prior benchmarks isolate these capabilities into narrow individual tasks. It is also the first in this space to pair process-level tool-use metrics with tolerance-aware numeric scoring. The benchmark comprises 403 extensive agentic tasks across three tracks (Fundamentals, Simulator-Grounded, and Document-Grounded Verification) and eight application domains with 24,500 verified execution steps. These results indicate that reliable Earth-science agents must go beyond tool access to coordinate heterogeneous workflows, parameterize tools precisely, and preserve artifact provenance.

19.
arXiv (CS.CL) 2026-06-18

Attention as Frustrated Synchronization

A network of oscillators that synchronizes perfectly computes nothing further, so an attention architecture built from synchronization must locate its computation in structured departures from agreement. We introduce the Frustrated Synchronization Network (FSN), whose token states are phases on a torus and whose entire value pathway is one learned complex coupling kernel over harmonics and a one-step delay. Each component of the kernel is a frustration in the sense of the synchronization literature. The complex phases are static Kuramoto-Sakaguchi frustration angles, the signed harmonics are repulsive Daido components, and the delay term, which couples each token to the successors of the tokens it attends to, is algebraically identical to Kuramoto-Sakaguchi coupling whose frustration angle is the data's own transition, so next-token prediction is implemented as synchronization frustrated by the data. At matched one-million-parameter and training budgets on character-level text and code, the FSN's validation loss is below a tuned RoPE-SwiGLU transformer's at every epoch measured, and the comparison survives training the baseline to convergence: every thirty-epoch enwik8 seed finishes below the transformer's converged fifty-epoch loss of 1.611, and the FSN's completed fifty-epoch runs converge to 1.5953 +/- 0.0014. A variant with every feed-forward block replaced by mean-field coupling to learned collective modes, leaving no multilayer perceptron in the stack, tracks the transformer. On natural text the unfrustrated base layer falls behind the converged transformer at every copy depth, worst on long-range copy events; the kernel reverses the deficit at every depth of four and beyond. Headline comparisons are at the one-million-parameter scale; a scale ladder is complete through four million parameters with the advantage persisting, and remaining arms are marked as in progress.

20.
arXiv (quant-ph) 2026-06-11

Expressivity of Quantum Reservoir Computers

arXiv:2501.15528v3 Announce Type: replace Abstract: Using Hamiltonian encoding to inject an input into parameterized quantum circuits (PQCs), the output of the PQC can be written as truncated Fourier series. In recent years, the expressivity of PQCs was established as the number of frequencies contained in this Fourier series. While this concept has also been applied to other quantum machine learning (QML) paradigms, a clear notion of expressivity for temporal information processing with quantum systems is still lacking. Here, we introduce such a notion to the field of quantum reservoir computing (QRC). We analytically derive an expression for the readouts showing that the output of a QRC can be interpreted as a multi-dimensional Fourier series. We give a formula for the growth of expressivity induced by the sequential information injection, which we corroborate with numerical simulations, calculating explicitly the number of multi-dimensional output functions which can be generated from the readouts. Our results show that the specific interplay between system size, input encoding, and memory time gives rise to a boundary on the system size beyond which it is obstructive to further increase the reservoir size in extreme scrambling systems. We propose a recipe for determining this maximal system size for a given QRC setup.

21.
PLOS Computational Biology 2026-06-15

WormSORT: A detection-based multiple object tracking model for individual silkworms in breeding environments

作者:

by Hongkang Shi, Linbo Li, Shiping Zhu, Haibo He, Minghui Zhu, Jianfei Zhang Variety breeding has long been a cornerstone of high-quality agriculture, and recent advances in artificial intelligence have opened new avenues for accelerating biological breeding. In this study, we applied multiple object tracking (MOT) technology to silkworm breeding to achieve efficient, non-invasive, and dynamic individual monitoring. Unlike pedestrian or vehicle tracking, silkworms pose unique challenges for MOT due to their small size, dense distribution, and high inter-individual similarity, which complicate accurate tracking and behavioral analysis. To address these issues, we propose WormSORT, an enhanced tracking method based on a tracking-by-detection framework with an optimized data association strategy. A pre-trained detection model identifies silkworms in each frame, and deep feature vectors are extracted using a re-identification network. Identity association is first performed using Intersection over Union (IoU) matching, followed by deep feature similarity for unmatched cases, improving both tracking accuracy and reliability. To further enhance tracking stability, we introduce a candidate input padding mechanism, including IoU padding and feature padding, ensuring that high-confidence unmatched trajectories and detections remain involved in the matching process. To validate the proposed tracking strategy, we constructed two multiple silkworm tracking (MST) datasets: MST-50, containing approximately 50 individuals over 1000 frames, and MST-100, containing approximately 100 individuals over 1200 frames. Experimental results demonstrate that WormSORT outperforms existing methods, including DeepSORT, StrongSORT, OCSORT, ByteTrack, and BotSORT, achieving superior tracking performance. This study provides a valuable reference for silkworm tracking and behavioral analysis, contributing to the advancement of high-quality silkworm rearing and management.

22.
bioRxiv (Bioinfo) 2026-06-11

An AI-Powered Trisomy 21 Research Assistant

Down syndrome, caused by trisomy 21, increases the risk of diverse co-occurring conditions. With more than 34,000 related publications indexed in PubMed as of early 2026, keeping pace with this expanding literature is challenging. While general-purpose large language models are widely used for information retrieval, they often rely on broad training data rather than specific evidence. Retrieval-augmented generation (RAG) improves rigor and reliability of responses by linking model outputs to source texts. In research, source texts are peer-reviewed articles. Standard implementations treat all manuscript sections equally, allowing background text to rank as highly as experimental results. To focus model outputs on experimentally supported responses, we developed the T21 Research Assistant, a section-aware RAG system that prioritizes Results sections to ground responses in primary experimental evidence. The system draws exclusively from 1,789 open-access Down syndrome publications from PubMed Central, including 327 NIH INCLUDE-funded studies, and uses a multistage pipeline for query validation, retrieval, reranking, synthesis, and citation verification. Built on NVIDIA Nemotron models, it generates structured, cited responses. Evaluation using expert-curated questions demonstrated strong performance, achieving a BERTScore F1 of 0.712 and recall of 0.758, comparable to or exceeding leading proprietary and open-source models. T21 Research Assistant is available at: https://bioinformatics.cuanschutz.edu/t21-res-assi/

23.
arXiv (CS.LG) 2026-06-17

Discovering Functionally Selective Brain Regions with a Deep Topographic Multimodal Model

arXiv:2606.09770v2 Announce Type: replace-cross Abstract: Nearby neurons in cortex share similar response profiles, producing systematic spatial organization across sensory and cognitive systems. Recent topographic models reproduce aspects of this structure but remain unimodal and spatially constrain each layer separately, yielding fragmented maps that capture neither the contiguity of cortical processing streams nor their integration across modalities. We introduce Topo-Omni, a topographic multimodal model in which visual, auditory, and language/cognitive processing share a single contiguous in-silico sheet. Built by fine-tuning a pretrained foundation model with a spatial smoothness objective, this architecture develops clusters across modalities that are consistent with human neuroimaging, from sensory to cognitive systems. Driving or suppressing a cluster selectively biases or impairs perception, paralleling human intervention studies. Finally, we use our model to screen for novel clusters in-silico and discover new natural landscape and animal networks which we validate in human data. A single spatial principle thus organizes representations across modalities and processing stages, yielding testable hypotheses about cortical organization.

24.
arXiv (quant-ph) 2026-06-15

Quantifying and detecting quantum-state texture

arXiv:2604.07257v2 Announce Type: replace Abstract: Quantum-state texture is a recently proposed quantum resource that characterizes the inhomogeneity of a quantum state's matrix element distribution in the computational basis, enriching our understanding of quantum state structure. To expand its quantification toolkit and establish detection methods, in this article, we investigate the resource theory of texture from both quantitative and detection perspectives. First, we construct a texture measure $\mathcal{T}^{GR}_{\alpha,z}(\rho)$ based on the $\alpha$-$z$ Rényi relative entropy and present some of its inherent properties. Second, we analyze the mathematical relationships between several existing texture measures, revealing connections among different quantifiers. Finally, drawing on the witness concept from other resource theories, we systematically introduce texture witnesses into the texture theory and provide examples of texture witnesses with special properties.

25.
arXiv (CS.AI) 2026-06-12

A Three-Layer Framework for AI in Scientific Discovery

作者:

arXiv:2606.13566v1 Announce Type: new Abstract: Current discussions of AI in scientific discovery are often dominated by two visible capabilities: search over existing knowledge and execution through optimization, simulation, and automation. Both are important, but neither fully captures the central act of discovery: the formation and evolution of models. This paper proposes a three-layer view of AI in discovery. Layer 1 is search and retrieval by large language models. Layer 2, as the main innovation of this paper, is model formation through qualitative reasoning: the capacity to recognize when a current framework is structurally inadequate and to understand the problem within a broader representational space, not through trial and error, but through structural insight into what is missing and where it can be found. Layer 3 is execution, optimization, and refinement. The main claim is that Layer 2 is both the most important and the least developed. Search without model formation remains confined to inherited frameworks, while execution without conceptual revision only amplifies an existing formulation. We illustrate Layer 2 reasoning through three case studies: S. S. Chern's intrinsic proof of the Gauss-Bonnet theorem, the resolution of the Nesterov Accelerated Gradient convergence problem via Lyapunov functions, and the autonomous disproof of the Erdos unit distance conjecture by OpenAI in 2026. Each case exhibits the same structural signature: a framework that had become inadequate, a missing conceptual object, and a resolution found in an unexpected neighboring field.