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01.
medRxiv (Medicine) 2026-06-17

A non-invasive liquid biopsy resolves the diagnostic blind spot in chronic kidney disease

Chronic kidney disease is a major global health burden, and its early detection is critical for delaying progression to kidney failure using recently developed targeted therapies. However, current diagnostic screening relies heavily on blood markers that are confounded by muscle mass, and on urine tests that frequently miss structural damage occurring without protein leakage. This creates a critical diagnostic blind spot that hinders timely intervention. Here we show a non-invasive liquid biopsy platform that quantifies a specific protein marker, MUC1, on urinary extracellular vesicles to accurately assess renal parenchymal integrity. By bypassing the systemic metabolic noise of traditional blood tests, our assay provides a remarkably stable, person-specific functional signature. Following extensive validation across diverse cohorts, our longitudinal analysis demonstrated that the discrepancy between this novel urine-based readout and standard blood tests unmasks hidden renal vulnerability, successfully predicting rapid functional decline. By comprehensively evaluating both tubular and glomerular integrity from a single spot urine sample, these findings establish a completely non-invasive, highly scalable prescreening tool that resolves the diagnostic blind spot, enabling broader early detection strategies and ushering in a new era of proactive risk management.

02.
arXiv (quant-ph) 2026-06-19

Stalls and Spequlation: Pipelined Execution for Fault Tolerant Quantum Computation

arXiv:2606.19593v1 Announce Type: new Abstract: Fault-tolerant quantum computation requires the coordinated action of three distinct systems: classical control logic, quantum hardware, and classical error decoders. Current scheduling models treat logical operations as atomic, hiding the fact that these subsystems operate sequentially and spend significant time idle. We present a pipelined execution framework that decomposes each logical operation into its component stages i.e. Control, Execute, and Decode. Building on this, we discuss some speculation strategies that allow successor operations to begin processing before their predecessors have completed decoding. We evaluate our framework on several common benchmarks and show that pipelining with speculation reduces total pipeline steps by 20-40% compared to a no-speculation baseline. The most aggressive strategy consistently outperforms conservative alternatives, even though partial rollback is needed at times, because the per-rollback penalty is small relative to the parallelism gained. We further show that speculation facilitates load balancing by distributing work more evenly across the heterogeneous subsystems of a fault-tolerant quantum computer, converting idle time into useful computation while also saving on execution time.

03.
arXiv (quant-ph) 2026-06-17

Efficient time-series prediction on NISQ devices via time-delayed quantum extreme learning machine

arXiv:2602.21544v2 Announce Type: replace Abstract: We proposed a time-delayed quantum extreme learning machine (TD-QELM) for efficient time-series prediction on noisy intermediate-scale quantum (NISQ) devices. By encoding multiple past inputs simultaneously, TD-QELM achieves shallow circuit depth independent of sequence length, thereby, mitigating noise accumulation and reducing computational complexity. Experiments using the NARMA benchmark on both noiseless simulations and IBM's 127-qubit processor demonstrate that TD-QELM consistently outperforms conventional quantum reservoir computing in prediction accuracy and noise robustness. These results highlight TD-QELM as a practical and scalable framework for time-series learning on current NISQ hardware.

04.
arXiv (CS.CV) 2026-06-16

All Eyes on the Workflow: Automated and Efficient Event Discovery from Video Streams

Disciplines such as business process management and process mining aid organizations by discovering insights about processes on the basis of recorded event data. However, an obstacle to process analysis is data multi-modality: for instance, data in video form are not directly interpretable as events. Existing approaches rely on a dictionary of activity label as input, cannot provide frame-by-frame labeling explanations, or rely on superseded computer vision techniques. In this work, we present SnapLog, an approach to extract event data from videos by converting frames to feature vectors using image embeddings and performing temporal segmentation through frame-wise similarity matrices. A generalized few-shot classification is then used to assign labels to the video segments, yielding labeled, timestamped sub-sequences of frames that are interpretable as events. Conventional process mining techniques can be used to analyze the resulting data. We show that our approach produces logs that accurately reflect the process in the videos.

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

CT-VDETR: Semi-supervised 3D Trauma Detection in Computed Tomography (CT) scans using Dense Vertex Relative Position Encoding

Accurate detection and localization of traumatic injuries in abdominal CT remain challenging because voxel-level annotations are limited and expensive to obtain. We present a label-efficient framework for 3D abdominal trauma detection that combines self-supervised pretraining with semi-supervised transformer-based detection. First, we use Masked Image Modeling (MIM) on 1098 CT volumes to pretrain a 3D U-Net encoder for anatomical representation learning. Next, we adapt V-DETR to dense volumetric CT through a feature adapter that converts the encoder feature grid into a compact token sequence for transformer decoding. The pretrained encoder is then integrated with V-DETR and 3D Vertex Relative Position Encoding (3D V-RPE) to improve the localization of irregularly shaped injuries. Finally, semi-supervised teacher-student consistency regularization leverages 2,000 additional unlabeled volumes during detector training. To the best of our knowledge, this is the first application of a 3D DETR-style detector to the RSNA abdominal trauma detection task. On this benchmark, the proposed method achieves 31.33% test mAP@0.50 using only 78 labeled training volumes, corresponding to a 1.53x improvement over supervised-only training. These results show that combining medical-domain pretraining with semi-supervised learning is an effective strategy for label-scarce 3D medical detection.

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

Phonikud: Overcoming Phonetic Underspecification for Hebrew Text-To-Speech

Text-to-speech (TTS) for Modern Hebrew is challenged by the language's orthographic complexity, with existing solutions ignoring underspecified phonetic features such as stress. We present a framework for more phonetically accurate Hebrew TTS with four contributions: (1) Phonikud, an open-source Hebrew grapheme-to-phoneme (G2P) system that outputs fully-specified International Phonetic Alphabet (IPA) transcriptions, designed by augmenting a base diacritizer. (2) The ILSpeech corpus of paired Hebrew audio, text, and expert IPA annotations. (3) A benchmark for the previously unmeasured task of Hebrew G2P conversion. (4) Hebrew audio-to-IPA models capturing previously disregarded phonetic details for automatic TTS evaluation. Our results show that Phonikud more accurately predicts Hebrew phonemes than prior methods, and that small, local TTS models with phonetic input from Phonikud approach large proprietary systems. We release our code, data, and models at https://phonikud.github.io.

07.
arXiv (quant-ph) 2026-06-11

Super-Heisenberg Non-Equilibrium Quantum Sensing with Waveguide-Coupled Emitters

arXiv:2606.11975v1 Announce Type: new Abstract: We explore an array of quantum emitters as non-equilibrium probes, coupled to a one-dimensional photonic waveguide, aiming to estimate its properties such as wave number which encodes the waveguide frequency and dispersive characteristics. By considering transient dynamics following initial excitation, we show that the quantum Fisher information (QFI) can be significantly enhanced through careful emitter positioning. For two-emitter probes, optimal spacing stabilizes populations and coherences in the single-excitation subspace, suppressing super radiant decay and extending both the magnitude and longevity of QFI. Randomized emitter configurations also reveal that vanishing waveguide-mediated cross decay maximizes both achievable sensitivity and the temporal duration over which information about the parameter remains accessible. Extending to multipartite probes, we demonstrate that the maximum QFI and its temporal integral scale with system size, exceeding the Heisenberg limit for all positioning strategies. Our results highlight the potential of waveguide-coupled emitter arrays as versatile quantum sensors, where collective radiative dynamics can be harnessed to achieve tunable, long-lived, and enhanced precision.

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

Improved Baselines with Representation Autoencoders

Representation Autoencoders (RAE) replace traditional VAE with pretrained vision encoders. In this paper, we systematically investigate several design choices and find three insights which simplify and improve RAE. First, we study a generalized formulation where the representation is defined as sum of the last k encoder layers rather than solely the final layer. This simple change greatly improves reconstruction without encoder finetuning or specialized data (e.g., text, faces). Second, we study the prevalent assumption that RAE (using pretrained representation as encoder) replaces representation alignment (REPA), which distills the same representation to intermediate layers instead. Through large-scale empirical analysis, we uncover a surprising finding: RAE and REPA exhibit complementary working mechanisms, allowing the same representation to be used as both encoder and target for intermediate diffusion layers. Finally, the original RAE struggles with classifier-free guidance (CFG) and requires training a second, weaker diffusion model for AutoGuidance (AG). We show that REPA itself can be viewed as x-prediction in RAE latent space. By simply re-parameterizing the output of the DiT model, it can provide guidance for "free". Overall, RAEv2 leads to more than 10x faster convergence over the original RAE, achieving a state-of-the-art gFID of 1.06 in just 80 epochs on ImageNet-256. On FDr6, RAEv2 achieves a state-of-the-art 2.17 at just 80 epochs compared to the previous best 3.26 (800 epochs) without any post-training. This motivates EPFID@k (epochs to reach unguided gFID < k) as a measure of training efficiency. RAEv2 attains an EPFID@2 of 35 epochs, versus 177 for the original RAE. We also validate our approach across diverse settings for text-to-image generation and navigation world models, showing consistent improvements. The code is available at https://raev2.github.io.

09.
arXiv (CS.AI) 2026-06-19

"**Important** You should give me full credits!": Exploring Prompt Injection Attacks on LLM-Based Automatic Grading Systems

arXiv:2606.03090v2 Announce Type: replace-cross Abstract: The emergence of large language models (LLMs) has significantly accelerated recent research on LLM-based automatic grading (AG) systems. Benefiting from the strong instruction-following capabilities and broad prior knowledge of LLMs, educators can deploy AG systems across diverse tasks using only natural language rubrics while achieving satisfactory grading performance. Despite these advantages, new security concerns may also arise. In particular, prompt injection (PI) attacks have recently become a major threat to LLM-based applications. In the context of AG, attackers can potentially exploit PI vulnerabilities to manipulate grading systems into assigning artificially high scores regardless of the actual answer quality. Such behavior poses serious risks to the fairness, reliability, and integrity of educational assessment. In this work, we study PI attacks in AG systems, and systematically investigate the effectiveness of such attacks in educational scenarios. We further evaluate the effectiveness of existing defensive strategies against these attacks. Through comprehensive experiments under rubric-based grading settings, we demonstrate that current LLM-based AG systems remain highly vulnerable to PI attacks. We hope that our findings raise awareness of this emerging threat and motivate future research toward secure, robust, and trustworthy LLM-based educational systems.

10.
bioRxiv (Bioinfo) 2026-06-11

Tumour evolution as ground truth for cancer whole-genome sequencing

Cancer genomes are shaped by evolutionary processes that couple mutagenesis, clonal selection, chromosomal instability, spatial growth and treatment response into structured genomic patterns, yet current benchmarking strategies largely ignore this evolutionary dependency. Here, we present SCOUT, a large-scale synthetic whole-genome sequencing resource of over 200 samples, designed for systematic benchmarking of tumour genomic analysis and evolutionary inference under controlled evolutionary ground truth. Unlike conventional task-specific simulations, SCOUT models tumour evolution as a latent generative process that simultaneously shapes mutations, copy-number alterations, variant allele frequencies, mutational signatures and clonal architectures. SCOUT recapitulates key features of solid and haematological malignancies, including driver mutations, chromosomal instability, intratumour heterogeneity, spatial sampling and treatment-associated evolutionary dynamics in tumour and matched-normal longitudinal and multi-region sequencing designs. Using SCOUT, we benchmarked widely used methods for somatic variant detection, copy-number analysis, mutational signature inference and tumour evolutionary reconstruction. Across analytical tasks, performance deteriorated in low-purity, highly subclonal and structurally complex tumours, while spatial sampling bias and hypermutation generated spurious evolutionary signals that confounded tumour interpretation across multiple inference layers. Evolutionary simulations further distinguished lineage-restricted genetic bottlenecks from multi-lineage resistance dynamics associated with tumour plasticity. Tumour purity consistently exerted a stronger effect on inference accuracy than sequencing depth. Together, our results establish evolutionary ground truth as a prerequisite for reproducible benchmarking and biologically interpretable analysis of cancer whole-genome sequencing data.

11.
arXiv (CS.CL) 2026-06-12

LLM-based Embeddings: Attention Values Encode Sentence Semantics Better Than Hidden States

Sentence representations are foundational to many Natural Language Processing (NLP) applications. While recent methods leverage Large Language Models (LLMs) to derive sentence representations, most rely on final-layer hidden states, which are optimized for next-token prediction and thus often fail to capture global, sentence-level semantics. This paper introduces a novel perspective, demonstrating that attention value vectors capture sentence semantics more effectively than hidden states. We propose Value Aggregation (VA), a simple method that pools token values across multiple layers and token indices. In a training-free setting, VA outperforms other LLM-based embeddings, even matches or surpasses the ensemble-based MetaEOL. Furthermore, we demonstrate that when paired with suitable prompts, the layer attention outputs can be interpreted as aligned weighted value vectors. Specifically, the attention scores of the last token function as the weights, while the output projection matrix ($W_O$) aligns these weighted value vectors with the common space of the LLM residual stream. This refined method, termed Aligned Weighted VA (AlignedWVA), achieves state-of-the-art performance among training-free LLM-based embeddings, outperforming the high-cost MetaEOL by a substantial margin. Finally, we highlight the potential of obtaining strong LLM embedding models through fine-tuning Value Aggregation.

12.
arXiv (CS.LG) 2026-06-16

Mixtures of Subspaces for Bandwidth Efficient Context Parallel Training

arXiv:2606.16384v1 Announce Type: new Abstract: Pretraining language models with extended context windows enhances their ability to leverage rich information during generation. Existing methods split input sequences into chunks, broadcast them across multiple devices, and compute attention block by block which incurs significant communication overhead. While feasible in high-speed clusters, these methods are impractical for decentralized training over low-bandwidth connections. We propose a compression method for communication-efficient context parallelism in decentralized settings, achieving a remarkable compression rate of over 95\% with negligible overhead and no loss in convergence. Our key insight is to exploit the intrinsic low-rank structure of activation outputs by dynamically constraining them to learned mixtures of subspaces via efficient reparameterizations. We demonstrate scaling billion-parameter decentralized models to context lengths exceeding 100K tokens on networks as slow as 300Mbps, matching the wall-clock convergence speed of centralized models on 100Gbps interconnects.

13.
arXiv (CS.CL) 2026-06-11

Beyond Third-Person Audits: Situated Interaction Auditing for User-Centered LLM Bias Research

Research on bias in large language models (LLMs) has predominantly focused on third-person audits, which study how models represent or evaluate demographic groups as external subjects. However, this paradigm overlooks a structural blind spot because the user is absent from the audit. In practice, LLMs are used in open-ended, personal interactions, during which the model implicitly represents the user and adjusts its responses accordingly. When identical requests yield different responses depending on who is asking, bias manifests not in how the model describes others but in how it treats its interlocutor. We propose Situated Interaction Auditing (SIA), a user-centered framework for studying how user profile signals – implicit sociodemographic markers, writing style, and stated identity – systematically shape LLM response quality, content, and tone. We demonstrate the framework through a case study that intersects gender and socioeconomic status signals across multiple task domains and outline a research agenda for SIA as a new mission for natural language processing.

14.
arXiv (CS.AI) 2026-06-12

Rarity-Gated Context Conditioning for Offline Imitation Learning-Based Maritime Anomaly Detection

arXiv:2606.13311v1 Announce Type: cross Abstract: Contextual anomaly detection aims to identify abnormal behavior conditional on context variables, but practical deployments often face highly imbalanced context distributions where rare regimes can be critical information. Under such frequency bias, context-conditioned models can produce unstable decisions and excessive false alarms in rare contexts. We propose Rarity-Gated Feature-wise Linear Modulation (RGFiLM), a rarity-aware conditioning module that combines feature-wise modulation (i.e., context-conditioned scaling and shifting of hidden features) with a gate controlled by a data-driven rarity score. The rarity score is estimated from the empirical distribution of context variables and regulates how strongly context modulates intermediate representations: the gate becomes more decisive under rare contexts while remaining conservative under frequent contexts. We evaluate RGFiLM on maritime trajectory anomaly detection using AIS motion sequences with ERA5 environmental context in an environment-sensitive detour scenario. When instantiated in a sequential anomaly scoring pipeline, RGFiLM achieves the best mean F1–False Positive Rate (FPR) trade-off among the compared context-agnostic and context-conditioned methods. These results suggest that explicitly accounting for context rarity is an effective approach for reducing false alarms in context-sensitive anomaly detection.

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

TimeVista: Exploring and Exploiting Vision-Language Models as Judges for Time Series Forecasting

arXiv:2606.16173v1 Announce Type: new Abstract: High-quality time series forecasting is pivotal for real-world decision-making. However, traditional point-wise metrics often fail to reveal complex temporal patterns and align poorly with human intuitive preferences. While the ''LLM-as-a-Judge'' paradigm has revolutionized text evaluation by providing flexible, human-aligned judgment, its application to time series remains largely unexplored. In this paper, we leverage Vision-Language Models (VLMs) as judges for time series forecasting, harnessing their ability to comprehend time series plots grounded in textual information. Specifically, we propose a novel framework integrating micro- and macro-level judgments informed by contextual information to evaluate time series forecasting. To this end, we introduce TimeVista, a comprehensive VLM-as-a-Judge benchmark comprising 5563 time series samples paired with detailed evaluation rubrics. Extensive meta-evaluations demonstrate that VLMs are highly reliable judges, achieving significantly higher consistency with human preferences than conventional metrics. Building upon our benchmark, we comprehensively assess recent Time Series Foundation Models (TSFMs) under the VLM-as-a-Judge paradigm. Our results demonstrate that VLMs serve as robust and interpretable judges, providing a comprehensive, human-aligned standard for evaluating time series models.

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

GraphInfer-Bench: Benchmarking LLM's Inference Capability on Graphs

Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood. We introduce GraphInfer-Bench, a benchmark for whether LLMs can perform this graph inference: producing an open-ended answer that no single node supports and no path retrieves. Existing graph-QA protocols cannot test this capability: algorithm simulation, node classification, single-node description, KG-QA, and GraphRAG all admit answers retrievable from one node or along a path. GraphInfer-Bench defines five tasks along Description (what a region is) and Comparison (how regions differ), each constructed so the ground truth lives in no single node. The release contains 42,000 samples across six real-world graphs, produced automatically and screened by a four-layer quality-control protocol. We evaluate four method families against the same tasks: graph-token alignment models, zero-shot frontier closed-source LLMs, Graph2Text supervised fine-tuning, and plain GNNs as a structural reference. No method family closes the gap. Graph-token alignment partially handles description tasks (relational, theme) but collapses on comparison tasks. Frontier LLMs lead on outlier detection and community partition among LLM-based methods but lag on masked-node prediction. Graph2Text SFT is the strongest LLM-based method on the description side yet falls behind frontier LLMs on comparison. Across every task, plain GNNs match or beat the strongest LLM-based row, with the largest margin on community detection. GraphInfer-Bench surfaces graph inference as an open capability gap rather than a property of any one architecture.

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

The Pragmatic Persona: Discovering LLM Persona through Bridging Inference

Large Language Models (LLMs) reveal inherent and distinctive personas through dialogue. However, most existing persona discovery approaches rely on surface-level lexical or stylistic cues, treating dialogue as a flat sequence of tokens and failing to capture the deeper discourse-level structures that sustain persona consistency. To address this limitation, we propose a novel analytical framework that interprets LLM dialogue through bridging inference – implicit conceptual relations that connect utterances via shared world knowledge and discourse coherence. By modeling these relations as structured knowledge graphs, our approach captures latent semantic links that govern how LLMs organize meaning across turns, enabling persona discovery at the level of discourse coherence rather than surface realizations. Experimental results across multiple reasoning backbones and target LLMs, ranging from small-scale models to 80B-parameter systems, demonstrate that bridging-inference graphs yield significantly stronger semantic coherence and more stable persona identification than frequency or style-based baselines. These results show that persona traits are consistently encoded in the structural organization of discourse rather than isolated lexical patterns. This work presents a systematic framework for probing, extracting, and visualizing latent LLM personas through the lens of Cognitive Discourse Theory, bridging computational linguistics, cognitive semantics, and persona reasoning in large language models. Codes are available at https://github.com/JiSoo-Yang/Persona_Bridging.git

18.
arXiv (CS.CV) 2026-06-15

GMN4AD: Graph Matching Network for Alzheimer's Disease Diagnosis with Test-Time Domain Adaptation using Multi-centered Structure Magnetic Resonance Imaging

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that affects millions of older adults, with prevalence expected to rise significantly in the coming years. Early diagnosis, particularly during the mild cognitive impairment (MCI) stage, is critical for timely intervention. Structural Magnetic Resonance Imaging (sMRI) has emerged as a key modality for detecting AD-related brain changes, but traditional graph-based approaches often struggle with modality and inter-site heterogeneity, limiting diagnostic performance. In this paper, we propose Graph Matching Network for Alzheimer's Disease Diagnosis (GMN4AD), designed to model interactions between heterogeneous brain graphs derived from neuroimaging data. Unlike conventional methods that treat each brain graph independently, GMN4AD leverages graph matching to capture cross-graph relationships, enhancing diagnostic precision. Furthermore, we introduce a test-time domain adaptation strategy that combines contrastive learning to mitigate domain shifts during inference. Extensive experiments on three public AD datasets demonstrate that GMN4AD achieves superior performance compared to state-of-the-art methods, offering a robust and generalizable solution for AD diagnosis.

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

From Mechanistic to Compositional Interpretability

arXiv:2605.08934v2 Announce Type: replace Abstract: Mechanistic interpretability aims to explain neural model behaviour by reverse-engineering learned computational structure into human-understandable components. Without a formal framework, however, mechanistic explanations cannot be objectively verified, compared, or composed. We introduce compositional interpretability, a category-theoretic framework grounded in the principles of compositionality and minimum description length. Compositional interpretations are pairs of syntactic and semantic mappings that must commute to enforce consistency between a model's decomposition and its observed behaviour. We deconstruct explanation quality into measures of faithfulness and complexity to cast interpretability as a constrained optimisation problem, and introduce compressive refinement to systematically restructure models into simpler parts without altering their function. Finally, we derive a parsimony criterion under which syntactic compression theoretically guarantees more concise, human-aligned explanations. Our framework situates prominent mechanistic methods as subclasses of refinement, and clarifies why their compressibility heuristics tend to align with human interpretability. Our work provides a measurable, optimisable blueprint for automating the discovery and evaluation of mechanistic explanations.

21.
bioRxiv (Bioinfo) 2026-06-16

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Performance bottlenecks in widely used genomics and bioinformatics software present a substantial and growing burden as biological datasets continue to increase in size and number. Relieving these bottlenecks relies largely on expert manual optimization and therefore remains difficult to scale. Here we present AutoZyme, an agentic framework for scientific software optimization. Given a target function, AutoZyme builds benchmarks, identifies bottlenecks, and iteratively tests code changes, retaining only those that improve runtime while preserving output. We evaluated AutoZyme on 45 functions, improving runtime without substantial memory increases in over 95% of cases considered. Across 38 functions from Seurat, Scanpy and related packages in genomics and bioinformatics, AutoZyme reduced runtime by a median of 8.52-fold, with the largest reductions exceeding 676-fold. The optimized functions are distributed through AutoZyme-Library as drop-in replacements for existing analysis pipelines. We also release AutoZyme as a reusable framework for optimizing additional user-specified packages and functions.

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

Context-Aware Multimodal Claim Verification in Spoken Dialogues

Every day, millions absorb claims from podcasts and streams that no fact-checker ever sees. Spoken misinformation is built through conversation, where credibility comes not from facts alone but from how claims are framed, reinforced, or left unchallenged across turns. Yet fact-checking has focused on isolated text, leaving dialogue audio under-studied. We introduce MAD2, a new Multi-turn Audio Dialogues benchmark for spoken claim verification, containing 1,000 two-speaker dialogues with 3,368 check-worthy claims and approximately 10 hours of audio, and propose calibrated multimodal fusion of a context-aware audio encoder and a dialogue-aware text model. Across settings, adding dialogue context improves verification, but the gains depend on scenario type. Using only preceding context often matches offline performance, supporting live-moderation settings, and audio contributes most when transcript-based models are destabilized by additional context. Overall, conversational structure matters more for verification than misinformation framing.

23.
bioRxiv (Bioinfo) 2026-06-10

Is level-1 blob reconstruction under the network multispecies coalescent easy?

作者:

Hybridization is an important evolutionary process, commonly modeled by the network multispecies coalescent. Reconstructing evolutionary histories under this model is notoriously costly, even for level-1 networks where hybridization events are isolated from each other. The widely used methods that combine speed with statistical guarantees rely on quartet concordance factors computed for all subsets of four species, resulting in an o(n^4k) bottleneck that severely limits scalability to large numbers of species (n) and genes (k). Among quartet-based methods, NANUQ+ is notable because it decomposes the problem into two steps: first reconstructing a tree of blobs, which compresses each non-treelike part of the network, called a blob, into a single vertex, and second reconstructing the internal structure of each level-1 blob, specifically its circular order and hybrid vertex. Here, we investigate whether level-1 blob reconstruction is difficult once the tree of blobs is known. We present a fast and statistically consistent algorithm, called NetCS, based on two simple primitives: majority voting and merge sort, circumventing the bottleneck of computing all quartet concordance factors. In simulations, NetCS achieved comparable accuracy to NANUQ+ and was dramatically faster, enabling analyses of 200 taxa and 1000 genes in only a few minutes. Both methods attained near-perfect accuracy when given the true tree of blobs; however, their performance degraded in end-to-end pipelines due to errors in tree of blobs reconstruction. Strikingly, even methods that reconstruct level-1 networks directly struggled to accurately predict hybrid ancestry. Our results suggest that reconstructing level-1 blobs is unexpectedly easy once the tree of blobs is known, and that a major challenge for phylogenetic network inference lies in accurate tree of blobs reconstruction.

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

SceneConductor: 3D Scene Generation from a Single Image with Multi-Agent Orchestration

Generating complete 3D scenes from a single image requires inferring globally consistent geometry, object relationships, and environmental context from inherently ambiguous visual evidence. Despite recent progress in joint layout-and-mesh generation, existing methods often rely on holistic or weakly decomposed pipelines that entangle many factors at once and demand extensive scene-level supervision, limiting their generalization to complex real-world environments. We propose a multi-agent orchestration framework that decomposes single-image 3D scene generation into three structured stages: scene initialization, environment construction, and multi-agent refinement. The initialization stage extracts image-derived object masks, builds object-level 3D representations, and predicts an initial spatial layout to form a coarse 3D scene. The environment-construction stage then leverages this initialization together with point-map geometry to build an environmental scaffold of supporting surfaces, room boundaries, materials, and illumination. Finally, in the refinement stage, a planner agent identifies structural and visual inconsistencies, applies simple corrections directly, and dispatches specialist agents for complex localized revisions that are reintegrated into the global scene. To provide reliable structural initialization while reducing reliance on scene-level annotations, we further introduce a geometry-aware layout predictor supervised by sparse geometric priors derived from point maps. Unlike fully supervised layout generators, the predictor can be trained from segmentation-level data and generalizes robustly to diverse real-world scenes. Extensive experiments on benchmark datasets show that our method consistently outperforms prior approaches in geometric accuracy, spatial consistency, and perceptual realism.

25.
arXiv (quant-ph) 2026-06-17

Dimension-Free Approximate Tensorization of Quantum Hypercontractivity for Qudit Depolarizing Semigroups

arXiv:2606.17729v1 Announce Type: new Abstract: We prove almost tensorization for hypercontractivity and logarithmic-Sobolev constants for a class of reversible quantum Markov semigroups satisfying the positive off-diagonal scaling (PODS) property. This class includes qubit examples and generalized depolarizing semigroups with respect to full-rank states in arbitrary finite dimensions. For any such semigroup $(\Phi_t)_{t\ge 0}$ and every tensor power $n$, we show that the log-Sobolev constant of the product semigroup $\Phi_t^{\otimes n}$ is at least $2/(3\ln 2)$, approximately 0.96, times the log-Sobolev constant of the single-site semigroup $\Phi_t$, independently of $n$ and the local dimension $d$. The proof first establishes exact tensorization of the $(q,2)$-hypercontractive inequality for integer $q$, in particular $q=3$, and then extends the estimate to all real $q>2$ by complex interpolation; the standard implication from hypercontractivity to logarithmic-Sobolev inequalities yields the stated almost tensorization result. As an application of the same method, we also obtain sharp $(q,2)$-hypercontractivity estimates for qubit depolarizing channels.