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01.
arXiv (CS.AI) 2026-06-17

Like a Hammer, It Can Build, It Can Break: Large Language Model Uses, Perceptions, and Adoption in Cybersecurity Operations on Reddit

arXiv:2604.09998v2 Announce Type: replace-cross Abstract: Large language models (LLMs) have recently emerged as promising tools for augmenting Security Operations Center (SOC) workflows, with vendors increasingly marketing autonomous AI solutions for SOCs. However, there remains a limited empirical understanding of how such tools are used, perceived, and adopted by real-world security practitioners. To address this gap, we conduct a mixed-methods analysis of discussions in cybersecurity-focused forums to learn how a diverse group of practitioners use and perceive modern LLM tools for security operations. More specifically, we analyzed 892 posts between December 2022 and September 2025 from three cybersecurity-focused forums on Reddit, and, using a combination of qualitative coding and statistical analysis, examined how security practitioners discuss LLM tools across three dimensions: (1) their stated tools and use cases, (2) the perceived pros and cons of each tool across a set of critical factors, and (3) their adoption of such tools and the expected impacts on the cybersecurity industry and individual analysts. Overall, our findings reveal nuanced patterns in LLM tools adoption, highlighting independent use of LLMs for low-risk, productivity-oriented tasks, alongside active interest around enterprise-grade, security-focused LLM platforms. Although practitioners report meaningful gains in efficiency and effectiveness in LLM-assisted workflows, persistent issues with reliability, verification overheads, and security risks sharply constrain the autonomy granted to LLM tools. Based on these results, we also provide recommendations for developing and adopting LLM tools to ensure the security of organizations and the safety of cybersecurity practitioners.

02.
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.

03.
arXiv (quant-ph) 2026-06-19

Universality in Ionic Three-body Systems Near an Ion-atom Feshbach Resonance

arXiv:2511.00325v3 Announce Type: replace-cross Abstract: We calculate bound and scattering properties of a system of two neutral atoms and an ion near an atom-ion Feshbach resonance. Our results indicate that long-range atom-ion interactions lead to significant deviations from universal behavior derived from contact or van der Waals potentials. We find that ionic systems display an overall suppression of inelastic transitions leading to recombination rates and lifetimes of Efimov state orders of magnitude smaller with respect to those for neutral atoms. We further characterize the dense spectra of triatomic molecular ions with extended lifetimes. Our results provide a deeper insight on the universality and structure of three-body ionic systems and establishing them as a promising platform for exploring novel few- and many-body phenomena with long-range interactions.

04.
arXiv (quant-ph) 2026-06-19

Quantifying Imaginarity in Neutrino Systems

arXiv:2412.01871v2 Announce Type: replace-cross Abstract: It is a fundamental question why quantum mechanics employs complex numbers rather than solely real numbers. In this work, we conduct the first analysis of imaginarity quantification in neutrino flavor and spin-flavor oscillations. As quantum systems in coherent superposition, neutrinos are ideal candidates for quantifying imaginarity within the resource theoretic framework, using measures such as the $\ell_1$-norm and the relative entropy of imaginarity. We show that in the case of two-flavor mixing, these measures of imaginarity are nonzero. The measures of imaginarity reach their extreme values when the probabilistic features of quantum theory are fully maximized, i.e., both the transitional and survival probabilities are approximately equal. Our study reveals that the imaginarity, as a resource, can be harnessed not solely from the presence of a complex phase in the mixing matrix but also from the intrinsic quantum dynamics of time evolution itself. We further extend our analysis to explore the dynamics of three-flavor neutrino mixing, incorporating the effects of a nonzero $CP$ phase.

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

Spatial Priors via Space Filling Curves for Small and Limited Data Vision Transformers

Though Vision Transformers (ViTs) have become the dominant backbone in many computer vision tasks, due to permutation equivariance, their attention mechanism lacks explicit spatial inductive biases. This become particularly important in two settings: when model capacity is small or training data is limited. Inspired by the attention masking strategies in Linear Transformers and the scanning patterns of Vision SSMs, we introduce VIOLIN, a lightweight masked attention mechanism that encodes spatial structure within attention via Space Filling Curves (SFCs) with less than 0.0015% extra parameters and negligible computational overhead. VIOLIN scans the image using multiple SFCs to construct curve-specific decay masks, which are then combined and multiplied with the attention matrix. Across a wide range of evaluations, VIOLIN consistently improves performance. In limited data regimes such as fine-tuning on VTAB-1K, it boosts accuracy across all task groups and by up to 8.7% on the tasks where spatial information is essential. It can be combined with parameter-efficient fine-tuning methods such as LoRA to further increase the performance. Beyond fine-tuning, VIOLIN improves various small scale ViT architectures (e.g., DeiT, DINO) during pretraining on ImageNet-1K. Additionally, on pixel-level CIFAR-100 training, a task that is highly dependent on location information, VIOLIN increases accuracy by up to 7.2%. Overall, VIOLIN provides a computationally efficient yet effective way to inject spatial inductive bias into ViTs, especially benefiting small models and limited data settings.

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

Asymmetric and chiral dynamics of two-component anyons with synthetic gauge flux

arXiv:2512.19139v3 Announce Type: replace-cross Abstract: In this work, we investigate the non-equilibrium dynamics in a one-dimensional two-component anyon-Hubbard model, which can be mapped to an extended Bose-Hubbard ladder with density-dependent hopping phase and synthetic gauge flux. Through numerical simulations of two-particle dynamics and the symmetry analysis, we reveal the asymmetric transport with broken inversion symmetry and two dynamical symmetries in the expansion dynamics. The expansion of two-component anyons is dynamically symmetric under spatial inversion and component flip, when the sign of anyonic statistics phase or the signs of gauge flux and interaction are changed. In the non-interacting case, we show the dynamical suppression induced by both the statistics phase and gauge flux. In the interacting case, we demonstrate that both chiral and antichiral dynamics can be exhibited and tuned by the statistics phase and gauge flux. The dynamical phase regimes with respect to the chiral-antichiral dynamics are obtained. These findings highlight the rich dynamical phenomena arising from the interplay of anyonic exchange statistics, synthetic gauge fields, and interactions in multi-component anyons.

07.
arXiv (CS.LG) 2026-06-12

DynamicPTQ: Mitigating Activation Quantization Collapse via Residual-Stream Dynamics

arXiv:2606.12487v1 Announce Type: new Abstract: Post-training quantization (PTQ) is essential for efficient large language model inference, but reliably quantizing activations remains challenging when weights, activations, and KV caches are all quantized to 4-bit precision. A key difficulty lies in massive activations, whose extreme values dominate the activation range and amplify quantization errors. State-of-the-art methods mainly mitigate massive activations through transformation-based smoothing, such as orthogonal rotations and affine scaling, but overlook the cross-layer dynamics of the residual stream. In this paper, we show that massive activations emerge and disappear in a phase-wise pattern across network depth, triggering large residual changes. These changes cause newly injected layer-wise updates to dominate the 4-bit quantization scale and weaken historical residual information. To characterize this behavior, we introduce Jump Ratio and Historical Feature SNR. This suggests that static transformation-based smoothing cannot fully resolve dynamic quantization instability caused by cross-layer residual changes. Based on this analysis, we propose DynamicPTQ, a Dynamic Post-Training Quantization policy for phase-aware mixed-precision activation quantization. DynamicPTQ identifies quantization-sensitive layers from residual-stream dynamics and assigns 8-bit activation precision only to these layers, while keeping weights, KV caches, and other activations in 4-bit precision. It can be directly integrated with strong PTQ baselines such as QuaRot, SpinQuant, and FlatQuant. Experiments on LLaMA-2 and LLaMA-3 show that DynamicPTQ consistently improves perplexity and zero-shot QA performance under W4A4KV4 quantization, while achieving 1.05 to 1.07 times throughput improvement with modest memory overhead. These results demonstrate a practical path toward robust low-bit LLM inference.

08.
arXiv (quant-ph) 2026-06-12

Reduced basis algorithm for solving nonlinear differential equations on quantum computers

arXiv:2606.13457v1 Announce Type: cross Abstract: As quantum computing moves toward scientific computing applications, nonlinear differential equations remain a central challenge since quantum evolution is intrinsically linear. In this work, we introduce a reduced basis algorithm (RBA) for polynomial nonlinear ordinary differential equations (ODEs) and spatially discretized partial differential equations (PDEs). After time discretization, the method composes the resulting polynomial update map over $m$ timesteps, identifies the reduced monomial basis appearing in this composed map, and constructs a linear RBA operator whose action recovers the exact $m$-timestep nonlinear dynamics. Thus, at the level of the chosen discrete update rule, the method introduces no additional approximation error beyond the time discretization error. The qubit number requirement is governed by the size of the reduced monomial basis. For an $n$-dimensional polynomial ODE system of degree $p>1$, the lifted register requires at most $q_m^{\mathrm{ODE}} = O(nm\log p)$ qubits in the full basis scenario. For PDEs discretized on $N^D$ grid points, a locality-based construction requires at most $q_m^{\mathrm{PDE}} = O(D\log N + n m^{D+1}\log p)$ qubits. Hence, the dependence on the grid size remains logarithmic, while the nonlinear overhead is controlled by local reduced basis size. The main computational burden is moved from the quantum computer to a classical preprocessing step, where the reduced monomial basis and RBA operator are constructed for the chosen timestep window. Through numerical tests on the Lorenz system and the one-dimensional Burgers equation, we verify that the RBA reproduces the corresponding discrete time nonlinear dynamics exactly, while exposing the trade-off between timestep composition, reduced basis growth, and locality.

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

Contrastive-Difference CKA Reveals Concept-Specific Structural Alignment Across Language Model Architectures

作者:

Do different LLM architectures encode high-level concepts in structurally compatible ways? We systematically characterize a geometric-functional universality dissociation: across multiple concept domains and architectural families, moderate geometric convergence coexists with near-perfect functional transfer. Using contrastive-difference CKA (CKA_Delta), a training-free diagnostic that computes kernel alignment on per-sample contrastive differences, we isolate concept-specific convergence from generic similarity – achieving significant discrimination where standard CKA cannot. The dissociation replicates across all six concept domains we test (five with p =70B models. We position CKA_Delta as a practical regime classifier and architectural outlier detector (Gemma: d = 1.08, AUC = 0.79) rather than an absolute transfer-accuracy predictor, providing a training-free diagnostic for cross-architecture concept monitoring.

10.
arXiv (CS.AI) 2026-06-15

Sorries Are Not the Hard Part: An Expert-Review Case Study of a Semi-Autonomous Formalization

arXiv:2606.13925v1 Announce Type: new Abstract: Large language models can often close proof gaps in interactive theorem provers, but a verified theorem is not the same thing as a reusable library contribution. We study this distinction through a detailed case study: a semi-autonomous formalization of Grothendieck's vanishing theorem. The initial version compiles with no sorries, but an expert review found serious problems in definitions, theorem generality, file organization, and the API. We then ran a review-driven refactor and compression process and obtained a second expert review. The before-and-after comparison shows a sharp split: agents adapted well to local, mechanically checkable feedback, but remained weak at choosing definitions and designing APIs. We argue that autoformalization should be evaluated not only by closed sorries, but by whether the resulting formalization survives expert review.

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

Non-Hermitian Delocalization Realizes Random Dirac Criticality in One Dimension

arXiv:2606.12089v1 Announce Type: cross Abstract: Non-Hermitian systems can evade Anderson localization and exhibit delocalized states even in one dimension. Here, we show that such non-Hermitian delocalized states under periodic boundary conditions (PBC) are intrinsically critical, realizing the universality class of one-dimensional random Dirac fermions. By linking spectral winding to topological Anderson transitions via Hermitization, we demonstrate that the delocalized PBC states exhibit a Dirac-type criticality with universal algebraic correlations. In contrast to Hermitian systems, where this criticality occurs only at fine-tuned transition points, it emerges generically in non-Hermitian systems as a consequence of spectral topology. These results identify a universal mechanism by which non-Hermiticity promotes criticality, providing a unified description of non-Hermitian delocalization in one dimension.

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

Efficient and simple Gibbs state preparation of the 2D toric code via duality to classical Ising chains

arXiv:2508.00126v2 Announce Type: replace Abstract: We introduce the notion of polynomial-depth duality transformations, which relates two sets of operator algebras through a conjugation by a poly-depth quantum circuit, and make use of this to construct efficient Gibbs samplers for a variety of interesting quantum Hamiltonians as they are poly-depth dual to classical Hamiltonians. This is for example the case for the 2D toric code, which is demonstrated to be poly-depth dual to two decoupled classical Ising spin chains for any system size, and we give evidence that such dualities hold for a wide class of stabilizer Hamiltonians. Additionally, we extend the above notion of duality to Lindbladians in order to show that mixing times and other quantities such as the spectral gap or the modified logarithmic Sobolev inequality are preserved under duality.

14.
Nature (Science) 2026-06-08

Targeting Cancer-Specific Mutations with RNA-Triggered Chromatin Shredding

作者:

Genetic mutations that drive cancer often occur in tumor suppressor proteins, including the p53 transcription factor which is altered in ~40-50% of cases1,2. However, current therapies fail to target most such mutations because the mutant proteins typically lack defined drug-binding pockets, and restoring the endogenous function has proven challenging. Here, we programmed CRISPR-Cas12a2, an RNA-guided nuclease with trans-nucleolytic cleavage activities3,4, to selectively kill cancer cells by targeting cancer-specific transcripts. This approach limits cell growth by inducing trans shredding of chromatin, triggering DNA damage responses and cell death. Unlike existing methods, RNA-guided Cas12a2 senses cellular RNA signatures, enabling precise targeting of undruggable mutations. Transcript-activated chromatin shredding provides a new approach to precision disease treatments for undruggable targets.

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

LaWAM: Latent World Action Models for Efficient Dynamics-Aware Robot Policies

arXiv:2606.15768v1 Announce Type: cross Abstract: Vision-Language-Action models (VLAs) leverage large-scale vision-language pretraining for semantic robot control, but often lack explicit foresight into how robot actions change the scene. World-Action Models (WAMs) address this limitation by conditioning policies on predicted futures, yet existing approaches typically rely on computationally expensive video generation with substantial pixel-level redundancy. We present LaWAM, a Latent World Action Model that exposes predictive dynamics to robot policies through compact latent visual subgoals instead of reconstructed future video. At the core of LaWAM is a latent-action-conditioned Latent World Model (LaWM). We obtain LaWM by training a latent action model in the latent space of a pretrained vision foundation model and repurposing its forward decoder to predict future observation features for scene evolution. LaWAM then conditions action generation on these predicted latent visual subgoals to enable dynamics-aware robot control. LaWAM achieves state-of-the-art or competitive success rates (SRs) across LIBERO (98.6% SR), RoboTwin (91.22% SR), and real-world manipulation tasks while retaining low-latency inference. LaWAM runs in 187 ms per action-chunk prediction and achieves up to 24x lower wall-clock latency than pixel-space WAMs.

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

Planning under Distribution Shifts with Causal POMDPs

arXiv:2602.23545v2 Announce Type: replace Abstract: In the real world, planning is often challenged by distribution shifts. As such, a model of the environment obtained under one set of conditions may no longer remain valid as the distribution of states or the environment dynamics change, which in turn causes previously learned strategies to fail. In this work, we propose a theoretical framework for planning under partial observability using Partially Observable Markov Decision Processes (POMDPs) formulated using causal knowledge. By representing shifts in the environment as interventions on this causal POMDP, the framework enables evaluating plans under hypothesized changes and actively identifying which components of the environment have been altered. We show how to maintain and update a belief over both the latent state and the underlying domain, and we prove that the value function remains piecewise linear and convex (PWLC) in this augmented belief space. Preservation of PWLC under distribution shifts has the advantage of maintaining the tractability of planning via $\alpha$-vector-based POMDP methods.

17.
arXiv (quant-ph) 2026-06-19

Complexity of detecting large coefficients in the Pauli basis

arXiv:2606.19545v1 Announce Type: new Abstract: We study the problem of deciding, given a mechanism to prepare a quantum state $\rho$ and a value $\varepsilon > 0$, whether there is some non-identity Pauli matrix $P$ such that $|Tr(P \rho)| \geq \varepsilon$. We consider that the state $\rho$ is described as the result of tracing out some of the qubits of a pure state prepared by a circuit $C$, and we assume the promise that either there is a Pauli matrix satisfying the stated condition or, instead, that for all non-identity Pauli matrices $P$ it is the case that $|Tr(P\rho)|\leq \varepsilon/2$. The problem is in $QCMA$, and we prove that if it belongs to $BQP$ then $NP \subseteq BQP$. The result is obtained through a reduction from the minimum-weight code problem, and it holds even when $\rho$ is assumed to be a pure state (i.e. when no qubits are discarded) and $\varepsilon$ is constant. This resolves an open question regarding the existence of efficient tomographic procedures to find the largest coefficients of a quantum state in the Pauli basis: namely, they do not exist under the standard hypothesis $NP \nsubseteq BQP$.

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

Learner-based Concept Drift Detection: Analysis and Evaluation

arXiv:2606.20216v1 Announce Type: cross Abstract: Machine learning algorithms deployed for evolving streaming environments must handle the non-stationary data distributions, commonly referred to as concept drift. The presence of concept drift poses a major challenge for many real-world applications because it can severely degrade their predictive performance, hindering their ability to support robust decision-making. Consequently, the timely and efficient detection of drift events is critical for sustaining high accuracy over time. This study examines theoretically the concept drift characteristics and numerous drift detection algorithms across several categories. Furthermore, we evaluate their performance on both synthetic and real-world datasets exhibiting diverse streaming scenarios and drift characteristics, such as abrupt and gradual changes. This study aims to enhance understanding of the complex notion of concept drift characteristics and behavior of drift detectors, along with their applicability to diverse contexts.

19.
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.

20.
arXiv (CS.CL) 2026-06-11

PRInTS: Reward Modeling for Long-Horizon Information Seeking

Information-seeking is a core capability for AI agents, requiring them to gather and reason over tool-generated information across long trajectories. However, such multi-step information-seeking tasks remain challenging for agents backed by language models. While process reward models (PRMs) can guide agents by ranking candidate steps at test-time, existing PRMs - designed for short reasoning with binary judgment - cannot capture richer dimensions of information-seeking steps, such as tool interactions and reasoning over tool outputs, nor handle the rapidly growing context in long-horizon tasks. To address these limitations, we introduce PRInTS, a generative PRM trained with dual capabilities: (1) dense scoring based on the PRM's reasoning across multiple dimensions of step quality (e.g., interpretation of tool outputs, tool call informativeness) and (2) trajectory summarization that compresses the growing context while preserving essential information for step evaluation. Extensive evaluations across FRAMES, GAIA (levels 1-3), and WebWalkerQA (easy-hard) benchmarks on multiple models reveal that best-of-n sampling with PRInTS enhances information-seeking in open-source models as well as specialized agents, matching or surpassing frontier models with a much smaller backbone agent and outperforming other strong reward modeling baselines.

21.
arXiv (CS.CL) 2026-06-16

Multimodal Evaluator Preference Collapse: Cross-Modal Contagion in Self-Evolving Agents

作者:

When AI agents use language models to evaluate their own outputs in a feedback loop, systematic biases emerge. We show that Evaluator Preference Collapse (EPC) is dramatically amplified in multimodal settings. Using GPT-4o to evaluate DeepSeek-chat across text and visual tasks, we find that a single strategy (step_by_step) absorbs 48.4% of all weight – 3.2x the collapse observed in text-only self-evaluation – while three visual-domain strategies receive only 9.1% combined weight. We then demonstrate a novel phenomenon we term cross-modal contagion: evaluator preferences acquired on one modality transfer to and corrupt strategy selection on another. Through a four-phase isolation training paradigm, we measure contagion coefficients and document strategy inversion – the optimal strategy for a modality reverses after cross-modal exposure. A Phase 3 statistical validation across four evaluator configurations (N=53 total independent repetitions, 15,592 API calls) reveals a clear hierarchy: cross-model evaluation (GPT-4o, N=8) produces strong but symmetric bidirectional contagion (mean gamma_{T->V}=1.176, gamma_{V->T}=1.089, Delta=-0.088, p=0.575, Cohen's d=0.29); high round counts (DashScope, 50 rounds) cause collapse to single-strategy dominance (70% zero contagion); and self-evaluation provides near-complete immunity – 97% of runs (N=30, DeepSeek-chat) yield exactly zero contagion (mean gamma=0.033, 95% CI [-0.031, 0.010], p=0.642, d=0.07). No evaluator condition shows statistically significant directional asymmetry. We introduce the contagion matrix indexed by evaluator identity, release the MM-EPC experimental framework, and identify cross-model evaluator architecture as the primary risk factor for preference contagion.

22.
arXiv (CS.AI) 2026-06-17

A homotopy-type-theoretic generalization of neurosymbolic inference

arXiv:2606.17851v1 Announce Type: new Abstract: A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $\sigma$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $\sigma$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Replacing the underlying sets by types, in the sense of homotopy type theory, preserves this information, and turns this functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.

23.
bioRxiv (Bioinfo) 2026-06-18

Accounting for allelic diversity and multicopy gene detection improves the accuracy of antibiotic resistance genotypic determination

Background Genomic prediction of antimicrobial resistance (AMR) relies on the accurate detection of resistance genes or allelic variants of core genes from raw or assembled genomes sequences. For several bacterial species and antibiotics, AMR genotype-phenotype discrepancies are common, indicating that important sources of error remain unresolved. For Enterococcus faecium, we focused on identifying the sources of discrepancies for tetracycline resistance, for which genotypic detection had shown particularly low accuracy. We investigated the effect of structural variation in antibiotic resistance genes (ARGs), including gene duplications, truncations, interruptions, and mixed configurations of complete and partial gene copies, as a source of genotype-phenotype discrepancies from short-read data. We conduct further extended investigations to other antibiotic families and into another bacterial species: Escherichia coli. Methods We analyzed collections of E. faecium and E. coli genomes, integrating high-quality complete assemblies, simulated Illumina short reads, and matched AMR phenotypic data. The integrity, copy number, and allelic diversity of ARGs were examined for multiple antibiotic classes, and their impact on ARG detection and accuracy of AMR determination was assessed using several commonly used bioinformatic tools (SRST2, ARIBA and AMRFinderPlus). Results For E. faecium, after ruling out the effect of specific tet allelic variants on tetracycline susceptibility, we found that the integrity and copy number of tet(M) had a major effect on detection accuracy. Duplicated and incomplete ARGs are also common in E. faecium genomes, particularly for macrolides (erm(B)) and aminoglycosides (ant(6)-Ia and aph(3')-IIIa). In E. coli, similar patterns were observed for tet(A), erm(B) and aminoglycoside-associated genes (aph(3')-IIIa and ant(6)-Ia). Across ARGs in both species, short-read mapping methods wrongly reported interrupted genes as complete in some instances, while assembly-based methods often failed to resolve complete copies of duplicated genes. Detection accuracy improved when tools were adapted to account for gene integrity and when extended AMR databases incorporating species-specific alleles were included. Conclusions Our findings reveal that bioinformatic limitations in dealing with ARG copy number and completeness, and in accounting for allelic variation, underly a substantial source of genotype-phenotype errors, highlighting the need for improved AMR databases and bioinformatic tools that consider these factors to achieve reliable genomic prediction of AMR.

24.
arXiv (CS.AI) 2026-06-16

DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

arXiv:2606.15931v1 Announce Type: cross Abstract: Historical medical archives and traditional medicines hold immense potential for drug discovery and remain a primary source for current drug development. However, pre-ontological prose and idiosyncratic taxonomies prevent the standardization and medical modernization of the data for use in current biomedical pipelines. Furthermore, no existing LLM agent system, whether tool-calling, retrieval-augmented, or agentic deep-research, can convert such text into verifiable drug-discovery leads at scale. We close this gap with DeepRoot, a multi-agent LLM system that jointly builds and utilizes a verified knowledge graph, showing that grounding and reasoning – often conflated – are separable axes the system can compose for therapeutic reasoning. Applied to the Shen Nong Ben Cao Jing, DeepRoot recovers $10$ of $21$ held-out compound-disease treatment pairs at R@$20$ ($47.6\%$ vs $4.8\%$ for a raw corpus LLM and $\sim\!2.4\%$ random) and dominates an LLM-as-judge audit for reasoning quality over baseline LLMs and LLMs with direct tool-call access to the same APIs DeepRoot itself queries. Tool-using LLMs hallucinate evidence on $87\%$ of claims, versus 7-10% for DeepRoot. Graph-only inference hallucinates $0\%$ but ranks lowest on reasoning coherence; DeepRoot KG+LLM is the only condition to win on both axes, pointing toward a route for systematic mining and repurposing of historical medical knowledge.

25.
arXiv (CS.AI) 2026-06-15

The Perceived Fragility of Explanations in Audio Models: Manipulation of Attribution with Unchanged Predictions

arXiv:2606.14466v1 Announce Type: cross Abstract: This paper investigates the fragility of post-hoc explanation methods in audio deepfake detection. While previous work on explanation manipulation focused on images using standard $L_p$ metrics, we introduce a psychoacoustic framework that optimizes inaudible perturbations to decouple model attributions from final classifications. We evaluate this vulnerability across state-of-the-art architectures under strict prediction-preserving constraints. By evaluating the manipulation cost through domain-specific perceptual audio quality metrics alongside explanation alignment criteria, our framework demonstrates that an adversary can systematically distort automated explanation heatmaps while preserving the predicted deepfake label. Full code available at: https://github.com/cncPomper/Audio-XAI