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01.
arXiv (quant-ph) 2026-06-11

Experimental straintronics in nanotube quantum dots

arXiv:2606.12180v1 Announce Type: cross Abstract: Single-wall carbon nanotubes (SWCNTs) are narrow ribbons of graphene with atomically precise edges and a single quantum transport channel, at experimentally-relevant dopings. This makes them ideal systems to harness quantum transport straintronics (QTS), i.e. using mechanical strain to control accurately quantum transport. We present QTS data from three single-wall carbon nanotube quantum dot (SWCNT-QD) transistors over a broad range of in-situ tunable and reversible uniaxial strain ($\Delta\varepsilon_mech\approx$ 0 to 3 %). We first present the nanofabrication of the suspended SWCNT transistors whose channel lengths are $\approx$ 30 nm. The channels are strained by moving gold clamps holding firmly the nanotubes. We present detailed charge transport data, $dI/dV_{B} - V_{B} - V_{G}$ and $dI/dV_{B} - V_{B} - \Delta\varepsilon_mech$, showing a large mechanical-gating effect of the SWCNT-QDs. The precise reversibility of the data, and their agreement with QTS theory, confirms that the tubes are strained elastically. We demonstrate that the mechanical control of the QD doping is not due to capacitive-gating effects, but to quantitatively predictable bandstructure changes including a strain-tunable bandgap. This precise mechanical control of the doping and bandgap of SWCNT-QDs could find applications in qubits, condensed matter physics, and homojunction molecular transistors.

02.
arXiv (CS.LG) 2026-06-15

Beyond a Single Explanation of the Adam–SGD Gap

arXiv:2606.14259v1 Announce Type: new Abstract: Prior work has identified several factors that can contribute to the performance gap between Adam and SGD, spanning data aspects, architecture design, and optimization properties. Yet these explanations are often studied in isolation, leaving their relative importance unclear. In this work, we revisit these hypotheses through a controlled empirical study across vision, language, genomics, and graph tasks, spanning modern and classical architectures, and carefully designed training setups. Our results suggest that no single factor consistently explains the Adam–SGD gap. For instance, the Adam advantage can (1) persist under a uniform vocabulary distribution yet nearly disappear under a heavy-tailed one; (2) reverse in favor of SGD in softmax-attention models; and (3) become larger under soft architectural modifications, e.g., when ReLU is replaced by a GeLU nonlinearity. This suggests that the gap arises from nontrivial data and architecture interactions, rather than from a single common factor. Yet, we observe a pattern across our settings: a crossover batch size at which the relative advantage shifts from SGD to Adam as the batch size scales. These empirical results are captured by our theoretical gap model, which predicts this batch-size-dependent crossover. Our perspective helps reconcile several existing hypotheses while offering practical insights across domains.

03.
bioRxiv (Bioinfo) 2026-06-10

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The extracellular matrix (ECM) is a fundamental metazoan innovation that provides structural support and regulatory cues essential for multicellular life. While core matrisome components are subject to strong functional constraints, their evolutionary dynamics at the molecular level remain incompletely characterized. Here, we present a comprehensive per-residue analysis of selection pressures across 272 human core matrisome proteins using high-quality orthologous sequences from up to 228 placental mammal species. We developed an automated pipeline integrating ortholog identification, codon-aware alignments, and site-specific selection analyses with the MEME and FUBAR methods from the HyPhy suite. Results reveal pervasive strong purifying selection across the matrisome, consistent with its structural and functional indispensability. This is accompanied by episodic positive selection and rarer pervasive positive selection, with collagens exhibiting significantly elevated episodic positive selection compared to glycoproteins and proteoglycans. To facilitate community access, we developed ECMME (ECM Molecular Evolution) browser, an intuitive open-access web resource that visualizes selection metrics plotted directly onto protein topologies. ECMME allows researchers to seamlessly browse and investigate the data, providing a powerful framework for interpreting functional sites. It is available online and requires no local installation or set-up (https://izzilab-ecmme.share.connect.posit.cloud/).

04.
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.

05.
arXiv (CS.AI) 2026-06-15

Applicability Condition Extraction for Therapeutic Drug-Disease Relations

arXiv:2606.14031v1 Announce Type: new Abstract: Identifying conditions that a certain drug takes therapeutic effect on a target disease is crucial for clinical decision-making support. However, most existing biomedical information extraction methods have focused on identifying only relations between drugs and diseases, while largely overlooking the context-specific conditions where such relations can apply. To address this problem, we introduce the task of applicability condition extraction for therapeutic drug–disease relations from biomedical research literature. We create the first dataset that has manually annotated triples of drugs, diseases, and applicability conditions on biomedical paper abstracts with 1,119 drug-disease pairs. Using this dataset, we systematically evaluate the performance of a range of existing methods. In addition, we propose a new method that enhances LoRA to consider relations between drugs and diseases. Our method consistently outperforms strong baselines across different evaluation settings. The source code and dataset of this paper can be obtained from: https://github.com/guantingluo98/Drug-ACE

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

When LLMs Analyze Scars: From Images to Clinically-Meaningful Features

Medical image classification faces a fundamental dilemma: while deep learning models achieve remarkable performance at scale, real-world clinical scenarios often suffer from severe data scarcity due to annotation costs, privacy constraints, and disease rarity. This challenge is particularly pronounced in pathological scar classification, where differentiating keloids from hypertrophic scars requires subtle expert knowledge and labeled images are extremely limited. We propose a novel paradigm that repositions large language models (LLMs) as knowledge-driven feature engineers rather than end-to-end classifiers. We call this framework ScaFE (Scar Feature Engineering). Our key insight is that LLMs encode rich medical knowledge that can be externalized as executable feature extraction code, enabling the transformation of high-dimensional images into low-dimensional, clinically interpretable representations. Specifically, we prompt an LLM with established scar assessment criteria to generate deterministic Python code that extracts features aligned with clinical scoring systems such as the Vancouver Scar Scale. Our approach offers three key advantages: (1) data efficiency, achieving robust performance with limited training samples by decoupling knowledge acquisition from statistical learning; (2) privacy preservation, as raw images are processed locally without exposure to external LLMs; and (3) interpretability, through explicit features grounded in clinical reasoning. Extensive experiments on scar classification demonstrate that our method consistently outperforms end-to-end deep learning baselines or using LLMs as black-box classifiers under limited data conditions, establishing a promising direction for integrating LLMs into data-efficient and clinically transparent medical AI systems.

07.
arXiv (CS.AI) 2026-06-18

MagpieTTS-LF: Inference-Time Long-Form Speech Generation Without Training on Long-Form data

arXiv:2606.18485v1 Announce Type: cross Abstract: Neural Text-to-Speech (TTS) systems achieve remarkable quality on short utterances but long-form speech generation shows prosodic drift, speaker inconsistencies and sentence boundary artifacts. Existing approaches either compress sequences, increase context length or naively concatenate independently synthesized chunks. We present an inference-time approach called MagpieTTS-LF that enables MagpieTTS to produce coherent long-form speech without model retraining. Our method introduces three key innovations: (1) soft attention priors to guide monotonic alignment while preserving past and future context; (2) a stateful inference algorithm that maintains context across sentence chunks, ensuring prosodic continuity; (3) history-aware text encoding that uses past text for discourse-level prosodic planning. Experiments on long texts show significant improvements in long-range intelligibility, prosodic coherence, speaker consistency, and boundary naturalness compared to other baselines.

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

FineVLA: Fine-Grained Instruction Alignment for Steerable Vision-Language-Action Policies

arXiv:2605.27284v2 Announce Type: replace-cross Abstract: Vision-Language-Action (VLA) models are increasingly expected to not only complete robot tasks, but also follow human instructions about how those tasks should be executed. However, existing robot datasets usually pair trajectories with coarse goal-level language, leaving execution-critical details such as active arm, approach direction, and contact region unspecified. This limits steerable policy learning and robotic video understanding. We introduce FineVLA, an open framework for action-aligned fine-grained VLA supervision. The framework includes: (1) a data construction tool that unifies 972,247 trajectories across 85K tasks from 10 open-source robot datasets and builds FineVLA-Data, a human-verified dataset of 47,159 fine-grained trajectories; (2) a held-out benchmark with 500 videos, 11,631 atomic facts, and 1,030 VQA questions; (3) a robotics-specialized VLM annotator for scalable fine-grained annotation; and (4) a steerable VLA policy trained with controlled mixtures of fine-grained and raw goal-level instructions. Our experiments yield three findings. First, fine-grained supervision does not sacrifice goal-level success: FG-only improves over Raw-only by +1.4 to +8.1 success-rate points across settings. Second, fine-grained and raw instructions are complementary, following a consistent inverted-U trend peaking at FG:Raw = 1:2 to 1:1. The best mixed setting reaches 86.8%/82.5% in RoboTwin simulation and 62.7/100 in real-world dual-arm manipulation (vs. 49.9 Raw-only). Third, fine-grained supervision improves steerable control: the largest real-world gains appear on pose (+23), color (+18), and approach direction (+18)–factors where goal-level instructions provide no guidance. Overall, fine-grained language should augment goal-level instructions: specifying how to execute alongside what to achieve. Project page: https://finevla.xlang.ai/

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

Closed-Loop Triplet Synergistic Generation for Long-Form Video

Multi-shot long-form video generation remains challenging due to identity drift and compounding inconsistencies across shots. While storyboard-driven pipelines improve controllability, they are often executed in a feed-forward manner, with limited mechanisms to incorporate generated visual evidence back into subsequent conditioning. We propose CoTriSyGen, an agentic framework that formulates multi-shot long video generation as a closed-loop visual-text-memory synergy process, where planned intent, persistent memory, and generated visuals are jointly leveraged for iterative correction and long-range coherence. A vision-language-model-based analyzer reasons over this triplet and produces updates to both prompts and memory along two pathways: (i) intra-shot refinement, which triggers targeted regeneration when semantic or compositional violations are detected and refines image-to-video prompt for coherent motions; and (ii) inter-shot refinement, which rewrites subsequent-shot prompts to propagate newly manifested entities or attributes and improve prompt quality (e.g., compositional grounding and cinematic fluency) based on generated evidence. The loop is grounded in an entity-centric memory modeled as a mutable visual state that evolves as the story progresses, which is continuously updated by both the generator and the analyzer by adding new and evolved entities to reflect appearance changes, accumulated multi-view evidence, and multi-entity compositions. Experiments on our curated StoryBench benchmark demonstrate substantial improvements in cross-shot consistency, prompt adherence, and cinematic continuity over representative methods.

10.
medRxiv (Medicine) 2026-06-16

Care Delivery Gap framework: a proof-of-concept patient-reported measure of guideline-referenced care-process omissions in sickle cell disease

Abstract Background:Sickle cell disease (SCD) is concentrated in sub-Saharan Africa, where delivery of guideline-referenced care remains challenging. Current evaluation approaches rely largely on access indicators and clinical outcomes, which do not directly measure care delivery. We developed the Care Delivery Gap (CDG) framework, a patient-reported approach for identifying care-process omissions, and conducted a proof-of-concept study to assess feasibility and explore variation across income strata. Methods: We conducted a cross-sectional framework-development study involving a proof-of-concept sample of 52 individuals with SCD or caregivers recruited through clinics and moderated SCD communities across Africa, North America, and Europe between June 2025 and March 2026. The CDG framework assessed patient-reported omissions in specialist involvement, follow-up continuity, cardiovascular screening, and biochemical surveillance. Analyses were descriptive. Results: Substantial multi-domain care-process omissions were identified despite high reported healthcare engagement. Across geographic income strata, cardiovascular screening was reported by 4/35 (11%) LMIC versus 16/17 (94%) HIC participants, and regular follow-up within the preceding 12 months by 14/35 (40%) versus 16/17 (94%), respectively. High CDG scores, representing 1 omissions across three or four domains, occurred in 20/35 (57%) LMIC compared with 1/17 (6%) HIC participants. Similar disparities were observed across specialist review and vitamin B12 surveillance domains. Conclusion: A structured patient-reported framework identified multi-domain omissions in guideline-referenced SCD care, including among individuals reporting healthcare access. The divergence between access indicators and reported care delivery suggests that service contact alone may not reflect care quality. The framework provides a feasible foundation for future process-level quality measurement in high-burden settings.

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

The Geometry of Phase Transitions in Generative Dynamics via Projection Caustics

arXiv:2606.13191v1 Announce Type: new Abstract: Continuous-state generative samplers, including diffusion and flow-matching models, evolve through continuous reverse-time dynamics, yet their samples often undergo abrupt qualitative changes: trajectories commit to modes, semantic alternatives collapse, and small perturbations in narrow time windows can produce large downstream effects. This paper develops a geometric account of such phase-transition-like behaviour. We view denoising as gradient descent on a free energy landscape and show that sharp transitions arise near projection caustics, where the nearest-point projection onto the data support ceases to be unique. Motivated by this perspective, we introduce the Critical Boundary Detector (CBD), as practical diagnostics for score-direction instability. Across toy models, standard diffusion models, and latent text-to-image diffusion models, CBD localises mode commitment, predicts intervention-sensitive windows, and supports targeted control in geometrically sensitive regions. Our results connect geometry of data and dynamics of diffusion generation.

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

Libra: Efficient Resource Management for Agentic RL Post-Training

arXiv:2606.03077v2 Announce Type: replace-cross Abstract: Reinforcement learning (RL) has emerged as a standard post-training paradigm for shaping large language models (LLMs) into capable agents. In agentic RL, the rollout stage generates trajectories while invoking tools, producing long-tailed and non-stationary workloads that expose two fundamental challenges in resource management. First, due to the long-tail distribution, a small fraction of trajectories dominates rollout makespan. Second, rollout and training are subject to cross-stage imbalance, as they exhibit strong asymmetry in compute patterns, memory demands, and sensitivity to sequence length. Compounding this asymmetry, the sequence length distribution drifts continuously as the policy evolves, rendering any static resource split progressively suboptimal. We present Libra, a resource management system to address both challenges via two core mechanisms. The first is a global resource planner that jointly optimizes GPU allocation across rollout and training clusters. It leverages an elastic hybrid pool to enable lightweight, non-blocking worker reallocation between stages. The second is a causality-driven multi-level feedback queue (C-MLFQ) scheduler, which routes requests to heterogeneous rollout buckets based on causal signals derived from tool-return outcomes, rather than relying on fragile length predictions. Evaluated on 48 A800 GPUs, Libra achieves up to 3.0x higher throughput and converges up to 2.5x faster in reward compared to the baselines.

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

Single-Round Clustered Federated Learning via Data Collaboration Analysis for Non-IID Data

arXiv:2601.09304v2 Announce Type: replace Abstract: Federated Learning (FL) enables distributed learning across multiple clients without sharing raw data. When statistical heterogeneity across clients is severe, Clustered Federated Learning (CFL) can im-prove performance by grouping similar clients and training cluster-wise models. However, most CFL approaches rely on multiple communication rounds for cluster estimation and model updates, which limits their practicality under tight constraints on communication rounds. We propose Data Collaboration-based Clustered Federated Learning (DC-CFL), a single-round framework that completes both client clustering and cluster-wise learning, using only the information shared in DC analysis. DC-CFL quantifies inter-client similarity via total variation distance between label distributions, estimates clusters using hierarchical clustering, and performs cluster-wise learning via DC analysis. Experiments on multiple open datasets under representative non-IID conditions show that DC-CFL achieves accuracy comparable to multi-round baselines while requiring only one communication round. These results indicate that DC-CFL is a practical alternative for collaborative AI model development when multiple communication rounds are impractical. Our source code is publicly available at https://github.com/souta-suga/DC-CFL.

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

Intrinsic Computational Functionalism and Simulated Consciousness

arXiv:2606.15348v1 Announce Type: cross Abstract: A common objection to artificial or simulated consciousness is that a simulated brain is no more conscious than simulated water is wet. We address this from the perspective of Intrinsic Computational Functionalism (ICF): if consciousness is computationally constituted, it depends not on externally imposed descriptions but on the computational structures a system physically realizes in virtue of its own causal-dynamical organization. In previous work we developed Canonical Functionalism as a mathematically precise special case of this anti-interpretivist program, identifying functional states by their complete future input-output roles under a fixed interface. Here we argue that this input-output construction, though important, is incomplete: as a behavioral boundary case of ICF, it makes lookup tables and unfolded systems that preserve the same boundary behavior canonically equivalent. A consciousness-relevant canonical representation must instead include internal mechanisms, interventions, and joint readouts belonging to the relevant intrinsic organization. We therefore define a mechanism-enriched canonical structure and use it to formulate Intrinsic Causal-Computational Realization (ICCR), a realization relation preserving physical implementation, intrinsic state individuation, transition structure, intervention profiles, and the relevant agent-body-world boundary. The central result is conditional: if conscious properties are invariants of intrinsic causal-computational organization, then any system satisfying ICCR realizes the same consciousness-relevant properties, whether biological, artificial, or simulated. We discuss objections including biological naturalism and integrated information theory. We conclude that to deny consciousness to a simulation, one must identify a consciousness-relevant intrinsic causal-computational structure that the simulation fails to realize.

15.
arXiv (quant-ph) 2026-06-16

Experimental quantum state learning with pairs of photons

arXiv:2606.16932v1 Announce Type: new Abstract: Tomography allows one to estimate the density matrix describing the state an ensemble of quantum systems are prepared in (for example, polarization tomography determines the polarization state of a beam of identically prepared photons). In general, it is not possible to uniquely decompose the density matrix into its pure state components. Agarwal et al. proposed a protocol which, for a mixture composed of any two pure states of a qubit (with arbitrary probabilities), allows an observer to infer not only the density matrix but the identity of those specific pure states and their weights - the additional requirement being that the qubits arrive in pairs, where both qubits in each pair are in the same state. We experimentally demonstrate this learning-from-pairs concept using photons in the polarization degree of freedom. We use tomography to measure a sequence of single photons and make use of their time-of-arrival information to 'pair up' the photons after the measurement. From here we are able to infer the photons' polarization states and their respective probabilities, and we demonstrate this for various different choices of polarization states and ratios. Finally, we investigate our ability to discriminate between two equal mixtures of distinct pairs of orthogonal polarization states. We find that on the order of approx. 10e4 photons is typically enough to achieve tomography fidelities of approximately 0.9999. This is sufficient to discriminate between two different preparations of the same mixed state, differing by angles of less than 5 degrees between the pure states used in the two preparations.

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

PANDA: An LLM-Enhanced Performance-Driven Analog Design Framework Bridging Design Intent and Layout Generation

arXiv:2606.15052v1 Announce Type: cross Abstract: Traditional design of analog circuits heavily relies on manual interventions across topology, sizing, and layout, with prior automation addressing stages in isolation. In this work, we propose PANDA, an LLM-enhanced framework that bridges high-level design intent to final layout by actively managing cross-stage dependencies through guided topology synthesis, substructure-aware sizing, and constraint-driven layout generation. This shifts automation from algorithm-centric execution to intent-centric co-design, reducing turnaround time from days or weeks to hours while improving design performance.

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

SCALE: Self-uncertainty Conditioned Adaptive Looking and Execution for Vision-Language-Action Models

arXiv:2602.04208v2 Announce Type: replace-cross Abstract: Vision-Language-Action (VLA) models have emerged as a promising paradigm for general-purpose robotic control, with test-time scaling (TTS) gaining attention to enhance robustness beyond training. However, existing TTS methods for VLAs require additional training, verifiers, and multiple forward passes, making them impractical for deployment. Moreover, they intervene only at action decoding while keeping visual representations fixed-insufficient under perceptual ambiguity, where reconsidering how to perceive is as important as deciding what to do. To address these limitations, we propose SCALE, a simple inference strategy that jointly modulates visual perception and action based on 'self-uncertainty', inspired by uncertainty-driven exploration in Active Inference theory-requiring no additional training, no verifier, and only a single forward pass. SCALE broadens exploration in both perception and action under high uncertainty, while focusing on exploitation when confident-enabling adaptive execution across varying conditions. Experiments on simulated and real-world benchmarks demonstrate that SCALE improves state-of-the-art VLAs and outperforms existing TTS methods while maintaining single-pass efficiency.

18.
arXiv (quant-ph) 2026-06-19

$K$-Theoretic Obstructions to Linearizing QCA Representations

arXiv:2606.19657v1 Announce Type: cross Abstract: Projective representations arise naturally in physics and representation theory, and determining whether they can be linearized has been a fundamental problem. In this work, we study the analogous problem for quantum cellular automata (QCA) representations, which incorporate locality constraints imposed by a metric space $X$. Over an arbitrary field $\mathbb{F}$, we develop an obstruction theory for the linearization of QCA representations, using the algebraic $K$-theory spectrum of QCA constructed in previous work of the authors. The resulting obstructions are governed by the homotopy type of the QCA spaces, from which we extract universal obstruction classes to linearization. In the complex algebraic and unitary case, we also fully compute the homotopy types of the QCA spaces over a point, a line, and a plane.

19.
arXiv (CS.AI) 2026-06-12

Mod-Guide: An LLM-based Content Moderation Feedback System to Address Insensitive Speech toward Indigenous Ethnic and Religious Minority Communities

arXiv:2606.13397v1 Announce Type: cross Abstract: Language operates as a mechanism of both marginalization and resistance, especially for minority communities navigating insensitive and harmful speech online. As content moderation increasingly depends on large language models (LLMs), concerns arise about whether these systems can recognize culturally insensitive speech-language that disregards or marginalizes the cultural and religious perspectives of historically underrepresented communities, often through implicit erasure, misrepresentation, or normative framing, rather than overt hostility. Focusing on Bangladesh's Hindu and Chakma communities – the country's largest religious and Indigenous ethnic minorities, respectively – this paper investigates the epistemic limits of LLM-based moderation systems and explores methods for incorporating minority perspectives. We co-created a culturally grounded corpus of insensitive speech with community members and integrated their narratives into moderation pipelines using retrieval augmented generation (RAG). Our tool, Mod-Guide, improves LLM sensitivity to minority viewpoints by leveraging contextual cues derived from lived experience. Through mixed-method evaluations involving both minority and majority participants, we demonstrate that RAG-enhanced moderation responses are more contextually accurate and perceived differently across ethnic lines. This work advances research in human-computer interaction, AI ethics, and social computing by foregrounding restorative justice and hermeneutical inclusion in the design of content moderation systems.

20.
Nature (Science) 2026-06-10

Whole-genome duplication shaped cell-type evolution in the vertebrate brain

Authors:

The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show one-to-one homology with amphioxus. Moreover, ohnologues, particularly those from the first WGD, were more important than small-scale duplication paralogues for vertebrate cell-type evolution. To explore whether ohnologues are mechanistically important for this process, we predicted ancestral cell-type states and compared them to amphioxus and experimentally investigated macroglia. The findings indicate that ohnologues had a role in early vertebrate cell-type diversification. Moreover, by examining paralogue expression across cell types and species, we show that expression changes were mainly driven by dosage selection and subfunctionalization. We also link ohnologues to cellular diversity at different anatomical and cell-type scales. Our findings demonstrate the importance of WGDs for the evolution of early vertebrate brain complexity and highlight that the resultant ohnologues continued to capacitate cell-type evolution long after they were formed. Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversification.

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

In-Domain Supervised Pathology Report Classification: A Reproducible Pipeline from Data Curation to Production-Matched Evaluation

We introduce an in-domain supervised pipeline designed to counter the out-of-distribution performance drop that hampers supervised biomedical NLP models, a problem observed when models trained on pathology reports are moved across cancer registries. Our contribution is a reproducible recipe for training a supervised classifier from routinely collected cancer registry data. It describes how to build the in-domain training set and a production-matched holdout, and to choose operating points that keep the false-negative rate (FNR) very low while keeping reviewer workload manageable. The pipeline standardizes data curation with facility-stratified sampling and separate handling of reports linked to registry cases, and includes a blinded manual audit to estimate positive-case prevalence and label noise. On a 418k-report holdout set, the Kentucky model achieved FNR 0.003 and false-positive rate (FPR) 0.097, improving over the Seattle-trained MOSSAIC OncoID baseline (FNR 0.010, FPR 0.183) and raising F1 from 0.860 to 0.922. In a blinded manual review of 600 reports, estimated positive prevalence declined from 0.500 to 0.398, indicating substantial label noise with errors concentrated in rare primary sites.

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

LegalHalluLens: Typed Hallucination Auditing and Calibrated Multi-Agent Debate for Trustworthy Legal AI

AI systems deployed in legal workflows hallucinate at rates that aggregate metrics report at ~52%, but this average conceals where errors concentrate and in which direction they run, leaving compliance officers without an actionable signal for trustworthy deployment. We present LegalHalluLens, an auditing framework with three components: typed hallucination profiles across four legally-motivated claim categories (numeric, temporal, obligation/entitlement, factual) over CUAD (Hendrycks et al., 2021); a Risk Direction Index (RDI) that reduces omission-versus-invention bias to a single deployment-comparable scalar; and a typed debate pipeline calibrated to both magnitudes and directions. Across 510 contracts and 249,252 clause-level instances we measure a within-model gap of approximately 38-40 pp between obligation/numeric and temporal claims that aggregate reporting hides, and show that two systems with matched 52% rates can carry opposite RDIs. The debate pipeline reduces fabricated detections by 45% with per-category gains tracking the diagnosis, matching commercial APIs with a substantially smaller backbone (4B active parameters). Typed profiles and RDI surface failure modes that aggregate metrics hide; we further show these diagnostics serve as calibration inputs for multi-agent debate pipelines, where Skeptic challenges and asymmetric gates targeted at measured failure modes outperform generically-tuned debate. The framework supports direction-aware procurement, accountability, and agent design for legal AI deployed in the wild.

23.
arXiv (quant-ph) 2026-06-11

On-Chip Quantum Randomness Amplification

arXiv:2606.12173v1 Announce Type: new Abstract: Randomness amplification, the task of extracting uniform private bits from biased seeds that may be partly known by a malicious third party, is of central importance in cryptography. The highest security in this task is provided by a class of quantum protocols known as device-independent, which however are challenging to integrate into scalable devices. Semi-device-independent (SDI) protocols are a promising alternative that guarantees security under few natural assumptions, such as bounds on the amount of energy used by the devices. Here, we provide the first demonstration of SDI randomness amplification on an integrated silicon photonic chip, achieving a throughput rate of 20 Mbps suitable for practical applications. This rate is achieved through a novel technique for SDI entropy certification, which delivers strictly tighter von Neumann entropy bounds compared to existing methods and remains valid even if the preparation and measurement devices share quantum correlations. Overall, the methods developed in this work enable the integration of SDI technology into portable telecom devices, opening up a new generation of quantum cryptographic hardware.

24.
bioRxiv (Bioinfo) 2026-06-18

Looking beyond stereotyped neuron structures reveals links between beading and morphological rearrangements in aging phenotypes.

Understanding how neuronal morphology changes during aging and acute stress is essential for elucidating mechanisms of neurodegeneration. The highly branched PVD neuron of Caenorhabditis elegans provides a powerful model for studying dendritic remodeling and degeneration-associated phenotypes such as dendritic beading. However, the complexity of this arbor presents substantial challenges for automated segmentation and quantitative analysis. In this study, we adapted a convolutional neural network (CNN)-guided region growing framework for automated dendrite tracing, coupled with two topology-based algorithms for categorizing dendritic segments by branching degree. The segmentation algorithm achieved high accuracy relative to manual tracing, with a median Dice coefficient of 0.82, while reducing analysis time by approximately tenfold. Automated dendrite categorization demonstrated strong agreement with manual annotations across branching orders, though position-based mapping performance declined with age due to progressive morphological distortion. Leveraging this platform, we investigated mechanistic differences in dendritic beading patterns observed during aging and cold shock. Consistent with prior work, aging was associated with decreased inter-bead spacing, whereas cold shock produced increased bead dispersion with stress severity. Structural analysis revealed that these trends were not driven by dendritic pruning or reduced arbor complexity. Instead, while a traditional anatomically unflexible paradigm falsely implicated lower-degree dendrites as highly vulnerable, our branching-informed framework revealed that age-dependent beading is fundamentally dictated by a segments history of successive branching events. Conversely, acute cold shock triggered systemic beading that expanded across all dendritic orders in a severity-dependent manner. Together, these findings demonstrate that chronic aging and acute stress engage distinct degenerative pathways (compartment-specific lineage vulnerability versus global architectural collapse) rather than gross morphological loss, as well as highlighting the need for paradigms that enable reliable analysis of changing morphologies.

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

MoVerse: Real-Time Video World Modeling with Panoramic Gaussian Scaffold

We present MoVerse, a real-time video world model that creates an interactively navigable scene from a single narrow-field-of-view image. This setting is challenging because the input observes only a small fraction of the environment, while interactive roaming requires a complete surrounding world, persistent geometry, controllable camera motion, and temporally coherent high-fidelity observations. MoVerse addresses this problem by separating world construction from observation rendering. It first expands the input into a gravity-aligned 360$^\circ$ panorama with topology-aware diffusion, closing the missing field of view before 3D reasoning. It then lifts the panorama into a persistent 3D Gaussian scaffold using panoramic geometry-aware residual prediction, yielding a dense and directly renderable spatial memory. Finally, a Gaussian-conditioned video renderer translates scaffold renderings along user-specified camera trajectories into photorealistic video. To make this renderer practical for interaction, we train a bidirectional diffusion teacher for high-quality conditional rendering and distill it into a causal autoregressive student for bounded-latency streaming. This design combines the controllability and long-range consistency of explicit 3D representations with the perceptual quality of generative video models. MoVerse supports real-time scene roaming at 8~FPS on a single NVIDIA RTX~4090 GPU, demonstrating a practical path toward single-image world creation with interactive video output.