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01.
arXiv (CS.CL) 2026-06-24

RoPE-Aware Bit Allocation for KV-Cache Quantization

Existing low-bit KV-cache quantizers often treat each cached key as a flat vector. Under RoPE, however, a key's contribution to a future attention logit decomposes into a position-dependent sum over two-dimensional frequency blocks. This makes key-cache quantization a block-wise bit-allocation problem: high-energy RoPE blocks are more sensitive to quantization error and should receive more bits. We introduce Block-GTQ, a RoPE-aware bit allocator for key-cache quantization built on TurboQuant-MSE(TQ-MSE). For each layer and KV head, Block-GTQ computes a label-free energy score for each RoPE block and greedily allocates integer bit widths by marginal gain. Under matched K/V bit budgets, Block-GTQ better preserves RoPE query-key logits on a ten-model diagnostic panel, cutting per-layer MAE by 32-80% at 2 and 3 b/dim K-only quantization and winning all 367/367 layer comparisons against uniform TQ-MSE. These fidelity gains translate to stronger downstream long-context retrieval, understanding, and reasoning. At K2V2 on Llama-3.1-8B-Instruct, Block-GTQ raises the six-task NIAH average from 70.6 to 97.4, and the LongBench-EN average from 36.87 to 53.31. On AIME 2024/2025 with DeepSeek-R1-Distill-Qwen-7B, without an fp16 recent-key buffer, Block-GTQ at K3V2 scores 51.7/37.5, close to fp16's 54.2/37.9, whereas uniform TQ-MSE collapses to 0.0/0.0. We further implement a packed-cache serving path. On a single H800 GPU with Qwen2.5-3B-Instruct, packed K3V3 achieves 3.24x KV-cache compression with fp16-comparable quality, runs 1.34x faster than fp16 FlashAttention2 at 128K context, reduces peak memory from 56.31 GB to 19.85 GB, and remains feasible at 256K and 512K where fp16 OOMs. Code is available at https://github.com/JIA-Lab-research/blockgtq.

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

Tensor-Coord: Algebraic Decomposition of Joint Plan Tensors for Conflict-Free Multi-Agent LLM Planning

Authors:

arXiv:2606.16478v1 Announce Type: new Abstract: Large language models (LLMs) remain limited in multi-agent planning because independently generated plans can create coordination failures such as spatial collisions, resource contention, and temporal deadlocks. We introduce Tensor-Coord, a multilinear algebra framework that represents the joint plan of N agents as a third-order tensor \(T \in R^{N \times H \times A}\) over agents, timesteps, and actions. Canonical Polyadic (CP) and Tucker decompositions are used to identify latent coordination structure. The minimal epsilon-approximate CP rank R* defines a computable coordination complexity measure, with \(CC(Pi)=(R*-N)/N\). We prove that R*=N is necessary and sufficient for plan independence. The residual \(E=T-T_{R*}\) defines a conflict score over agent pairs, timesteps, and actions, localizing failures without domain-specific rules. Tucker factors provide interpretable agent roles, temporal phases, and action clusters that are converted into natural language constraints for iterative LLM replanning. Experiments on multi-robot delivery tasks across Easy (2 agents, 5x5 grid), Medium (3 agents, 5x5 grid), and Hard (4 agents, 5x5 grid) settings show convergence to conflict-free plans in 100% of 2-agent cases within 1.4 iterations on average, 80% of 3-agent cases within 3.2 iterations, and 60% of 4-agent cases within 4.0 iterations. CP rank scaled approximately linearly as \(R*(N) = 3.9N + 0.5\), supporting its use as a predictor of coordination complexity.

03.
arXiv (CS.CL) 2026-06-19

Disentangling Linguistic Relatedness from Task Alignment in Cross-Lingual Transfer

We study cross-lingual transfer by fine-tuning seven large language models (4B–671B parameters) on Arabic and evaluating zero-shot reading comprehension on Semitic languages and non-Semitic controls. Across dense and Mixture-of-Experts architectures, we find no evidence of Semitic-specific transfer: models with weak baselines improve dramatically across all languages, while strong-baseline models show only marginal gains regardless of language family. A chain-of-thought ablation reinforces this finding – the same models that benefit most from fine-tuning benefit equally from inference-time reasoning, suggesting both mechanisms address task-format alignment rather than cross-lingual knowledge transfer.

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

C2-Faith: Benchmarking LLM Judges for Causal and Coverage Faithfulness in Chain-of-Thought Reasoning

Large language models (LLMs) are increasingly used as judges of chain-of-thought (CoT) reasoning, yet it remains unclear whether they can reliably assess process faithfulness rather than merely answer plausibility. We introduce C2-Faith, a benchmark built from PRM800K that explicitly decomposes faithfulness into two complementary dimensions: causality (whether each step logically follows from prior context) and coverage (whether essential intermediate inferences are present). Using controlled perturbations, we construct examples with known causal error positions by replacing a single step with a logically inconsistent variant, and with controlled coverage deletions at varying rates, enabling direct measurement against reference labels. We evaluate three frontier LLM judges across three tasks: binary causal detection, causal step localization, and coverage scoring. Our results reveal that judge reliability is highly task-dependent, with no single model dominating across settings. While models often detect that an error exists, they struggle to accurately localize it, indicating a substantial gap between detection and attribution. Moreover, all judges systematically overestimate reasoning completeness, assigning high coverage scores even when substantial portions of intermediate reasoning are missing. These findings expose fundamental limitations of LLM judges in process-level evaluation and highlight the need for more reliable and calibrated methods when using LLMs to assess reasoning quality.

05.
arXiv (CS.CL) 2026-06-12

Entity Binding Failures in Speech LLM Reasoning: Diagnosis and Chain-of-Thought Intervention

Speech Large Language Models (SLLMs) underperform their text counterparts on complex reasoning. We reveal that this gap is not a uniform cognitive deficit. Evaluating two architecturally diverse SLLMs, we show speech-to-text (S2T) matches or exceeds text-to-text (T2T) on spatial, syntactic, and factual tasks. Yet on logical tasks requiring entity tracking, S2T accuracy collapses to chance. We diagnose this as an entity binding failure: continuous speech features blur precise entity-property associations during implicit reasoning. To validate this diagnosis, we introduce Entity-Aware Chain-of-Thought (EA-CoT), a lightweight inference-time intervention forcing SLLMs to enumerate entities and bind them to claims before reasoning. EA-CoT bridges the gap, even when spoken names are misrecognized, yielding up to a 24.4 percentage-point accuracy gain. Ablations confirm the gains stem from explicit semantic binding, reframing the gap as an elicitation failure rather than a missing capability.

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

Divination by Prompt: LLM-Mediated Xuanxue on Chinese Social Media

arXiv:2606.12418v1 Announce Type: cross Abstract: The rapid proliferation of large language models (LLMs) has produced a striking cultural practice: using conversational AI for divination. This paper offers one of the first systematic studies of LLM-mediated divination in the context of Xuanxue, an internet-native umbrella term for mystical and spiritual practices on Chinese social media. Using a mixed-methods design, we analyze 23000+ posts and comments from Xiaohongshu and conduct 32 semi-structured interviews with users and professional diviners. Users primarily consult LLMs about pragmatic concerns - romantic relationships, careers, exams, and in-game gacha draws - via two intersecting pathways: trend-driven curiosity enabled by viral visibility and zero-cost access, and event-driven anxiety under conditions of uncertainty. A defining feature is collaborative prompt refinement, which turns users into active prompt engineers. Among commenters expressing a clear stance, perceived efficacy skews positive, with "accuracy" often justified through biographical fit and retrospective confirmation, consistent with Barnum and confirmation bias. Users also develop verification practices such as repeated trials and cross-model comparison. Professional diviners, by contrast, portray LLMs as lacking the "spiritual power" required for genuine divination, reflecting both ontological commitments and economic boundary-work. We also show how participants navigate tensions between scientific and metaphysical frames when interpreting AI-generated readings. Situating these findings in anthropological and cognitive-evolutionary theories of divination, we argue that LLM divination preserves core functions of traditional practice while introducing scalability, repeatability, and prompt-driven co-production that reshape how divinatory authority is constructed and evaluated.

07.
bioRxiv (Bioinfo) 2026-06-21

Antibody-Antigen Affinity Prediction with Chain-Aware Protein Language Modeling

Motivation: Antibody-antigen affinity determines which antibodies advance in therapeutic discovery, repertoire analysis and affinity maturation, but experimental measurements are sparse relative to the scale of sequence libraries. Structure-based predictors can exploit interface geometry when reliable complexes are available, yet early discovery often requires ranking many heavy-light chain pairs against antigens for which no complex structure exists. Existing sequence-based models are scalable, but frequently compress heavy and light chains into a single antibody representation or concatenate antibody and antigen features obscuring the chain-specific and epitope-specific signals that drive binding. Results: We present AbAffinity, a sequence-only chain-aware three-stream architecture that maintains heavy chain, light chain and antigen as distinct streams. It integrates frozen ESM-2 embeddings with heavy-chain CDR-focused pooling, heavy-light self-attention, adaptive fusion gating and gated cross-attention, training only a compact interaction module. On the SAAINT-DB benchmark, AbAffinity achieves strong predictive performance under ten-fold cross-validation and maintains robust accuracy on novel antigens. It consistently outperforms recent sequence-based models across external benchmarks including SAbDab, AB-Bind and SKEMPI 2.0. Ablation studies highlight the contributions of chain-specific representations, CDR-focused pooling and the gated interaction pathway. Integrated Gradients attributions recover known paratope and epitope residues at structurally validated interfaces. AbAffinity provides a lightweight, explainable sequence-first framework for antibody triage and prioritisation when structural information is limited or unavailable.

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

Can Agents Distinguish Visually Hard-to-Separate Diseases in a Zero-Shot Setting? A Pilot Study

The rapid progress of multimodal large language models (MLLMs) has led to increasing interest in agent-based systems. While most prior work in medical imaging concentrates on automating routine clinical workflows, we study an underexplored yet clinically significant setting: distinguishing visually hard-to-separate diseases in a zero-shot setting. We benchmark representative agents on two imaging-only proxy diagnostic tasks, (1) melanoma vs. atypical nevus and (2) pulmonary edema vs. pneumonia, where visual features are highly confounded despite substantial differences in clinical management. We introduce a multi-agent framework based on contrastive adjudication. Experimental results show improved diagnostic performance (an 11-percentage-point gain in accuracy on dermoscopy data) and reduced unsupported claims on qualitative samples, although overall performance remains insufficient for clinical deployment. We acknowledge the inherent uncertainty in human annotations and the absence of clinical context, which further limit the translation to real-world settings. Within this controlled setting, this pilot study provides preliminary insights into zero-shot agent performance in visually confounded scenarios.

09.
arXiv (quant-ph) 2026-06-19

Quantum Algebraic Diversity: Single-Copy Density Matrix Estimation via Group-Structured Measurements

arXiv:2604.03725v3 Announce Type: replace Abstract: We extend the algebraic diversity (AD) framework from classical signal processing to quantum measurement theory. The Quantum Algebraic Diversity (QAD) Theorem establishes that a group-structured positive operator-valued measure (POVM) applied to a single copy of a quantum state produces a full-rank, group-averaged density matrix estimator whose eigenbasis and eigenvalue ordering track those of the true density matrix, with a bias toward the symmetrized state, analogous to the classical recovery of covariance eigenstructure from a single observation. We establish a Classical-Quantum Duality Map connecting classical covariance estimation to quantum state tomography, and an Optimality Inheritance Theorem showing that classical group optimality transfers to quantum settings via the Born map within the group-averaged family. SIC-POVMs are identified as AD with the Heisenberg-Weyl group and mutually unbiased bases as AD with the Clifford group, revealing the hierarchy $\mathrm{HW}(d) \subseteq \mathcal{C}(d) \subseteq S_d$ that mirrors the classical $\mathbb{Z}_M \subseteq G_{\min} \subseteq S_M$. The double-commutator eigenvalue theorem gives polynomial-time adaptive POVM selection. A worked qubit example shows the group-averaged estimator from a single computational-basis measurement, averaged over a matched $\mathbb{Z}_2$ group, reaching fidelity 0.99 where standard single-basis tomography gives a rank-1 estimate of fidelity 0.80. Monte Carlo simulations for $d = 2$ to $13$ confirm fidelity above 0.90 from a single outcome while standard fidelity degrades as $\sim 1/d$. The growing ratio reflects collapse of the rank-1 standard estimator, not fewer copies per parameter: the biased single-copy estimator reduces the number of distinct measurement settings, not the per-parameter sampling cost, and a genuine copy reduction holds only under exact symmetry.

10.
arXiv (quant-ph) 2026-06-19

Fidelity bounds for adiabatic gates and other quantum operations with time-dependent dissipation

arXiv:2606.20501v1 Announce Type: new Abstract: As quantum-computing platforms are susceptible to noise, the fidelity of quantum operations is limited by decoherence. Understanding this limitation is crucial for building utility-scale quantum processors. In previous works [Phys. Rev. Lett. 129, 150504 (2022); Quantum 9, 1684 (2025)], we presented analytical formulae for the average gate fidelity of multi-qubit operations under static Markovian noise processes, including operations that temporarily leave the computational subspace. However, some quantum-computing architectures dynamically modulate qubit or coupler frequencies to implement two-qubit gates, e.g., baseband flux gates; such modulation can lead to dissipation rates varying in time. In this Letter, we therefore generalize the fidelity-reduction formulae to encompass time-dependent dissipation. Applying our generalized formula, we obtain a fidelity bound for adiabatic operations and demonstrate that flux-dependent noise sensitivity, combined with qubit-coupler hybridization, significantly reduces the fidelity of adiabatic controlled-Z (CZ) gates in superconducting quantum computers. Our work thus provides essential theoretical tools for evaluating error budgets and optimizing the design of quantum operations in tunable quantum-computing architectures, and may also find applications in quantum-sensing and quantum-communication protocols that are affected by time-dependent dissipation.

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

DYNA : Dynamic Episodic Memory Networks for Augmenting Large Language Models with Temporal Knowledge Graphs in Continuous Learning

Large Language Models (LLMs) struggle to incorporate new knowledge without forgetting or costly retraining. We propose DYNA, a lightweight framework that augments a frozen LLM with a temporal knowledge graph where events are nodes and temporal relations are directed, timestamped edges. The graph serves as an external, updatable memory. At query time, DYNA retrieves relevant nodes via random walks and centrality measures, then augments the LLM's response. Evaluated on three temporal recall tasks, DYNA reduces catastrophic forgetting by ~7% compared to fine-tuning and improves temporal ordering by ~5% over standard RAG. Higher graph clustering coefficients correlate with better retrieval, showing that graph structure matters. Contributions: (1) episodic memory as temporal KG, (2) retraining-free LLM augmentation, (3) graph properties as predictors of retrieval performance.

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

Equivariant Flow Matching for Symmetry-Breaking Bifurcation Problems

arXiv:2509.03340v4 Announce Type: replace-cross Abstract: Bifurcation phenomena in nonlinear dynamical systems often lead to multiple coexisting stable solutions, particularly in the presence of symmetry breaking. Deterministic machine learning models are unable to capture this multiplicity, averaging over solutions and failing to represent lower-symmetry outcomes. In this work, we formalize the use of generative AI, specifically flow matching, as a principled way to model the full probability distribution over bifurcation outcomes. Our approach builds on existing techniques by combining flow matching with equivariant architectures and an optimal-transport-based coupling mechanism. We generalize equivariant flow matching to a symmetric coupling strategy that aligns predicted and target outputs under group actions, allowing accurate learning in equivariant settings. We validate our approach on a range of systems, from simple conceptual systems to physical problems such as buckling beams and the Allen–Cahn equation. The results demonstrate that the approach accurately captures multimodal distributions and symmetry-breaking bifurcations. Moreover, our results demonstrate that flow matching significantly outperforms non-probabilistic and variational methods. This offers a principled and scalable solution for modeling multistability in high-dimensional systems.

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

VidCRAFT3: Camera, Object, and Lighting Control for Image-to-Video Generation

Controllable image-to-video (I2V) generation transforms a reference image into a coherent video guided by user-specified control signals. While precise control over camera motion, object motion, and lighting is essential for high-fidelity creation, existing methods often treat these factors independently. This overlooks the physical coupling among viewpoint, geometry, and illumination in dynamic scenes, leading to visual inconsistencies such as mismatched shadows and perspective drift under simultaneous changes. We present VidCRAFT3, a unified and flexible I2V framework that explicitly models cross-factor interactions among geometry, motion, and illumination, enabling both independent and joint control over camera motion, object motion, and lighting direction. Image2Cloud provides explicit 3D geometric priors for accurate camera motion control. ObjMotionNet encodes sparse object trajectories into multi-scale motion features to guide realistic object motion. A Spatial Triple-Attention Transformer integrates lighting direction through lighting cross-attention for consistent relighting. To address the scarcity of jointly annotated data, we construct the VideoLightingDirection (VLD) dataset with accurate per-frame lighting direction annotations, and introduce a three-stage progressive training strategy that enables robust learning without fully joint annotations. Extensive experiments demonstrate that VidCRAFT3 achieves state-of-the-art performance in control precision and visual coherence across diverse scenarios.

14.
arXiv (CS.CV) 2026-06-17

Quantum Enchanced Multi-Scale CNN with Bi-directional Mamba for Crop Field Analysis

Hyperspectral image (HSI) crop analysis is essential for precision agriculture because it captures rich spectral and spatial information for accurate crop monitoring and assessment. However, HSI classification remains challenging due to high spectral dimensionality, spatial complexity, class imbalance, and limited labeled samples. To address these challenges, this paper proposes a BiSpectral Mamba-based framework that combines multi-scale convolutional feature extraction, spectral attention, bidirectional state-space modeling, and quantum-inspired learning. A multi-scale CNN backbone first extracts hierarchical spatial-spectral representations through feature fusion across multiple resolutions. A spectral attention mechanism then emphasizes informative bands while suppressing redundant and noisy channels. The refined features are processed by a BiSpectral Mamba module that captures long-range dependencies in both forward and backward directions by modeling hyperspectral feature maps as sequential tokens. In addition, class-weighted optimization and feature fusion strategies are incorporated to improve training stability and mitigate class imbalance. Experimental evaluation on the UAVHSI-Crop dataset demonstrates the effectiveness of the proposed framework, achieving an overall accuracy of 84.83%. The results show that integrating convolutional, attention-based, and state-space modeling components enables robust spatial-spectral feature learning for crop classification. The proposed framework also shows potential for broader agricultural and remote sensing applications, including crop disease detection, yield prediction, and soil moisture estimation, while highlighting the effectiveness of structured state-space and quantum-inspired architectures for hyperspectral image analysis.

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

AnonShield: Scalable On-Premise Pseudonymization for CSIRT Vulnerability Data

arXiv:2606.15650v1 Announce Type: cross Abstract: We present AnonShield, a high-throughput, on-premise pseudonymization system that combines GPU-accelerated NER, streaming processing, caching, and schema-aware configuration. Evaluated on datasets up to 550 MB (70,951 records), AnonShield reduces processing time from over 92 hours to under 10 minutes (up to 738x speedup) while achieving up to 94.2% F1-score and 96.7% recall. Our results show that scalable pseudonymization of vulnerability data is feasible without sacrificing analytical utility, enabling compliant data sharing in operational CSIRT environments.

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

HyDRA: Hybrid Dynamic Routing Architecture for Heterogeneous LLM Pools

Production LLM deployments increasingly maintain heterogeneous model pools spanning order-of-magnitude cost differences. Existing routers make binary strong-vs-weak decisions and couple learned parameters to specific model identities, requiring retraining whenever the catalog changes. We present HyDRA (Hybrid Dynamic Routing Architecture), a framework that predicts fine-grained, multi-dimensional capability requirements per query and matches them against configuration-defined model profiles via shortfall matching. A ModernBERT encoder with K=4 independent sigmoid heads scores each query along reasoning, code generation, debugging, and tool use; a shortfall-matching algorithm then selects the cheapest model whose capabilities meet the predicted requirements. The deployed predictor runs at 86 ms median CPU inference latency in production, and is fully decoupled from the model catalog – adding or removing models requires only a configuration change, with zero retraining. On SWE-Bench Verified (5-model pool: GPT-5.4-mini, Claude Haiku 4.5, GPT-5.3 Codex, Claude Sonnet 4.6, GPT-5.4), HyDRA's tunable shortfall threshold spans three regimes: peak-quality exceeds the always-strong Claude Sonnet 4.6 baseline (75.4% vs. 74.2% resolution) at 12.9% cost savings; iso-quality matches Sonnet at 54.1% cost savings, a 6x improvement over our prior in-house binary router at 9.1%; aggressive pushes savings to 72.5% for a 3.2-point quality trade. Results generalize across LiveCodeBench, BigCodeBench, and tau-bench. HyDRA is deployed to all users in GitHub Copilot's VS Code Chat auto-mode and – to our knowledge for the first time in the LLM routing literature – demonstrates language-invariant routing across CJK, European, and other script families.

17.
arXiv (CS.CL) 2026-06-19

When Does Streaming Tool Use Help? Characterizing Tool-Intent Stabilization in Streaming Retrieval-Augmented Generation

Streaming Retrieval-Augmented Generation (Streaming RAG) reduces user-perceived latency by issuing tool queries in parallel with ongoing user input, before the utterance is complete. Reported gains are aggregate, yet the mechanism's benefit is fundamentally query-intrinsic: speculation can only help when the correct tool query becomes determinable before the user stops speaking or typing. We isolate and measure this property – tool-intent stabilization, the point in the input stream at which a speculative query's retrieval converges to the answer-bearing result. On the CRAG benchmark (1371 validation questions) we (i) measure the distribution of stabilization, (ii) derive a model-agnostic bound H on the portion of tool latency that can be hidden behind the user's remaining input, as a function of tool latency L and input cadence {\delta}, (iii) validate against a working streaming pipeline that realized savings meet or exceed this bound, and (iv) identify which query properties predict early versus late stabilization. The study requires no model training and runs on commodity CPU hardware. We find that at a realistic operating point (L=600ms, {\delta}=3w/s, {\theta}=0.8), 73.9% of queries across the full benchmark admit substantial latency hiding – a blended figure that mixes sufficiency stabilization on the 21.3% of questions where gold evidence is verbatim-present and BM25-retrievable (95.2% streamable on this favorable slice) with a grounding-free top-1-settling fallback on the remainder. On the favorable slice, {\phi}_suf is bracketed to [0.26, 0.281] by exact and relaxed grounding – both early. Question type produces a significant but coarse early/late split (Kruskal-Wallis p=0.017, epsilon^2=0.04), directly informing when a learned speculative trigger is worth its cost.

18.
medRxiv (Medicine) 2026-06-10

Towards the Virtual Amyotrophic Lateral Sclerosis Patient: Inferring Cortical Excitability through Whole-Brain Dynamical Modeling

Amyotrophic lateral sclerosis (ALS) is increasingly recognized as a multisystem neurodegenerative disorder in which motor-neuron degeneration is accompanied by widespread alterations in cortical dynamics. Among its most reproducible neurophysiological signatures is cortical hyperexcitability, yet how this local excitability imbalance shapes distributed whole-brain activity remains poorly understood. Here, we combined source-reconstructed resting-state MEG data, tractography-informed whole-brain modeling, and simulation-based inference to investigate whether ALS-related alterations in large-scale brain dynamics can be mechanistically explained by changes in cortical excitability. First, we characterized empirical brain dynamics using complementary features spanning regional activity amplitude and variability, functional connectivity, and avalanche-based metrics. These analyses revealed significant alterations in ALS patients relative to healthy controls, as well as associations with clinical impairment and disease staging. To mechanistically interpret these changes, we employed a reduced Wong-Wang whole-brain model in which local recurrent excitation modulates emergent large-scale neural dynamics. Simulations showed that increasing excitability systematically reproduced the empirical dynamical signatures observed in ALS. We then applied a simulation-based inference framework to estimate latent excitability parameters directly from empirical observations. Whole-brain model inversion revealed increased excitability in ALS patients compared with controls. The recovered excitability parameter was associated with disease staging, supporting its clinical relevance as a model-derived descriptor of ALS progression. Finally, by extending the model to estimate frontal and non-frontal excitability separately, we found that ALS-related alterations were predominantly associated with increased frontal excitability, whereas non-frontal regions appeared comparatively less affected. The recovered parameters related to disease staging. Together, these findings provide a mechanistic framework linking altered large-scale brain dynamics in ALS to selective cortical hyperexcitability, explaining how local excitability changes can give rise to global network reorganization. More broadly, they show how computational model inversion can recover latent multiscale pathophysiological processes from empirical neural recordings, offering a non-perturbative alternative to complex experimental paradigms typically required to causally probe local-to-global mechanisms.

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

Human genetic evidence is associated with drug approval across therapeutic areas: an observational analysis of 26,278 target-disease pairs with temporal validation and feature ablation

Genetic evidence is enriched among approved drug targets: in an observational analysis of 26,278 target-disease pairs from Open Targets and ChEMBL, targets with any genetic association had a 3.25-fold higher approval rate than those without (OR = 3.25, 95% CI 2.79-3.79, p = 1.91e-42). A target-level analysis accounting for non-independence of pairs sharing the same gene gave OR = 2.79 (bootstrap 95% CI 2.22-3.53); the oncology pair-level OR of 6.72 attenuates to 2.71 at the target level, illustrating how non-independence inflates area-specific estimates. The enrichment replicated in post-2015 approvals (OR = 3.51, p = 1.72e-8). Feature ablation across six evidence types revealed that literature mining alone accounts for most classifier performance (AUPRC = 0.099 versus 0.109 for all features), consistent with temporal leakage from post-approval publications. Excluding literature, remaining evidence types retain above-baseline signal (AUPRC = 0.084, 1.63x baseline). Sensitivity analyses bracket the pair-level OR between 3.25 and 4.93. Genetic evidence alone yields only a 1.0-percentage-point absolute AUPRC gain and the best model has poor calibration; the classifier has limited practical predictive value. We catalogue 1,433 genetically supported Phase 1/2 pairs as a hypothesis-generating resource. All findings are observational.

20.
arXiv (CS.AI) 2026-06-18

TRIDENT: Breaking the Hybrid-Safety-Physics Coupling for Provably Safe Multi-Agent Reinforcement Learning

arXiv:2606.18308v1 Announce Type: cross Abstract: Safe coordination in networked cyber-physical systems forces learning algorithms to simultaneously handle hybrid discrete-continuous actions, hard training-time safety constraints, and physics-governed dynamics. We show that these three features form a directed cycle of biases that defeats any naive composition of off-the-shelf modules, and formalize this as a three-way coupling lemma. We then introduce TRIDENT, the first MARL framework whose three components are co-designed to cancel each leak: a Richardson-Romberg gradient correction reducing Gumbel-Softmax bias from O(tau) to O(tau^2), a Lyapunov-constrained sequential trust-region update enforcing per-iterate feasibility, and a physics-informed residual critic that decomposes value rather than reward. We prove an O~(1/sqrt(K)) convergence rate to a constrained Nash equilibrium and an O(sqrt(K)) cumulative-violation bound. On multi-UAV mobile-edge computing, autonomous intersection management, and a hybrid SMAC variant, TRIDENT cuts training-time violations by 95.5% over MADDPG and 76.3% over MACPO, while improving reward by 13.5% over the strongest unconstrained baseline.

21.
bioRxiv (Bioinfo) 2026-06-12

The Geometry of Allostery: A Laplacian Minor Hierarchy for Many-Body Protein Communication

Quantifying how cooperative, many-body relationships drive allostery in protein networks remains a major challenge. To address this, we develop the Laplacian minor hierarchy, a mathematical framework that characterizes the geometric invariants of a protein network. Lower-order minors yield standard metrics including the partition function and effective distances, whereas higher-order minors define novel topological measures: cooperation indices, each bounded between zero and one, that characterize pathway correlations at increasing levels of complexity, the third-order minor determines whether allosteric pathways are correlated or uncorrelated, and the fourth-order minor quantifies how distinct pathways communicate through intermediary residues. We apply this framework to analyze the evolutionary adaptation of the PSD95pdz3 domain from Class I to Class II ligand specificity via mutations G330T and H372A. The cooperation index demonstrates a distinct evolutionary hierarchy: the G330T mutation establishes distributed pathway couplings that the H372A mutation subsequently exploits, whereas H372A alone produces minimal global changes. Furthermore, the fourth-order analysis identifies His317 as a critical intermediary node bridging the class-switching (330-372) and class-bridging (330-400) allosteric pathways. These results demonstrate that allosteric dependencies emerge only when mutations accumulate in specific combinations, with a hierarchical organization of pathways structured around position 330 and intermediary nodes His317 and Phe400. Rather than predicting allosteric mechanisms, this framework provides a mechanistic explanation for why and how allostery emerges during protein evolution.

22.
arXiv (CS.AI) 2026-06-11

Toward Trustworthy AI: Multi-Target Adversarial Attacks and Robust Defenses for Continuous Data Summarization

arXiv:2606.11804v1 Announce Type: new Abstract: Trustworthy AI requires reliable data-processing pipelines, not only robust downstream predictive models. As an upstream component, data summarization determines which information is retained and passed to subsequent learning or decision modules. Therefore, adversarial perturbations to the summarization process can compromise trustworthy AI in an upstream manner: they may alter the selected summary, reduce its representativeness, and further degrade the utility of subsequent learning tasks. In this paper, we study adversarial attacks on continuous data summarization under similarity-level perturbations through DR-submodular optimization. We show that a class of multi-resolution image summarization objectives can be formulated as multilinear extensions of non-negative submodular set functions and satisfy DR-submodularity with $m$-weak monotonicity. We then formulate multi-target attack generation as a min-max problem, where one admissible perturbation of the similarity structure is optimized to degrade multiple target summarization models. To mitigate such perturbations, we formulate robust defense against mixed attack types as a regularized max-min problem. For both problems, we develop approximation algorithms with theoretical guarantees. Experiments on real-data and controlled clustered benchmarks show that the proposed attack is effective in representative low-to-moderate budget regimes and can induce downstream task-performance loss. The proposed defense improves the robustness–mitigation trade-off in structured settings, while also revealing the parameter sensitivity of robust protection on real data.

23.
arXiv (CS.CV) 2026-06-12

QueryOcc: Query-based Self-Supervision for 3D Semantic Occupancy

Learning 3D scene geometry and semantics from images is a core challenge in computer vision and a key capability for autonomous driving. Since large-scale 3D annotation is prohibitively expensive, recent work explores self-supervised learning directly from sensor data without manual labels. Existing approaches either rely on 2D rendering consistency, where 3D structure emerges only implicitly, or on discretized voxel grids from accumulated lidar point clouds, limiting spatial precision and scalability. We introduce QueryOcc, a query-based self-supervised framework that learns continuous 3D semantic occupancy directly through independent 4D spatio-temporal queries sampled across adjacent frames. The framework supports supervision from either pseudo-point clouds derived from vision foundation models or raw lidar data. To enable long-range supervision and reasoning under constant memory, we introduce a contractive scene representation that preserves near-field detail while smoothly compressing distant regions. QueryOcc surpasses previous camera-based methods by 26% in semantic RayIoU on the self-supervised Occ3D-nuScenes benchmark while running at 11.6 FPS, demonstrating that direct 4D query supervision enables strong self-supervised occupancy learning. https://research.zenseact.com/publications/queryocc/

24.
arXiv (quant-ph) 2026-06-17

Effects of Josephson Junction Non-idealities on Adiabatic Quantum Flux Parametron Circuits

arXiv:2606.17338v1 Announce Type: new Abstract: Adiabatic quantum flux parametron (AQFP) gate is a promising approach to scale up the cryogenic microwave electronics for superconducting qubit multiplexed control. However, the performance of these circuits depends on the quality of the Josephson junctions which are ideally superconductor-insulator-superconductor (SIS) type following the ideal sinusoidal relation between current and quantum phase. We demonstrate how the non-sinusoidal current-phase relation in Superconductor-Normal metal-Superconductor (SNS) and weak link (WL) junctions affects the speed, delay, and margin of the AQFP gates. The JJ models are defined in the Keysight ADS simulator using symbolically defined device (SDD) method.

25.
arXiv (CS.CL) 2026-06-18

BCL: Bayesian In-Context Learning Framework for Information Extraction

Existing information extraction (IE) tasks increasingly adopt in-context learning (ICL) with large language models. However, current approaches either show inconsistent performance across model scales or lack systematic optimization and generalizability. Building on this, we propose BCL (Bayesian In-Context Learning Framework for Information Extraction), the first optimization framework that uses particle filtering with Bayesian updates to systematically refine label representations across IE tasks. Through four steps initialization, observation, weight update, and resampling, BCL generalizes to both sequence labeling and relation classification paradigms. Extensive experiments demonstrate substantial and consistent improvements over existing approaches.