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01.
arXiv (CS.LG) 2026-06-12

One Step Closer to Ground Truth: A Multi-Scale Residual-Aware Representation Learning Pipeline for Predicting Time Series Data

arXiv:2606.10678v2 Announce Type: replace Abstract: Transformer-based models have emerged as leading paradigms in time-series forecasting in recent years, employing self-attention mechanisms to capture long-range dependencies. Despite their success, these single-stage forecasting architectures exhibit persistent systematic residual biases arising from structural discrepancies, unmodeled stochastic components, or inadequate multi-scale temporal representations. This limitation persists when residuals are treated as irreducible noise, precluding adaptive correction of structured error patterns. To address this limitation, we introduce a two-stage, model-agnostic framework that explicitly decouples forecasting and residual learning into distinct stages of representation learning. A base transformer first generates the initial predictions. Subsequently, a dedicated meta-corrector dynamically models structured error patterns across multivariate channels, preserves cross-variable dependencies, and iteratively refines the residual bias of the base transformer. By formalizing this pipeline as a hypothesis space expansion, our framework addresses approximation limitations inherent in single-stage architectures, removes reliance on restrictive assumptions, and enables end-to-end learning of complex error dynamics. Evaluated on eight popular benchmark datasets using established protocols, our approach achieves state-of-the-art performance, with significant improvements in standard metrics (MSE, MAE). The results demonstrate the framework's ability to mitigate systematic biases and enhance robustness to complex temporal dynamics, advancing the practical applicability of transformer-based forecasting models.

02.
arXiv (CS.CV) 2026-06-12

GAE: Unleashing Physical Potential of VLM with Generalizable Action Expert

Vision-language models demonstrate strong reasoning and planning abilities, yet grounding these predictions into precise robot actions remains a central challenge. Existing Vision-Language-Action methods typically entangle reasoning and action generation, leading to limited generalization. We propose Generalizable Action Expert (GAE), a task-agnostic model that converts sparse geometric plans into dense robot actions. Our approach introduces a sparse geometric interface: the VLM predicts sparse 3D waypoints representing high-level intention, while GAE maps these waypoints together with real-time point cloud observations to continuous action trajectories. GAE is pretrained on a large-scale pointcloud-trajectory dataset comprising 150k trajectories from both simulation and real-world robots. To further improve efficiency and generalization, we introduce an Action Pre-training, Pointcloud Fine-tuning (APPF) scheme that decouples learning action dynamics from geometry grounding. After pretraining, GAE is frozen and reused across downstream tasks, requiring only lightweight fine-tuning of the VLM to produce the sparse interface. Experiments show that our method achieves strong performance and generalization across diverse visual domains, camera viewpoints, and natural language instructions.

03.
arXiv (CS.AI) 2026-06-12

Hallucination in Medical Imaging AI: A Cross-Modality Analytical Framework for Taxonomy, Detection, and Mitigation under Regulatory Constraints

arXiv:2606.13211v1 Announce Type: new Abstract: AI systems are being deployed across medical imaging faster than their failure modes are understood. At this point in time, the failure of greatest clinical concern is hallucination: clinically plausible but factually incorrect outputs, including fabricated anatomical structures, missed findings, incorrect laterality, and invented measurements in generated reports, with direct consequences, for example, for biopsy decisions, staging, and treatment planning. This structured narrative synthesizes peer-reviewed studies, benchmark datasets, and FDA regulatory guidance across five imaging modalities to produce a cross-modality analysis of hallucination taxonomy, etiology, detection, and mitigation. Specifically, we address three questions in this study: (1) how can existing taxonomies be unified across modalities?, (2) how do medical-specialized foundation models hallucinate less than general-purpose ones?, and (3) which mitigation strategies are effective and compatible with FDA lifecycle oversight? We note that three taxonomic frameworks together cover the imaging pipeline in a way no single framework does alone. We also highlight that general-purpose foundation models outperform medical-specialized models on hallucination-specific benchmarks, indicating that narrow domain fine-tuning can introduce overfitting-induced confabulation. At the same time, the oversight of radiologists remains essential; for instance, a very high percentage of of AI-generated flags required expert correction before clinical use. Physics-informed architectural constraints, Chain-of-Thought prompting, and human-in-the-loop safeguards each address different failure modes and is effective when combined. All findings are mapped to the FDA's Total Product Lifecycle and Predetermined Change Control Plan frameworks, which treat hallucination management as a lifecycle obligation rather than a pre-deployment checklist.

04.
arXiv (CS.CL) 2026-06-17

GameCraft-Bench: Can Agents Build Playable Games End-to-End in a Real Game Engine?

Game generation is an emerging application of coding agents, requiring models to transform natural-language specifications into playable interactive systems. Unlike traditional coding tasks, game generation takes place within a game engine, where scripts, scenes, assets, rendering, and runtime interactions must jointly produce coherent gameplay. We formalize end-to-end game generation as the problem of producing a complete game artifact that realizes a specification through observable player-game interaction in a target environment. We argue that evaluating this setting requires three desiderata: Engine Grounding, Artifact Completeness, and Interactive Verification. We propose an interaction-grounded evaluation framework that assesses executable gameplay through replayed demonstrations and rubric-guided multimodal judging. We instantiate this framework as GameCraft-Bench, a benchmark comprising 140 Godot tasks across 15 game families. Evaluations of frontier coding agents show that end-to-end game generation remains highly challenging: the strongest agent achieves only 41.46%, and most agents score below 40%. Further analysis reveals that while agents often implement recognizable mechanics, they struggle to deliver complete games with sufficient content, functional visual feedback, and coherent presentation. See https://tongxuluo.github.io/gamecraft-bench-website for demos, code, and data.

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

Encoder Winners Do Not Reliably Transfer Across VLA Backbone Scale: A Frozen-Backbone Grafting Diagnostic

Vision-language-action (VLA) policies typically inherit their vision encoder from upstream VLM releases, but it is unclear whether an encoder choice validated on a small VLA transfers to a larger backbone. We introduce a frozen-backbone grafting diagnostic: the vision tower of a released VLA is replaced by a candidate encoder under a fixed protocol (adaptive average pooling, LayerNorm, and a single trainable linear projector), with the language model and action expert frozen. Across four encoders, two LIBERO suites, two backbones (SmolVLA-450M and $\pi_{0.5}$-3.3B), and two-to-three seeds per cell (40 main grafting runs plus native, LoRA, pooling, and zero-/shuffled-image controls, all scored by offline action MSE), the small-backbone winner does not reliably select the large-backbone top tier: SigLIP is best on SmolVLA across both suites, while on $\pi_{0.5}$ DINOv2-small leads the spatial suite and the object suite is a seed-sensitive near-tie band; three of the four backbone-suite comparisons (and 11 of 12 seed-level cells) support backbone-dependent rankings. The grafting wrapper is itself non-neutral with opposite sign across backbones (+45-56% MSE on the SmolVLA native tower, -50-52% on $\pi_{0.5}$), so all conclusions are conditional on the fixed grafting protocol. We position frozen grafting as a cheap target-backbone diagnostic to run before committing to an encoder at scale, not as a closed-loop deployment claim.

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

JADE: Expert-Grounded Dynamic Evaluation for Open-Ended Professional Tasks

arXiv:2602.06486v2 Announce Type: replace Abstract: Evaluating agentic AI on open-ended professional tasks faces a fundamental dilemma between rigor and flexibility. Static rubrics provide rigorous, reproducible assessment but fail to accommodate diverse valid response strategies, while LLM-as-a-judge approaches adapt to individual responses yet suffer from instability and bias. Human experts address this dilemma by combining domain-grounded principles with dynamic, claim-level assessment. Inspired by this process, we propose JADE, a two-layer evaluation framework. Layer 1 encodes expert knowledge as a predefined set of evaluation skills, providing stable evaluation criteria. Layer 2 performs report-specific, claim-level evaluation to flexibly assess diverse reasoning strategies, with evidence-dependency gating to invalidate conclusions built on refuted claims. Experiments on BizBench show that JADE improves evaluation stability and reveals critical agent failure modes missed by holistic LLM-based evaluators. We further demonstrate strong alignment with expert-authored rubrics and effective transfer to HealthBench and DR.BENCH, covering medical and 10-domain professional evaluation settings. Code and data are available at https://github.com/smiling-world/JADE.

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

Ex-Omni: Enabling 3D Facial Animation Generation for Omni-modal Large Language Models

Omni-modal large language models (OLLMs) aim to unify multimodal understanding and generation, yet extending them to jointly produce speech and 3D facial animation remains largely unexplored despite its importance for natural human-computer interaction. A key challenge is the mismatch between the discrete semantic reasoning of LLMs and the dense temporal dynamics required for 3D facial motion. We propose Expressive Omni (Ex-Omni), an open-source model that augments OLLMs with native speech-accompanied 3D facial animation. Ex-Omni decouples semantic reasoning from temporal generation through a blendshape-aware speech unit generator and a blendshape decoder, where speech units provide temporal scaffolding and hidden speech representations carry facially relevant cues. We further introduce a unified token-as-query gated fusion (TQGF) mechanism for controlled semantic injection, as well as InstructS2SF-1200K, a dataset consisting of 1200K samples for pre-training. Extensive experiments show that Ex-Omni maintains competitive speech understanding and generation ability while achieving better audio-visual synchronization and lower face-generation latency than cascaded pipelines.

08.
medRxiv (Medicine) 2026-06-12

High coverage, persistent gaps: quality of Antenatal Care and its determinants in Zambia based on the 2024 Demographic and Health Survey.

Abstract Background Evaluating antenatal care (ANC) quality is critical to reducing maternal and neonatal mortality. In Zambia, despite high basic ANC attendance, comprehensive national evidence on the clinical content and quality of services remains limited. This study assessed the coverage of WHO-recommended ANC interventions and identified factors associated with care quality using the latest national data. Methods A cross-sectional analysis was conducted using data from the 2024 Zambia Demographic and Health Survey. The final analytic sample comprised 4,829 women aged 15-49 with a live birth in the preceding 5 years. A composite index of 15 selected, equally weighted WHO-recommended components evaluated clinical assessment, counseling/screening, preventive interventions, and utilization. Survey-weighted Poisson regression estimated adjusted incidence rate ratios (aIRRs) for the count of ANC components received. Results The mean ANC quality score was 12.5 out of 15 (95% CI: 12.4-12.6), and 78.5% (95% CI: 77.0-80.0) of women achieved adequate ANC ([≥] 12/15 components). While individual clinical and counseling coverage generally exceeded 90%, only 47.2% (95% CI: 45.3-49.0) of women initiated care during the first trimester, and just 4.8% (95% CI: 4.1-5.6) achieved [≥] 8 ANC contacts. Maternal education was the strongest and most stable predictor of quality across all models. Compared to no education, higher education was associated with an 8.0% higher expected quality score (aIRR = 1.080, 95% CI: 1.051-1.110). Lower ANC quality was significantly associated with unwanted pregnancies (aIRR = 0.970, 95% CI: 0.956-0.993) and with residence in Western (aIRR = 0.923, 95% CI: 0.897-0.951) and North Western (aIRR = 0.966, 95% CI: 0.937-0.996) provinces. Absence of distance barriers and residence in Eastern, Luapula, and Copperbelt provinces were associated with higher quality scores. Conclusion While average ANC component coverage in Zambia is high, critical gaps persist in early initiation and total contact frequency. Care adequacy is strongly influenced by maternal education, relationship status, pregnancy intention, and regional inequities. These findings underscore the need for interventions targeted at uneducated women, preventing unintended pregnancies, and underserved regions such as Western and North Western Provinces. Keywords: Antenatal care quality, ANC content, Zambia, maternal education.

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

Teacher-Student Structure for Domain Adaptation in Ensemble Audio-Visual Video Deepfake Detection

The rapid advancement of generative AI models is leading to more realistic deepfake media, encompassing the manipulation of audio, video, or both. This raises severe privacy and societal concerns. Numerous studies in this area have yielded promising intra-domain results; however, these models frequently exhibit decreased efficacy when faced with data from dissimilar domains. Consequently, recent deepfake detection approaches focus on enhancing the generalization ability through multiple techniques that incorporate all input modalities, including audio, images, and their interactions. In this regard, we propose the EAV-DFD method, a generalized deep ensemble audio-visual model (EAV-DFD) combined with a domain adaptation mechanism utilizing a teacher-student framework to enhance the model's ability to perform and generalize effectively across unseen domains. To evaluate the model's performance, we used the FakeAVCeleb dataset as the primary domain and the DFDC, Deepfake_TIMIT, and PolyGlotFake datasets as an unseen domain. Our experimental results demonstrate that the proposed framework is efficient in domain adaptation, improving AUC performance of the model by 4.09%, 17.94%, and 0.5% on three unseen datasets, using only a small portion of them to train the student model. This leads to a novel deepfake detection model capable of adapting to new domains and interpreting which modality has been manipulated, highlighting the potential of our approach for real-world applications.

10.
medRxiv (Medicine) 2026-06-12

Immunologically Optimized Zmp1 Peptides Reveal a Translational Serological Biomarker Platform for Tuberculosis Diagnosis Across Disease Manifestations

Tuberculosis (TB) diagnosis remains challenging, particularly for extrapulmonary TB (EPTB), where invasive sampling, low bacillary burden, and suboptimal sensitivity of nucleic acid-based tests in peripheral specimens hinder timely detection. Here, we report an immunology-driven strategy for biomarker discovery and development of a peptide-based serological assay targeting Mycobacterium tuberculosis zinc metalloprotease-1 (Zmp1). Leveraging fundamental principles of adaptive immunity that antigenic regions containing overlapping B-cell and CD4 T-helper cell epitopes would preferentially generate high antibody titers through linked recognition and cognate T-cell help, we used an immunoinformatics pipeline to identify two nested immunodominant peptide regions within Zmp1 (Mtb-Zp-NT and Mtb-Zp-CT) enriched for overlapping B- and T-cell epitopes. The diagnostic potential of these peptides was evaluated through ELISA-based serological assays. A blinded pilot study (N=137) demonstrated a clear discrimination between active TB and TB-recovered individuals. The assay was subsequently validated in an expanded cohort (N=875) by screening 6,086 individuals, which identified 457 TB-positive cases. The cohort included pulmonary TB (PTB), EPTB, TB-recovered individuals, household contacts, non-specific infections, and healthy controls. Receiver operating characteristic analyses, supported by DeLong and bootstrap comparisons, revealed superior diagnostic performance of the peptide-based assays relative to full-length Zmp1. Mtb-Zp-CT exhibited the highest accuracy (AUC=0.93; specificity >90%), while Mtb-Zp-NT also demonstrated strong discriminatory power (AUC{approx}0.89). These findings establish that the immunologically optimized Zmp1 peptides are highly promising serological biomarkers for TB and EPTB. More broadly, they demonstrate how mechanistically informed epitope selection can accelerate translation of pathogen-specific immune signatures into sensitive, minimally invasive, and potentially point-of-care diagnostic platforms for resource-limited settings.

11.
PLOS Computational Biology 2026-06-01

Histology-informed spatial domain identification through multi-view graph convolutional networks

作者:

by Huihui Zhang, Jiaxing Chang, Zirong Li, Yue Sun, Pinli Hu, Haoxiu Wang, Hang Yang, Yonglin Ren, Xingtan Zhang, Zehua Chen, Kok Wai Wong, Haojing Shao Identifying spatial domains is crucial in spatial transcriptomics, yet effectively integrating gene expression, spatial location, and histology remains challenging. We present STESH, a Spatial Transcriptomics clustering method that combines Expression, Spatial information and Histology. STESH extracts histological features using a convolutional neural network and generates expression, histology, spatial, and collaborative convolution modules for a multi-view graph convolutional network with a decoder and attention mechanism. We evaluated STESH on multiple tissue types and technology platforms. STESH consistently outperformed ten state-of-the-art methods, achieving superior clustering accuracy with the highest scores in adjusted Rand index, normalized mutual information, and Fowlkes-Mallows index.

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

From Brewing to Resolution: Tracing the Internal Lifecycle of Code Reasoning in LLMs

arXiv:2606.17648v1 Announce Type: new Abstract: Standard accuracy metrics cannot explain why LLMs handle variable tracking but fail on semantically equivalent loops. We study an internal lifecycle of code reasoning in which models first brew the answer, making it linearly recoverable many layers before it becomes self-decodable, and then diverge into one of four resolution outcomes: Resolved, Overprocessed, Misresolved, or Unresolved. Understanding this lifecycle matters because similar task accuracies can mask fundamentally different failure modes that surface-level evaluation cannot detect. We introduce a dual diagnostic framework pairing layer-wise linear probing with Context-Stripped Decoding (CSD) and apply it to six code-reasoning task families across 16 models spanning Qwen, Llama, and DeepSeek architectures. All four outcomes carry substantial mass in every task family: overall Resolved is only 41.5%, with multiple tasks below 30%. Controlled sweeps over structure, depth, and operators expose task-specific failure bottlenecks: Function Call Resolved plunges from 61.1% to 2.5% as call depth increases from one to three. Across architectures and scales, the brewing scaffold remains stable, with normalized brewing duration 24-42% across all 16 models, while resolution success varies with capability. This indicates that the scaffold is a stable empirical regularity across the tested decoder-only Transformer families, whereas resolution success covaries with capability, scale, and training. Code: https://github.com/euyis1019/llm-brewing

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

On Subquadratic Architectures: From Applications to Principles

arXiv:2606.12364v1 Announce Type: new Abstract: Transformers dominate modern sequence modeling, but their quadratic attention incurs substantial computational cost. Subquadratic architectures offer a scalable alternative. However, it remains unclear which designs yield the most effective sequence models. We compare three leading approaches: xLSTM, Mamba-2, and Gated DeltaNet. We evaluate these models on tasks with complex dependencies: (1) code-model pre-training, (2) distillation of code models from large language models, and (3) pre-training of time-series foundation models. Across these settings, xLSTM delivers the strongest overall performance. To explain xLSTM's advantage, we present a unified formulation and analyze the underlying architectural mechanisms, focusing on state tracking and memory dynamics. Our results show that xLSTM enables more flexible and stable memory correction via its gating scheme. We corroborate these findings on controlled synthetic length-generalization tasks. Overall, our findings indicate that xLSTM's gains on complex tasks stem from robust state tracking and accumulation.

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

MamBOA: State-Space Architecture for Video Recognition

Fine-grained action recognition demands temporal reasoning that general-purpose architectures address through different cost-accuracy tradeoffs: 3D dense operators couple computation to the input volume, while difference-based methods approximate motion through rigid, hand-crafted subtraction of uncontextualized features - each reflecting a deliberate design choice with corresponding limitations in expressiveness or flexibility. We present MamBOA, a backbone-agnostic temporal framework built upon a novel interleaved scan structure that recasts the selective state-space recurrence (S6) as a native motion synthesizer. By interleaving consecutive feature representations extracted from a pretrained backbone into a single alternating sequence, the proposed scan structurally drives the recurrence to encode both temporal observations of each position within a shared hidden state, separated by only a single decay step - rendering the inter-frame transition an intrinsic component of the state dynamics rather than an externally computed quantity. A cascade of dedicated alignment and decoding operations then distills this joint encoding into an explicit motion representation, which a dual-path pooling mechanism adaptively aggregates by balancing attention-driven selection with uniform temporal coverage. The framework interfaces seamlessly with CNN, Transformer, and Mamba backbone families, adding only ~2.1 GFLOPs per feature pair. On Diving48, MamBOA achieves 85.02% Top-1 accuracy with an image-pretrained backbone and 86.24% with a video-pretrained backbone processing the entire video in a single forward pass - demonstrating that structurally induced state-space dynamics constitute a principled and general foundation for motion modeling.

15.
arXiv (CS.CV) 2026-06-17

HLS-GPT: A Generative Pretrained Transformer (GPT) for Continental-Scale NASA Harmonized Landsat and Sentinel-2 (HLS) Reflectance Reconstruction Across All Bands on Arbitrary Dates

Recent deep learning methods for Landsat and Sentinel-2 reflectance time series reconstruction remain limited by restricted spectral coverage, limited geographic scalability, or patch-based designs with short temporal contexts. We present HLS-GPT, a large-scale generative pretrained Transformer model for reconstructing NASA Harmonized Landsat Sentinel-2 30 m surface reflectance for all bands, any date, and any pixel location. HLS-GPT uses a hierarchical Transformer architecture to handle the different spectral band configurations of Landsat and Sentinel-2 and operates on single-pixel 12-month time series. To capture geographic and seasonal variability, the model was trained with nine years of HLS time series from more than 0.25 million training pixels across the conterminous United States. A random cropping and masking strategy extracts 12-month periods with varying start dates across epochs, masks 50% of valid observations, and trains the model to reconstruct the masked reflectance values from the remaining observations. Evaluation using more than 62,000 independent test pixels shows robust reconstruction under diverse land surface conditions, including complex crop phenology and sparse, irregular observations. Leave-one-observation-out evaluation achieved reconstruction RMSE below 0.026 for all HLS spectral bands, with relative RMSE below 35% for visible bands and below 13% for other bands. Red-edge band errors were comparable to red and near-infrared errors despite the absence of red-edge bands on Landsat. Sensitivity analyses that randomly masked 10% to 90% of test observations showed only modest degradation when 10% to 50% of observations were masked, with all-band RMSE below 0.028. Image reconstruction over nine independent 109 by 109 km CONUS HLS tiles further demonstrates that HLS-GPT outperforms two conventional methods and the NASA-IBM Prithvi model.

16.
arXiv (CS.AI) 2026-06-17

MathVis-Fine: Aligning Visual Supervision with Necessity via Progressive Dependency-Guided Training for Multimodal Mathematical Reasoning

arXiv:2606.17888v1 Announce Type: new Abstract: Chain-of-Thought (CoT) reasoning has extended from purely linguistic domains to multimodal scenarios; however, existing approaches often treat visual inputs as homogeneous or auxiliary signals, failing to capture the intricate and sample-specific dependencies between text and images in mathematical problem-solving. This gives rise to two core issues: first, the supervisory signals for visual content are generalized and coarse-grained, lacking adaptation to the actual necessity of visual information in each sample; second, training feedback becomes inaccurate when visual rewards are uniformly applied without distinguishing the complementary relationships among inputs. These limitations hinder models from achieving precise multimodal reasoning. In this work, we propose a framework for modeling fine-grained visual dependencies in mathematical reasoning. We first construct the MathVis-Fine dataset, augmenting fine-grained visual annotations with visual dependency ratings. Building upon this dataset, we introduce a two-stage progressive visual enhancement training paradigm that balances answer correctness rewards and visual grounding rewards according to the intrinsic visual dependency level of each sample, thereby mitigating reward bias and improving supervision accuracy. Extensive experiments demonstrate that the MathVis-Fine framework effectively enhances visual perception progressively based on visual dependency, offering a more precise training framework for multimodal mathematical reasoning. We will release the dataset upon acceptance.

17.
arXiv (CS.LG) 2026-06-16

p-PSO: A Penalized Particle Swarm Optimization Technique for Finding D-Optimal Designs with Mixed Factors in Generalized Linear Models

arXiv:2606.15962v1 Announce Type: cross Abstract: Finding D-optimal designs for generalized linear models (GLMs) is challenging due to the dependence of the Fisher information matrix on unknown parameters and the lack of closed-form solutions, particularly when input factors include both discrete and continuous variables. Although classical algorithms and recent metaheuristic approaches have offered partial solutions, there remains a need for robust and computationally efficient methods. In this paper, we propose a penalized Particle Swarm Optimization (PSO) approach, named $p$-PSO. Here we introduce a new, general-purpose penalty formulation for constrained optimization and demonstrate its effectiveness in optimal design problems. The formulation is algorithm-agnostic and applicable to a broad class of black-box optimization methods. Results show that the method is highly efficient, with its primary contribution being a penalty formulation that enables the direct use of an off-the-shelf PSO algorithm and extends naturally to more general constrained optimization tasks.

18.
arXiv (CS.LG) 2026-06-17

From Reasoning Traces to Reusable Modules: Understanding Compositional Generalization in Language Model Reasoning

arXiv:2606.18089v1 Announce Type: new Abstract: Post-training pipelines that combine supervised fine-tuning (SFT) with reinforcement learning (RL) have emerged as the key recipe for transforming large language models (LLMs) into robust reasoners. We argue that this combined success is driven by compositional generalization, which we formalize through a hierarchical latent selection model. In this framework, reasoning traces are generated by a cascade of discrete latent selection variables corresponding to reusable atomic modules, including both skills (local operations) and routing mechanisms (how intermediate information is selected, reused, and composed). Within this model, we theoretically show that SFT and RL play asymmetric, complementary roles: SFT supplies the raw module materials in compositional traces, and RL decomposes those traces to identify the latent atomic modules and enable compositional generalization. We design controlled experiments to validate this theory. Our results demonstrate that RL can extract atomic modules from compound traces supplied by SFT and recombine them to solve new configurations. Moreover, we find that training on compound traces yields stronger generalization than training on isolated atomic modules. Finally, we investigate the relationship between SFT and RL data and identify an effective protocol in which SFT ensures coverage of all atomic modules through compositional traces, while RL focuses on novel compositions outside the SFT support to drive exploration.

19.
arXiv (CS.CL) 2026-06-11

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

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

20.
PLOS Computational Biology 2026-06-11

A zero-parameter first-principles gate framework for full-length TP53 missense variant interpretation

by Masamichi Iizumi Missense variant interpretation often achieves useful predictive performance but remains mechanistically opaque, particularly in proteins that combine structured domains with intrinsically disordered regions (IDRs). We developed Gate & Channel, a zero-parameter, first-principles framework for full-length TP53 missense variant analysis in which each prediction is generated by explicit IF-THEN gates derived from physicochemistry, geometry, structural constraints, and polymer physics rather than fitted weights. Variants are evaluated across independent channels representing distinct physical failure modes; a variant is predicted disruptive if any gate closes. A second hierarchical layer (“Geta”) encodes physically grounded post-closure exceptions, allowing sensitivity and specificity to be improved on disjoint variant populations. The v18 framework consists of 12 channels and 2 Getas spanning structured domains and IDRs, capturing DNA-contact disruption, Zn coordination, burial-dependent packing, secondary-structure compatibility, post-translational modification chemistry, short linear motif disruption (including a multi-partner coupled-folding face), proline-directed kinase recognition, and IDR-specific proline and glycine backbone constraints. Across 1,369 TP53 missense variants, the framework achieved 84.5% sensitivity and 89.1% positive predictive value, with 90.9% sensitivity preserved in the DNA-binding core and all 9/9 hotspot mutations captured. A post hoc audit of discordant IDR calls indicated that many apparent false positives had plausible molecular rationales, consistent with a distinction between molecular mechanism disruption and clinical penetrance. Applied to KRAS, TDP-43, and BRCA1, the same channels capture the dominant pathogenic mechanisms in each protein as a proof of principle, while residual missed variants name specific gates yet to be written. The framework is distributed as the open-source Python package pathogenicity-gates (v0.5.1, MIT). These results show that a substantial fraction of full-length TP53 missense variation can be resolved through explicit, auditable physical gates that carry meaning beyond TP53, with each remaining failure naming the next rule to be written.

21.
arXiv (CS.AI) 2026-06-19

Bi-Anchor Interpolation Solver for Accelerating Generative Modeling

arXiv:2601.21542v3 Announce Type: replace-cross Abstract: Flow Matching (FM) models have emerged as a leading paradigm for high-fidelity synthesis. However, their reliance on iterative Ordinary Differential Equation (ODE) solving creates a significant latency bottleneck. Existing solutions face a dichotomy: training-free solvers suffer from significant performance degradation at low Neural Function Evaluations (NFEs), while training-based one- or few-steps generation methods incur prohibitive training costs and lack plug-and-play versatility. To bridge this gap, we propose the Bi-Anchor Interpolation Solver (BA-solver). BA-solver retains the versatility of standard training-free solvers while achieving significant acceleration by introducing a lightweight SideNet (1-2% backbone size) alongside the frozen backbone. Specifically, our method is founded on two synergistic components: 1) Bidirectional Temporal Perception, where the SideNet learns to approximate both future and historical velocities without retraining the heavy backbone; and 2) Bi-Anchor Velocity Integration, which utilizes the SideNet with two anchor velocities to efficiently approximate intermediate velocities for batched high-order integration. By utilizing the backbone to establish high-precision ``anchors'' and the SideNet to densify the trajectory, BA-solver enables large interval sizes with minimized error. Empirical results on ImageNet-256^2 demonstrate that BA-solver achieves generation quality comparable to 100+ NFEs Euler solver in just 10 NFEs and maintains high fidelity in as few as 5 NFEs, incurring negligible training costs. Furthermore, BA-solver ensures seamless integration with existing generative pipelines, facilitating downstream tasks such as image editing.

22.
arXiv (quant-ph) 2026-06-12

Kerr-induced nonreciprocal transparency and group delay in a hybrid cavity magnomechanical system

arXiv:2606.13412v1 Announce Type: new Abstract: We propose a scheme for realizing nonreciprocal transparency, Fano resonances, and slow/fast light in a hybrid cavity magnomechanical system containing two YIG spheres and a mechanical resonator. The nonreciprocal behavior originates from the magnon Kerr nonlinearity, which induces direction-dependent frequency shifts and modifies the interference pathways among cavity photons, magnons, and phonons. We show that the hybrid system supports multiple transparency windows arising from magnon- and magnomechanical-induced interference processes. The Kerr interaction strongly reshapes these transparency features, producing asymmetric Fano line shapes and enabling controllable nonreciprocal transmission. Furthermore, the associated dispersion exhibits pronounced directional asymmetry, leading to giant differences in the group delay for opposite propagation directions and allowing reversible switching between slow- and fast-light regimes. We investigate the roles of hybrid coupling strengths and dissipation channels and identify parameter regimes where the nonreciprocal response is maximized. These findings establish Kerr-engineered magnomechanical systems as promising platforms for integrated nonreciprocal microwave photonics and quantum information technologies.

23.
medRxiv (Medicine) 2026-06-15

The clinical utility of functional testing in fibroblasts to diagnose primary mitochondrial disease

Genome sequencing of the heterogeneous primary mitochondrial disorders (PMD) frequently reveals variants of uncertain significance that require functional tests for diagnosis, and does not identify variants in all patients. We analyzed mitochondrial enzyme assays, blue native polyacrylamide gel electrophoresis (BN-PAGE) with in-gel activity staining, complex I assembly blot, and select protein abundances in fibroblasts of a case series of 204 PMD patients divided into functional classes, in comparison to 51 controls and 53 differential diagnostic conditions. Overall, sensitivity and specificity for respiratory chain enzyme assays were 46% and 93% respectively, for BN-PAGE 40% and 98%, for complex I assembly assay 49% and 99%. The overall sensitivity of all tests was 76%, specificity 93%, with positive predictive value 96% and negative predictive value 67%. Categories with high sensitivity were isolated complex deficiencies, nuclear DNA-encoded mitochondrial protein synthesis defects, co-factor defects, and mitochondrial amino-acyl-tRNA synthetase conditions when aided by protein abundance. Mitochondrial DNA mutations and maintenance disorders showed poor sensitivities. Secondary dysfunctions were rare. A complete battery of functional tests showed strong diagnostic clinical utility in fibroblasts.

24.
arXiv (quant-ph) 2026-06-16

Grid-state deformation in a no-jump non-Hermitian bosonic dimer

arXiv:2606.17036v1 Announce Type: new Abstract: We study the no-jump evolution of ideal grid states in a lossy bosonic dimer with differential decay. The effective non-Hermitian quadratic dynamics induces a complex symplectic flow in phase space that deforms both the primitive lattice vectors and the origin seed. The average decay rate controls common attenuation, while coherent hopping and differential decay control the reduced dimer deformation. The reduced sector contains elliptic, parabolic, and hyperbolic regimes with imaginary spectra, an exceptional point, and real spectra, producing oscillatory, linear, and exponential lattice deformations. Although projected lattice areas can change, the deformation comes from a determinant-one complex symplectic flow on the full four-dimensional phase space. For a Gaussian regularization of the origin seed, we derive the associated complex width matrix and identify the positivity conditions that preserve Gaussian form. For an initial two-mode qunaught product state, the lossless limit recovers the standard beam-splitter generation of a square GKP$+$ Bell pair, while the no-jump dynamics produces its non-Hermitian deformation with a postselection cost set by the no-jump probability.

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

Do You Really Need a GPU to Guard Your LLM? CPU-Class Classifiers and Multi-Stage Pipelines for Safety Enforcement at Scale

Safety classifiers that screen LLM inputs for jailbreak attempts have become standard deployment components, yet almost all production systems rely on GPU-based models: fine-tuned transformers and LLM-as-a-judge pipelines. These approaches impose significant per-query latency and infrastructure cost. Very little research has asked whether CPU-based classifiers, such as support vector machines and gradient-boosted trees trained on TF-IDF features, can match their accuracy across the conditions that production deployments encounter. We evaluate five CPU classifier families, Mamba-130M as an SSM-based GPU classifier, and transformer-based GPU models (DeBERTa-v3 and Gemma-2B with LoRA) across nine jailbreak sources and three regimes: in-distribution (D1), out-of-distribution (D2), and adversarially obfuscated (D3). On D1, the best CPU classifier matches the best transformer GPU model at roughly one-fifth the deployment cost. On D2, CPU classifiers fail via confident miscalibration, producing high-confidence false negatives that bypass escalation entirely. On D3, CPU classifiers outperform transformer GPU models by more than 26 percentage points in F1. Based on these complementary failure modes, we design GuardChain, a three-stage safety pipeline (Regex -> CPU -> GPU) that routes each prompt to the cheapest stage capable of a confident decision. The CPU stage alone resolves 80\% of in-distribution prompts at near-peak accuracy, and the GPU stage recovers the out-of-distribution failures. For practitioners deploying LLM safety at scale, this work provides evidence that GPU-class infrastructure is unnecessary for the majority of traffic.