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01.
arXiv (CS.CL) 2026-06-11

Steering the Noise: Turning Random Perturbations into Effective Descent for Memory-Efficient LLM Fine-Tuning

Fine-tuning large language models (LLMs) achieves strong performance but is often limited by the memory overhead of backpropagation. Zeroth-order (ZO) optimization avoids this overhead by estimating gradients through forward passes alone, yet it typically converges slowly because random Gaussian perturbations yield high-variance gradient estimates in high-dimensional parameter spaces. In this paper, we propose a plug-and-play framework that turns random perturbations into more effective descent directions. The key idea is to draw a small pool of candidate perturbations, evaluate their loss values, and then select or combine those that are best aligned with the optimization objective. We develop two instantiations of this idea: MeZO-GV, which forms a guiding vector from the contrast between low-loss and high-loss perturbation groups, and MeZO-Greedy, which keeps the single best perturbation within a fixed evaluation budget. We theoretically show that both strategies yield a larger per-step reduction in the objective than standard ZO estimation, leading to improved convergence rates. Experiments on LLMs of different scales and architectures confirm that the proposed methods integrate naturally with existing ZO optimizers and consistently improve convergence speed and task accuracy. On OPT-13B, our approach outperforms all ZO baselines across 11 benchmarks and exceeds gradient-based methods on 9 of them, while retaining the memory efficiency of forward-only optimization.

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

Does the Judge Prefer English? Evaluating Language-Switching Invariance in LLM-as-a-Judge

作者:

Large language models (LLMs) are now widely used as automatic judges for open-ended instruction-following evaluation. This practice is convenient, scalable, and often more semantically aware than reference-based metrics, but it also introduces a new reliability question: does a judge evaluate the quality of an answer, or does it also react to the language in which the comparison is presented? We propose Judge-LS, a lightweight meta-evaluation protocol that transforms LLMBar response-pair items into English, Chinese, and Chinese-English language-switched variants. A reliable judge should preserve its preference under label-preserving language transformations and should not prefer a language when two answers are translation-equivalent. We evaluate four API-accessible judges on the full 419-item LLMBar benchmark, producing 13,408 successful pairwise judgments. Across models, Chinese and language-switched presentations induce 10.7–14.4% preference flips relative to English, and all judges achieve their highest accuracy in English. However, translation-equivalent tie probes do not reveal a systematic English preference: most probes are judged as ties, and non-tie decisions more often favor Chinese. We add confidence intervals, paired significance tests, and an automatic transformation audit with a sensitivity analysis that excludes mechanically flagged high-risk variants. The experiment requires no model training, uses only API calls, and is feasible on modest local hardware.

03.
arXiv (quant-ph) 2026-06-11

Measurement-Free Toric-Code Memory in Array Globally Controlled Rydberg Array

arXiv:2606.12030v1 Announce Type: new Abstract: The central prerequisite of any fault-tolerant quantum architecture is a quantum memory: a block of encoded physical qubits whose logical state is actively preserved against noise across many rounds of error correction. In neutral-atom Rydberg arrays, realizing such a memory is obstructed not by the entangling gates themselves, which are already fast and high-fidelity, but by the auxiliary operations that a conventional error-correction cycle requires: mid-circuit fluorescence measurement, inter-zone atom transport, and locally focused single-qubit addressing. Each of these introduces latency, atom loss, or optical crosstalk that exceeds the cost of the underlying gates by orders of magnitude. These costs accumulate cycle after cycle, progressively degrading the very logical information the code is meant to protect. Here we propose a protocol that stabilizes a toric-code quantum memory without moving, measuring or local addressing atoms. The key is to use a three-species Rydberg atom array for the complete stabilizer cycle, including syndrome extraction, coherent correction, and ancilla reset, under global, species-selective laser pulses. Numerical simulation of a $4 \times 4$ rotated toric code shows a longer qubit lifetime when the physical error rate is below a pseudo-threshold $p^\star \approx 0.034$. The scheme offers a concrete, hardware-efficient route to topological quantum memory in neutral-atom platforms.

04.
arXiv (CS.LG) 2026-06-19

Pose6DAug: Physically Plausible Multi-view Object Swapping for Robot Data Augmentation

arXiv:2606.20118v1 Announce Type: cross Abstract: Vision-language-action (VLA) policies have shown strong potential for general-purpose manipulation, yet they often fail on novel, out-of-distribution objects whose appearance or geometry deviates from the training distribution. The standard remedy is to collect multi-view teleoperation data for every failure case, but this scales poorly in both cost and time. We introduce Pose6DAug, a failure-driven data augmentation framework that turns a policy's own successful episodes into targeted demonstrations for its failure modes, without any new data collection. Our key insight is that each successful episode already encodes a physically valid action trajectory together with calibrated multi-view observations. By swapping only the manipulated object while preserving this trajectory, we obtain new and physically grounded demonstrations. However, naive 2D video editing breaks multi-view consistency and physical plausibility, particularly under heavy occlusion and egocentric viewpoints. Our method instead operates directly in 3D, anchoring the target object with an explicit mesh driven by a temporally coherent 6D pose trajectory, ensuring geometrically consistent renderings across all camera views. Fine-tuning a VLA on data augmented by our method improves success rates by 16.5% relative to the state-of-the-art baseline on novel objects, while preserving in-distribution performance. These results show that multi-view and physically consistent augmentation is a practical path to scalable VLA generalization.

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

Diffusion Offline Reinforcement Learning for Fair and Energy-Efficient UAV-Assisted Wireless Networks

arXiv:2606.16331v1 Announce Type: new Abstract: The integration of generative artificial intelligence with wireless communication and signal processing systems has opened new avenues for intelligent, data-driven decision-making in future 6G networks. This work proposes a diffusion soft actor-critic (Diffusion-SAC) approach that leverages offline reinforcement learning (RL) enhanced by denoising diffusion probabilistic models (DDPMs) to optimize trajectory and scheduling control in unmanned aerial vehicle (UAV) networks. While offline RL methods, such as conservative Q-learning (CQL), can learn from static datasets, they often struggle to generalize in low-data or dynamic conditions. To address this, we combine the robustness of CQL with the generative power of diffusion models, enabling expressive and signal-aware policy learning that generalizes beyond behavior policies. Applied to a UAV-assisted wireless network, the proposed framework minimizes transmission energy and improves fairness among devices. Simulations show that Diffusion-SAC outperforms standard offline RL baselines, achieving more stable convergence and higher rewards even with limited datasets. The method enhances data efficiency, reduces energy consumption, and increases throughput by more than 35 % compared to existing algorithms, demonstrating its potential for robust policy learning in next-generation wireless control systems.

06.
medRxiv (Medicine) 2026-06-22

The direct economic impact of surgical non-response in orthopaedic hip, knee, and spine surgery for osteoarthritis: a cost-utility analysis

Background Annually, nearly 2 million hip, knee, and spinal inpatient surgeries are performed in Canada and the US for osteoarthritis (OA), costing over $37 billion in hospital expenditures. However, 15-30% of patients experience limited or no improvement, resulting in poor value for money. This study evaluated the one-year cost-utility of joint and spine procedures for OA by comparing non-responders to responders, considering various responder definitions. Methods Individual micro-costing data were collected for 1,175 elective hip, knee, and spine patients enrolled in the Longitudinal Evaluation in the Arthritis Program - Osteoarthritis (LEAP-OA) between 2014 and 2018. Quality-adjusted life years (QALYs) were derived using the SF-6D utility index. One-year incremental cost-utility ratios (ICURs) were calculated from the hospital perspective. Results Responder rates varied by definition, ranging from 78%-94% for hip replacements, 64%-90% for knee replacements, 60%-64% for spine fusions, and 50%-68% for spine decompressions. Corresponding ICURs were: $45,956-$51,773/QALY for responders versus $108,593-$485,762/QALY for non-responders for hip replacements; $54,831-$71,151/QALY for responders versus $200,486-$1,203,596/QALY for non-responders for knee replacements; $65,980-$74,422/QALY for responders versus $262,039-$729,686/QALY for non-responders for spine fusions; and $29,947-$42,168/QALY for responders versus $63,195-$662,586/QALY for non-responders for spine decompressions. Conclusions While surgical response rates were highly dependent on the responder definition, ICURs for non-responders were significantly higher than those for responders across all definitions. Beyond the negative impact on patients, there is a compelling economic argument for investment in improved pre-operative identification of patients at risk of surgical non-response. Such efforts could enable more personalized, value-based care pathways and reduce the provision of low-value surgical interventions.

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

GeoNatureAgent Benchmark: Benchmarking LLM Agents for Environmental Geospatial Analysis Across Frontier and Open-Weight Foundation Models

arXiv:2606.12821v1 Announce Type: new Abstract: Environmental scientists spend disproportionate effort on data wrangling rather than analysis, and AI agents that automate geospatial workflows remain unvalidated: no benchmark evaluates agents operating through structured tool calling against real APIs. We introduce the GeoNatureAgent Benchmark, the first benchmark for environmental analysis agents that operate via structured tool calls to a production-style geospatial API. It comprises 93 tasks across 18 categories, covering municipality analysis, multi-turn conversation, spatial reasoning, cross-indicator synthesis, error handling and recovery, ranking, comparison, multilingual understanding, habitat analysis, and task rejection. Tasks are evaluated against an open, self-hostable API serving three environmental indicators across Spain and Portugal via sixteen tools. We evaluate seven LLMs (Claude Sonnet 4, DeepSeek V3.2, GLM-5, Gemini 2.5 Pro, Qwen3-235B, GPT-OSS-120B, Llama 4 Scout) under three temperature-1.0 seeds, reporting capability and per-case cost as orthogonal axes. We find: (1) Claude Sonnet 4 leads at 60.8% +/- 0.8%, followed by DeepSeek V3.2 at 56.3% +/- 3.1%, with no other model above 51%; (2) the cost-accuracy Pareto frontier is occupied mostly by open-weight models, with DeepSeek V3.2 offering 93% of Claude's capability at 11x lower cost ($0.011/case); (3) comparison tasks remain universally unsolved (0% on close-value comparisons), exposing systematic reasoning limits; and (4) structured tool calling against a real API is more discriminative than general-purpose GIS benchmarks, with accuracies 25-35 points lower. We further show extensibility by integrating BigEarthNet V2 land cover for Portugal alongside Spanish CO2 and erosion indicators. The benchmark, harness, and self-hostable API are publicly available.

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

A Multi-Level Architecture for Reusable Materials Ontologies – The OntoCrafter Ceramics Ontology (OCO) as Reference Implementation

arXiv:2606.14814v1 Announce Type: cross Abstract: The Materials Science and Engineering ontology landscape is fragmented along multiple axes simultaneously. Horizontally: a recent survey identified 94 ontologies of which over 40 are structurally incompatible; each new application domain – ceramics, polymers, batteries, smart materials – typically restarts ontology design from scratch. Vertically: EU regulation (CSRD, CSDDD, PPWR, CBAM, R2R, AI Act, ESPR) forces material, manufacturing, supply-chain, and lifecycle data into integrated digital product passports, leaving ontologies that only address horizontal fragmentation incomplete for any contemporary consumer. And mechanistically: a vocabulary that records that BNT-BT has $d_{33} \approx 580$ pC/N stores a fact but cannot surface why – Bi-6s$^2$ lone-pair stereo-activity, anomalous Born effective charges, soft modes, defect chemistry – without a systematic explanation skeleton. We propose a multi-level modular architecture with two independent classification axes – level of abstraction (L0 bridges, L1 material-agnostic laboratory-notebook, L2 material-class-specific, L3 categorical reasoning) and consumer audience (material vs. compliance) – in which the material-specific level is internally organised by a seven-tier mechanistic-explanation skeleton (Symmetry, Energy/DFT, Thermo/CALPHAD, Kinetics, Microstructure, Defect chemistry, Bonding) applicable to any crystalline ionic oxide. The level-and-audience modularity dissolves the horizontal fragmentation, the compliance audience absorbs the vertical regulation pressure, and the seven-tier organisation of Level 2 delivers the mechanistic explanation depth. We instantiate the architecture as the OntoCrafter Ceramics Ontology (OCO v0.94): 5,196 classes across 44 modules; 167,348 OWL axioms (40,454 logical); 1,674 properties; 829 cross-ontology bridge mappings; 1,172 SHACL shapes; 163 published competency questions.

09.
arXiv (quant-ph) 2026-06-17

Intrinsic Pointer Basis and Irreversible Classicality from Coherence Contraction

arXiv:2604.23304v4 Announce Type: replace Abstract: This work analyzes an operational route to classical behavior for reduced quantum states using the intrinsic reference basis (IRB). Relative to a fixed physical conjugation, the IRB separates intrinsic populations from a real antisymmetric cohesion sector. A globally bounded cohesion index is defined and its exponential contraction is proved for phase-free dephasing dynamics aligned with the IRB; for general aligned dephasing, the corresponding modulus-based coherence functional contracts at the same computable rates. The results provide distance bounds to the IRB-diagonal description and a logarithmic upper bound on the time required to reach a prescribed experimental tolerance. The IRB projectors constitute state-derived candidate pointer sectors, and they become dynamically stable pointer sectors when the effective dephasing generator is aligned with them and damps the relevant inter-sector coherences. Degenerate population sectors lead naturally to block-classicality and protected intra-block coherence. In a two-level active sector, the cohesion index equals fringe visibility, giving a direct interferometric test of the contraction law. The construction is independent of any spacetime- or unification-emergence hypothesis and is intended as a channel-level complement to environment-induced einselection.

10.
arXiv (quant-ph) 2026-06-11

Circulators Based on Coupled Quantum Anomalous Hall Insulators and Resonators

arXiv:2505.07770v2 Announce Type: replace Abstract: Integrated plasmonics is advancing rapidly, enabling a wide range of functionalities to be incorporated onto a single chip. Applications span information processing, computation, quantum sensing, and dark-matter detection. This progress has driven the development of integrated non-reciprocal devices, which are essential for preventing unwanted feedback that can degrade system performance. While non-reciprocal devices have been realized in edge magnetoplasmon materials via classical interference effects, their operation is often limited by the input power range. Here, we demonstrate that topological circulators utilizing asymmetric coupling offer improved input power range, isolation, and insertion loss. In this configuration, we demonstrate the coupling between a chiral edge magnetoplasmonic resonator and a pair of LC resonators is well described by an effective non-Hermitian two-site Hatano-Nelson model with asymmetric directional couplings, resulting in nonreciprocal behavior. The coherent photon-plasmon interaction enables a circulator with up to 50 dB of isolation across a broad range of excitation power. These results suggest that magnetic topological insulators provide a promising platform for realizing asymmetric non-Hermitian couplings at radio frequencies and for exploring regimes of strong directional suppression and possible exceptional-point physics. More broadly, they highlight the potential of topological-material-based microwave devices for future integration with superconducting quantum information platforms.

11.
arXiv (quant-ph) 2026-06-19

Quantum-Accelerated Self-Consistent Field: A Hybrid Algorithm

arXiv:2606.20176v1 Announce Type: new Abstract: We present the Grover adaptive search self-consistent field (GAS-SCF) algorithm. GAS-SCF leverages quantum arithmetic to construct an efficient oracle that marks target states (Fock states) which improve upon some initial classical energy estimate. Amplitude amplification then increases the probability of measuring these states. This approach offers a theoretical quadratic speed-up for the optimization problem encountered in SCF quantum chemistry and establishes a baseline against which structured optimization algorithms, such as QAOA and DQI may be compared. In this work, we classically simulate three examples as proofs of concept of the algorithm, the largest consisting of 26 qubits. We then extend our analysis to two larger systems, with O3 representing the largest case at 330 qubits. These examples are chosen to probe classically challenging SCF regimes. Achieving chemically relevant applications of GAS-SCF will require large-scale, fault-tolerant quantum hardware.

12.
arXiv (CS.AI) 2026-06-15

An Analysis of the Coordination Gap between Joint and Modular Learning for Job Shop Scheduling with Transportation Resources

arXiv:2604.24117v2 Announce Type: replace Abstract: Efficient job-shop scheduling with transportation resources is critical for high-performance manufacturing. With the rise of "decentralized factories", multi-agent reinforcement learning has emerged as a promising approach for the combined scheduling of production and transportation tasks. Prior work has largely focused on developing novel cooperative architectures while overlooking the question of when joint training is necessary. Joint training denotes the simultaneous training of job and automatic guided vehicle scheduling agents, whereas modular training involves independently training each agent followed by post-hoc integration. In this study, we systematically investigate the conditions under which joint training is essential for optimal performance in the job-shop scheduling problem with transportation resources. Through a rigorous sensitivity analysis of resource scarcity and temporal dominance, we quantify the coordination gap – the performance difference between these two training modalities. In our evaluation, joint training outperforms the majority of dispatching rule combinations and modular training approaches. However, the coordination gap advantage diminishes in bottleneck environments, particularly under severe transport and processing constraints. These findings indicate that modular training represents a viable alternative in environments where a single scheduling task dominates. Overall, our work provides practical guidance for selecting between training modalities based on environmental conditions, enabling decision-makers to optimize reinforcement learning-based scheduling performance.

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

Towards Scalable Customization and Deployment of Multi-Agent Systems for Enterprise Applications

Large language model (LLM)-based multi-agent systems demonstrate strong performance on complex reasoning and task execution, enabling broad enterprise applications. However, production deployment remains challenging due to domain-specific customization requirements and high latency and inference costs in agentic workflows. We propose a unified framework for customization and efficient deployment of multi-agent systems in real-world settings. The first stage, Agentic Model Customization, combines continual pretraining, supervised fine-tuning, and preference optimization to adapt a compact model to specialized domains while retaining strong agentic capabilities. The second stage, Inference Optimization, integrates speculative decoding and FP8 quantization with targeted calibration to enable cost-efficient serving with minimal quality loss. Across enterprise workloads, our framework enables rapid domain adaptation and achieves a 4.48x speedup in throughput while maintaining performance and improving robustness on long-tail scenarios.

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

Fed-FBD: Federated Functional Block Diversification for Isolation, Privacy, and Surgical Unlearning

arXiv:2606.12679v1 Announce Type: new Abstract: Federated learning (FL) enables collaborative model training without sharing raw patient data, but standard approaches such as FedAvg treat each client as a black box and provide no mechanism for isolating an adversarial contributor, auditing per-client influence, or honoring a departed participant's right to be forgotten. We present Fed-FBD (Federated Functional Block Diversification), a modular federated architecture that decomposes a ResNet backbone into six functional blocks (the stem, four residual groups, and the classification head) and maintains a warehouse of N color variants, each assembled from independently tracked and contributor-stamped blocks. Fed-FBD provides three capabilities absent in FedAvg: (i) architecturally guaranteed block-level isolation, so that an adversarial or mislabelled client cannot contaminate the clean colous; (ii) privacy-by-design, where membership inference advantage is already indistinguishable from chance before any privacy mechanism is applied; and (iii) surgical machine unlearning of a departed participant's contribution at sub-second cost and without retraining. Experiments on six MedMNIST-2D datasets, PathMNIST at 224x224, and CIFAR-10 show that Fed-FBD trades a modest 0.3%-3.1% IID accuracy gap on the adequately sized datasets for these guarantees, remains within 0.8%-4.0% of FedAvg at Dirichlet alpha=1.0 on three of four datasets, and confines all six adversarial attacks we study to the poisoned client's own blocks with at most +/-0.01 AUC drift on the clean colors.

15.
PLOS Computational Biology 2026-06-22

GrassSV – hybrid method to detect structural variants in high throughput DNA-seq data

by Dominik Witczak, Krzysztof Sychla, Julia Wysocka, Artur Laskowski, Wojciech Frohmberg, Marta Glowacka, Alicja Dzik, Piotr Lukasiak, Jacek Blazewicz, Aleksandra Swiercz Genetic diversity is crucial for populations to adapt and survive in dynamic environments. This diversity arises from genetic mutations, which manifest in the genome as structural variants (SVs). Several types of SVs exist, but not all are equally easy to detect. Current SV detection tools tend to specialize in certain SV types or require the use of multiple tools to obtain a comprehensive variant profile, which increases computational cost and complexity. While some methods excel at identifying breakpoints, they often struggle with accurately classifying variant types, and their precision depends strongly on data quality and sequencing technology. At present, the majority of available genomic data originates from high-quality short reads, which remain the most affordable sequencing technology. In this manuscript, we introduce GrassSV, a novel and computationally efficient method that employs a hybrid pattern-matching approach to detect all major classes of structural variants using short-read sequencing data. GrassSV integrates depth-of-coverage analysis with contig-based pattern recognition to ensure both sensitivity and precision while minimizing false positives and runtime. Its robustness was demonstrated on the human Genome in a Bottle dataset, as well as on synthetic data derived from the yeast genome, where it achieved high accuracy across all SV types at a lower computational cost compared to existing methods. This makes GrassSV a practical alternative to multi-tool pipelines typically required for comprehensive SV detection. GrassSV is available at https://github.com/Domomod/GrassSV under GPL-3.0 license and the benchmark at: https://github.com/Domomod/GrassBenchmark.

16.
arXiv (quant-ph) 2026-06-19

Smooth time-dependent control of dipolar Bose-Einstein condensates

arXiv:2606.20507v1 Announce Type: cross Abstract: We consider protocols for control of dipolar Bose-Einstein condensates where the critical role is played by the long-range anisotropic interatomic magnetic dipole-dipole interaction. The phase diagram of such a condensate has been explored theoretically and experimentally with certain values of the interatomic scattering length corresponding to superfluid and supersolid phases, where supersolidity appears as a modulation in the ground state density. Preparation of this modulated ground state is challenging, since excitations appear as a result of a finite-time evolution required to produce qualitative changes in the wavefunction density. To solve this problem we consider the time-dependent control of a dipolar Bose-Einstein condensate using shortcuts to adiabaticity techniques, concentrating on design of the time-dependent scattering length, a parameter of the system easily tunable by contemporary experiments. The first technique is the variational approach based on the Euler-Lagrange equations for a separable ansatz describing the evolution of the superfluid state. Secondly, we study the transition from superfluid to supersolid using a direct optimization protocol. We discuss the fidelity of the developed protocols in terms of the evolution time.

17.
bioRxiv (Bioinfo) 2026-06-18

Robust Conditional Diffusion with Noisy Templates for Antibody Sequence-Structure Design

Antibodies specifically recognize antigens and play a central role in therapeutic discovery. Designing antibodies for a given antigen remains challenging because antigen-antibody complex data are limited, whereas the sequence and conformational spaces of complementarity-determining regions (CDRs) are large. Retrieved CDR templates from databases or candidate libraries can narrow the design space and improve controllability, but retrieval for novel antigens is often sparse and imperfect; treating retrieved templates as hard conditions can bias the denoising process and cause negative transfer. To address this problem, we propose Robust Conditional Diffusion with Noisy Templates for antibody sequence-structure design (NT-ABDiff), a joint diffusion framework that treats candidate CDR-only templates as optional and potentially unreliable conditions. NT-ABDiff uses reliability-aware template modulation to estimate the context-conditioned usefulness of each candidate and to adaptively reweight and fuse multiple templates during conditioning. We further train the model with mixed-quality and corrupted templates as conditional perturbation regularization, encouraging the denoiser to exploit informative templates while remaining stable when templates are uninformative. Experiments under controlled template shifts and a train-set retrieval evaluation show that NT-ABDiff improves CDR-H3 sequence recovery and structural accuracy over strong baselines, while retaining robustness to missing, mismatched, and corrupted templates. Under a stringent random-template CDR-H3 evaluation, NT-ABDiff improves amino-acid recovery (AAR) from 30.03% to 39.47% and reduces RMSD from 3.160 to 2.915A; with train-set retrieval candidates, it achieves 39.50% AAR and 2.76 {ring} A RMSD. Code, processed splits, {ring} configuration files, and evaluation scripts are available at https://github.com/ShiDeng7rz/NT-ABDiff.

18.
Nature (Science) 2026-06-10

A 5.3-million-year-old deep-sea whale necropolis in the Diamantina Zone

Whale falls are biodiversity oases at seabeds1–6, yet their record from the oceans has remained sparse and fragmentary6,7. Here we report the discovery of a vast whale necropolis in the Diamantina Zone (4,616- to 7,001-m depth), extending about 1,200 km along the sea floor of the southeastern Indian Ocean. This area has a deep and extensive accumulation comprising five modern natural whale-fall communities and 476 fossil cetaceans recorded. We show that carcasses host specialized communities dominated by brittle stars, bone-boring worms and chemosynthesis-based bivalves and that the fossil record in this area comprises both extant and extinct deep-diving beaked whales. Isotopic dating shows that whale falls in this region have occurred since at least 5.3 million years ago. These findings reshape the understanding of the limits and biogeography of whale-fall ecosystems and establish some deep sea floors as a fossil archive for tracing cetacean evolution over geological time. Researchers uncovered an enormous deep-sea accumulation of whale remains in the southeastern Indian Ocean, showing long-term, specialized ecosystems and an extensive fossil record that offers new insight into deep-ocean biodiversity and whale evolutionary history.

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

NAMESAKES: Probing Identity Memorization in Text-to-Image Models

Text-to-image (T2I) models generate realistic likenesses of some individuals when prompted with their names, raising privacy concerns. However, distinguishing whether a generated face is memorized or fabricated currently requires ground-truth photos, access to training data, or white-box access to model internals, limiting applicability. We introduce a fully black-box behavioral probe that distinguishes between these regimes while requiring no reference photos or prior knowledge of training data. To benchmark this task, we present the NAMESAKES dataset of over one thousand names and faces of public figures spanning a wide range of fame levels, along with perturbed, less famous names. Experiments on state-of-the-art T2I models show that our probe substantially predicts identity memorization and separates memorized from unrecognized names, with further insights into differences across model families.

20.
arXiv (CS.CV) 2026-06-16

Visual Generation in the New Era: An Evolution from Atomic Mapping to Agentic World Modeling

Recent visual generation models have made major progress in photorealism, typography, instruction following, and interactive editing, yet they still struggle with spatial reasoning, persistent state, long-horizon consistency, and causal understanding. We argue that the field should move beyond appearance synthesis toward intelligent visual generation: plausible visuals grounded in structure, dynamics, domain knowledge, and causal relations. To frame this shift, we introduce a five-level taxonomy: Atomic Generation, Conditional Generation, In-Context Generation, Agentic Generation, and World-Modeling Generation, progressing from passive renderers to interactive, agentic, world-aware generators. We analyze key technical drivers, including flow matching, unified understanding-and-generation models, improved visual representations, post-training, reward modeling, data curation, synthetic data distillation, and sampling acceleration. We further show that current evaluations often overestimate progress by emphasizing perceptual quality while missing structural, temporal, and causal failures. By combining benchmark review, in-the-wild stress tests, and expert-constrained case studies, this roadmap offers a capability-centered lens for understanding, evaluating, and advancing the next generation of intelligent visual generation systems.

21.
arXiv (CS.CV) 2026-06-17

SPATIA: Multimodal Generation and Prediction of Spatial Cell Phenotypes

Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but existing methods typically analyze these modalities in isolation or at limited resolution. We address the problem by introducing SPATIA, a multi-level generative and predictive model that learns unified, spatially aware representations by fusing morphology, gene expression, and spatial context from the cell to the tissue level. SPATIA also incorporates a spatially conditioned generative framework with confidence-aware OT reweighting and morphology-profile alignment for modeling target-state morphology distributions. Specifically, we propose a confidence-aware flow matching objective that reweights weak optimal-transport pairs based on uncertainty. We further apply morphology-profile alignment to encourage biologically meaningful image generation, enabling the modeling of microenvironment-dependent phenotypic transitions. We assembled a multi-scale dataset consisting of 25.9 million cell-gene pairs across 17 tissues. We benchmark SPATIA against 18 models across 12 tasks, spanning categories such as phenotype generation, annotation, clustering, gene imputation, and cross-modal prediction. SPATIA achieves improved performance over state-of-the-art models, improving generative fidelity by 8% and predictive accuracy by up to 3%.

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

Fixed-Point Reasoners: Stable and Adaptive Deep Looped Transformers

arXiv:2606.18206v1 Announce Type: new Abstract: Looped architectures provide an inductive bias toward learning step-by-step procedures for tasks that require compositional reasoning. The number of effective layers reached by looping determines the quality of the solution these models find. Like deep architectures, looped architectures are prone to a signal propagation problem induced by depth as the halting decision is postponed. In this paper, we address this signal propagation issue using pre-norm layers and residual scaling. Building on these architectural modifications, we propose FPRM, a Transformer-based Fixed-Point Reasoning Model that uses fixed-point convergence as an end-to-end halting mechanism in a looped architecture. We show that fixed-point halting allows FPRM to adapt its compute to task difficulty. FPRM is effective on common reasoning benchmarks, namely Sudoku, Maze, state-tracking, and ARC-AGI.

23.
bioRxiv (Bioinfo) 2026-06-11

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele- and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

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

PathRouter: Aligning Rewards with Retrieval Quality in Agentic Graph Retrieval-Augmented Generation

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from answer-path reward aliasing, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits search-update ambiguity, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

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

GPT-Based Fast Simulation of CLAS12 Detector Hits via Conditional Autoregressive Generation

arXiv:2606.16035v1 Announce Type: cross Abstract: Modern particles physics experiments have demonstrated an increasing need for fast, high-fidelity detector simulation as detector components have improved and subsequent computational requirements approach the limits of available resources. Recently, deep generative models have emerged as a promising alternative to traditional Monte-Carlo methods, with recent works drawing inspiration from large language models (LLMs) and self-supervised next-token prediction methods. In this work, we present an application of a GPT-style autoregressive transformer as a fast surrogate model for the calorimeter inside the CLAS12 experiment at the Thomas Jefferson National Accelerator Facility. The model is conditioned on incident momentum and generates realistic detector hits autoregressively across all nine calorimeter layers as sequences of strip, ADC, and TDC tokens. We demonstrate that the model faithfully reproduces hit multiplicity, spatial distributions, energy deposits, and the energy-momentum response of the electromagnetic calorimeter. The generator achieves inference rates exceeding 700 events per second on a single GPU, providing a substantial speedup over traditional Geant4-based simulations while maintaining physics fidelity essential for high-luminosity experimental programs.