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

HANCLIP: A Family of Hyperbolic Angular Negation Vision Language Models

Vision-Language Models (VLMs) are typically pre-trained on large-scale image-text datasets to capture semantic correspondences between visual content and natural language. However, they remain surprisingly brittle to negation: models often rely on shallow word co-occurrence and are easily distracted by misleading or irrelevant textual cues, even when their overall retrieval or classification performance is strong. Moreover, directly finetuning on negation data can interfere with previously acquired knowledge, causing noticeable degradation on standard vision-language benchmarks. To tackle these issues, this work introduces HANCLIP (Hyperbolic + Angular + Negation), a family of VLMs that explicitly restructures the embedding space to encode "what an image is not" alongside "what it is." HANCLIP is trained on a compact set of 20,000 image-text quadruplets and combines a hyperbolic formulation, which models hierarchical semantic relations and asymmetries, with an angular triplet objective that drives systematic separation between negated descriptions and their corresponding positives. This geometry-aware design strengthens negation sensitivity while preserving the global structure of pretrained representations, rather than overwriting them. Extensive experiments across multiple vision-language tasks show that HANCLIP delivers consistent gains on the negation-focused NegBench benchmark, while maintaining competitive or improved performance on standard classification and image-text retrieval benchmarks. The framework is model-agnostic and can be plugged into CLIP, LongCLIP, SmartCLIP, and HiMo-CLIP without large-scale retraining, demonstrating that a carefully designed geometric objective can substantially extend the reasoning capabilities of existing VLMs using only modest additional data.

02.
medRxiv (Medicine) 2026-06-19

Rumination as a cognitive vulnerability factor in perinatal bereavement: evidence from the CARING study

Purpose. Perinatal loss is associated with a high risk of persistent psychological distress, including prolonged grief, depression, anxiety, and post-traumatic stress symptoms. Cognitive processes such as rumination may play a crucial role in maintaining and amplifying distress following loss, yet their specific contribution in perinatal bereavement remains underexplored. Methods. The CARING (Cognitive Analysis and Rumination INvestigation in perinatal Grief) study employed a cross-sectional design involving 298 parents who experienced perinatal loss within the previous five years. Participants completed an anonymous online survey including measures of depressive rumination (Ruminative Response Scale, RRS), angry rumination (Anger Rumination Scale, ARS), perinatal grief (Perinatal Grief Scale, PGS), general psychopathology (SCL-90), and post-traumatic stress symptoms (NSESSS). Non-parametric analyses were conducted to examine associations between rumination patterns and psychological outcomes. Results. Higher levels of rumination were significantly associated with greater perinatal grief, depressive and anxiety symptoms, and post-traumatic stress. Depressive rumination showed consistently stronger associations with all outcomes compared to angry rumination. Participants presenting both depressive and angry rumination exhibited the highest levels of grief intensity, psychological distress, and PTSD symptoms, suggesting a graded relationship between rumination patterns and severity of distress. Rumination levels were not significantly associated with gestational age at loss or with having received psychological support. Conclusions. Rumination, particularly in its depressive form, appears to function as a transdiagnostic cognitive vulnerability factor in perinatal bereavement. These findings highlight rumination as a potential target for early screening and tailored psychological interventions aimed at reducing long-term distress following perinatal loss.

03.
arXiv (CS.CV) 2026-06-16

HairLRM: Strand-based Hair Modeling via Large Reconstruction Models

The fundamental limitation of traditional strand-based modeling is not simply data scarcity, but the ill-posedness of inferring complex 3D fields from 2D imagery without structural constraints. This unconstrained regression leads to catastrophic failures in resolving both global occlusion (e.g., in ponytails) and local directionality (e.g., in curls), resulting in over-smoothed, plausible-but-incorrect geometries. To resolve this, we integrate the strong geometric priors of Large Reconstruction Models (LRMs) into the strand generation pipeline. Using the LRM mesh as a structural anchor, we employ a novel Dual Orientation AutoEncoder to lift coarse geometry into high-fidelity strands. By resolving vector field singularities through latent-space optimization and surface-guided refinement, our method effectively disentangles complex topological structures, setting a new benchmark for robustness and accuracy in hair reconstruction.

04.
arXiv (CS.CV) 2026-06-16

A Comprehensive Survey of Medical Image Segmentation: Challenges, Benchmarks, and Beyond

Medical image segmentation plays a critical role in clinical diagnostics, treatment planning, disease monitoring, and neurological disorder identification. This article presents a comprehensive review of its systematic development, covering widely used public datasets, representative methods built on the U-Net, Transformer, and SAM architectures, and key evaluation metrics with their differences, followed by an analysis of major challenges from multiple perspectives. Unlike surveys that focus on a single model family or a specific clinical application, this review organizes U-Net-, Transformer-, and SAM-based methods within a unified analytical framework, with a particular focus on their effectiveness in improving segmentation accuracy and efficiency. This work aims to guide future research and support clinical translation of medical image segmentation, with all related resources publicly available in our GitHub repository: https://github.com/andrew-pengyu/Awsome_MedSeg/tree/main.

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

Prediction Bottlenecks Don't Discover Causal Structure (But Here's What They Actually Do)

arXiv:2605.09169v2 Announce Type: replace-cross Abstract: A Mamba state-space model trained only for next-step prediction appears to recover Granger-causal structure through a simple readout $S = |W_{out} W_{in}|$, with early experiments suggesting the phenomenon generalized across architectures and benefited from interventional data at $p < 10^{-5}$. We package the protocol used to test that claim – standardized synthetic generators (VAR/Lorenz/CauseMe-style), three intervention semantics ($do(X=c)$, soft-noise, random-forcing), edge-provenance cards on three real datasets, and size-matched control arms – as a reusable falsification benchmark, and walk the claim through it in five stages. The method-level claim does not survive: (i) a plain linear bottleneck does as well or better; (ii) tuned Lasso beats the bottleneck on synthetic CauseMe-style benchmarks, and on Lorenz-96 (the only real benchmark with unambiguous ground truth) classical PCMCI and Granger lead a tight cluster in which the bottleneck trails; (iii) the headline intervention advantage is roughly 60% a sample-size confound, and the residual disappears under standard $do(X=c)$ interventions, surviving only under a non-standard random-forcing scheme; (iv) even that residual reproduces, with a larger effect, in classical bivariate Granger – the effect is method-agnostic. What survives is a narrow characterization result; the benchmark is the lasting artifact, and each stage above is one of its control arms.

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

DRA-GRPO: Your GRPO Needs to Know Diverse Reasoning Paths for Mathematical Reasoning

Post-training LLMs with Reinforcement Learning, specifically Group Relative Policy Optimization (GRPO), has emerged as a paradigm for enhancing mathematical reasoning. However, standard GRPO relies on scalar correctness rewards that are often non-injective with respect to semantic content: distinct reasoning paths receive identical rewards. This leads to a Diversity-Quality Inconsistency, where the policy collapses into a narrow set of dominant modes while ignoring equally valid but structurally novel strategies. To bridge this gap, we propose Diversity-aware Reward Adjustment (DRA), a theoretically grounded framework that calibrates the reward signal using the semantic density of sampled groups. By leveraging Submodular Mutual Information (SMI), DRA implements an Inverse Propensity Scoring (IPS) mechanism that effectively de-biases the gradient estimation. This creates a repulsive force against redundancy, driving the policy to achieve better coverage of the high-reward landscape. Our method is plug-and-play and integrates seamlessly with GRPO variants. Empirical evaluations on five math benchmarks demonstrate that DRA-GRPO consistently outperforms strong baselines, achieving an average accuracy of 58.2% on DeepSeek-R1-Distill-Qwen-1.5B with only 7,000 training samples and $55 cost, highlighting the critical role of diversity calibration in data-efficient alignment. The code is available at https://github.com/xiwenc1/DRA-GRPO.

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

REFLEX: Reflective Evolution from LLM Experience

Authors:

Large multimodal language models (LLMs) have emerged as powerful tools for guiding evolutionary search toward interpretable programmatic policies. However, existing frameworks rely on a monolithic model call to simultaneously interpret visual behavioral evidence and synthesize corrective code. This diagnosis-repair entanglement creates an opaque feedback loop, obscuring the rationale behind mutations and preventing the retention of algorithmic insights across independent runs. To achieve auditable and efficient policy search, we argue that visual diagnosis must be structurally decoupled from code generation. We present REFLEX, a train-free evolutionary framework that operationalizes this decoupling. In REFLEX, a vision-enabled Critic first distills task-specific behavioral evidence into structured, auditable diagnoses. Subsequently, a text-optimized Actor synthesizes child policies using these diagnoses alongside a persistent, self-evolving Skill Memory of reusable code snippets. This architecture not only provides transparent mutation traces but also enables cross-run programmatic knowledge transfer. Extensive evaluations across control benchmarks (Lunar Lander, Acrobot, Pendulum) and a 36-dimensional antenna array synthesis task demonstrate exceptional sample efficiency. Notably, REFLEX solves Acrobot and Pendulum in under 10 LLM calls and reaches a best Normalized Weighted Score of 1.092 on Lunar Lander, achieving highly competitive final performance while significantly accelerating the early-stage discovery of transparent policies.

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

Sub-Semantic Image Segmentation

Images can be segmented based on visual cues (i.e., texture segmentation) or into objects (i.e., semantic segmentation). We propose a new category of sub-semantic image segmentation that blurs the line between the two. In sub-semantic image segmentation, language is not used to name whole objects. Instead, it is used to partition an image into stable appearance patterns that can be described by language. To do that, we couple a general-purpose vision-language model to SAM 3, a promptable segmentation backbone whose native text pathway can ground rich descriptions into masks. Simple coupling fails for a number of reasons that we identify in the paper, and we overcome them by introducing DETECTURE that resolves three concrete failure modes – language leakage between texture regions, prompt competition inside the segmentation backbone, and semantic distortion at the language-to-mask interface. Since there is no dataset of sub-semantic image segmentation, we introduce one, termed TextureADE. The new dataset is derived from the ADE20K dataset using a system we designed. We compare DETECTURE to a number of baselines and find that it achieves the strongest performance on several datasets using different metrics. Code is available at https://github.com/Scientific-Computing-Lab/TextureDetecture.

09.
arXiv (CS.AI) 2026-06-19

MakeupMirror: Improving Facial Attribute Preservation in Diffusion Models for Makeup Transfer

arXiv:2606.20094v1 Announce Type: cross Abstract: Makeup transfer models enable fun augmented reality (AR) experiences as well as virtual try-on (VTO) for online makeup shopping. While recent state-of-the-art diffusion based solutions such as Stable-Makeup dramatically improve the accuracy and realism of makeup transfer, they still face limitations in identity and skin color preservation, making production-level VTO for makeup shopping unrealistic. In this work, we propose MakeupMirror, a diffusion-based approach to makeup transfer that makes significant progress towards preserving facial features and skin tone. We introduce several technical innovations over Stable-Makeup: (1) integration of facial geometry conditioning with ControlNets to maintain facial fidelity; (2) region-specific makeup transfer control to enable precise makeup application across facial regions such as skin, eyes and lips; (3) skin tone-based makeup transfer modulation that prevent skin tone alteration in cross-subject transfer scenarios; and (4) integration of a Levenberg-Marquardt Langevin sampler to speed up inference while maintaining generation quality. Our experiments on CPM-Real, Makeup Wild, and (herein newly collected, more diverse) MakeupSelfies datasets show that MakeupMirror improves relative facial recognition similarity by +60%, reduces relative skin tone difference by -50% over Stable-Makeup, with a latency of 0.7s, while achieving expert acceptance rate of 94% across core facial identity preservation criteria.

11.
arXiv (CS.CL) 2026-06-18

Simulating Hate Speech Cascades with Multi-LLM Agents: Empirical Grounding, Modeling Fidelity, and Intervention Strategies

Authors:

Faithful modeling of hateful content propagation on online platforms remains an open problem for moderation research. Classical cascade models that do not explicitly represent the profile, community, and content factors associated with hateful-content propagation may yield moderation strategies that behave less effectively when deployed in real-world scenarios. Multi-agent large language model (LLM) systems can, in principle, make each reshare decision depend on the user's profile, the surrounding community, and the post's content, but it remains unclear whether this added flexibility actually reproduces real hateful cascades more faithfully than classical baselines. We study three hateful Bluesky cascades and a size-matched benign control. In the empirical Bluesky data, we found that: 97.4–99.7\% of reposters take a hostile stance; toxicity-engagement homophily is higher on the diffusion tree than on the follower graph for hateful cascades; topology is star-like for the hateful cascades (most reposts come directly from the root) versus tree-like for the benign cascade (reposts propagate through multi-hop chains). In simulation, a multi-LLM-agent simulator reproduces the stance monoculture and the toxicity-delta direction. A structured ablation identifies agent heterogeneity as the leading fidelity factor, and amplifier targeting on dense networks yields 7.5–12.9\% reduction at 5.7\% benign collateral.

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

MapSatisfyBench: Benchmarking Satisfaction-Aware Map Agents through Behavior-Grounded Implicit Decision Factors

arXiv:2606.17453v1 Announce Type: new Abstract: Large language model agents are increasingly integrated into map services. Since map services are embedded in everyday-life scenarios rather than professional task settings, users often express their needs informally, resulting in underspecified queries with many unspoken needs, namely, implicit decision factors that are critical for user satisfaction. Although clarification is an effective way to mitigate this issue, it increases user burden in daily interaction, and a capable agent should first proactively recover such factors from available information sources. However, evaluating this ability is challenging. The first challenge is to determine which implicit decision factors are suitable for evaluation. A factor is evaluable only if it affects user acceptance and can be recovered from information available to the agent before it responds. Second, user satisfaction cannot be reliably represented by a single reference answer, requiring a benchmark that converts satisfaction-relevant factors into objective and quantifiable evaluation targets. To address these challenges, we propose a restore-identify-filter framework that reconstructs complete user needs from behavior-chain evidence, identifies implicit decision factors, and retains only those supported by pre-query evidence. Building on this methodology, we construct MapSatisfyBench from large-scale, real-world anonymized user data and annotate ground truth from five dimensions and enables full-chain evaluation of satisfaction-aware map agents. Experiments show that current agents generally perform well on explicit task completion, but remain limited in satisfying implicit decision factors and proactively acquiring the evidence needed for satisfaction-aware decisions. These findings establish MapSatisfyBench as a benchmark for shifting map-agent evaluation from task completion toward satisfaction-aware spatial decision making.

13.
medRxiv (Medicine) 2026-06-18

The Effectiveness of aromatherapy and its supportive Interventions on anxiety and pain among breast cancer patients: A systematic review and meta-analysis

Introduction: Breast cancer treatments are often associated with pain and anxiety, which can hinder physical functioning and overall quality of life, even after treatment. Complementary therapies, such as aromatherapy, can be used to alleviate pain and reduce anxiety in breast cancer patients. This project aimed to synthesize current global evidence on the effectiveness of aromatherapy. Method: This systematic review followed the PRISMA 2020 guidelines, with a comprehensive, systematic search conducted in PubMed, CINAHL, Cochrane Library, and SCOPUS for randomized controlled trials (RCTS) published from 2015 to 2025. Eligible studies included adult women breast cancer surgery patients who received aromatherapy during various periods of breast cancer. Where possible, data from the included studies were pooled using meta-analysis. GRADE approach was used to assess certainty of findings. Results: The search yielded 84 studies. Out of these, six were included in this review. On average, aromatherapy reduces pain and anxiety scores by 0.79 (standard mean difference (SMD)=-0.79, 95% CI -1.42, -0.16) and 0.53 (SMD=-0.53, 95 CI=-0.90, -0.16) units, respectively, compared to control condition [Low-quality of evidence]. The combination of aromatherapy with music reduces pain and anxiety by 1.26 (SMD= -1.26, 95 CI=-1.65, -0.87) and 1.08 (SMD = -1.08, 95 % CI: -1.45, -0.70) units respectively compared to standard care [Low-quality of evidence]. Conclusion: There is a potential role for the use of aromatherapy and music therapy, to alleviate anxiety and pain, especially for non-preoperative anxiety and pain. Further research is needed to inform the integration of aromatherapy into the management of anxiety and pain.

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

EPM-JEPA: Operator-Side Experience Modulation in JEPA-Family World Models

Authors:

arXiv:2606.12979v1 Announce Type: new Abstract: JEPA-family world models use a static predictor whose weights do not adapt when test-time dynamics diverge from training. We compare two mechanisms for incorporating accumulated experience into a JEPA predictor under distribution shift: operand-side injection, where a compressed experience representation is added as a residual to the predictor's hidden state (EI-JEPA), and operator-side modulation, where the same representation generates low-rank weight deltas via LoRA applied to the predictor's weights (EPM-JEPA). On a pre-registered comparison (Moving MNIST, gravity shift), EPM-JEPA (D_shift^{n=50} = 0.7848 +/- 0.0078, three seeds) differs from EI-JEPA (0.8238) by delta = 4.74% - Outcome C: a null result - by our stated criterion, a valid outcome. As a secondary, non-pre-registered observation, EPM-JEPA improves 1.90% over a no-memory baseline (0.8000), consistently across seeds, while EI-JEPA underperforms the baseline, indicating the benefit is specific to weight-level modulation. Our primary contribution is a mechanism analysis: the D_shift^{n=50} trajectory reflects three independent dynamical processes - buffer cycling, EMA target drift, and an intrinsic LoRA settling transient of +0.021 - rather than convergence to equilibrium. These findings motivate PEM-JEPA, a physics-grounded successor addressing this dynamical-peak limitation.

15.
Nature (Science) 2026-06-17

Navigating a crowded developing brain leaves neurons with broken DNA

As neurons migrate to their final destinations in the forming brain, their DNA gets damaged. The brain has evolved a fix, but there can be lasting consequences if repair fails. As neurons migrate to their final destinations in the forming brain, their DNA gets damaged. The brain has evolved a fix, but there can be lasting consequences if repair fails.

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

Formalizing Numerical Analysis: An Agent Pipeline and Quality Audit Beyond Kernel Acceptance

arXiv:2606.14000v1 Announce Type: new Abstract: Recent work has demonstrated that coding agents can formalize entire advanced mathematics textbooks in Lean 4, yet existing efforts concentrate on branches of mathematics already well-represented in mathlib and measure success solely through kernel acceptance. We address both limitations by applying a coding agent to formalize Numerical Methods for Ordinary Differential Equations, a textbook in numerical analysis that is largely absent from mathlib, stressing the agent's capacity to develop new theory from scratch. We further introduce a systematic, reproducible three-dimensional framework for evaluating the quality of agent-produced formalizations beyond compilation: semantic correctness, Mathlib reuse, and cross-file reuse via LLM-as-judge methods. Applying this framework to our own formalization and to the released outputs of RepoProver and M2F, we uncover recurring unfaithful formalization patterns, including incomplete multi-part statements, added weakening hypotheses, and parameter restrictions, that kernel acceptance entirely obscures. Our results suggest that compilation-based metrics substantially overstate formalization quality, and we provide a reproducible audit methodology to support more rigorous evaluation of future autoformalization systems.

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

Superconductor-"Metal" Transition of One-dimensional Interacting Bosons with Ohmic Quantum Dissipation

arXiv:2605.30746v2 Announce Type: replace-cross Abstract: The phase diagram of a system of interacting bosons (Cooper pairs) hoping on a one-dimensional (1D) lattice with onsite phase dissipation describing the Josephson tunneling to a nearby diffusive normal-metal electrode is studied. Starting from the system at commensurate lattice filling, it is shown by a combination of analytical techniques that the phase diagram contains two quantum phases: A dissipative Bose-Einstein condensate (D-BEC) or superconductor with long-range phase coherence, and a dissipative Mott insulator (D-Mott) or "metal" with exponentially decaying phase correlations in space and local imaginary-time correlations decaying as the local pairing correlations of the electrode. The D-Mott/metal phase can be described as a 1D array of dissipative boson puddles, weakly coupled by Josephson tunneling. The puddle size roughly corresponds to the length scale beyond which phase slips suppress phase coherence. The dissipative time-dependent Ginsburg-Landau theory phenomenologically used by Sachdev, Werner, and Troyer [Phys. Rev. Lett. {\bf 92} 237003 (2004)] for the superconductor-metal transition in quasi-1D wires is derived from this microscopic puddle picture. Thus, the criticality of the D-Mott/D-BEC transition is shown to belong to the Wilson-Fisher universality class with dynamical exponent $z\approx 2$. At small doping, the D-Mott/metal phase remains stable due to its finite compressibility, which is computed to leading order in a perturbation expansion of the dissipation strength and the inter-puddle Josephson coupling. At larger doping, using a mapping to a pseudospin chain combined with bosonization, the D-BEC/superconductor phase is the ground state for non-vanishing but arbitrarily small dissipation. Similarities and differences with deconfinement transition of an array 1D bosonic Mott insulators in anisotropic optical lattices are also discussed.

18.
medRxiv (Medicine) 2026-06-23

Innate immunity associates with protection from pneumococcal colonisation, but colonisation does not confer capsule-independent protection

Nasopharyngeal colonisation with Streptococcus pneumoniae is a prerequisite for transmission and disease and represents an important immunising event. While colonisation induces serotype-specific immunity, the mechanisms underlying heterologous protection remain unclear. We developed a controlled human infection model using pneumococcal serotype 15B and investigated colonisation dynamics, immunogenicity, and cross-protection against subsequent heterologous challenge with serotype 6B. Fifty-four healthy adults were intranasally inoculated with 15B at escalating doses. Colonisation rates peaked at 31.4% with 8 x 10 CFU per naris, lower than those historically observed with 6B and 3 strains. Density was also lower than previously observed with other strains. In vitro assays demonstrated that 15B adhered more readily to epithelial cells than 6B, but was less efficiently internalised, potentially reducing attack rates and colonisation density. Colonisation with 15B induced capsular polysaccharide-specific serum IgG, but baseline humoral immune measures did not predict protection from acquisition. Prior colonisation with 15B did not reduce acquisition of 6B upon re-challenge. Analysis of nasal microbiopsy samples revealed distinct innate activation signatures. Resistance to colonisation was associated with elevated baseline MIP-1 and MIP-1{beta} responses upon in vitro stimulation, whereas carriage was associated with enhanced chemokine and IL-6 responses. Local innate immune activation, rather than circulating antibody responses alone, may therefore contribute to colonisation control. We demonstrate that experimental colonisation with 15B does not confer heterologous protection against 6B and highlight the importance of mucosal innate immune conditioning in serotype-independent defence. Strategies enhancing nasal innate immune recruitment and activation may be required for broader protection against pneumococcal colonisation.

19.
bioRxiv (Bioinfo) 2026-06-16

Expanding gene regulatory networks from transcriptome data through graphical modeling with heterogeneous priors

Gene regulatory network inference is widely used to reconstruct large-scale networks and identify functional genes from transcriptome data. Meanwhile, in many biological fields, core regulatory genes have been extensively studied, leading to the establishment of small-scale gene regulatory networks, and novel genes connected to these networks remain to be identified. However, methods for expanding existing gene networks by identifying novel regulatory interactions, rather than reconstructing the entire network, are not well established. Here, we propose a method for gene network expansion that incorporates known regulatory relationships and evaluates each candidate gene individually to infer its regulatory connections to the existing network. Using simulated datasets from the DREAM4 benchmark and the PRECISE-1K experimental dataset, our method outperformed conventional methods by incorporating prior knowledge. In particular, it improved the ability to distinguish true regulatory interactions from indirect associations arising from strong correlations among genes in the existing network. The method also showed strong performance for interactions involving genes with high outdegree or centrality. Furthermore, it maintained stable performance as the size of the existing network increased and was robust to noise in prior information. These results demonstrate that our method provides an effective framework for expanding existing gene regulatory networks by leveraging prior knowledge.

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

Trust but Verify: Mitigating Medical Hallucinations via Post-Hoc Adversarial Auditing and Multi-Agent Feedback Loops

arXiv:2606.14149v1 Announce Type: new Abstract: Large Language Models (LLMs) are increasingly deployed in healthcare settings, yet their tendency to hallucinate poses risks when clinical decisions are involved. This study examine whether LLMs recommend recently banned or withdrawn pharmaceuticals when answering clinical questions and tests an agent-based method for reducing such errors. We developed a five-agent "Trust but Verify" system using a single LLM backbone. To measure regulatory knowledge obsolescence, we created an adversarial dataset of 103 clinical MCQs where historically correct answers now refer to banned substances. This scale ensures statistical significance across various therapeutic classes. We evaluated three open-access model families (GPT-OSS, Llama-3, Falcon-3) under vanilla and agentic conditions. Performance was measured via pointwise score, label accuracy, Hallucination Error Rate (HER), and Component Fidelity (CF) score. We also observed clinical safety regression in proprietary models. In default configurations, all models showed high hallucination rates, consistently selecting banned drugs that matched training data patterns. Our proposed agentic architecture reduced HER by approximately 53% across models. Pointwise scores shifted from -0.25 (unsafe recommendation) toward 0.0 (appropriate refusal). The safety audit intercepted dangerous outputs even when models' parametric knowledge favored the banned substance. The proposed multi-agent framework offers a model-agnostic method for enforcing regulatory compliance that prioritizes patient safety over fluent text generation. Our work demonstrates a practical approach for deploying autonomous AI systems in safety-critical healthcare settings. It shows how real-time regulatory data can be integrated into LLM pipelines to support clinical decision-making.

21.
bioRxiv (Bioinfo) 2026-06-11

DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics

De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides without relying on protein sequence databases. Recent advances in deep learning have substantially improved the performance of de novo sequencing methods, but the rapid emergence of new models has led to heterogeneous evaluation practices and limited comparability. To address this, we introduce DLDN-Bench, a benchmark framework including a set of benchmark datasets derived from human muscle biopsy mass spectrometry data retrieved from PRIDE and annotated through consensus across multiple widely used database search engines. Using these datasets, we systematically benchmark recent deep learning-based de novo sequencing tools alongside traditional approaches. Performance is assessed using established metrics, including precision and coverage relative to a pseudo-ground truth defined by cross-engine agreement. To demonstrate the utility of DLDN-Bench, we benchmark four recent deep learning models and make all results publicly available. This benchmark framework provides a standardized basis for comparing state-of-the-art methods and offers an extensible resource for evaluating future tools in de novo peptide sequencing.

22.
bioRxiv (Bioinfo) 2026-06-11

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

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

23.
arXiv (CS.AI) 2026-06-15

CoRe-MoE: Contrastive Reweighted Mixture of Experts for Multi-Terrain Humanoid Locomotion with Gait Adaptation

arXiv:2606.04718v3 Announce Type: replace-cross Abstract: Humans primarily rely on walking and running to traverse complex terrains. Similarly, humanoid robots should be able to smoothly transition between walking and running while maintaining natural and stable locomotion. However, unifying gait transition and multi-terrain adaptation within a single policy remains challenging due to gradient interference between tasks and the distribution shift caused by terrain variations. Although Mixture-of-Experts (MoE) architectures can mitigate multi-skill interference, direct joint training often fails to achieve clear expert specialization. To address these challenges, we propose CoRe-MoE, a two-stage reinforcement learning framework that decouples gait generation from terrain adaptation. In the first stage, a stable locomotion policy is learned to produce natural walking and running behaviors with smooth transitions. In the second stage, a terrain-aware MoE branch is introduced, and the gating network is trained with a contrastive objective to learn structured terrain representations and promote expert specialization. The final action is obtained through weighted fusion of the base gait policy and the terrain-aware branch, enabling the policy to preserve stable locomotion while adapting to complex terrains. Extensive simulation results demonstrate that the proposed method outperforms baseline approaches in terms of success rate, locomotion stability, and multi-terrain adaptability. Furthermore, zero-shot deployment on a Unitree G1 humanoid robot validates the effectiveness of our framework, achieving robust walking and running across stairs, slopes, steps, obstacles, and unstructured outdoor terrains while maintaining accurate foothold control and dynamic stability.

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

Equity with Efficiency: An Empirical Study of Tokenizers for Multilingual Large Language Models

Multilingual large language models (LLMs) depend on subword tokenization to bridge discrete text and continuous neural representation. State-of-the-art multilingual LLMs often use Byte-level Byte-Pair Encoding (BPE) tokenizers that structurally favor high-resource languages and Latin scripts. For speakers of underrepresented languages, particularly those across Southeast Asia, this bias inflates inference costs and widens cross-lingual capability gaps. We present the first systematic comparison of equitable tokenizers on a unified benchmark spanning 11 Southeast Asian languages. Beyond tokenizer-level analysis of compression efficiency and cross-lingual equity, we assess downstream task performance through controlled 1.5B-parameter language model training using the same training data. Our results show that Parity-aware BPE lies on the Pareto frontier of the efficiency-equity trade-off, achieving strong compression parity at competitive cost. Morphology-Driven Byte Encoding delivers the best semantic reasoning performance through morphologically richer representations, albeit at a higher computational expense. Byte Latent Transformer underperforms on downstream tasks, possibly because its architectural assumptions misalign with the constraints of limited low-resource training data. Together, our findings demonstrate that cross-lingual fairness and tokenization efficiency are not fundamentally at odds, and offer practical guidance for designing equitable multilingual models.

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

From "Aha Moments" to Controllable Thinking: Toward Meta-Cognitive Reasoning in Large Reasoning Models via Decoupled Reasoning and Control

arXiv:2508.04460v2 Announce Type: replace Abstract: Large Reasoning Models (LRMs) can exhibit step-by-step reasoning, reflection, and backtracking, but these behaviors are often unregulated, leading to overthinking. As a result, LRMs continue generating redundant reasoning even after reaching high-confidence conclusions. This increases inference cost and latency, limiting practical deployment. The root cause is the absence of an intrinsic mechanism to monitor the reasoning state and decide when to continue, backtrack, or stop. We propose MERA, a meta-cognitive reasoning framework that decouples reasoning from control to enable independent optimization of control strategies. MERA constructs high-quality reasoning-control supervision data via a takeover-based pipeline, and transforms long-horizon traces into structured reasoning-control alternating sequences for training. The model is trained with supervised fine-tuning to internalize the structured separation, and further optimized with Control-Segment Policy Optimization (CSPO), which combines segment-wise GRPO with control masking to focus learning on control segments. Experiments across reasoning benchmarks show that MERA improves both efficiency and accuracy.