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01.
arXiv (quant-ph) 2026-06-17

Helical Dirac Current with Local Coupling to a Chiral Potential

arXiv:2606.17618v1 Announce Type: new Abstract: We show that exact Dirac eigenstates in cylindrical confinement carry a definite helical conserved-current texture even in the zero orbital angular momentum channel l = 0. For the lowest confined mode, the Dirac current contains a nonvanishing azimuthal component together with longitudinal transport and exhibits opposite handedness in the two spin-resolved sectors. The structure also persists into the evanescent region. We further derive the channel-resolved matrix-element kernel generated by a static chiral scalar potential acting on the confined l = 0 Dirac modes. The resulting spin-selective coupling arises from the Dirac current texture and the scalar chiral potential, and yields a geometric selection rule in which diagonal channels vanish while off-diagonal conversion channels survive. The coupling strength is governed by an internal sampled-current overlap Jchi(k), defined as the integral from 0 to R of f(rho) times jphi_up(rho, k) times rho d rho. This quantity measures the spatial overlap between the chiral radial profile and the spin-up azimuthal Dirac-current density. The mechanism is fully local and texture-based, without external magnetic fields or spin-orbit coupling. Within standard Dirac theory, this work identifies the minimal static Dirac-geometric kernel underlying spin-selective response, establishing a baseline structure from which dynamical-medium, scattering, and transport formalisms can be systematically developed toward a complete description of spin-polarization phenomena such as CISS.

02.
arXiv (CS.LG) 2026-06-18

Does VLA Even Know the Basics? Measuring Commonsense and World Knowledge Retention in Vision-Language-Action Models

arXiv:2606.19297v1 Announce Type: new Abstract: Embodied Vision-Language-Action (VLA) models are typically obtained by fine-tuning powerful pretrained VLMs on robotics data, yet it is unclear how much commonsense and factual knowledge they retain after adaptation. Failures on knowledge-sensitive tasks are ambiguous, conflating missing knowledge with poor generalization of low-level control. We introduce Act2Answer, a lightweight protocol that adapts VLM knowledge benchmarks to VLA evaluation by requiring agents to answer through action. Each question becomes a short tabletop episode where the agent performs a single object-placement action to select among candidate answers, yielding an action-grounded success rate with reduced control confounds. We curate a test suite of such environments across diverse commonsense and world-knowledge categories and introduce layerwise intent probing to localize answer-relevant information across the VLM backbone and action head. In a large-scale study of 7 VLA models and 9 VLM baselines, we systematically rank models across categories, finding that VLAs show solid performance on simple concepts while exhibiting larger gaps on richer semantic categories relative to their source VLMs, that VQA co-training is associated with better knowledge retention, and that answer-relevant signals peak in middle VLA layers but attenuate in upper layers. Act2Answer is available at https://tttonyalpha.github.io/act2answer/.

03.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

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

Unified Multimodal Autoregressive Modeling with Shared Context-Visual Tokenizer is Key to Unification

Unified Multimodal Modeling aims to integrate visual understanding and generation within a single system. However, existing approaches typically rely on two disparate visual tokenizers, which splits the representation space and hinders truly unified modeling. We propose UniAR, a unified autoregressive framework where a single discrete visual tokenizer serves as the key bridge between understanding and generation, enabling a shared context in which the model can directly interpret its own generated visual tokens without additional re-encoding. UniAR adapts a pretrained vision encoder with multi-level feature fusion and a lookup-free bitwise quantization scheme, preserving both high-level semantics and low-level details while scaling the effective visual vocabulary at minimal cost. Building on this, the unified autoregressive model adopts parallel-bitwise-prediction to jointly predict spatially grouped, multi-level visual codes, substantially reducing visual sequence length and accelerating generation. Finally, a diffusion-based visual decoder operates on discrete visual tokens to decode high-fidelity images. Through large-scale pre-training, followed by supervised fine-tuning and reinforcement learning, UniAR achieves state-of-the-art performance on image generation and image editing while remaining competitive on multimodal understanding benchmarks. The project page is available at https://sharelab-sii.github.io/uniar-web.

05.
arXiv (CS.LG) 2026-06-18

TS-Fault: Benchmarking Time Series Forecasters Against Structural Faults

arXiv:2606.18539v1 Announce Type: new Abstract: Time series forecasting (TSF) underpins consequential decisions in energy, transportation, finance, and healthcare, yet TSF models are almost universally ranked by a single number (e.g., average error) on clean held-out data, under the implicit assumption that it predicts deployed reliability. However, real faults are not i.i.d noise but structured events with temporal shape, broken cross-variable dependencies, regime change coupled with missingness, and causal propagation across a sensing pipeline. Treating TSF robustness as a data-quality problem, we present TS-Fault, a benchmark that evaluates forecasting models under explicit, parameterized fault scenarios with controllable semantic difficulty. TS-Fault organizes recurring failures into four modes along two orthogonal axes (observation- vs mechanism-level; univariate vs multivariate) and injects each fault into the most prediction-critical window via a unified importance score. This design enables robustness to be tested against the structures models actually rely on, rather than reduced to generic noise sensitivity. We evaluate 21 models across 6 datasets, 4 modes, and 5 difficulty levels under a paired clean/corrupt protocol. The results reveal three findings that contradict common leaderboard intuition: (i) clean-data accuracy anti-correlates with robustness; (ii) clean rankings are preserved under observation-level faults but reshuffled under mechanism-level faults; and (iii) all catastrophic failures occur under mechanism-level faults, with foundation models achieving the highest clean-data accuracy yet exhibiting the greatest fragility. The code is publicly available at https://github.com/Ray-zyy/TS-Fault.

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

Speaker Verification with Speech-Aware LLMs: Evaluation and Augmentation

arXiv:2603.10827v2 Announce Type: replace-cross Abstract: Speech-aware large language models (LLMs) can accept speech inputs, yet their training objectives largely emphasize linguistic content or specific fields such as emotions or the speaker's gender, leaving it unclear whether they encode speaker identity. First, we propose a model-agnostic scoring protocol that produces continuous verification scores for both API-only and open-weight models, using confidence scores or log-likelihood ratios from the Yes/No token probabilities. Using this protocol, we benchmark recent speech-aware LLMs and observe weak speaker discrimination (EERs above 20% on VoxCeleb1). Second, we introduce a lightweight augmentation that equips an LLM with ASV capability by injecting frozen ECAPA-TDNN speaker embeddings through a learned projection and training only LoRA adapters. On TinyLLaMA-1.1B, the resulting ECAPA-LLM achieves 1.03% EER on VoxCeleb1-E, approaching a dedicated speaker verification system while preserving a natural-language interface.

07.
arXiv (CS.CL) 2026-06-15

An Empirical Study of Automating Agent Evaluation

Agent evaluation requires assessing complex multi-step behaviors involving tool use and intermediate reasoning, making it costly and expertise-intensive. A natural question arises: can frontier coding assistants reliably automate this evaluation process? Our study shows that simply prompting coding assistants is insufficient for this task. Without domain-specific evaluation knowledge, frontier coding assistants achieve only a 30% execution success rate and produce over-engineered evaluations averaging 12+ metrics per agent, indicating that strong coding ability does not automatically translate to reliable agent evaluation. We introduce EvalAgent, an AI assistant that automates the end-to-end agent evaluation pipeline. EvalAgent encodes evaluation domain expertise as evaluation skills (procedural instructions, reusable code and templates, and dynamically retrieved API documentation) that compose into a trace-based pipeline producing complete evaluation artifacts including metrics, executable code, and reports. To systematically assess generated evaluations, we introduce a meta-evaluation framework alongside AgentEvalBench, a benchmark comprising 20 agents, each paired with evaluation requirements and test scenarios. We further propose the Eval@1 metric to measure whether generated evaluation code both executes and yields meaningful results on the first run. Our experiments show that EvalAgent produces focused evaluations, improving Eval@1 from 17.5% to 65%, and achieving 79.5% human expert preference over baseline approaches. Further ablation studies show that evaluation skills are critical for handling complex evaluation: removing them causes Eval@1 to drop significantly from 65% to 30%.

08.
arXiv (CS.LG) 2026-06-12

Viral Proteins Reveal Geometry of Protein Language Models

arXiv:2606.12609v1 Announce Type: new Abstract: Protein language models are trained on highly imbalanced datasets, raising the question of how they represent underrepresented biological sequences. Using viral proteins as a case study across ESM model families, we identify a dominant nativeness axis in embedding space, aligned with masked reconstruction perplexity, that orders sequences from well-modeled cellular proteins through viral proteins to shuffled and random sequences. Scaling contracts this axis unevenly across viral families. Despite this, protein language model embeddings retain viral-specific signal: viral proteins remain linearly separable beyond zero-shot perplexity and shallow sequence features. Together, these results suggest that pLM representations are structured by a general notion of nativeness while preserving information specific to distinct biological groups.

09.
arXiv (CS.CL) 2026-06-12

G-Long: Graph-Enhanced Memory Management for Efficient Long-Term Dialogue Agents

While Large Language Models (LLMs) have advanced open-domain dialogue systems, maintaining long-term consistency remains a challenge due to inherent limitations in long-context reasoning and the inefficiency of processing extensive raw text. Existing approaches typically rely on either unstructured memory storage, which is prone to information loss, or computationally expensive LLMs that incur high latency. To address these limitations, we propose G-Long, a graph-enhanced framework that utilizes a fine-tuned small Language Model (sLM) for structured triplet extraction and associative retrieval, significantly reducing operational costs. Furthermore, we introduce the novel attention-aware importance scoring mechanism that leverages the intrinsic cross-attention signals of a T5 summarizer to identify salient memories. Extensive experiments across diverse benchmarks demonstrate that G-Long achieves state-of-the-art performance in both response generation and memory retrieval, yielding performance gains of up to 9.8% in response quality on MSC and 40.8% in retrieval recall on LME, while significantly minimizing computational overhead.

10.
arXiv (CS.AI) 2026-06-12

Boosting Direct Preference Optimization with Penalization

作者:

arXiv:2606.12505v1 Announce Type: cross Abstract: Offline preference optimization has become a practical substitute for reinforcement learning from human feedback, but pairwise objectives such as Direct Preference Optimization (DPO) and its variants use only the chosen and rejected responses stored in a static dataset. This leaves a useful signal unused: the response that the reference model itself would generate for the same prompt. We propose Direct Preference Optimization with Penalization (DPOP), a simple extension of DPO that augments the base preference loss with a gated penalty on reference-greedy responses. DPOP activates this penalty only when the current policy still assigns a lower likelihood to the preferred response than to the rejected response. On AlpacaEval 2.0, DPOP improves length-controlled win rate over DPO, SimPO, and AlphaDPO on both Llama-3-8b-it and Gemma-2-9b-it, achieving relative gains of 5.3\% and 4.4\% over baselines on the two models, respectively. Ablations further show that a SimNPO-style length-normalized penalty is stronger than NPO and token-level unlikelihood in this setting.

11.
medRxiv (Medicine) 2026-06-16

Adverse Childhood Experiences and Growth Outcomes in Childhood: A Longitudinal EHR-Based Study

Question Are adverse childhood experiences (ACEs) associated with altered growth trajectories in childhood? Findings In this cohort study of 412,549 children and adolescents, ACEs were associated with lower height throughout childhood, earlier pubertal timing, and shorter final stature. Height differences emerged approximately 2 years before ACE documentation and were greatest among those with earlier documentation. Meaning These findings suggest that early adversity affects physical growth in children and may serve as a measurable indicator of the biological consequences of early-life stress, especially in those with documentation of ACEs prior to the onset of typical pubertal growth. Importance Adverse childhood experiences (ACEs) are among the strongest risk factors for long-term mental and physical health complications, yet their impact on physical growth in childhood remains incompletely understood. Objective To determine the association of ACEs on childhood growth trajectories and growth dynamics. Design, Setting and Participants Retrospective cohort study using longitudinal electronic health record data. Data was collected from participants between February 1999 and August 2025. A large academic medical center biobank linked to deidentified electronic health records in the southeastern United States. A total of 412,549 individuals with at least 2 recorded height measurements between the ages of 2 and 20 were included in the primary analysis. Growth curve analyses were performed in a subset of 199,844 individuals with at least 3 height measurements spanning at least 2 years. Genetic analyses were performed in a subset of 10,114 individuals of primarily European ancestry. Exposure(s) Documented exposure to adverse childhood experiences before age 18 years identified through a natural language processing algorithm. Main Outcome(s) and Measure(s) Height-for-age z-scores across childhood, final attained height, and growth curve parameters estimated using SuperImposition by Translation and Rotation (SITAR) modeling. Results Among 412,549 participants, 18,502 (4.5%) had clinically documented ACEs during childhood. ACE documentation was associated with lower height-for-age z-scores throughout childhood and adolescence. Final attained height was significantly lower among ACE-documented individuals, with mean differences of -3.0 cm among males (174.0 cm vs 177.0 cm, p < 0.001) and -1.3 cm among females (161.8 cm vs 163.1 cm, p < 0.001). Height differences emerged approximately 2 years before clinical ACE documentation. Earlier age at first ACE documentation was associated with progressively shorter final attained height, with each year decrease in age at ACE documentation associated with a decrease in final height of -0.20 cm in females and -0.35 cm in males. Those with first ACE documented prior to pubertal age also showed the most pronounced growth dynamic differences, with males demonstrating a mean reduction in size of 5.25 cm (95% CI, -6.79 cm to -3.70 cm) and 1.26-year earlier pubertal timing (95% CI, -1.50 to -1.03 years), and females demonstrating a reduction in growth curve size of 3.62 cm (95% CI, -4.83 to -2.41 cm) and 1.14-year earlier pubertal timing (95% CI, -1.29 to -0.99 years). Conclusions and Relevance In this large clinical cohort, clinically documented ACEs were associated with time-dependent reductions in stature, earlier pubertal timing, and short final attained height. These findings suggest that early childhood adversity may have lasting effects on physical development and highlight growth trajectories as a potential marker of the biological consequences of early-life stress.

12.
medRxiv (Medicine) 2026-06-18

Can Vision-Language Models See the Vital Signs? Benchmarking and Fine-Tuning for Intraoperative Monitor Reading

Background Vital-sign deterioration is a leading contributor to preventable perioperative death, yet manual monitor reading is intermittent, error-prone, and subject to alarm fatigue. Automating this perceptual step could enable continuous surveillance, but existing solutions depend on device-specific hardware integration or cloud-hosted vision-language models (VLMs), which raise privacy, cost, and connectivity barriers in resource-limited healthcare facilities. Methods We constructed a benchmark of 200 in-the-wild intraoperative monitor photographs (spanning multiple vendors, angles, and illumination conditions) annotated for eight vital-sign parameters: heart rate, SpO2, ETCO2, respiratory rate, systolic/diastolic/mean blood pressure, and temperature. We evaluated an optical character recognition (OCR)-based pipeline, nine instruction-tuned VLMs (four commercial, five open-weight ranging from [&le;]4B to 31B parameters) under two prompting regimes, and a compact open model (Qwen3.5-9B) adapted via low-rank fine-tuning (LoRA, 0.46% of parameters updated). Results Under a domain-aware prompt, frontier VLMs reached 0.98-0.997 exact-match accuracy zero-shot, whereas the OCR pipeline and [&le;]4B model scored approximately 0.20 lower, defining a 9B-class usable floor. LoRA fine-tuning Qwen3.5-9B on 80-120 images raised accuracy from 0.953 to 0.994 (statistically indistinguishable from the best commercial model) and reduced the critical-error rate fivefold (0.0313 [-&gt;] 0.0063). Ablations showed that performance saturated at 80 training images and rank-8 adapters. Conclusion Monitor reading is a solved perception problem for VLMs above the 9B scale. A lightweight fine-tuned open model achieves frontier accuracy while running entirely on local hardware, preserving data privacy, offline capability, and near-zero marginal cost. Residual errors stem from blood-pressure source ambiguity and are addressable with explicit disambiguation logic.

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

FutureOmni: Evaluating Future Forecasting from Omni-Modal Context for Multimodal LLMs

Although Multimodal Large Language Models (MLLMs) demonstrate strong omni-modal perception, their ability to forecast future events from audio-visual cues remains largely unexplored, as existing benchmarks focus mainly on retrospective understanding. To bridge this gap, we introduce FutureOmni, the first benchmark designed to evaluate omni-modal future forecasting from audio-visual environments. The evaluated models are required to perform cross-modal causal and temporal reasoning, as well as effectively leverage internal knowledge to predict future events. FutureOmni is constructed via a scalable LLM-assisted, human-in-the-loop pipeline and contains 919 videos and 1,034 multiple-choice QA pairs across 8 primary domains. Evaluations on 13 omni-modal and 7 video-only models show that current systems struggle with audio-visual future prediction, particularly in speech-heavy scenarios, with the best accuracy of 64.8% achieved by Gemini 3 Flash. To mitigate this limitation, we curate a 7K-sample instruction-tuning dataset and propose an Omni-Modal Future Forecasting (OFF) training strategy. Evaluations on FutureOmni and popular audio-visual and video-only benchmarks demonstrate that OFF enhances future forecasting and generalization. We publicly release all code (https://github.com/OpenMOSS/FutureOmni) and datasets (https://huggingface.co/datasets/OpenMOSS-Team/FutureOmni).

14.
arXiv (CS.CL) 2026-06-19

DeepSeek-V4: Towards Highly Efficient Million-Token Context Intelligence

We present a preview version of DeepSeek-V4 series, including two strong Mixture-of-Experts (MoE) language models – DeepSeek-V4-Pro with 1.6T parameters (49B activated) and DeepSeek-V4-Flash with 284B parameters (13B activated) – both supporting a context length of one million tokens. DeepSeek-V4 series incorporate several key upgrades in architecture and optimization: (1) a hybrid attention architecture that combines Compressed Sparse Attention (CSA) and Heavily Compressed Attention (HCA) to improve long-context efficiency; (2) Manifold-Constrained Hyper-Connections (mHC) that enhance conventional residual connections; (3) and the Muon optimizer for faster convergence and greater training stability. We pre-train both models on more than 32T diverse and high-quality tokens, followed by a comprehensive post-training pipeline that unlocks and further enhances their capabilities. DeepSeek-V4-Pro-Max, the maximum reasoning effort mode of DeepSeek-V4-Pro, redefines the state-of-the-art for open models, outperforming its predecessors in core tasks. Meanwhile, DeepSeek-V4 series are highly efficient in long-context scenarios. In the one-million-token context setting, DeepSeek-V4-Pro requires only 27% of single-token inference FLOPs and 10% of KV cache compared with DeepSeek-V3.2. This enables us to routinely support one-million-token contexts, thereby making long-horizon tasks and further test-time scaling more feasible. The model checkpoints are available at https://huggingface.co/collections/deepseek-ai/deepseek-v4.

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

Beyond Scalars: Evaluating and Understanding LLM Reasoning via Geometric Progress and Stability

arXiv:2603.10384v3 Announce Type: replace Abstract: Evaluating LLM reliability via scalar probabilities often fails to capture the structural dynamics of reasoning. We introduce TRACED, a framework that assesses reasoning quality through theoretically grounded geometric kinematics. By decomposing reasoning traces into Progress (displacement) and Stability (curvature), we reveal a distinct topological divergence: correct reasoning manifests as high-progress, stable trajectories, whereas hallucinations are characterized by low-progress, unstable patterns (stalled displacement with high curvature fluctuations). Leveraging these signatures, our probabilistic framework achieves competitive performance and superior robustness across diverse benchmarks. Crucially, TRACED bridges geometry and cognition by mapping high curvature to ''Hesitation Loops'' and displacement to ''Certainty Accumulation'', offering a physical lens to decode the internal dynamics of machine thought.

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

Concrete Subspace Learning based Interference Elimination for Multi-task Model Fusion

arXiv:2312.06173v2 Announce Type: replace Abstract: Merging models fine-tuned from a common, extensively pre-trained large model but specialized for different tasks has been demonstrated as a cheap and scalable strategy to construct a multi-task model that performs well across diverse tasks. Recent research, exemplified by task arithmetic, highlights that this multi-task model can be derived through arithmetic operations on task vectors. Nevertheless, current merging techniques frequently resolve potential conflicts among parameters from task-specific models by evaluating individual attributes, such as the parameters' magnitude or sign, overlooking their collective impact on the overall functionality of the model. In this work, we propose the CONtinuous relaxation of disCRETE (Concrete) subspace learning method to identify a common low-dimensional subspace and utilize its shared information to track the interference problem without sacrificing much performance. Specifically, we model the problem as a bi-level optimization problem and introduce a meta-learning framework to find the Concrete subspace mask through gradient-based techniques. At the upper level, we focus on learning a shared Concrete mask to identify the subspace, while at the inner level, model merging is performed to maximize the performance of the merged model. We conduct extensive experiments on both vision domain and language domain, and the results demonstrate the effectiveness of our method. The code is available at https://github.com/tanganke/subspace_fusion

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

FlowMPC: Improving Flow Matching policies with World Models

arXiv:2606.16286v1 Announce Type: cross Abstract: Flow Matching (FM) is a powerful approach for behavior cloning in multimodal action spaces [Jiang et al., 2025], but because it is not trained to directly maximize expected return, there is still room to improve how FM policies act at test time. This work investigates whether a learned world model can improve FM policies by enabling Model Predictive Path Integral (MPPI) planning over candidate action sequences proposed by the policy. Building on TD-MPC2 [Hansen et al., 2024], I introduce FlowMPC, a framework that combines an imitation-learned FM policy with a learned world model for test-time planning in ManiSkill manipulation tasks [Tao et al., 2025]. Across PickCube and PickSingleYCB, adding the world model improved performance over the FM policy alone, with especially clear gains in end-of-episode success. These results suggest that world-model-based planning can effectively complement flow-based imitation policies without modifying the FM training objective.

18.
bioRxiv (Bioinfo) 2026-06-11

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecules, providing a unique opportunity to study transcriptional and epitranscriptomic regulation within a single experiment. However, comprehensive analysis of DRS data remains challenging, as existing workflows typically focus on individual processing steps and often require manual integration of multiple software packages for expression analysis, modification detection, statistical testing, and visualization. Furthermore, integrated differential expression and differential RNA modification analysis at both gene and isoform resolution remains poorly supported by current workflows. Here, we present DModE (Differential Modification and Expression Analysis), an end-to-end framework for integrated analysis of Nanopore DRS data. DModE combines an Epi2ME-compatible Nextflow preprocessing workflow with a dedicated Python package for downstream statistical analysis, visualization, and reporting. The framework supports differential gene and isoform expression analysis, differential RNA modification analysis at genome and transcript level, metagene profiling, exploratory epitranscriptomic analyses, and integrated assessment of relationships between expression and modification dynamics. Results are automatically summarized in interactive HTML reports, facilitating reproducible and accessible data interpretation. By integrating transcriptomic and epitranscriptomic analyses within a single framework, DModE substantially simplifies comprehensive DRS data analysis and lowers the barrier for studying RNA modification biology using Nanopore sequencing.

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

3D Classification of Paramagnetic Rim Lesions in Multiple Sclerosis via Asymmetric QSM-FLAIR Modeling

Paramagnetic rim lesions (Rim$^+$) identified on susceptibility-sensitive MRI have recently emerged as a specific biomarker of chronic active inflammation in Multiple Sclerosis (MS) and are associated with long-term disability progression. However, susceptibility imaging and expert interpretation remain limited to specialized centers, visual assessment is time-consuming and variable, and the low prevalence of Rim$^+$ lesions poses severe class imbalance challenges for automated analysis. We propose a 3D multimodal deep learning framework for lesion-level Rim$^+$/Rim$^-$ classification from Quantitative Susceptibility Mapping (QSM) and FLAIR MRI. The architecture explicitly models modality asymmetry by treating QSM as the primary susceptibility-driven signal and conditioning it with FLAIR-derived structural context. To improve robustness under limited data, we employ self-supervised multimodal pretraining followed by supervised fine-tuning with contrastive regularization. The method was evaluated on a clinically acquired cohort of 88 people with MS with expert lesion annotations as reference standard. Results highlight improved performance compared to prior architectures, supporting the effectiveness of asymmetric multimodal modeling for automated chronic active lesion identification.

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

Spectral Analysis of Molecular Features: When Richer Features Do Not Guarantee Better Generalization

arXiv:2510.14217v2 Announce Type: replace Abstract: The spectral properties of feature embeddings offer critical insights into model generalization and representation quality. While deep learning models are widely used for molecular property prediction, kernel methods remain competitive in low-data regimes, yet their spectral behavior is largely unexplored. We present the first comprehensive spectral analysis of kernel ridge regression across diverse representations-including molecular fingerprints (ECFP), pretrained transformers, graph neural networks, and 3D descriptors-evaluated on QM9 and 3 MoleculeNet benchmarks. Surprisingly, richer spectral features do not consistently yield better generalization performance, contradicting common representation heuristics used in self-supervised learning (SSL). Across 4 spectral metrics, only ECFP-based kernels show a strictly positive correlation with performance. Transformer and global 3D representations exhibit mixed behavior, whereas local 3D representations show consistently negative correlations. Truncation analysis further emphasizes this disparity: for local 3D representations on thermodynamic targets, fewer than 2\% of eigenvalues (and occasionally as few as 0.02\%) are needed to recover 95\% of performance, whereas ECFP and transformer kernels require significantly more. By demonstrating a strong dependence on both task and representation, our results challenge the heuristic that richer spectra inherently improve generalization, providing new guidance for evaluating representations in SSL and in label-limited scientific tasks.

21.
arXiv (CS.CV) 2026-06-12

ECA: Efficient Continual Alignment for Open-Ended Image-to-Text Generation

Incremental Learning (IL) for Open-ended Image-to-Text Generation (OpenITG) enables models to continuously generate accurate, contextually relevant text for new images while preserving previously acquired knowledge. Unlike prior studies, this paper addresses a more practical scenario in which the predominant category of visual data shifts over time as environments evolve. In this context, we introduce a new notion of continual alignment, which incrementally adapts the alignment module within pre-trained VLMs to preserve high-quality cross-modal representations. Based on this idea, we propose Efficient Continual Alignment (ECA), a novel exemplar-free IL approach for OpenITG. The key challenge is enabling the model to acquire new, task-specific features while minimizing interference with the established alignment without accessing raw data from previous tasks. To address this, ECA employs three core mechanisms: a Mixture of Query (MoQ) module that adapts task-specific query tokens, a Fisher Dynamic Expansion (FeDEx) that dynamically expands model structure based on a Fisher Information Matrix (FIM)-based metric, and an embedding dictionary with Dictionary Replay (DR) to retain past knowledge. To evaluate ECA's performance, we construct four new IL OpenITG benchmarks that better reflect real-world scenarios. Experimental results demonstrate that ECA significantly mitigates catastrophic forgetting and improves IL performance compared to baseline methods. Code and benchmarks are available at https://github.com/Snowball0823/ECA.

22.
arXiv (CS.AI) 2026-06-16

Heteroskedastic Signals in Budgeted LLM Verification: Structural Heterogeneity Limits Optimization Gains

作者:

arXiv:2606.15841v1 Announce Type: new Abstract: Large language model (LLM) systems increasingly use uncertainty signals to allocate limited computation across verification, test-time scaling, tool execution, and other selective-compute decisions. Such policies rely on a global signal comparability assumption: equal scores should carry comparable decision value across inputs. Using budgeted verification as a controlled diagnostic setting, we identify a failure mode of this assumption: uncertainty quality is heteroskedastic across cost strata, with some regions exhibiting near-random discriminability despite concentrating many errors. Under an explicit local model, we characterize the resulting distortion of global allocation and show that its upper bound scales with cross-stratum signal-quality dispersion. We separate weak signals, optimization instability, and structural heterogeneity through a controlled intervention hierarchy: Threshold, MP-Adapt, MP-Strat, and a deliberately simple cost-stratified thresholding intervention (CST). Across MBPP and MATH using Qwen3-8B, LLaMA3-8B, and GPT-4o-mini, global online adaptation yields inconsistent gains over static thresholding; MP-Strat partially recovers performance, while CST improves hit rate by up to 17 percentage points in strongly heterogeneous settings without gradient updates. These results identify structural heterogeneity, rather than optimizer weakness alone, as the primary bottleneck in the observed settings. More broadly, misaligned feedback structure cannot always be repaired by stronger optimization.

23.
arXiv (CS.AI) 2026-06-16

Provenance-Enhanced Statements in Knowledge Graphs

arXiv:2606.15246v1 Announce Type: cross Abstract: Provenance-enhanced statements of the form "according to $X$, $\varphi$" are pervasive in contemporary knowledge graphs, especially in domains where graph content primarily represents claims, interpretations, and hypotheses (capta) rather than observer-independent facts (data). Current provenance models can record who asserted what, but they typically treat provenance as semantically neutral, leaving underspecified how attributed claims relate to factual commitment, to one another, and to reasoning. In this paper we introduce DEC, a framework that interprets provenance predicates as indicators of epistemic stance and groups provenance-homogeneous sets of statements into cognitive worlds. Drawing on cognitive modal logics (doxastic, epistemic, and conjectural), DEC characterizes locality, rationality, and controlled permeation between cognitive worlds and a distinguished factual core ("reality"), thereby enabling principled reasoning over attributed content without collapsing disagreements into inconsistencies. We formalize a DEC interpretation for RDF datasets that is conservative over RDF~1.2 semantics, clarify the role of intensionality and identity (including the Superman paradox), and illustrate the approach on common Semantic Web representations (named graphs, quoted triples/RDF-star, and reification). Finally, we describe our prototype DEC reasoner implemented as a Fuseki dataset module, supporting controlled factualisation and explicit detection of disagreements and delusions.

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

Phase-Aware Guidance Injection for Recurrent MAPPO in Assembly-Line Disruption Recovery

arXiv:2606.16330v1 Announce Type: new Abstract: Disruption recovery in industrial assembly lines requires timely decisions under machine faults, worker absence, and emergency orders. Existing methods either rely on rigid handcrafted recovery logic or learn adaptive policies that do not readily exploit heterogeneous external recovery knowledge at decision time to reduce abnormal recovery time (ART) and preserve on-time delivery (OTD). To address this gap, we propose a phase-aware guidance injection framework that augments a trained recurrent MAPPO (RMAPPO) scheduling policy through logit-level action bias during evaluation. The framework provides a unified decision-time interface for rule-based, replay-based, and online LLM-based guidance, while activating intervention only during abnormal and recovery phases. Experiments on a custom AssemblyLineEnv show that high-quality rule guidance yields the strongest gains, replay-based guidance degrades smoothly under imperfect availability, and online LLM guidance still provides useful intermediate improvements. These results show that decision-time guidance injection can exploit heterogeneous recovery hints without redesigning the actor.

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arXiv (CS.CL) 2026-06-19

Beyond the GUI Paradigm: Do Mobile Agents Need the Phone Screen?

Recent advances in mobile agents are dominated by the GUI paradigm, in which agents perceive UI information and emit screen interactions. However, mobile platforms also expose a command-line interface (CLI) that provides direct access to device services and data. We argue CLI deserves first-class consideration alongside GUI. We evaluate three coding agents (Claude Code, Terminus-2, mini-swe-agent) across four model APIs on AndroidWorld and MobileWorld without any mobile-specific post-training, comparing against three reproducible GUI baselines (GUI-Owl-1.5-32B, MAI-UI, Qwen3-VL-32B). Claude Code (Opus 4.7) reaches 71.8\% and 51.9\%, outperforming every reproducible GUI baseline (69.3/68.1/57.8\% on AndroidWorld; 43.2/26.3/13.3\% on MobileWorld), while every other CLI configuration remains competitive. To establish the paradigm's ceiling, we provide oracle CLI solutions that reach 88.8\% on AndroidWorld (103/116 tasks CLI-solvable) and 86.3\% on MobileWorld (101/117 tasks CLI-solvable), indicating substantial room for future improvement. To cover everyday user intents beyond the GUI scope, we introduce the CLI-Advantage Task Suite, comprising 45 templates across five categories: bulk operations, multi-condition filtering, aggregation, cross-app workflows, and hidden device state. Every CLI agent outperforms every GUI baseline in all five categories, with substantially fewer steps per task (10.7 vs.\ 18.6). To support future research on mobile CLI agents, we will open-source agent implementations, oracle solutions, the CLI-Advantage suite, and evaluation infrastructure.