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

GeoT2V-Bench: Benchmarking 3D Consistency in Text-to-Video Models via 3D Reconstruction

Camera-prompted text-to-video (T2V) models are increasingly used to synthesize virtual camera captures, such as orbiting objects or moving through static scenes. For these outputs, visual plausibility is insufficient: the generated frames should also provide coherent multi-view evidence for a single static 3D scene. We introduce GeoT2V-Bench, a reconstruction-based diagnostic benchmark for evaluating whether camera-prompted T2V clips can support explicit rigid 3D reconstruction. Our pipeline estimates per-frame camera intrinsics and poses with VGGT-style geometry estimation, fits DeformableGS, derives a static MedianGS proxy by temporal-median aggregation, and renders this proxy along the estimated camera path. Instead of producing a pass/fail label or a single scalar score, GeoT2V-Bench reports a continuous reconstruction profile covering apparent image motion, estimated trajectory behavior, MedianGS static rendering error, static-render flow agreement, and the gap between flexible and static fits. On a fair-format four-seed evaluation with 3,840 completed reconstructions from 12 open-weight model configurations and 80 GeCo-Eval static-scene prompts, we find that visible motion, static rendering error, flow agreement, and flexible-vs-static behavior often disagree. GeoT2V-Bench therefore captures complementary failure modes that emerge when generated videos are tested as global static-scene acquisitions.

02.
arXiv (CS.AI) 2026-06-11

Embodied-R1.5: Evolving Physical Intelligence via Embodied Foundation Models

arXiv:2606.11324v1 Announce Type: cross Abstract: We introduce Embodied-R1.5, a unified Embodied Foundation Model (EFM) that integrates comprehensive embodied reasoning capabilities, spanning embodied cognition, task planning, correction, and pointing, within a single architecture toward general physical intelligence. Leveraging three automated data construction pipelines to significantly expand the data coverage of critical capabilities, we build a large-scale data system of over 15B tokens, and design a multi-task balanced RL recipe to alleviate heterogeneous task conflicts. We further introduce a Planner-Grounder-Corrector (PGC) closed-loop framework that enables a single model to autonomously execute and self-correct over long-horizon tasks. With only 8B parameters, Embodied-R1.5 achieves SOTA on 16 out of 24 embodied VLM benchmarks, surpassing leading models like Gemini-Robotics-ER-1.5 and GPT-5.4. Benefiting from the internalized embodied capabilities, Embodied-R1.5 can be fine-tuned into a VLA with only a small amount of data, outperforming leading VLA models like $\pi_{0.5}$ across 4 popular manipulation benchmark suites. We further conduct extensive zero-shot real-robot experiments, validating performance in instruction following, affordance grounding, articulated object manipulation, and long-horizon complex tasks, demonstrating strong generalization to the physical world. We open-source model weights, datasets, training code, and EmbodiedEvalKit, an evaluation framework tailored for embodied tasks, to facilitate future research in EFMs.

03.
arXiv (CS.CV) 2026-06-11

A Scalable PyTorch Abstraction for Multi-GPU Gaussian Splatting

Gaussian splatting methods have become increasingly popular for neural reconstruction of the real world. However, they are often limited in scale and resolution due to compute and memory constraints. We present a multi-GPU Gaussian splatting approach that scales reconstruction to higher resolutions and larger scenes while abstracting away the code complexity typically associated with distributing a model. To accomplish this, we propose a PyTorch backend that distributes the Gaussian parameters and splatting operators across GPUs via CUDA unified memory and NVLink. Because distribution occurs at the operator level, the model code requires no explicit cross-device communication. More broadly, the backend exposes multiple GPUs as an aggregate PyTorch device and supports other PyTorch operators. We demonstrate city-scale reconstructions with street-level detail consisting of over 1 billion Gaussian splats, more than 25 times as many as the current state of the art.

04.
arXiv (math.PR) 2026-06-19

Power-law hypothesis and (un)fairness of PageRank on undirected multi-type PAMs

arXiv:2606.19583v1 Announce Type: new Abstract: The preferential attachment model (PAM) describes the sequential growth of a network based on the "rich-get-richer" principle. Several versions of it have become established for modeling, e.g., citation networks, capturing a power-law degree distribution. Directed versions of the preferential attachment model where the edges are directed from the new to the old vertices have been the subject of extensive research. They have been shown to exhibit remarkable properties such as heavier tails for the limiting graph-normalized PageRank than for the in-degrees. By contrast, for the undirected version, we recently showed that PageRank has similar tails as the degree. In the present paper, we discuss the PageRank asymptotics for a multi-type version of the undirected PAM (here vertices have different colors), complementing previous results of Antunes, Bhamidi, Banerjee and Pipiras on the asymptotics of PageRank on similar directed multi-type or colored PAMs. Our studies are motivated by the aim to go beyond the rigid rule of edge orientation in directed preferential attachment models. As the main result, for the case of a finite set of colors, we show that the power-law hypothesis for PageRank is fulfilled also for the colored undirected PAM, where, by contrast to the directed case, the power-law exponent is color-dependent for some choices of the initial color distribution and the attractiveness function. For the specific case of a two-type model, we discuss implications of our results on fairness in sampling underrepresented nodes from the network.

05.
Nature (Science) 2026-06-10

Structural basis for chaperone-guided assembly of RNA-induced silencing complex

The RNA-induced silencing complex (RISC), comprising an Argonaute (AGO) protein and a small RNA, is the central effector in RNA silencing. Small RNAs are loaded onto AGO as bulky duplexes in an HSP70- and HSP90-dependent process1–3, but the molecular mechanism remains poorly understood. Here we identify the human AGO–HSP90–p23 complex, which captures AGO in an RNA-free state, termed the AGO maturation complex (AMC). The purified AMC enables RNA loading and AGO folding, faithfully recapitulating de novo RISC assembly. Using cryogenic electron microscopy, we determined the structure of AMC bound to a microRNA duplex. In contrast to its conformation in the RISC, AGO adopts a highly open conformation in the AMC: the N domain and the RNA-binding module (PAZ–MID–PIWI) are fully detached and anchored to opposite sides of the HSP90 dimer, connected solely by the unfolded L1 linker. This arrangement exposes a positively charged cleft that accommodates an RNA duplex. AGO folding is facilitated by a small RNA duplex containing a 5′-terminal phosphate—but not by single-stranded RNAs—revealing a role for the RNA duplex as a chaperone-like cofactor that directs AGO domain assembly. These findings elucidate the RISC assembly mechanism and establish the AMC as a molecular tool for probing optimal RNA features and chemical modifications for the rational design of small interfering RNA therapeutics. Our study also sheds light on how chaperones, together with ligands, can guide the folding of client proteins. Structures of the AGO maturation complex reveal how chaperones and an RNA duplex drive assembly of the RNA-induced silencing complex.

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

Addressing Detail Bottlenecks in Latent Diffusion for RGB-to-SWIR Image Translation

Latent diffusion models (LDMs) enable efficient image-to-image translation but discard fine spatial details during compression, degrading downstream perception tasks. We identify two bottlenecks: the autoencoder, which loses spatial information, and the conditioning pathway, which further degrades the source signal through naive downsampling. We propose two lightweight, backbone-agnostic fixes: a Source-Conditioned Autoencoder (SCAE) that injects high-resolution source features into the decoder via skip connections, and a Learnable Guidance Encoder (LGE) that replaces naive downsampling with a learned conditioning signal. Evaluated on RGB-to-SWIR translation for driving scenes with two denoiser backbones (U-Net and DiT), our approach improves detection mAP by up to 2x over the latent diffusion baseline, with up to 3.4x gains on small objects (COCO-small,

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

Oops, Wait: Discourse Tokens Matter in Reasoning Model

Recent studies suggest that even data-efficient training with ($\simeq$1K) reasoning trajectories can induce non-trivial reasoning capabilities in large language models through post-training. Such training corpora often contain iconic tokens such as "wait", "so", and "alternatively", which frequently appear in reasoning trajectories and may play a role in this process. This paper focuses on characterizing observable token-level patterns in post-training and a case study of how data-efficient supervised fine-tuning (SFT) differs from, and falls short of, large-scale post-training. To this end, we first identify tokens that correlate with correct answers along reasoning trajectories across models and training setups. We then focus on the distribution and (functional) roles of the "wait" token to primarily study the model trained in a data-efficient manner compared with the counterpart. Our study finds that discourse tokens are associated with correctness and a reasoning accuracy jump, even in data-efficient SFT. This suggests data-efficient SFT can partially reproduce discourse-token patterns to mimic meaningful reasoning behavior, but the patterns are less aligned with high-confidence answer transitions than those from large-scale post-training.

08.
arXiv (CS.CV) 2026-06-24

ForensicsTok: Forensics-Guided Tokenized Modeling for Image Tampering Localization

Multi-modal Large Language Models (MLLMs) offer powerful reasoning for forensic tasks, yet existing approaches utilizing exogenous segmentation decoders often suffer from suboptimal localization. The reliance on stitched pipelines introduces information bottlenecks during backpropagation, which dilutes spatial signals and is limited by semantic priors of the segmentor. To address these limitations, we propose ForensicsTok, which reformulates image manipulation localization as an autoregressive sequence generation task. ForensicsTok directly generates spatially grounded token sequences, enabling precise mask prediction without intermediary supervision. Specifically, we introduce a Token Splatting Decoder (TSD) to map tokens to binary masks via codebook-aware code smoothing, which mitigates sharp gradients from deterministic detokenizers. Furthermore, to capture diverse tampering clues, we propose a Hierarchical Expert Fusion (HEF) module that injects multi-scale features from a forensic expert model. This unified architecture effectively compensates for the lack of forensic priors in standard MLLMs. Extensive experiments on six benchmarks show that ForensicsTok substantially improves over existing MLLM-based baselines and slightly improves over strong forensic expert baselines, while exhibiting stronger robustness to perturbations.

09.
arXiv (quant-ph) 2026-06-16

Phase controlled spectral topology, dynamic stability and sensitivity in Non-Hermitian Cavity Magnonics

arXiv:2606.16522v1 Announce Type: new Abstract: We theoretically investigate a non-Hermitian cavity-magnon platform in which coherent photonmagnon interactions and reservoir-mediated dissipative coupling interfere through a single externally tunable phase. We show that this interference phase provides a universal control parameter that continuously rotates the effective coupling between Hermitian and anti-Hermitian regimes, enabling dynamic transitions between level repulsion and level attraction without modifying intrinsic system parameters. The resulting phase-controlled non-Hermitian topology gives rise to exceptional points, linewidth engineering, and zero-damping conditions. Owing to the propagation-direction dependence of the dissipative interaction, the system further exhibits strong nonreciprocal transport and phase-tunable isolation arising from asymmetric hybridization of the cavity and magnon modes. Beyond its spectral and transport properties, we establish a direct connection between nonHermitian spectral topology and nonequilibrium population dynamics. The interference phase governs the stability of the hybrid modes, driving transitions between stable relaxation, critical slowing down near exceptional points, oscillatory energy exchange, and exponentially amplified dynamics. We further demonstrate that the same phase-controlled exceptional topology can be exploited for enhanced sensing, where the eigenvalue response exhibits the characteristic square-root scaling associated with exceptional-point physics. Our results provide a unified framework linking spectral topology, directional transport, dynamical stability, and sensing functionality through reservoirengineered interference in cavity magnonic systems.

10.
arXiv (CS.CL) 2026-06-19

ShoppingBench: A Real-World Intent-Grounded Shopping Benchmark for LLM-based Agents

Existing benchmarks in e-commerce primarily focus on basic user intents, such as finding or purchasing products. However, real-world users often pursue more complex goals, such as applying vouchers, managing budgets, and finding multi-products seller. To bridge this gap, we propose ShoppingBench, a novel end-to-end shopping benchmark designed to encompass increasingly challenging levels of grounded intent. Specifically, we propose a scalable framework to simulate user instructions based on various intents derived from sampled real-world products. To facilitate consistent and reliable evaluations, we provide a large-scale shopping sandbox that serves as an interactive simulated environment, incorporating over 2.5 million real-world products. Experimental results demonstrate that even state-of-the-art language agents (such as GPT-4.1) achieve absolute success rates under 50% on our benchmark tasks, highlighting the significant challenges posed by our ShoppingBench. In addition, we propose a trajectory distillation strategy and leverage supervised fine-tuning, along with reinforcement learning on synthetic trajectories, to distill the capabilities of a large language agent into a smaller one. As a result, our trained agent achieves competitive performance compared to GPT-4.1.

11.
medRxiv (Medicine) 2026-06-18

Evaluating Deep-Learning Based Quantification of Breast Arterial Calcification on Mammography for Cardiovascular Risk Assessment

Purpose: To develop and evaluate a deep learning model for automated quantification of breast arterial calcification (BAC) on screening mammography and to assess whether AI-derived BAC burden predicts major adverse cardiovascular events (MACE) in women. Methods: In this retrospective study, 202,006 women who underwent screening mammography without history of MACE were included. A BAC segmentation model was trained on an expert-annotated dataset using a multi-task U-Net with a ResNet-18 encoder to detect and segment BAC. BAC burden was quantified as area (mm{superscript 2}) from model-generated masks using DICOM pixel spacing and categorized by tertiles into low, intermediate, and high. The PREVENT score and incident MACE were identified from electronic health records. Cox proportional hazards models were developed to evaluate AI-derived BAC burden and PREVENT score alone, and combined models for 5 - and 10-year cardiovascular risk prediction. Results: Among 202,006 women (mean age 54.8{+/-}11.7 years), 23.1% had AI-detected BAC, and 7,701 (3.8%) developed incident MACE during a median follow - up of 7.5 years. On the geographically held-out test set, the BAC model achieved an AUROC of 0.97, Dice score of 0.6678, and Pearson correlation of 0.961 between AI-derived and manually annotated BAC burden. BAC burden increased with age and was higher among women who developed MACE. Five - year MACE incidence increased across BAC categories from 1.5% in women without BAC to 6.9% in those with high BAC burden. BAC burden alone showed modest prediction of MACE, with 5-year and 10-year AUROCs of 0.661 and 0.650, respectively, while PREVENT achieved AUROCs of 0.781 and 0.771. Adding BAC to PREVENT produced minimal improvement in discrimination. Conclusion: Deep learning-based BAC quantification from routine mammography is feasible, accurate, and associated with future cardiovascular risk. Although BAC added little to PREVENT for overall discrimination, it may serve as a scalable opportunistic imaging biomarker to identify women at elevated cardiovascular risk and support preventive care.

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

DIPHINE: Diffusion-based $\Phi$-ID Neural Estimator

arXiv:2606.18997v1 Announce Type: new Abstract: Uncovering the true informational architecture of real-world complex systems requires disentangling how their components uniquely store, redundantly share, and synergistically integrate information over time. Integrated Information Decomposition ($\Phi$ID) is a framework for decomposing the information dynamics of multivariate systems into sixteen non-overlapping atoms that characterize redundant, unique, and synergistic modes of information storage, transfer, and integration. Existing methods to compute $\Phi$ID are restricted to Gaussian or discrete systems, preventing its application to continuous non-Gaussian dynamical systems. We address this limitation by proposing DIPHINE (Diffusion-based $\Phi$-ID Neural Estimator), the first neural estimator that leverages score-based diffusion models to jointly estimate all the mutual information terms required by $\Phi$ID from a single amortized network, recovering the sixteen atoms through Möbius inversion. We provide a theoretical analysis of error propagation through the inversion, showing that the Jacobian of the mapping from mutual informations to atoms is integer-valued and that the synergy-to-synergy atom is provably the hardest to estimate. We demonstrate accurate recovery of ground-truth atoms on synthetic benchmarks, superior performance compared to established mutual information estimators, and the ability to extract physiologically interpretable information-dynamic structure on an application involving real data without any distributional assumptions.

13.
arXiv (CS.LG) 2026-06-12

Multi-Token Residual Prediction

arXiv:2605.18817v2 Announce Type: replace Abstract: Diffusion Language Models (DLMs) generate text by iteratively denoising masked token sequences, offering a tradeoff between parallelism and quality compared to autoregressive models. In current practice, the number of tokens decoded per step is controlled by a confidence threshold, and quality degrades monotonically as more tokens are denoised per step. We introduce Multi-token Residual Prediction (MRP), a lightweight module that enables dependency-aware multi-token denoising within a single backbone forward pass. MRP exploits a key property of the denoising process: the logit distributions at adjacent denoising steps are remarkably similar. Rather than running the backbone a second time to obtain the next-step logits, MRP predicts the residual between steps from the backbone's hidden states, effectively denoising more tokens per backbone forward at a fraction of the cost. We apply MRP across the two operating regimes of DLM decoding. In the high-quality-low-throughput static denoising regime, MRP serves as a drafter for speculative decoding: its proposals are verified against the backbone, yielding lossless acceleration of up to 1.4x in SGLang. In the low-quality-high-throughput dynamic denoising regime, MRP instead drives a remasking scheme that revokes over-eager reveals, recovering most of the accuracy lost to aggressive low-threshold decoding and improving accuracy by up to 22.6 points on code generation task HumanEval and 17.7 points on reasoning task GSM8K.

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

Understanding helpfulness and harmless tension in reward models

Reward models are a key component of reinforcement learning from human feedback (RLHF), aligning language models toward both helpful and harmless behaviour. However, the internal mechanisms underlying these objectives and their conflicts remain poorly understood. We study alignment tension in reward models trained under helpfulness-only, harmlessness-only, and mixed-objective settings. We find that mixed-objective models often underperform single-objective models, indicating interference between objectives. Using activation-based methods, we identify neurons associated with each objective and study their functional roles via targeted ablations. We find that these neurons causally support their corresponding objectives while often negatively affecting the opposing one. We find that a substantial proportion of neurons are shared between helpfulness and harmlessness, and that these shared neurons exert a disproportionate influence on model behaviour, contributing to alignment tension. Additionally, our results provide insights and mechanistic interpretation into how alignment objectives are represented in reward models and why multi-objective alignment remains challenging, motivating future work on disentangled and controllable alignment methods.

15.
medRxiv (Medicine) 2026-06-22

UKBAnalytica: an integrated R package for scalable phenotyping and reproducible epidemiological analysis within the UK Biobank Research Analysis Platform

作者:

UK Biobank provides longitudinal health-related data for approximately 500,000 participants, and its Research Analysis Platform (RAP) has shifted large-scale analyses toward secure cloud-based computation. However, many existing tools address only specific steps of the analytical workflow, leaving a need for an integrated framework that connects multi-source disease phenotyping, survival-ready cohort construction, and downstream analysis on the RAP. Here, we present UKBAnalytica, an extensible R package for scalable phenotyping and integrated analysis of UK Biobank data within the RAP environment. It currently includes 52 predefined baseline variables and a built-in library of 331 curated disease definitions. These definitions are based on multiple UK Biobank data sources, including ICD-10, ICD-9, self-reported conditions, death registry records, algorithmically defined outcomes, and OPCS-4 procedure codes. UKBAnalytica distinguishes prevalent and incident cases, constructs follow-up time, generates analysis-ready survival datasets, and summarizes participant flow. Beyond phenotype construction, UKBAnalytica provides integrated modules for epidemiological analysis, omics analysis, and machine-learning-based modeling and interpretation. By linking endpoint definition with downstream modeling under a consistent data structure, UKBAnalytica reduces repetitive scripting and improves analytical transparency. Furthermore, we demonstrate the package's practical utility through a case study on chronic obstructive pulmonary disease (COPD) proteomics. The findings align closely with previously reported conclusions, underscoring the robustness and reliability of our analytical framework. This phenotype-centered framework complements existing UK Biobank tools and facilitates reproducible RAP-based biomedical research. UKBAnalytica is freely available at https://github.com/Hinna0818/UKBAnalytica.

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

On the Geometry of On-Policy Distillation

arXiv:2606.07082v2 Announce Type: replace-cross Abstract: On-policy distillation (OPD) is increasingly used to improve large language model reasoning, but its training dynamics remain poorly understood. We characterize the trajectory of OPD updates in parameter space and compare it with supervised fine-tuning (SFT) and reinforcement learning with verifiable rewards (RLVR). A suite of parameter-space diagnostics consistently places OPD in a relaxed off-principal regime: compared with SFT, its updates affect fewer weights and avoid principal directions more strongly, while compared with RLVR, they remain less tightly constrained. Beyond this static localization, OPD exhibits subspace locking: its cumulative updates rapidly enter a narrow low-dimensional channel. Constraining training to the update subspace formed early in training preserves OPD performance but substantially degrades SFT, indicating that the locked subspace is functionally sufficient for OPD. Control experiments further show that sparsifying the update tokens and shifting rollout generation off-policy preserve the rank dynamics, whereas mixing the OPD objective with RLVR changes them. Overall, these results suggest that OPD is not merely an intermediate point between SFT and RLVR, but induces its own update geometry in parameter space.

17.
medRxiv (Medicine) 2026-06-11

Incremental costs of transitioning from four to eight WHO-recommended antenatal care visits in Uganda: A costing analysis from a societal perspective

Background In 2016, the World Health Organization revised its antenatal care (ANC) recommendation from four to eight visits. For low- and middle-income countries like Uganda, where achieving even four visits remains a challenge, this transition has significant cost implications for both the health system and households. This study estimated the incremental costs of adopting the eight-visit model from a societal perspective. Methods The study was conducted in six government health facilities in southwestern Uganda. A micro-costing approach estimated health facility costs (personnel, equipment, consumables, and overhead). Costs incurred at patients end (transport, ultrasound, medical expenses, and time) were collected from 785 women using a questionnaire, with all costs in 2025 USD. Results For an average of 4.3 visits, total cost per woman was $100.1: facility costs $43.7 (43.7%), and patient costs $56.4 (56.3%). Transitioning to eight visits would increase total cost by $57.8 (57.8%), of which $36.4 (63.0%) would fall on households, equivalent to 68.8% of average monthly household income. Total costs would rise by 55.4% ($115.5 to $179.5) at Health Center IVs and 64.3% ($102.3 to $168.1) at Health Center IIIs, with facility costs up 43.4% and 62.9% and patient costs up 61.2% and 65.7%, respectively. Conclusion Transitioning to eight ANC visits would impose a large financial burden on households, with the incremental patient cost equivalent to more than two-thirds of average monthly household income. Equitable implementation requires improving availability of medicines and diagnostics, subsidizing transport, exploring telemedicine or community-based models, and improving efficiency at lower-tier health centers.

18.
arXiv (CS.CL) 2026-06-19

Manifold Bandits: Bayesian Curriculum Learning over the Latent Geometry of Large Language Models

Reinforcement learning (RL) is a central approach for improving reasoning capabilities in large language models (LLMs), where training efficiency depends critically on how problems are sampled during optimization. Existing adaptive curriculum learning methods typically prioritize prompts of intermediate difficulty, treating problem selection as a standard bandit problem with independent arms and overlooking the structured, heterogeneous nature of the task space. In this work, we frame problem sampling as a manifold-structured bandit problem with endogenous non-stationarity: problems are related through the model's latent representation space, and sampling decisions can steer how learning signals evolve across that space. To operationalize this perspective, we introduce Bayesian Manifold Curriculum (BMC), a structure-aware framework that organizes problems into a hierarchical task tree and applies Bayesian learning to guide sampling. Empirically, we find that different sampling strategies induce non-trivial tradeoffs between productivity (learning signal), diversity (coverage of the task manifold), and utility (evaluation relevance). These results show that prioritizing difficulty alone is insufficient for strong downstream performance, highlighting the importance of incorporating structure and type-awareness into problem sampling.

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

Re-feeding Is Not Replaying: Measuring Replay Noise in Counterfactual Token-Credit Estimation

Per-token counterfactual credit estimation asks which token in a language-model rollout caused the final answer to be right or wrong: cut the transcript at a pivot, substitute an alternative token, replay continuations, and compare outcomes. Published methods re-feed the transcript prefix as a fresh prompt, assuming this reproduces the state the model passed through during generation. We measure what that assumption costs on a stock inference engine, with a three-pass design: continuations resumed from the verified decode-time KV state, an identical second exact pass (a replica noise floor), and a re-feed pass. Across six configurations and three models (including a GRPO-trained checkpoint), at low-margin decision tokens, re-feeding changes the credit estimate at rates 14-28 percentage points above the replica floor (7-21pp under a treatment-independent conditioning; problem-clustered t = 2.9-6.4). Most changes are zero-boundary crossings of the quantized estimator rather than polarity reversals, and the perturbation is consistent with mean-zero, so averaged quantities are largely safe; but selection is not: a critical-token set chosen by thresholding $|\hat{A}_t|$ under re-feed overlaps the exact-resume selection at Jaccard 0.34-0.90, versus a 0.63-0.96 replica ceiling. A causal confirmation closes the loop: under vLLM's batch-invariant kernels all three passes are identical on every measured channel, with both disagreement rates exactly zero. Replica passes themselves disagree on 9-23% of eligible estimates: single-sample credit measurements at decision tokens are unreliable under any replay. Settings were fixed in advance; exact-pass cache hits in the second campaign are instrumented (100% hit rate, 3,434 pivots); total compute was under 10 USD. We recommend that counterfactual credit studies resume decoder state or use batch-invariant kernels, and report a replica floor.

20.
arXiv (CS.LG) 2026-06-15

A theoretical model for task routing in mixture-of-expert transformers

arXiv:2606.14398v1 Announce Type: new Abstract: Mixture-of-experts (MoE) layers enable the scaling of transformer models while keeping the inference compute fixed. While task-expert specialization has been observed in empirical studies of frontier MoE transformer models, existing theoretical work analyzes this using continuous mixture models that cannot be used to model natural language effectively. An important open question is to theoretically explain task-expert specialization in transformer MoE models using discrete models of language. To address this, we represent structured knowledge via syntactic templates and finite key-value dictionaries, and prove formally that a single-layer MoE transformer can encode knowledge by using experts that specialize in the corresponding tasks. Our construction shows how queries are routed to unique, task-specific experts whose size depends solely on the intrinsic complexity of the given task (i.e. the combined size of its syntactic templates and factual dictionary). Our construction provides a theoretical support for empirical results on localized knowledge circuits in MoE models. We support our theoretical findings with experiments evaluating model performance under varying MoE loss functions.

21.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.

22.
arXiv (CS.AI) 2026-06-24

MGI: Member vs Generated Inference

arXiv:2606.23872v1 Announce Type: cross Abstract: As generative models increasingly produce samples that are indistinguishable from human-created content, it becomes difficult to determine whether a given data point was part of a model's natural training set or was generated by the model itself, especially when models memorize and reproduce training data. We formalize this challenge as Member vs Generated Inference (MGI): given a sample and a target generative model, infer whether the sample is a true training member or a generated output of that model. Focusing on image generation, we show that existing membership inference methods systematically misclassify generated samples as training members, while attribution-based methods often misclassify true members as generated. This failure arises because both approaches rely on likelihood-related signals that are similarly elevated for training examples and for the model's own outputs. To address MGI, we propose Data Circuit Breaker (DCB), a three-stage method that combines complementary signals from a generative model's autoencoder and latent generator to distinguish training members from generated samples. Across multiple generative models, including image autoregressive and diffusion models, DCB consistently addresses the shortcomings of membership inference and attribution methods, remains effective even when models reproduce near-duplicates of training samples, and generalizes to challenging model derivative settings in which new models are trained on generated data.

23.
bioRxiv (Bioinfo) 2026-06-16

MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics

Metaproteomic peptide identification is constrained by the structure and size of the protein search space. Pooled gene catalogues provide coverage but obscure genome-level evidence, and current workflows for data-dependent (DDA) and data-independent (DIA) acquisition diverge in their database strategies. We present MetaPilot, a genome-aware workflow that uses conserved marker-protein evidence to rank candidate genomes from MGnify catalogues and construct adaptive, sample-specific search spaces. Applied to paired DDA/DIA datasets of defined mixtures and fecal samples, MetaPilot adapted genome selection to community complexity and reproduced published peptide evidence while expanding the detectable peptide space. In DDA-independent reanalysis of Orbitrap human gut DIA data, MetaPilot identified 24.4% more peptides than the published DDA-derived library and 2.06-fold more than the matched DDA-assisted DIA search. On timsTOF DIA-PASEF mouse intestinal data, it outperformed uMetaP by 41.8~119.7%, enabling genome-resolved functional interpretation without DDA-PASEF input.

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

Damage-TriageFormer: A Foundation-Model Framework for Typology-Based Building Damage Assessment from Mono-Temporal Imagery

Decision-relevant building damage assessment is critical for prioritizing resources and recovery after a disaster, yet most automated methods either flatten damage into a single severity scale (no damage, minor, major, destroyed) or require paired pre- and post-event imagery that is often unavailable for emerging hazards. This paper presents Damage-TriageFormer, a single-image, post-event, footprint-conditioned model that produces a damage typology rather than a severity scale. We contribute: (1) DamageTriage-Bench, a new benchmark built from NOAA Emergency Response Imagery across Hurricane Michael (2018), Hurricane Helene (2024), and the 2025 Los Angeles wildfire complex, with five typology classes that distinguish roof damage from structural damage and, within each, partial from total extent; and (2) Damage-TriageFormer, which extends a DINOv3 ViT-L backbone with a Simple Feature Pyramid for higher-resolution instance pooling, a two-stage gated damage head, and an auxiliary severity-regression objective. Our model achieves macro F1 of 0.624 on validation and 0.619 on a held-out stratified test set, performing strongest where operational triage needs it most, with per-class F1 of 0.91 and 0.84 on undamaged buildings and total structural collapse, respectively. While the rare Total Roof Damage class remains difficult due to its limited examples and an inherently ambiguous label boundary, our results show that single-image post-event imagery can support actionable building damage typing, enabling targeted emergency response and resource allocation without a pre-event reference.

25.
arXiv (CS.AI) 2026-06-24

Detecting AI Coding Agents in Open Source: A Validated Multi-Method Census of 180 Million Repositories

arXiv:2606.24429v1 Announce Type: cross Abstract: Generative AI coding agents are entering the open-source supply chain, yet their diverse and often invisible traces leave their prevalence poorly understood. We introduce a multi-layered detection framework that integrates configuration-file scanning, commit-message analysis, author-identity matching, and bot-signature lookup across World of Code (180M+ Git repositories), classifying agent traces into four behavioral types. No single method captures more than a fraction of activity: multi-method detection identifies 850,157 Claude Code commits in one snapshot, of which bot-account lookup_the signal most adoption studies rely on_recovers only 28,154 (3.3%), a 30x relative-recall gap, so single-signal prevalence estimates are biased low by at least this factor. Every detection pattern is hand-validated (495 labels) with per-cell precision and Wilson confidence intervals. Across snapshots from December 2024 to April 2026, commit-attributed agents generate over 320,000 commits per month; Claude Code leads (886,122 commits across 17,295 projects) and dominates silent, configuration-file-only adoption (21,078 projects). Compared against an independent pull-request census (AIDev), the two channels capture nearly disjoint agent populations_a PR census misses 79% of commit-detected Claude Code adopters and essentially all Codex adopters_and different kinds of work: PR-deployed cloud agents (Codex, Cursor) surface as feature work, while commit-deployed in-editor agents (Claude Code, OpenHands, Aider) surface as maintenance. The observed work profile follows deployment and detection mode rather than the tool itself, so no single channel is representative.