Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

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

Reward hacking in physical reinforcement learning revealed by turbulent drag reduction

arXiv:2606.06227v2 Announce Type: replace-cross Abstract: A reinforcement-learning agent maximises its reward, which can diverge from the outcome its designer intended. In physical control the reward rarely closes that gap, and drag reduction in wall turbulence makes it concrete. A mass-conservation projection couples agents' outputs and erases the per-agent credit the policy gradient needs; a memoryless policy cannot resolve the slow near-wall cycle it acts on; and a pressure-gradient reward pays for nominal drag reduction by pumping power through the wall. Two degenerate controllers achieve large drag reductions while total dissipation rises, so the reported figure can mask a more wasteful flow. We trace each fault to its cause and fix it: a differentiable projection that restores credit, a recurrent policy with a widened sensing stencil, and a reward scored on the true wall power. The corrected controller acts on the flow within a closed energy budget, earning a conservative $17\%$ under honest accounting.

02.
arXiv (CS.LG) 2026-06-17

A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer

arXiv:2606.17491v1 Announce Type: cross Abstract: Binary data factorization is common, but real-valued methods ignore discreteness and yield hard-to-interpret factors. Boolean Matrix Factorization (BooMF) instead decomposes a binary matrix into two lower-rank binary matrices via logical AND and OR, expressing the data as a Boolean disjunction of interpretable patterns. In cancer genomics, BooMF can reveal coordinated feature changes that may drive tumor evolution, unlike rotational or additive decompositions. Most existing BooMF methods are heuristic, greedy, sensitive to initialization, prone to local optima, and do not support principled model selection or uncertainty quantification. We introduce Bayesian Boolean Matrix Factorization (BBMF), a fully conjugate generative model with sparsity-inducing priors. It enforces Boolean constraints, yields interpretable latent factors with coherent uncertainty quantification, and admits Gibbs sampling with closed-form full conditionals. Because cancer evolution often involves widespread, near-simultaneous chromosome-number changes (e.g., whole-genome duplication followed by instability and selection), Boolean factorizations capture these patterns more naturally than additive models. Applied to arm-level copy-number alteration data in multiple myeloma, where entries indicate presence/absence of chromosomal-arm amplifications, BBMF finds a small set of interpretable bicliques linking patient subsets to recurrently co-altered chromosomal arms, providing a compact, biologically meaningful summary of tumor heterogeneity and demonstrating BBMF's utility for uncovering discrete latent structure in complex binary data.

03.
medRxiv (Medicine) 2026-06-15

Wellbeing After Stroke-2 (WAterS-2): a feasibility study with process evaluation exploring inclusive, accessible, online psychological support after stroke

Objectives: Explore feasibility and acceptability of upskilling a workforce to deliver a co-developed intervention, based on Acceptance and Commitment Therapy (ACT), to support psychological adjustment post-stroke targeting underserved groups. Design: Multi-site, single-arm feasibility study with embedded mixed-methods process evaluation (ISRCTN17628580). Setting: Four NHS community stroke services across England. Participants: 1. Stroke survivors [≥]18 years of age, [≥]4 months post-stroke, reporting psychological difficulties adjusting to stroke, able to consent and access remote group sessions in English; 2. Group facilitators from NHS stroke services, not ACT specialists. Intervention: WAterS-2: an eight-session, remotely-delivered ACT-informed group intervention. Outcome measures: Recruitment, fidelity, safety, acceptability and perceived value were assessed using fidelity checklists, post-intervention surveys and semi-structured interviews with stroke survivors and facilitators. Clinical outcomes including mood (HADS), wellbeing (ONS4), psychological flexibility (AAQ-ABI), measured post-group and three-months later. Results: Nineteen stroke survivors recruited (mean 9.6 months post-stroke; n=5 (26%) minoritised ethnicities; n=10 (52%) with aphasia). Thirteen facilitators - including two peer support workers - delivered the intervention with fidelity following structured training across four services. Drop-out was low (2/19; 11%); with 15 (79%) attending [≥]5/8 sessions. Remote data collection was feasible (79% follow-up completion), with no adverse events recorded. Acceptability was high: survivors valued peer connection, grounding and mindfulness practices. ACT metaphors were helpful for some but challenging for others, including some with aphasia. Online delivery was suitable but limited informal connection. Facilitators reported increased capability, incorporating ACT skills into routine care. NHS workforce pressures and geographically-constrained referral pathways limited recruitment reach. Conclusions: WAterS-2 is feasible, safe, acceptable and inclusive. A mixed workforce, including NHS peer support workers, can be upskilled to deliver with fidelity. Inclusion of underserved groups is achievable but requires active strategies beyond standard NHS referral routes. Findings inform a provisional logic model and a future pragmatic trial.

04.
arXiv (CS.CV) 2026-06-12

Trajectory-Level Redirection Attacks on Vision-Language-Action Models

Vision-language-action (VLA) policies bring natural language into closed-loop robot control, enabling robots to execute manipulation tasks directly from text instructions. The same interface gives text a recurring role in control because the prompt is reused at every replanning step, and each prompt-conditioned action changes the future observations on which the policy acts. Existing VLA attacks study adversarial prompts that elicit targeted low-level actions or make such actions persist across changing images. We identify a stronger trajectory-level failure mode: a prompt that still $appears$ to specify the intended task but redirects the final physical outcome. We mathematically formalize this setting as $command-preserving trajectory redirection$, a prompt-only threat model in which the attacker chooses one prompt before the episode, all policy and environment components remain fixed, and the prompt must stay close to the benign instruction while omitting target words and correction language. To find such prompts, we introduce an on-policy prompt search method that uses rollouts to discover perturbations whose closed-loop behavior tracks a target task while satisfying the command-preserving constraints. Experiments in simulation and on hardware show that near-benign prompt perturbations can redirect VLA rollouts to attacker-specified targets. These results expose a trajectory-level vulnerability in VLA instruction grounding: text that appears to preserve the intended command can still give an adversary control over the robot's final physical outcome. Project website: https://vla-redirection-attack.github.io/

05.
arXiv (quant-ph) 2026-06-11

Consistent Evaluation of Operators Involving the Position Operator in the Bloch Representation: Application to the Orbital Moment

arXiv:2606.11679v1 Announce Type: cross Abstract: The position operator plays a central role in condensed-matter observables such as velocity, orbital moment, and electric polarization. In solid-state physics, the evaluation of operators incorporating the position operator has not reached a consensus, as observed in the operator-level discrepancy between the local circulation of Wannier functions and the self-rotation of wave packets. Here, to achieve a consistent evaluation of such operators, we propose three rules for evaluating operators involving the position operator in the Bloch representation. The rules are devised to satisfy physical conditions: independence from the choice of unit cell, preservation of Hermitian conjugacy for the product of operators, and recovery of the correct intraband velocity. We further address the gauge dependence of the position operator and introduce a scheme termed gauge filtration, which systematically removes gauge-dependent contributions from the operators containing the position operator. This methodology ensures that the quantities obtained from the operator evaluation correspond to observable physical phenomena. By applying our framework, we reconcile the results concerning the self-rotation of the wave packet and the local circulation of the Wannier function. We expect our proposal to establish a consistent framework for evaluating operators involving the position operator.

06.
arXiv (math.PR) 2026-06-24

The one-point Schreier Poisson boundary of Thompson's group $F$

arXiv:2606.23896v1 Announce Type: new Abstract: We identify the Poisson boundary of the one-point Schreier-chain random walk obtained by projecting the simple symmetric random walk on Thompson's group $F$ to the dyadic orbit point $1/2$. For the associated simple labelled-generator walk on the dyadic Schreier graph, the full Poisson boundary is the skeleton end boundary. The proof combines the known description of this Schreier graph as a binary-tree skeleton with recurrent one-dimensional ray attachments with an explicit trace computation. After tracing to the grey skeleton and deleting holding probabilities, the walk becomes a reversible nearest-neighbor walk on the rooted binary tree with two unequal classes of edge conductance. This reduces the boundary identification to standard Poisson–Martin theory for transient walks on trees and leaves a finite electrical-network calculation for the harmonic measure. Following Kaimanovich's coding of skeleton ends by odd 2-adic integers [{Groups, Graphs and Random Walks}, London Math. Soc. Lecture Note Ser.~436, pp.~300–342, 2017], the hitting measure is a biased Bernoulli product measure with explicitly computed bias. It is singular with respect to Haar measure, has full topological support, and is exact-dimensional; these properties and the exact constants are proved here.

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

Odds Law: The Decomposition Algebra On How Intelligence Organizes Itself to Solve Difficult Problems Reliably

作者:

arXiv:2606.15712v1 Announce Type: cross Abstract: We ask a structural question: given unreliable elementary problem-solvers, what organizations of them solve hard problems reliably, and what are the limits? We develop a $decomposition~algebra$: elementary solvers are morphisms in a stochastic category, and four combinators (sequential composition, parallel ensembling, verification gating, and recursive reduction) generate the space of compound solvers. We equip this algebra with two homomorphisms, a $reliability$ valuation into the ordered monoid $([0,1],\le)$ and a $cost$ valuation into a commutative semiring, and we derive the composition laws that govern how reliability flows through structure. Our central results are (i) a $verification~odds~law$ (the result that names this report), showing that a verification gate multiplies the odds of correctness by the verifier's likelihood ratio $\Lambda$, so that $k$ conditionally independent gates yield geometric amplification; (ii) a $reliability~amplification~theorem$, giving target reliability $1-\delta$ at $O(\log 1/\delta)$ verification depth whenever $\Lambda>1$; and (iii) a $threshold~dichotomy$: above the critical parameters reliability can be driven arbitrarily close to one at logarithmic cost, while at or below them no amplification is possible. We then show that $self-organization$ is the least fixed point of a monotone improvement operator on the complete lattice of strategies, and that this fixed point equalizes marginal log-odds gain per unit cost. Finally, we prove matching limits: an information ceiling bounds per-gate amplification by a divergence quantity; shared error causes create a strictly positive voting floor, so diversity is $necessary$ for unbounded amplification. Reliability, in short, is neither free nor magical: it is bought with independent information, arranged by composition, and bounded by the verifier.

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

SAAS: Self-Aware Reinforcement Learning for Over-Search Mitigation in Agentic Search

Agentic search enables LLMs to solve complex multi-hop questions through iterative reasoning and external search. Despite the effectiveness, these systems often suffer from a critical limitation in practice: agents fail to recognize their own knowledge boundaries, blindly triggering searches when internal knowledge suffices and failing to terminate search even when adequate evidence has been collected. The lack of self-awareness leads to severe over-search, incurring substantial inference latency and prohibitive computational cost. To this end, we propose SAAS, a novel RL framework designed to cultivate dynamic self-awareness that precisely regulates search behavior without compromising accuracy. SAAS introduces three key components: (i) a search boundary modeling mechanism, which identifies the search boundary under the evolving policy by contrasting search-disabled and search-enabled rollouts; (ii) a boundary-aware reward module, which translates this boundary awareness into trajectory-level penalties, suppressing unnecessary and redundant searches; and (iii) a stage-wise optimization strategy, which leverages a sequential curriculum to prioritize reasoning over search regularization, thereby avoiding reward hacking. Extensive experiments demonstrate that SAAS substantially reduces over-search, while maintaining accuracy. Our code and implementation details are released at https://github.com/XMUDeepLIT/SAAS.

09.
arXiv (CS.CL) 2026-06-11

Which Models Are Our Models Built On? Auditing Invisible Dependencies in Modern LLMs

Modern LLM training pipelines increasingly rely on other models to generate data, filter corpora, judge outputs, and guide development decisions. These dependencies are recursive: a model may depend on an upstream artifact whose own dependencies are documented only in separate releases and artifacts. As a result, the full dependency structure is fragmented across heterogeneous public artifacts, with complexity and recursive depth far outpacing humans' ability to trace. We introduce ModSleuth, an agentic system that recursively reconstructs LLM dependency graphs from public artifacts with source-grounded evidence. We find that the primary challenge is no longer information extraction, but defining what constitutes a dependency and reconciling artifact references across inconsistent documentation. We address these challenges through a formalization that distinguishes direct and indirect dependencies, represents heterogeneous pipeline roles through operation-centered relationships, and resolves artifact identities across names, versions, and repositories. Applying ModSleuth to four public-artifact-rich LLM releases, we recover 1,060 source-verified dependencies and construct large-scale dependency graphs of modern LLM development. These graphs reveal multi-hop license obligations, train-evaluation coupling, discrepancies between released and training-time artifacts, and documentation inconsistencies that would otherwise be difficult to uncover. We release ModSleuth and the resulting dependency graphs to support transparent analysis of the increasingly complex ecosystems underlying modern LLMs.

10.
arXiv (CS.CL) 2026-06-17

ConSA: Controllable Sparsity in Hybrid Attention via Learnable Allocation

Hybrid architectures combining full attention (FA) and sliding-window attention (SWA) are a promising paradigm for efficient LLM inference. However, existing methods typically rely on hand-crafted rules or simple post-hoc heuristics for FA/SWA allocation and offer limited analysis of the attention behaviors underlying these designs. We propose Controllable Sparsity in Hybrid Attention (ConSA), a framework that learns optimal FA/SWA assignment under a user-specified sparsity target. ConSA employs L0 regularization to learn binary masks selecting between FA and SWA for each attention unit, while an augmented Lagrangian constraint enforces the target sparsity at either layer or KV-head granularity. We evaluate ConSA on two LLMs at the 0.6B and 1.7B scales. Learned allocations consistently outperform rule-based baselines, with KV-head-wise allocation yielding clear gains over layer-wise allocation. The learned patterns place SWA in the bottom layers and concentrate FA into contiguous middle-layer blocks, diverging from evenly interleaved patterns in rule-based methods. This structure persists across model scales, sparsity levels, and allocation granularities, revealing a fine-grained spectrum of intrinsic attention behaviors that underlies the learned allocation.

11.
arXiv (CS.CL) 2026-06-24

Aspect-Based Sentiment Evolution and its Correlation with Review Rounds in Multi-Round Peer Reviews: A Deep Learning Approach

Mining sentiment information from the textual content of peer review comments offers valuable insights into the scientific evaluation process. However, previous studies are often constrained by coarse-grained analysis and the lack of differentiation across review rounds. Notably, the dynamic shifts in reviewers' focus and sentiment tendencies throughout multiple review stages remain underexplored. To address this gap, the present study investigates the distribution and evolution of aspect-level sentiments and examines their correlation with the number of review rounds. We begin by segmenting the multi-round review comments of 11,063 accepted papers from Nature Communications and identifying fine-grained review aspect clusters. A manually annotated corpus of approximately 5,000 review sentences is then constructed. Using this dataset, we train a series of deep learning-based aspect sentiment classification models. Among them, the LCF-BERT-CDM model achieves the best performance, with a Macro-F1 score of 82.65%. Subsequent statistical analysis reveals a consistent trend: as the number of review rounds increases, the proportion of positive sentiments rises, while negative sentiments decline. Correlation analysis further indicates that aspect sentiment scores are negatively associated with the total number of review rounds. Key aspects exhibiting stronger correlations include "experiments", "research significance" and "result analysis".

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

G-IdiomAlign: A Gloss-Pivoted Benchmark for Cross-Lingual Idiom Alignment

Idioms are difficult to transfer across languages due to their non-compositionality and weak surface-form grounding, making literal mappings unreliable. We present G-IdiomAlign, a gloss-pivoted benchmark where each idiom is anchored by an English gloss from Wiktionary. We further construct a high-confidence reference alignment set for reproducible evaluation. G-IdiomAlign supports two protocols: (1) a controlled Multiple-Choice Idiom Equivalence with typed distractors for error attribution; and (2) a Gloss-Contrastive Generation contrasting No-gloss and With-gloss inputs to isolate the effect of an explicit semantic pivot. Across diverse LLMs, a bias to literal translation is a dominant failure mode, especially when the target is a low-resource language. Glosses consistently improve Gloss-Contrastive Generation under an embedding-based semantic proxy, but performance remains modest, indicating substantial headroom in the open output space. Subsequent analysis on Qwen3-8B further suggests that cross-condition differences are concentrated more in attention heads than in layers, while better With-gloss generations coincide with stronger gloss anchoring.

13.
arXiv (CS.AI) 2026-06-16

Decision-Aware Memory Cards: Counterfactual-Inspired Context Selection and Compression for Tool-Using LLM Agents

arXiv:2606.08151v2 Announce Type: replace Abstract: Modern large language model (LLM) agents do not simply need longer contexts; they need decision-relevant evidence at the moment of action. We study decision-aware context selection: ranking retrieved files, tests, traces, rules, and memories by their expected effect on an agent's next action rather than by semantic similarity alone. We present the Counterfactual-Inspired Context Layer (CICL), which builds an instance context graph, estimates decision-oriented utility for candidate units, and compresses selected evidence into typed memory cards. The same schema can be instantiated with hosted LLM judges, local surrogates, or lightweight rankers, making the selection protocol auditable across model choices. On 50 SWE-bench Verified file-retrieval instances, Qwen3.6-Plus reranking of BM25 top-50 candidates improves hit@1 from 0.58 to 0.78 and MRR@10 from 0.634 to 0.790, with all 2,500 judgments parseable. Controlled diagnostics show that CICL identifies action-critical evidence: removing the top-utility semantic unit reduces F1 from 0.245 to 0.000. In selected-then-compressed mode, memory cards save 44.93 tokens per query while preserving selected evidence. CICL provides a practical layer for measuring, ranking, and compressing decision-critical context for tool-using agents. Code is available at https://github.com/stephen-guan-researcher/CICL.

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

PACT: Privileged Trace Co-Training for Multi-Turn Tool-Use Agents

Multi-turn tool-use agents must reason, call tools, and adapt to observations across several interaction turns. Post-training such agents is challenging, as reinforcement learning often suffers from sparse rewards and weak credit assignment despite matching the prompt-only inference setting, while supervised fine-tuning on expert traces provides dense process supervision but can over-constrain the model to fixed trajectories. To tackle this, we propose PACT, a Privileged trAce Co-Training framework for multi-turn tool-use agents. The key idea is to use expert traces only as training-time optimization signals rather than rollout-time hints. PACT keeps rollout generation prompt-only, then uses expert traces to guide optimization through two complementary signals: a trace-conditioned RL surrogate that evaluates prompt-only rollouts under expert-trace context, and a component-aware SFT loss that supervises reasoning prefixes and tool-calls with annealed strength. To reduce over-reliance on the training-only trace context, PACT further introduces a prompt-only anchoring. We also provide a latent-trace view that connects the two trace-based objectives and explains how expert traces can guide optimization without being used during rollout generation. Experiments on FTRL, BFCL, and ToolHop show that PACT consistently improves over strong SFT- and RL-based baselines, highlighting the value of privileged trace co-training for multi-turn tool-use learning.

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

Faster algorithm for achieving minimal-size quantum decision diagrams

arXiv:2606.24789v1 Announce Type: new Abstract: The decision diagram (DD) data structure enables fast linear-algebra calculations by bringing vectors into a normal form and subsequently merging equivalent ones, yielding a minimally-sized DD modulo the equivalence relation. A fruitful application area is quantum-circuit simulation, where the vectors represent quantum states. The Local Invertible Map Decision Diagram (LIMDD) type, merges LIM-equivalent (typically Pauli-gate equivalent) vectors, can efficiently simulate Clifford circuits as well as some high-T-count circuits, and has theoretically been proven exponentially faster for simulation than other well-developed data structures, including other common DD variants. However, these exponential advantages have not fully materialized yet in existing implementations, for which the normal-form procedure, which is a highly complex algorithm, is either absent or only partially implemented. We here present a novel normal-form algorithm for Pauli-LIMDDs, achieving a worst-case speedup from $O(n^3)$ to $O(n^2)$ for an $n$-qubit DD node with a single child node while keeping the $O(n^3)$ run time in case of two distinct children nodes. We implement the algorithm as part of QolDDer, our Pauli-LIMDD simulator for quantum circuits, written from scratch in C/C++. The implementation realizes the theoretically-proven advantages of Pauli-LIMDDs on Clifford circuits, is significantly faster than the existing LIMDD simulators on such circuits, and on a public quantum-circuit data set often outperforms them by an order of magnitude. In the future, we envision that our work will enable further application and development of LIMDD variants, not only for quantum design tasks, but also for analysis of linear-algebra-based systems in general.

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

Quantum Field-Theoretic Predictions of {\Psi}-Epistemic Models of Quantum Mechanics

arXiv:2605.12546v2 Announce Type: replace Abstract: {\Psi}-epistemic models of quantum mechanics imply that the quantum state does not correspond to physical reality, but instead reflects the observer's knowledge of the underlying quantum system. The epistemic view of the quantum state has the potential to shed light on several foundational problems of quantum theory and has attracted considerable attention in the literature. On the other hand, the Pusey-Barrett-Rudolph theorem demonstrated that broad classes of {\psi}-epistemic models must lead to predictions that deviate from those of quantum mechanics. Although the original theorem involved entangled joint measurements on composite systems, alternative no-go theorems involving measurements on single quantum systems were developed shortly thereafter. Experimental investigations of the deviations predicted by {\psi}-epistemic models from quantum mechanics are still ongoing. So far, such tests have been performed within the framework of non-relativistic quantum mechanics and predominantly rely on quantum information based measurement procedures. In this work, we show that {\psi}-epistemic models can give rise to deviations from standard quantum field-theoretic predictions through modifications of polarized scattering cross sections and decay widths. Our results do not require a relativistic formulation of ontological models or of the Harrigan-Spekkens criterion; the essential assumption is merely that measurements implemented through relativistic processes can still be represented within the ontological framework by well-defined response functions and probabilities. The present work constitutes a proof-of-principle study demonstrating that particle physics tests of the ontological status of the quantum state are possible and that {\psi}-epistemic models may exhibit experimentally distinguishable signatures in particle phenomenology.

17.
arXiv (CS.LG) 2026-06-16

Latent space mapping of interpretable structural coordinates from stochastic single-molecule signals

arXiv:2606.16950v1 Announce Type: cross Abstract: Nanopores are versatile single-molecular sensors, but their utility is fundamentally constrained by stochastic translocation dynamics warping any encoded information. We resolve it by shifting from time-domain analysis to a learned latent-space mapping via a contrastive encoder trained exclusively on simulated signals from a physics-informed model. This encoder maps solid-state nanopore signals of engineered DNA barcodes into an interpretable molecular coordinate system. The learned representation is responsive to structural barcode parameters while remaining invariant to acquisition conditions and translocation conformation, allowing data pooling across devices. Molecule identification requires a single pass through the encoder, reducing computational cost by three orders of magnitude relative to alignment-based methods. We experimentally validate through mixture quantification, rare-variant detection, consensus barcode reconstruction, and real-time signal acquisition. This shift from temporal analysis to mapping structural coordinates into a latent space changes the paradigm behind analyzing stochastic sensor signals by linking classification to interpretable encoded molecular information.

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

LARE: Low-Attention Region Encoding for Text-Image Retrieval

Image retrieval in crowded scenes is particularly challenging due to the salience bias of conventional visual encoders, which tend to focus on dominant objects while neglecting low-attention regions that are often crucial for fine-grained retrieval. We propose LARE (Low-Attention Region Encoding), a framework that explicitly models these overlooked regions. LARE adopts a dual-encoding strategy that encodes low-attention regions of an image and the full image in parallel, leading to more diverse and informative image embeddings. To evaluate image retrieval performance in challenging crowded scenes, we introduce Dense-Set, a challenging subset derived from COCO and Flickr30K. In this subset, images are re-captioned to provide richer descriptions of low-attention or previously overlooked regions. This dataset highlights the limitations of existing retrieval models and enables a more rigorous evaluation under densely crowded scene conditions. Experimental results demonstrate that the proposed framework improves retrieval performance by preserving subtle, non-dominant visual cues within the shared latent space.

19.
bioRxiv (Bioinfo) 2026-06-18

A data-driven rediscovery of the specificity-conferring code of adenylation domains in nonribosomal peptide synthetases

Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that assemble structurally diverse peptides, many of pharmacological importance, including antibiotics and immunosuppressants. Within each NRPS module, the adenylation (A) domain selects the substrate to be incorporated, a choice governed by a small set of residues lining the binding pocket. For two decades, computational prediction of A-domain substrate specificity has relied on residue sets - most prominently the Stachelhaus code and the 34-residue "8 Angstrom code" - that were defined by spatial proximity to the substrate rather than by demonstrated predictive value. Here we revisit which residues govern substrate specificity from a purely data-driven perspective. We assembled a non-redundant dataset of 5,366 A-domain sequences (4,693 bacterial and 673 fungal) and used information-theoretic measures to rank alignment positions by their statistical association with substrate identity, without restricting candidate positions to any predefined structural shell. This procedure yielded two compact, kingdom-specific codes: IG15B (15 positions) for bacterial and IG13F (13 positions) for fungal A-domains. Both match or exceed the predictive accuracy of the 34-residue 8 Angstrom code while using fewer than half its positions, and both independently recover the majority of the classical Stachelhaus positions. Notably, our analysis identifies four positions (242, 280, 281, and 284) that lie outside all conventional codes yet carry non-redundant specificity information and co-localize with classical determinants on two helices flanking the binding pocket. These positions provide new candidate sites for the rational engineering of A-domain specificity.

20.
arXiv (quant-ph) 2026-06-24

The $\omega$-Effect from a Multimode Squeezed Graviton State

arXiv:2606.24613v1 Announce Type: cross Abstract: The $\omega$-effect in entangled neutral-meson systems provides a sensitive probe of CPT violation induced by quantum-gravitational environments. In open quantum systems, interactions with inaccessible gravitational degrees of freedom can render the reduced meson dynamics non-unitary, causing the CPT operator to become ill-defined, even when the underlying microscopic Hamiltonian is CPT invariant. We present a microscopic derivation of the $\omega$-effect arising from a multimode squeezed gravitational environment generated by an axion cloud around a Kerr black hole. Using the Takagi decomposition of the associated complex symmetric squeezing kernel, the graviton field is expressed in terms of independent squeezed supermodes possessing anomalous correlators. These correlators provide a microscopic quantum counterpart of the stochastic fluctuations that appear in earlier D-particle foam descriptions of the $\omega$-effect, replacing phenomenological variances of flavour-changing D-particle recoil by calculable graviton correlation functions. After tracing over the graviton bath, the anomalous correlators and the weak-interactions-induced mixing combine to generate transitions between the antisymmetric and symmetric two-meson sectors. This results in a small exchange-symmetric admixture, parametrised by $\omega$, in the otherwise antisymmetric EPR state. We obtain an explicit expression for $\omega$ in terms of a sum over Takagi supermodes weighted by their squeezing amplitudes and phases together with the weak-interaction flavour-mixing matrix element. The resulting framework suggests that the $\omega$-effect may be a generic signature of non-classical states of gravitational environments, extending beyond the specific axion-cloud scenario considered here. The observability of the $\omega$-effect from other astrophysical and microscopic black-hole sources is discussed.

21.
arXiv (CS.AI) 2026-06-24

On the Smallness of the Large Language Models Scaling Exponents

arXiv:2606.24504v1 Announce Type: new Abstract: We discuss reasons why the scaling exponents of current Large Language Models (LLMs) applications are indicating an unsustainable regime in terms of energy resources. We further show that attributing the smallness of such exponents to a numerical bias due to the neglect of a non-zero value of the loss function in the limit of infinite data (``pedestal effect") does not remove the unsustainability issue. Finally, the effects of the smoothness (roughness) of the data on the scaling exponents is commented upon based on an analogy with phenomenological models of fluid turbulence.

22.
bioRxiv (Bioinfo) 2026-06-23

EnrichViz: An Interactive R Shiny Application for Visualization of Pathway Enrichment Results from Omics Data

Pathway and functional enrichment analysis is a cornerstone of omics data interpretation, enabling researchers to map differentially expressed proteins or genes onto curated biological processes, signaling cascades, and molecular functions. While tools such as Ingenuity Pathway Analysis (IPA), g:Profiler, and Enrichr are widely used to generate ranked enrichment results, translating these tabular outputs into clear, publication-ready figures remains a time-consuming step that typically requires custom scripting and familiarity with visualization libraries, a significant barrier for researchers without a computational background. Here we present EnrichViz, a self-contained, browser-based R Shiny application that enables interactive, code-free visualization of pathway and functional enrichment results from quantitative proteomics, transcriptomics, and metabolomics experiments. EnrichViz accepts three standard CSV files as input, a normalized abundance matrix, a sample annotation or metadata file, and enrichment results from any platform that exports tabular output, and produces six complementary, publication-ready visualizations: bar and bubble plots for ranking enriched terms by significance, chord diagrams for exploring pathway-molecule connectivity, clustered heatmaps for displaying Z-score normalized expression patterns across experimental groups, and boxplots or violin plots for examining the abundance distribution of individual proteins, genes, or metabolites. The application supports both raw p-values and pre-transformed -log10(p) values through automatic detection, and all plot parameters are adjustable in real time through a graphical sidebar. Every figure can be exported as a high-resolution PNG file at 300 dpi. EnrichViz is implemented in R using the Shiny, ggplot2, pheatmap, and circlize packages, and is freely available at https://rgmilian.shinyapps.io/EnrichViz/

23.
arXiv (quant-ph) 2026-06-24

Quantum Entanglement Halves the Oblivious Update Bandwidth

作者:

arXiv:2605.19248v2 Announce Type: replace Abstract: We consider $(n,k)$ MDS-coded distributed storage over $\mathbb{F}_q$ with per-node storage $\alpha$ symbols. For the oblivious update problem, where a single message symbol changes and neither helpers nor the stale node know which, the classical lower bound is $\alpha k \log_2 q$ bits. We prove that when the $k$ contacted helpers share prior quantum entanglement, the update bandwidth is $\lceil \alpha/2 \rceil \cdot k \log_2 q$ bits-equivalent, a factor approaching 2 reduction. For $\alpha = 2$, a $[[k, k-2]]_q$ CSS code achieves bandwidth $k \log_2 q$ with one qudit per helper. For general $\alpha$, a $[[\lceil \alpha/2 \rceil k, \lceil \alpha/2 \rceil k - \alpha]]_q$ CSS code achieves the bound with $\lceil \alpha/2 \rceil$ qudits per helper. The matching converse uses the superdense coding bound: the stale node holds all transmitted qudits and hence the entangled partners, so each helper's channel supports at most $D^2$ distinguishable signals for dimension $D$. The result holds for all $(n,k)$ pairs with sufficiently large prime $q$.

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

High-harmonic generation driven by temporal-mode quantum states of light

arXiv:2512.06602v2 Announce Type: replace Abstract: We develop a theoretical framework for high-harmonic generation (HHG) driven by quantum states of light based on a temporal-mode expansion of the electromagnetic field. This approach extends previous single plane-wave mode treatments to realistic pulse configurations and arbitrary multi-mode states of light, resolving conceptual inconsistencies arising from non-normalizable infinite plane waves and establishing consistency between analytical and numerical methods. We derive a correction factor that quantifies deviations from the diagonal approximation (in which the yield becomes a statistical average over classical-field simulations) both for the response of a single atom and in the many-atom regime. Our results confirms that the HHG spectrum for atoms driven by any quantum state of light in free space is accurately described by averaging semi-classical calculations over the Husimi distribution, with no observable genuine quantum effects in the spectrum. We also demonstrate that in the many-atom regime, the mean-field coherent-state approximation underlying this treatment does not preserve probabilities, although unitarity is restored by in the diagonal approximation. The absence of genuine quantum effects in the HHG yield is attributed to the large photon numbers ($\sim 10^{11}$) required to reach HHG intensities in free space, which render quantum fluctuations negligible. We discuss nanophotonic environments with ultrasmall mode volumes as potential platforms where few-photon strong-field processes could exhibit genuine quantum signatures.

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

Guiding Federated Graph Recommendation with LLM-encoded knowledge

arXiv:2606.15277v1 Announce Type: cross Abstract: Graph-based recommender systems are highly effective at extracting collaborative signals from user–item interactions, and federated learning (FL) allows these models to be trained while preserving user privacy. However, aggregating graph representations across distributed, non-IID clients remains a challenge; structural embeddings learned locally often misalign, and naive averaging fails to capture meaningful cross-client relationships. Most existing federated graph methods rely exclusively on structural aggregation, neglecting the rich, global semantic context available in large language models (LLMs). In this paper, we propose a novel framework that uses LLM-encoded knowledge to guide federated graph recommendation. Specifically, clients learn structural representations from local graphs while simultaneously summarizing their typical interaction patterns into compact semantic vectors via a frozen LLM. The central server then uses these LLM-encoded semantic signals to discover related preference patterns across clients, guiding the selective aggregation of their structural representations. This enables semantically informed cross-client collaboration without exposing raw data. Extensive experiments on standard benchmarks show that guiding structural alignment with LLM-encoded knowledge consistently improves recommendation accuracy over existing federated graph baselines.