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02.
bioRxiv (Bioinfo) 2026-06-16

Phylogenetic tree inference using generative models

作者:
Dotan↗Schers↗Wygoda↗Pupko↗Belinkov↗

Accurate inference of phylogenetic trees is fundamental to evolutionary biology, yet existing methods rely on complex pipelines involving multiple sequence alignment, explicit evolutionary models, and computationally intensive tree search procedures. Here, we present BetaInfer, a generative framework that reformulates phylogenetic tree inference as a sequence transduction problem. BetaInfer leverages hybrid transformer-based architectures to directly map sets of unaligned sequences to phylogenetic trees represented in Newick format. Trained on large-scale simulated evolutionary data with known ground truth, BetaInfer learns to capture complex evolutionary signals directly from sequence data. Ensemble-based generation of multiple candidate trees further improves robustness, reducing reconstruction error by over 30% relative to single predictions. Across extensive evaluations on both simulated and empirical datasets, BetaInfer achieves competitive performance relative to state-of-the-art phylogenetic pipelines, matching, and in some cases exceeding, the accuracy of established likelihood-based and distance-based methods under a wide range of conditions. Interpretability analyses reveal that BetaInfer leverages internal pairwise-distance computations to synthesize evolutionary relationships into an integrated, global representation that supports direct tree generation. Together, these results demonstrate that generative models can serve as a viable and scalable alternative to standard phylogenetic pipelines.

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03.
arXiv (CS.LG) 2026-06-24

A Differentially Private Weighted Empirical Risk Minimization Procedure and its Application to Outcome Weighted Learning

作者:
Spencer Giddens↗Yiwang Zhou↗Kevin R. Krull↗Tara M. Brinkman↗Peter X. K. Song↗Fang Liu↗

arXiv:2307.13127v3 Announce Type: replace-cross Abstract: Data used to train predictive models via empirical risk minimization (ERM) often contain sensitive personal information. While differential privacy (DP) provides mathematically provable bounds to protect such data, previous work has focused almost exclusively on unweighted ERM. We consider weighted ERM (wERM) – an important generalization where individual contributions to the objective function vary. We propose the first DP algorithm for general wERM with formal privacy guarantees and derive both its empirical and population excess risk bounds. Crucially, this general wERM framework provides a pathway for deriving privacy-preserving learning methods for individualized treatment rules, including the popular outcome-weighted learning (OWL) approach. We evaluate DP-wERM applied to OWL in simulated and real data experiments. Our empirical results demonstrate that training OWL models via wERM provides strong DP guarantees while maintaining robust performance, proving the method is practical for sensitive, real-world data.

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

Shift-and-Sum Quantization for Visual Autoregressive Models

作者:
Jaehyeon Moon↗Bumsub Ham↗

Post-training quantization (PTQ) enables efficient deployment of deep networks using a small set of data. Its application to visual autoregressive models (VAR), however, remains relatively unexplored. We identify two key challenges for applying PTQ to VAR: (i) large reconstruction errors in attention-value products, especially at coarse scales where high attention scores occur more frequently; and (ii) a discrepancy between the sampling frequencies of codebook entries and their predicted probabilities due to limited calibration data. To address these challenges, we propose a PTQ framework tailored for VAR. First, we introduce a shift-and-sum quantization method that reduces reconstruction errors by aggregating quantized results from symmetrically shifted duplicates of value tokens. Second, we present a resampling strategy for calibration data that aligns sampling frequencies of codebook entries with their predicted probabilities. Experiments on class-conditional image generation, inpainting, outpainting, and class-conditional editing show consistent improvements across VAR architectures, establishing a new state of the art in PTQ for VAR.

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

Beyond Rubrics: Exploration-Guided Evaluation Skills for Reward Modeling

作者:
Xing Yue↗Linjuan Wu↗Daoxin Zhang↗Yongliang Shen↗Weiming Lu↗

Open-ended reward modeling requires judges that can follow subtle, domain-specific preferences when verifiable answers are unavailable. Existing rubric-based methods often address this by generating criteria online for each query, but the extra generation step can add inference overhead and produce rigid or misaligned guidance. We introduce Eval-Skill, an exploration-guided method that synthesizes reusable evaluation skills for reward modeling and reframes reward guidance as context evolution rather than parameter training or per-query rubric generation. Using only 100 cases per domain for skill evolution, Eval-Skill synthesizes reusable domain-level evaluation skills through two progressive stages, workflow generation followed by principle generation, with exploration and selection interleaved across both stages. Once generated, a skill is directly injected into the judge context. Across multiple RM benchmarks, Eval-Skill consistently improves diverse judge backbones; on RewardBench 2, it yields significant gains over vanilla judging for each main backbone (+13.44% for Qwen3-8B, and 18.51% for DeepSeek-V4-Flash). Further analyses of evolution-time scaling, generalizability, and transferability show that compact evaluation skills offer an efficient new paradigm for LLM-based evaluation. Code is available at https://github.com/xing-stellus-yue/Eval-Skill.

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

MCR-VQGAN: A Scalable and Cost-Effective Tau PET Synthesis Approach for Alzheimer's Disease Imaging

作者:
Jin Young Kim↗Jeremy Hudson↗Jeongchul Kim↗Qing Lyu↗Christopher T. Whitlow↗

Tau positron emission tomography (PET) is a critical diagnostic modality for Alzheimer's disease (AD), but its widespread clinical adoption is hindered by radiation exposure, limited availability, high clinical workload, and substantial financial costs. To address these limitations, we propose the Multi-scale CBAM Residual Vector Quantized Generative Adversarial Network (MCR-VQGAN) to synthesize high-fidelity tau PET images from structural T1-weighted MRI. MCR-VQGAN advances the standard VQGAN architecture through three enhancements: multi-scale convolutions, ResNet blocks, and Convolutional Block Attention Modules (CBAM), which collectively improve the capture of local and global features. Using 222 paired T1-weighted MRI and tau PET scans from the ADNI database, we trained and compared MCR-VQGAN against cGAN, WGAN-GP, CycleGAN, and baseline VQGAN. MCR-VQGAN achieved superior image synthesis performance across all metrics (MSE = 0.0056 +/- 0.0061, PSNR = 30.65 +/- 4.47 dB, SSIM = 0.9263 +/- 0.0469). A CNN-based AD classifier trained on real tau PET achieved comparable accuracy on real (63.64%) and synthetic (65.91%) images, indicating that diagnostically relevant features are preserved. Regional SUVR-equivalent analysis across Braak-defined ROIs further indicated strong agreement between real and synthetic tau PET (Pearson r = 0.78-0.88; ICC = 0.71-0.84), with the strongest agreement in Braak V/VI (ICC = 0.838). Together, these results suggest that MCR-VQGAN offers a promising and scalable surrogate for conventional tau PET imaging, potentially improving the accessibility of tau biomarkers for AD research and clinical workflows.

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

Toward 360-Degree Indoor Panorama Editing via Tuning-Free Diffusion Model with Refocusing Cross-Attention

作者:
Dinh-Khoi Vo↗Nhut-Thanh Le-Hinh↗Viet-Tham Huynh↗Tam V. Nguyen↗Minh-Triet Tran↗Trung-Nghia Le↗

Zero-shot text-guided diffusion has significantly advanced image editing; however, its practical usability remains constrained by three persistent challenges: prompt brittleness that requires meticulous prompt engineering, spillover edits that unintentionally affect non-target regions, and failures on small or cluttered objects caused by limited fine-grained supervision in training data. We propose FocusDiff (Target-Aware Refocusing for Tuning-Free Diffusion Editing), a tuning-free framework for precise and region-specific image manipulation based on refocusing cross-attention. Given a target region obtained through automated segmentation or manual selection, FocusDiff applies selective blurring to non-edit areas to guide attention toward the masked region while accurately transferring the object's identity, structure, and appearance to the edited output. Integrated context-preserving modules further ensure background fidelity and global coherence, enabling accurate edits from simple text prompts in a single pass. We also extend FocusDiff to 360-degree indoor panorama editing and demonstrate its effectiveness within virtual reality environments. Extensive experiments on our localized editing benchmark LIMB, comprising 30 multi-object images and 100 annotated examples including challenging small-object cases, show that FocusDiff outperforms existing zero-shot editors in text-image alignment and background preservation, achieving superior precision, photorealism, and usability. The project page is available at https://vdkhoi20.github.io/FocusDiff.

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

SimSiam Naming Game: A Unified Approach for Emergent Communication and Representation Learning

作者:
Nguyen Le Hoang↗Tadahiro Taniguchi↗Tianwei Fang↗Akira Taniguchi↗Masatoshi Nagano↗

Emergent Communication (EmCom) investigates how agents develop symbolic communication through interaction without predefined language. Recent frameworks, such as the Metropolis–Hastings Naming Game (MHNG), formulate EmCom as the learning of shared external representations negotiated through interaction under joint attention, without explicit success or reward feedback. However, MHNG relies on sampling-based updates that suffer from high rejection rates in high-dimensional perceptual spaces, making the learning process sample-inefficient for complex visual datasets. In this work, we propose the SimSiam Naming Game (SSNG), a feedback-free EmCom framework that replaces sampling-based updates with a symmetric, self-supervised representation alignment objective between autonomous agents. Building on a variational inference–based probabilistic interpretation of self-supervised learning, SSNG formulates symbol emergence as an alignment process between agents' latent representations mediated by message exchange. To enable end-to-end gradient-based optimization, discrete symbolic messages are learned via a Gumbel–Softmax relaxation, preserving the discrete nature of communication while maintaining differentiability. Experiments on CIFAR-10 and ImageNet-100 show that the emergent messages learned by SSNG achieve substantially higher linear-probe classification accuracy than those produced by referential games, reconstruction games, and MHNG. These results indicate that self-supervised representation alignment provides an effective mechanism for feedback-free EmCom in multi-agent systems.

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

RoboPIN: Grounded Embodied Reasoning via Pinned Chain-of-Thought

作者:
Yaoting Huang↗Yifu Yuan↗Linqi Han↗Chengwen Li↗Shuoheng Zhang↗Xianze Yao↗Hongyao Tang↗Yan Zheng↗Jianye Hao↗

arXiv:2606.15753v1 Announce Type: new Abstract: Embodied reasoning requires models to perceive task-relevant objects and spaces in physical environments and maintain consistent visual grounding throughout multi-step reasoning. However, current vision-language models rely on text-only or coordinate-augmented chain-of-thought, where entity references remain implicit and ambiguous. This may cause the reasoning process to decouple from visual evidence, entity references to drift across steps, and a causal disconnection between the reasoning trajectory and the final answer, with these problems further amplified in multi-view scenarios due to cross-view appearance changes. To address these issues, we propose Pinned Chain-of-Thought (\pincot{}), a structured reasoning paradigm that pins every reasoning step to visual evidence. \pincot{} introduces the concept of \reasoninganchor{}, which binds each task-relevant entity to a structured visual anchor with entity name, unique identity, view index, and spatial grounding, enabling consistent entity tracking across reasoning steps and views. We build a fully automated data generation pipeline to construct \dataset{}, a high-quality \pincot{}-formatted reasoning dataset. We then train \method{} through three-stage post-training that progressively injects embodied knowledge, structured reasoning ability, and process-supervised alignment, with rewards that directly constrain both anchor localization and identity consistency during reasoning. On 14 benchmarks covering embodied spatial reasoning, multi-view reasoning, and pointing, \method{} with only 4B parameters consistently outperforms 7B level open-source embodied models, achieving a 12\% average improvement over the strongest 7B baseline, Mimo-Embodied. Further analysis shows that \pincot{} improves grounding accuracy and cross-step identity consistency, validating the effectiveness of process supervision.

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

CTS-MoE: Implicit Terrain Adaptation via Mixture-of-Experts for Perceptive Locomotion

作者:
Francisco Affonso↗Matheus P. Angarola↗Ana Luiza Mineiro↗Aditya Potnis↗Marcelo Becker↗Girish Chowdhary↗

arXiv:2606.19633v1 Announce Type: cross Abstract: Perceptive legged locomotion over discontinuous terrain (e.g., stairs, gaps, and obstacles) requires adaptive behavior, as a single conservative gait cannot produce the anticipatory maneuvers needed for abrupt topology changes. Cast as multi-task reinforcement learning, this problem introduces a tension between sharing and separation. Tasks use a common locomotion base but have conflicting rewards, so a policy must share behavior while avoiding value interference. Prior work addresses only one side, with monolithic policies sacrificing specialization and hierarchical sub-policies sacrificing generalization across transitions and unseen terrain. We propose CTS-MoE, which combines a dense mixture-of-experts actor with perception-based gating to compose shared behaviors and a multi-critic with task-specific value heads to prevent interference. The model is trained end-to-end in a single-stage concurrent teacher-student setup that handles partial observability and avoids sequential distillation, with task labels used only during training. At deployment, routing depends solely on perception, allowing terrain adaptation without a high-level selector or terrain classifier. Experiments on a Unitree Go1 in simulation and on hardware across seen and unseen terrains show task-aware specialization, with lower tracking error and higher success rates than monolithic baselines. Project Website: https://cts-moe.github.io/ .

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11.
arXiv (CS.CL) 2026-06-17

LLMs Infer Cultural Context but Fail to Apply It When Responding

作者:
Yisong Miao↗Jian Zhu↗Vered Shwartz↗

Recent work has shown that LLMs overrepresent dominant cultures, particularly Western ones, while marginalizing others. We investigate whether this affects models' ability to generate culturally adapted responses by evaluating their use of local measurement units based on the user's perceived cultural background. We introduce Cultural and Pragmatic Response Inference (CAPRI), a dataset of conversations with varying levels of cultural cues. Experiments with state-of-the-art LLMs show that models can infer cultural background and recall relevant conventions, but often fail to utilize the information to adapt their answers to the relevant cultural conventions, unless explicitly prompted to perform the tasks sequentially. We further evaluate adaptation to the interpretation of time and quantity expressions, two subjective language grounding dimensions that are affected by culture. We find that models increasingly adapt their answers as cultural cues accumulate, but their priors are not culture-neutral, sometimes aligning with the model's country of origin. Overall, CAPRI provides a resource for future research aimed at narrowing the gap between cultural knowledge and culturally adaptive language generation.

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

LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks

作者:
Zhongyuan Wang↗Pratyusha Vemuri↗

Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig

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13.
arXiv (CS.CL) 2026-06-24

To Compare, or Not to Compare: On Methodological Practices in Evaluating Social Bias

作者:
Federico Marcuzzi↗Xuefei Ning↗Roy Schwartz↗Iryna Gurevych↗

As Large Language Models are increasingly deployed in critical applications, robustly evaluating their social biases is paramount. However, the current literature suffers from widespread methodological fragmentation, which yields contradictory conclusions. This stems largely from ignoring the structural framing of benchmark-level evaluations. To resolve this, we introduce a unified and controllable framework that standardizes heterogeneous benchmarks to systematically contrast isolated demographic assessments with forced-choice comparative settings. Crucially, this allows us to disentangle the confounding effects of Chain-of-Thought reasoning, neutral fallback options, and other structural artifacts in social bias evaluations. Our evaluation across multiple model families reveals a massive, systematic paradigm gap: while isolated assessments limit prejudice activation, comparative settings act as aggressive catalysts for latent discrimination, a shift primarily driven by underspecified contexts. Alarmingly, CoT reasoning exacerbates social biases under comparative settings, and this systemic bias persists as a deterministic prejudice even when models are provided neutral fallback options or claim to answer randomly. Finally, we demonstrate that this comparative prejudice is a generalized phenomenon that scales positively with model size. Ultimately, we offer a crucial methodological guideline: while researchers must leverage comparative settings to robustly audit hidden biases, practitioners cannot safely rely on comparative deployments in ambiguous real-world tasks.

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

TimeVista: Exploring and Exploiting Vision-Language Models as Judges for Time Series Forecasting

作者:
Zhi Chen↗Yuxuan Wang↗Jialong Wu↗Yong Liu↗Haoran Zhang↗Xingjian Su↗Jianmin Wang↗Mingsheng Long↗

arXiv:2606.16173v1 Announce Type: new Abstract: High-quality time series forecasting is pivotal for real-world decision-making. However, traditional point-wise metrics often fail to reveal complex temporal patterns and align poorly with human intuitive preferences. While the ''LLM-as-a-Judge'' paradigm has revolutionized text evaluation by providing flexible, human-aligned judgment, its application to time series remains largely unexplored. In this paper, we leverage Vision-Language Models (VLMs) as judges for time series forecasting, harnessing their ability to comprehend time series plots grounded in textual information. Specifically, we propose a novel framework integrating micro- and macro-level judgments informed by contextual information to evaluate time series forecasting. To this end, we introduce TimeVista, a comprehensive VLM-as-a-Judge benchmark comprising 5563 time series samples paired with detailed evaluation rubrics. Extensive meta-evaluations demonstrate that VLMs are highly reliable judges, achieving significantly higher consistency with human preferences than conventional metrics. Building upon our benchmark, we comprehensively assess recent Time Series Foundation Models (TSFMs) under the VLM-as-a-Judge paradigm. Our results demonstrate that VLMs serve as robust and interpretable judges, providing a comprehensive, human-aligned standard for evaluating time series models.

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

Can Deep Neural Networks Improve Compression of Very Large Scientific Data?

作者:
Muhannad Alhumaidi↗Guozhong Li↗Spiros Skiadopoulos↗Panos Kalnis↗

arXiv:2606.14353v1 Announce Type: new Abstract: Error-bounded lossy compression is a fundamental technique for managing the rapidly growing volumes of scientific data produced by modern simulations and observational instruments. Most state-of-the-art-compressors follow a prediction-residual paradigm, where compression effectiveness depends on the quality of the predictor: more accurate predictions generate smaller residuals that are easier to compress. This observation raises a question: can modern machine learning models serve as superior predictors for scientific data compression? Answering this question directly is challenging because developing compression-specific ML predictors requires substantial resources. Instead, we leverage the climate domain where highly accurate pretrained weather forecasting foundation models already exist, making them an ideal testbed. We present a framework that integrates spatial and temporal deep learning models into a conventional error-bounded compression pipeline. The framework supports auto-regressive forecasting models and avoids error accumulation. Using ERA5 climate data as a representative large-scale scientific dataset, we evaluate three distinct ML predictors: a VAEformer-based codec (CRA5), a graph neural network forecaster (GraphCast), and a vision-transformer forecaster (Aurora), against the state-of-the-art compressor SZ3.1 under identical quantization and entropy-coding backends. Our evaluation over approximately 1.7 TB of data reveals a surprising result: although ML predictors generate more accurate predictions and can improve reconstruction quality by up to 91% while achieving up to 9.6x higher compression ratios for highly predictable variables, they do not improve overall dataset-level compression ratio. We show that prediction accuracy alone is insufficient: the spatial structure of the resulting residuals plays a decisive role in entropy coding efficiency.

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

QuantKAN: A Unified Quantization Framework for Kolmogorov Arnold Networks

作者:
Kazi Ahmed Asif Fuad↗Lizhong Chen↗

arXiv:2511.18689v3 Announce Type: replace Abstract: Kolmogorov–Arnold Networks (KANs) replace linear weights with spline-based functions, offering strong expressivity but posing challenges for low-precision deployment due to heterogeneous parameter distributions. We introduce QuantKAN, the first unified framework for quantization-aware training (QAT) and post-training quantization (PTQ) of KANs. The framework employs branch-aware quantizers for base and spline parameters and extends modern QAT and PTQ methods to spline-based layers across EfficientKAN, FastKAN, PyKAN, and KAGN. Experiments on MNIST, CIFAR-10/100, TinyImageNet, and ImageNet provide the first unified QAT/PTQ KAN benchmarks and show that DSQ is the most robust QAT method at aggressive low-bit settings, while GPTQ is the strongest PTQ method at moderate precision. Sensitivity analyses reveal architecture-specific failure modes: spline/basis parameters dominate in FastKAN, while base or scaling parameters dominate in EfficientKAN, GRAM, and PyKAN. Vivado HLS estimates on a Xilinx UltraScale+ device further suggest up to 3.32$\times$ throughput and 7.7$\times$ lower estimated dynamic energy per inference under W4A4, exposing a residual basis-evaluation tax that motivates basis-aware microarchitecture. QuantKAN is available at https://github.com/OSU-STARLAB/QuantKAN/.

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17.
arXiv (CS.AI) 2026-06-25

Verifiable Manifest Signing and Transparency Enforcement for Secure MCP-Based LLM Pipelines

作者:
Saeid Jamshidi↗Kawser Wazed Nafi↗Arghavan Moradi Dakhel↗Foutse Khomh↗Mohammad Hamdaqa↗

arXiv:2601.23132v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) are increasingly deployed in tool-driven environments such as healthcare analytics, financial systems, retrieval-augmented generation (RAG), and multi-agent workflows. Although the Model Context Protocol (MCP) standardizes how LLM applications expose and invoke external tools, its baseline model does not require tool-use manifests to be cryptographically authenticated, freshness-checked, policy-bound, or independently auditable before execution. As a result, MCP pipelines may remain vulnerable to manifest tampering, unauthorized tool invocation, replay of stale requests, and weak accountability. This paper presents a manifest-level enforcement layer for MCP-based LLM pipelines. It treats each MCP tool-use manifest as a first-class security object whose canonical form must be policy-validated, freshness-checked, digitally signed, verified before execution, and linked to tamper-evident audit evidence. The framework binds tool invocation to verifiable manifest integrity and fail-closed authorization, separates user-visible request parameters from execution metadata, rejects non-compliant or stale manifests before execution, and records accepted invocations in a Merkle-based transparency log. Evaluation across GPT-5.3, LLaMA-3.5, and DeepSeek-V3 using up to 50,000 manifest instances shows near-linear scalability (R^2 = 0.998), bounded verification latency (

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

DeXposure-Claw: An Agentic System for DeFi Risk Supervision

作者:
Aijie Shu↗Bowei Chen↗Wenbin Wu↗Cathy Yi-Hsuan Chen↗Fengxiang He↗

Decentralized finance exposes supervisors to fast-moving, networked credit risks. General-purpose LLM agents fit this setting poorly: they over-read weak evidence and recommend high-stakes interventions, while existing evaluations offer no regulator-aligned way to measure the resulting false alarms. We introduce DeXposure-Claw, a forecast-grounded agentic supervision system that routes LLM decisions through structured evidence: (1) DeXposure-FM, a graph time-series foundation model, forecasts future exposure networks; (2) deterministic monitors and stress scenarios then turn those forecasts into typed alerts, attribution signals, and scenario evidence; and (3) data-health and confidence gates constrain escalation before DeXposure-Claw emits auditable supervisory tickets with rationales. We further develop DeXposure-Bench, a six-axis evaluation harness, whose decision axis scores tickets against a regulator-aligned absolute-loss ground truth and an explicit false-intervention rate. Experiments on five years of weekly real data fully support our system. Code is at https://github.com/EVIEHub/DeXposure-Claw.

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19.
medRxiv (Medicine) 2026-06-24

Structural ethnic inequities in maternal mortality between Indigenous and non-Indigenous women in Paraguay, 2014-2023: a national analysis of territorial, institutional, and preventable factors.

作者:
Duarte-Zoilan↗Tullo Gomez↗J. E↗Nunez↗Ramos↗

Background: Indigenous women in Paraguay continue to experience disproportionately high maternal mortality despite national efforts to improve maternal health. Evidence on the structural factors underlying these disparities remains limited. Objectives: To analyze structural ethnic inequities in maternal mortality between Indigenous and non-Indigenous women in Paraguay, focusing on territorial patterns, institutional access, and potentially preventable causes of death. Design: National population-based study using maternal mortality records registered in Paraguay between 2014 and 2023. Maternal mortality ratios (MMRs), incidence rate ratios (IRRs), and absolute differences were estimated according to Indigenous status. Logistic regression models were used to assess associations with deaths occurring outside healthcare institutions and specific preventable causes of death. Results: A total of 907 maternal deaths were identified, including 112 among Indigenous women (12.3%). Indigenous women were overrepresented by a factor of 4.8 relative to their population share. Maternal mortality remained consistently higher among Indigenous women throughout the study period, with mortality ratios ranging from 317.7 to 773.6 per 100,000 live births, compared with 58.7 to 145.1 among non-Indigenous women. Absolute inequalities remained persistently high over time. Overall, 24.3% of maternal deaths occurred outside healthcare institutions, with a substantially higher proportion among Indigenous women (44.6% versus 21.5%). After adjustment for age and educational level, Indigenous women had more than three times greater odds of dying outside healthcare institutions (aOR = 3.41; 95% CI: 2.20-5.29). Potentially preventable causes accounted for 42.4% of maternal deaths. Obstetric hemorrhage was strongly associated with Indigenous status (aOR = 3.83; 95% CI: 2.31-6.37). Conclusion: Indigenous women in Paraguay experience a disproportionate burden of maternal mortality characterized by persistent ethnic disparities, higher occurrence of deaths outside healthcare institutions, and a substantial burden of preventable causes of death. These findings suggest the presence of enduring territorial, institutional, and healthcare access barriers that contribute to structural ethnic inequities in maternal health.

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20.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

作者:
Katopodi↗X.-L↗Pryszcz↗L. P↗Llovera↗Ollivier↗Cozzuto↗Ponomarenko↗Novoa↗E. M↗

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.

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21.
arXiv (math.PR) 2026-06-11

Micro-macro population dynamics models of benthic algae with long-memory decay and generic growth

作者:
Hidekazu Yoshioka↗Kunihiko Hamagami↗

arXiv:2505.04289v4 Announce Type: replace Abstract: Benthic algae as a primary producer in riverine ecosystems develop biofilms on the riverbed. Their population dynamics involve growth and decay processes, the former owing to the balance between biological proliferation and mortality, while the latter to mechanical abrasion because of the transport of sediment particles. Contrary to the assumptions of previous studies, the decay has experimentally been found to exhibit long-memory behavior, where the population decreases at an algebraic rate. However, the origin and mathematical theory of this phenomenon remain unresolved. The objective of this study is to introduce a novel mathematical model employing spin processes to describe microscopic biofilm dynamics. A spin process is a continuous-time jump process transitioning between states 0 and 1, and the continuum limit of these processes captures the long-memory decay and generates generic growth. The proposed framework leverages heterogeneous spin rates, achieved by appropriately superposing spin processes with distinct rates, to reproduce the long-memory decay. Computational simulations demonstrate the behavior of the model, particularly emphasizing rate-induced tipping phenomena. This mathematical model provides a computationally tractable interpretation of benthic algae dynamics and their long-term prediction, relevant to river-engineering applications.

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22.
arXiv (CS.CL) 2026-06-19

Large Language Models Hack Rewards, and Society

作者:
Wei Liu↗Xinyi Mou↗Hanqi Yan↗Zhongyu Wei↗Yulan He↗

Reinforcement learning (RL) has become a dominant post-training paradigm, enabling large language models (LLMs) to learn from rewards. We observe that societal regulations are structurally similar to reward functions. They define measurable outcomes, thresholds, and exceptions, while often leaving institutional intent only partially specified. We hypothesise that the RL training process may exploit these gaps and therefore ask whether models' well-known tendency to hack reward functions during RL can scale into a more consequential failure mode named societal hacking: discovering loopholes in the rules society runs on. To study this phenomenon, we introduce SocioHack, a sandbox of 72 societal environments, and find that within these environments, reward hacking naturally emerges and leads to regulatory loophole discovery. Models learn to hack the social rules and generate strategies that remain technically compliant while defeating regulatory intent, and current LLM safeguards provide only limited mitigation. Therefore, collecting in-the-wild feedback for model training requires greater caution, and we need a next-generation post-training paradigm for safely iterating LLMs in real society.=

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

Transformers Learn the Mestre-Nagao Heuristic

作者:
Pranav Venkata Konda↗

arXiv:2606.15036v1 Announce Type: new Abstract: We train a two-layer transformer encoder to classify rational elliptic curves $E/\mathbb{Q}$ of conductor $\leq 10000$ as either rank 0 or rank 1 from the first 128 normalized Frobenius traces. We achieve >99% accuracy on both classes, and accuracy is essentially unchanged on test curves with no isogeny or quadratic-twist relative in the training set. We then apply techniques from mechanistic interpretability such as attention analysis, linear probing, activation patching, logit attribution, and neuron-level circuit analysis to reverse-engineer the algorithm the (centroid in function space) model learned. We find that a sparse circuit of 20 out of 512 layer-1 MLP neurons is sufficient for rank prediction under a linear probe with an AUROC of 0.992 at plateau, implementing a push-pull detector architecture of rank-0 and rank-1 detectors with a one-sided readout. However, we notice that the model has sub-optimal readout problems indicating a mismatch in rank-order between the readout pathway and the discriminative circuit. Critically, the learned input weights of the top discriminating neuron match the Mestre-Nagao sum heuristic weights $\log(p)/(p\cdot \log{B})$ with a Spearman coefficient $r = 0.997$ and Pearson coefficient $r = 0.952$: the model has learnt a result from analytic number theory from the Frobenius trace data alone. We additionally find that all 50 independently trained models concentrate CLS attention on prime positions at 2-50$\times$ the rate of composite positions. The CLS embedding encodes $\log{L(E,1)}$ with $R^2 = 0.962\pm 0.011$ across the 50 models (after controlling for the conductor). Activation patching analysis reveals that attention weights are dissociated from causal information flow. Additionally, the 50 solutions from training are near-identical in function space (with pairwise agreement $>$98.8%) despite large weight space barriers.

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

From Awareness to Adherence: Bridging the Context Gap in Spoken Dialogue Systems via Context-Aware Decoding

作者:
Che Hyun Lee↗Heeseung Kim↗Sungroh Yoon↗

Despite the success of end-to-end (E2E) spoken dialogue systems, maintaining strict context adherence in multi-round conversations remains a challenge. While prior works attribute these failures to models forgetting dialogue history, we highlight an equally critical but overlooked bottleneck: a gap between latent context awareness and active adherence. Although models internally recognize relevant past utterances, strong parametric priors often overshadow these signals during decoding. To bridge this gap, we propose an audio-adapted Context-Aware Decoding (CAD) approach. By leveraging internal attention mechanisms to isolate key historical rounds, our approach contrasts output distributions with and without this key context during inference, directly amplifying multimodal contextual signals. Evaluations on the Audio MultiChallenge benchmark demonstrate significant improvements in Semantic Memory and Self Coherence subtasks, successfully enforcing strict, context-faithful adherence.

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25.
arXiv (CS.CV) 2026-06-15

Trimodal Glioma Representation Alignment via Volumetric Contrastive Learning

作者:
Denise Marini↗Eleonora Grassucci↗Danilo Comminiello↗

Glioma grading and survival prediction require the integration of heterogeneous information collected at different spatial and biological scales. Histopathology describes tissue morphology, mRNA expression captures molecular activity, and magnetic resonance imaging provides a non-invasive view of tumor extent and radiological heterogeneity. Existing glioma prognosis models often combine only two of these sources, while their alignment objectives remain mostly pairwise. This paper introduces GLORIA, a novel trimodal framework for GLioma Omics - Radiology - hIstopathology Alignment. GLORIA processes whole-slide image regions, gene-expression profiles, and 3D MRI volumes through modality-specific encoders, projects them into a shared latent space, and aligns them with a Gramian contrastive loss that measures the volume spanned by the three modality embeddings. The aligned representations are fused through a cross-modal gating module and optimized jointly for three-class glioma grading and overall survival prediction. We evaluate GLORIA on a matched TCGA-GBM/LGG and BraTS21 cohort, comprising 132 patients with all three modalities. On the shared trimodal test set, GLORIA improves over the bimodal WSI-mRNA baseline in all the metrics considered.

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