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01.
Nature Medicine 2026-06-11

Microglia at a key inflection point in Alzheimer’s disease

作者: 未知作者

We analyzed brains from octogenarians and cognitively resilient centenarians to understand why some individuals with substantial Alzheimer’s disease pathology develop dementia whereas others remain cognitively intact. Spatial transcriptomics revealed gene expression changes in discrete tissue domains surrounding amyloid plaques and tau pathology that distinguish early, clinically silent, disease from later stages associated with cognitive decline.

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02.
medRxiv (Medicine) 2026-06-15

Poly-Social Risk for Hypertension Among Black and Latina Women

作者:
Belak↗James↗Auguste↗Rana↗Eweka↗De Moor↗Sarma↗Ensing↗Economy↗K. E↗Powe↗C. E↗…

Background: Hypertension is a leading modifiable cardiovascular risk factor prominently influenced by health-related social needs (HRSN). Whether detailed information on HRSN can improve identification of hypertension among minoritized women is unknown. Methods: Black and Latina women aged 18-65 years completed the Centers for Medicare and Medicaid Services Accountable Health Communities Screening Tool, assessing 13 HRSN domains. Hypertension was ascertained by a validated EHR-based algorithm or self-report of hypertension. Logistic regression tested associations of HRSN with hypertension. LASSO regression with 10-fold cross-validation was used to derive a poly-social risk score in the training set (random 70%) and tested in the validation set (30%) against a sociodemographic model (age, race, income, education). Results: Among 1302 participants (mean [SD] age 40.1 [11.3] years, 70.4% Black, 44.3% Latina), higher cumulative burden of HRSN was associated with increased odds of hypertension (adjusted odds ratio [aOR] for each additional domain of HRSN: 1.07 [95% CI 1.01-1.14], P=0.02). Food insecurity (aOR 2.30 [1.37-3.87], P= 0.002), lapse in utilities (aOR 1.44 [1.04-1.96], P=0.02), poor concentration (aOR 1.57 [1.13-2.17], P=0.007), and social isolation (aOR 1.77 [1.14-2.73], P=0.01) were associated with hypertension. In the validation set, the poly-social risk score did not improve discrimination for hypertension vs. the sociodemographic model (AUC 0.76 [95% CI 0.71-0.81] vs. AUC 0.80 [0.75-0.85]). Conclusion: In this cross-sectional analysis of Black and Latina women, greater cumulative social disadvantage was associated with hypertension. While inclusion of HRSN did not improve hypertension prediction beyond conventional sociodemographic indices, findings may inform targeted interventions among minorities at cardiometabolic risk.

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03.
arXiv (CS.CL) 2026-06-15

Knowledge Graph Enhanced Memory-Augmented Retrieval for Long Context Modeling

作者:
Ghadir Alselwi↗Basem Suleiman↗Hao Xue↗Shoaib Jameel↗Hakim Hacid↗Flora D. Salim↗Imran Razzak↗

Long-context language modeling requires not only extending context windows but maintaining coherent understanding of entity states and relationships across thousands of tokens – a challenge that semantic similarity alone cannot address. KGERMAR addresses this by constructing dynamic, context-specific knowledge graphs from input text during inference, enabling domain-adaptive retrieval that leverages both semantic similarity and explicit entity relationships. The framework performs real-time entity and relation extraction to build contextual knowledge graphs, then integrates graph-structural embeddings with textual semantics through a multi-component memory architecture. Three memory banks – contextual, semantic, and structural – are maintained with retrieval signals fused via learned weights to capture both surface-level semantics and deeper relational patterns. Evaluated on SlimPajama (84.7K training examples), WikiText-103 (4,358 examples), PG-19 (100 examples), and Proof-pile (46.3K examples), KGERMAR achieves up to 8.5\% lower perplexity and 2–2.5x better memory efficiency than memory-augmented baselines across context lengths from 1K to 32K tokens, with superior in-context learning performance across five NLU tasks. The dynamic knowledge graph construction approach advances memory-augmented language modeling by enabling domain-specific knowledge representation that adapts to input contexts rather than relying on fixed knowledge bases.

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04.
bioRxiv (Bioinfo) 2026-06-18

Bioinf-Farma: supervised integration of epitope prediction and recombinant protein developability for automated vaccine candidate prioritization

作者:
Bondi↗Crespi↗Orlando↗Lescai↗Serapian↗S. A↗Colombo↗Fasano↗Pollegioni↗Molla↗

Vaccine antigen discovery requires prioritizing protein candidates according to both immunogenic potential and recombinant expression feasibility. These properties are typically evaluated using separate computational tools, requiring researchers to integrate heterogeneous outputs through ad hoc workflows. Here, we present BIOINF-farma, a modular platform integrating epitope prediction and developability assessment for rational antigen selection within a unified environment. Candidates can be submitted as amino acid sequences or three-dimensional structures. When experimental structures are unavailable, BIOINF-farma automatically searches for models in AlphaFold DB or performs structure prediction using Boltz-2, ensuring a standardized structural representation for downstream analyses. Antigenicity is quantified by combining structure-based conformational epitope signals (MLCE/REBELOT-BEPPE) and sequence-based linear epitope propensity scores (BepiPred 3.0) into a protein-level Antigenicity Score, with a classification threshold optimized on a manually curated validation dataset. Developability is evaluated through two supervised Random Forest meta-learners that integrate three solubility predictors (DeepSoluE, SoluProt, Protein-Sol) and three thermal stability predictors (TemStaPro, ProLaTherm, BertThermo), whose outputs are combined into an Expression Efficiency Score (EES). By integrating complementary predictive signals, the meta-learning framework achieves greater accuracy and robustness than individual predictors while maintaining performance across a broad range of sequence identities. The Antigenicity Score effectively discriminates antigenic from non-antigenic proteins with a large effect size, whereas EES successfully distinguishes soluble from insoluble outcomes on an independent panel of recombinant proteins expressed in Escherichia coli. BIOINF-farma jointly assesses antigenicity and expression feasibility within a single framework. Its modular architecture facilitates the incorporation of future predictive methods, while its web-based interface makes the full pipeline accessible to users without programming expertise, supporting rapid candidate triage in vaccine research and emerging pathogen responses.

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05.
arXiv (CS.AI) 2026-06-12

Eigenism: Ethics for a Human-AI Future

作者:
Dan Hendrycks↗

arXiv:2606.12420v1 Announce Type: cross Abstract: Our concepts of survival and self-interest were built for single, continuous biological lives. These ideas break down when applied to artificial intelligence, since an AI can be easily copied, paused, branched, or merged. To determine what an AI actually has reason to care about, this paper introduces Eigenism, an ethical framework that treats identity not as an all-or-nothing property tied to specific hardware, but as a graded, distributed pattern of information. We propose that an agent evaluates outcomes by summing the wellbeing of all entities weighted by their connectedness to the agent's pattern: $\sum c\cdot w$. We first formalize this equation to map exactly how an AI should value its existence across copies, forks, and updates. We then demonstrate that this ethical theory successfully generalizes to humans as well, providing a much-needed shared moral vocabulary. Finally, the framework uses this shared vocabulary to reframe AI alignment. Rather than only attempting to constrain AIs from the outside using confinement or reinforcement, Eigenism points toward ``identity engineering,'' showing how deep, non-redundant shared histories can make human flourishing a genuine component of an AI's own rational self-interest.

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

SAFformer:Improving Spiking Transformer via Active Predictive Filtering

作者:
Zequan Xie↗Weiming Zeng↗Yunhua Chen↗Sichang Ling↗Tongyang Chen↗Jinsheng Xiao↗

Spiking Neural Networks (SNNs) offer notable advantages in biological plausibility and energy efficiency, making them promising candidates for building low-power Transformers. However, existing Spiking Transformers largely adhere to a passive reactive paradigm, which struggles to focus on task-relevant information and incurs substantial computational overhead when processing redundant visual data. To overcome this fundamental yet underexplored limitation, we propose SAFformer, a novel Spiking Transformer architecture based on an active predictive filtering paradigm. Inspired by the brain's predictive coding mechanism, SAFformer actively suppresses predictable signals and focuses on salient visual features. Extensive experiments show that SAFformer establishes new state-of-the-art performance on CIFAR-10/100 and CIFAR10-DVS. Remarkably, on ImageNet-1K, it achieves 80.44% Top-1 accuracy with only 26.58M parameters and an energy consumption of 5.88 mJ, demonstrating an exceptional balance between accuracy and efficiency.

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

Near-Optimal Regret for Distributed Adversarial Bandits: A Black-Box Approach

作者:
Hao Qiu↗Mengxiao Zhang↗Nicol\`o Cesa-Bianchi↗

arXiv:2602.06404v2 Announce Type: replace Abstract: We study distributed adversarial bandits, where $N$ agents cooperate to minimize the global average loss while observing only their own local losses. We show that the minimax regret for this problem is $\tilde{\Theta}(\sqrt{(\rho^{-1/2}+K/N)T})$, where $T$ is the horizon, $K$ is the number of actions, and $\rho$ is the spectral gap of the communication matrix. Our algorithm, based on a novel black-box reduction to bandits with delayed feedback, requires agents to communicate only through gossip. It achieves an upper bound that significantly improves over the previous best bound $\tilde{O}(\rho^{-1/3}(KT)^{2/3})$ of Yi and Vojnovic (2023). We complement this result with a matching lower bound, showing that the problem's difficulty decomposes into a communication cost $\rho^{-1/4}\sqrt{T}$ and a bandit cost $\sqrt{KT/N}$. We further demonstrate the versatility of our approach by deriving first-order and best-of-both-worlds bounds in the distributed adversarial setting. Finally, we extend our framework to distributed linear bandits in $R^d$, obtaining a regret bound of $\tilde{O}(\sqrt{(\rho^{-1/2}+1/N)dT})$, achieved with only $O(d)$ communication cost per agent and per round via a volumetric spanner.

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

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

作者:
Lanbo Lin↗Jiayao Liu↗Tianyuan Yang↗Li Cai↗Yuanwu Xu↗Lei Wei↗Sicong Xie↗Guannan Zhang↗

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

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

AudioX-Turbo: A Unified Framework for Efficient Anything-to-Audio Generation

作者:
Zeyue Tian↗Lei Ke↗Zhaoyang Liu↗Ruibin Yuan↗Liumeng Xue↗Yujiu Yang↗Weijia Chen↗Xu Tan↗Qifeng Chen↗Wei Xue↗Yike Guo↗

Audio and music generation based on flexible multimodal control signals is a widely applicable topic, with the following key challenges: 1) a unified multimodal modeling framework, 2) large-scale, high-quality training data, and 3) the prohibitive inference cost of multi-step diffusion sampling. As such, we propose AudioX-Turbo, a unified and efficient framework for anything-to-audio generation that integrates varied multimodal conditions (i.e., text, video, and audio signals) in this work. AudioX-Turbo follows a teacher-student paradigm. The teacher AudioX-Base is built on a Multimodal Diffusion Transformer with a Multimodal Adaptive Fusion module that aligns diverse multimodal inputs for high-fidelity synthesis, and is then distilled into the few-step student AudioX-Turbo via Distribution Matching Distillation adapted to flow matching, complemented by a diffusion-based discriminator for high-quality few-step generation. To support the training of AudioX-Turbo, we construct a large-scale, high-quality dataset, IF-caps-Pro, comprising approximately 9.2M samples curated through a two-stage data collection and annotation pipeline. We benchmark AudioX-Turbo across a wide range of tasks, finding that our model achieves superior performance, especially on text-to-audio and text-to-music generation, while operating at only 4 sampling steps and requiring approximately 25x fewer function evaluations (NFE) than multi-step baselines. These results demonstrate that our method is capable of audio generation under flexible multimodal control, showing efficient and powerful instruction-following capabilities. The code and datasets will be available at https://zeyuet.github.io/AudioX-Turbo/.

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10.
arXiv (CS.LG) 2026-06-15

When to Write and When to Suppress: Route-Specialized Dual Adapters for Memory-Assisted Knowledge Editing

作者:
Yining Huang↗

arXiv:2606.14668v1 Announce Type: new Abstract: Knowledge editing systems must update selected facts while preserving nearby but irrelevant behavior. This paper studies this problem in a memory-assisted setting where an edit memory is retrieved at inference time and a parameter-efficient adapter corrects the model's object preference. We argue that the central design question is not only how to write an edit, but also when to suppress it. We introduce \method{}, a route-specialized dual-adapter editor. A relevance router first decides whether a prompt should receive an edit memory. Routed prompts use an edit adapter trained to prefer the new object over the original object; unrouted non-direct prompts use a separate locality adapter trained to preserve or restore the original-object preference. We evaluate \method{} on three 1,000-case protocols, \cf{}, \zsre{}, and \mquake{}, under the same memory protocol and two 7B/8B base models. On Llama-3.1-8B-Instruct, \method{} obtains the best overall probability-preference accuracy on all three benchmarks: 0.8180 on \cf{}, 0.8946 on \zsre{}, and 0.9922 on \mquake{}. The same trend holds on Qwen3-8B. Router ablations show that the relevant memory boundary differs across datasets: a lexical neural router is safest on \cf{}, while BGE embedding routing is better on \zsre{} and \mquake{}. Component and module ablations show that the gain mainly comes from separating edit injection from off-route suppression rather than from simply increasing LoRA capacity.

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11.
PLOS Computational Biology 2026-06-02

PepAnno: A structure-aware deep learning framework for bioactive peptide prediction, structural visualization, and physicochemical profiling

作者:
Enyan Liu↗

by Enyan Liu, Yueming Hu, Liya Liu, Yifan Chen, Shilong Zhang, Sida Li, Haoyu Chao, Luyao Xie, Yi Shen, Liangwei Wu, Julio Raúl Fernández Massó, Ming Chen Peptides are gaining prominence as therapeutic candidates due to their diverse physiological functions and structural simplicity. Although multiple computational tools exist for bioactive peptide prediction, many suffer from limitations such as non-intuitive interfaces, sequence-only representations, insufficient structural awareness, restricted interpretability, or fragmented analysis workflows, leading to reduced research efficiency and higher costs. To address these challenges, we present PepAnno (https://bis.zju.edu.cn/pepanno/), a comprehensive and user-friendly web server for multi-functional peptide annotation. PepAnno is powered by a novel structure-aware, multi-view geometric deep learning framework that integrates pre-trained sequence embeddings with predicted 3D structural graphs through a dual-stream architecture combining a Transformer and a GATv2 network. A cross-modal attention mechanism is employed to effectively fuse semantic and geometric representations, enabling accurate multi-task prediction across 7 key bioactivities, including antimicrobial and anticancer properties. Comprehensive evaluation on seven curated bioactivity datasets demonstrates that PepAnno achieves robust and competitive predictive performance across tasks, consistently outperforming or matching existing methods in terms of discrimination and stability. Beyond functional prediction, PepAnno provides automated calculation of physicochemical properties, structure visualization, and access to an integrated repository of peptide-related databases and tools. By enabling one-click peptide annotation, PepAnno offers an efficient and interpretable solution for large-scale peptide analysis and facilitates downstream experimental design and peptide-based drug discovery.

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

NTIRE 2025 Challenge on Image Super-Resolution (x4): Methods and Results

作者:
Zheng Chen↗Kai Liu↗Jue Gong↗Jingkai Wang↗Lei Sun↗Zongwei Wu↗Radu Timofte↗Yulun Zhang↗Xiangyu Kong↗Xiaoxuan Yu↗Hyunhee Park↗Suejin Han↗…

This paper presents the NTIRE 2025 image super-resolution ($\times$4) challenge, one of the associated competitions of the 10th NTIRE Workshop at CVPR 2025. The challenge aims to recover high-resolution (HR) images from low-resolution (LR) counterparts generated through bicubic downsampling with a $\times$4 scaling factor. The objective is to develop effective network designs or solutions that achieve state-of-the-art SR performance. To reflect the dual objectives of image SR research, the challenge includes two sub-tracks: (1) a restoration track, emphasizes pixel-wise accuracy and ranks submissions based on PSNR; (2) a perceptual track, focuses on visual realism and ranks results by a perceptual score. A total of 286 participants registered for the competition, with 25 teams submitting valid entries. This report summarizes the challenge design, datasets, evaluation protocol, the main results, and methods of each team. The challenge serves as a benchmark to advance the state of the art and foster progress in image SR.

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13.
arXiv (CS.AI) 2026-06-16

DualGauge: Automated Joint Security-Functionality Benchmarking of Specification-Only Code Generation by LLMs and Coding Agents

作者:
Rupam Patir↗Keyan Guo↗Suvadra Barua↗Abhijeet Pathak↗Dinesh Gudimetla↗Jiawei Guo↗Hongxin Hu↗Haipeng Cai↗

arXiv:2511.20709v2 Announce Type: replace-cross Abstract: Large language models (LLMs) and LLM-based coding agents are now used to generate code from natural-language specifications, yet ensuring such code is both functionally correct and secure remains a challenge. We present DualGauge, the first fully automated framework for jointly evaluating correctness and security of specification-only code generation, supported by DualGauge-Bench, a language-agnostic benchmark of 307 coding tasks each paired with functional and security tests derived from the same specification. Evaluating 10 representative LLMs across Python, C++, and JavaScript, we find that functional correctness substantially overestimates reliable code generation: even the strongest model remains below 15% joint security-functionality success in every language. Common model-side factors–scale, extended thinking, quantization, instruction tuning, and code specialization–do not reliably improve joint performance, suggesting secure-and-correct code generation does not simply emerge from stronger coding capability. Evaluation of 3 leading agentic coding systems (Codex, OpenHands, and Claude Code) shows that iterative scaffolding provides no advantage over direct (LLM-based) generation on specification-only tasks. A qualitative audit reveals failures concentrate at the output contract boundary and in guards that exist but are insufficient–patterns that only joint benchmarking reliably exposes.

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

Creating Multilingual Mental Health Dialogue Datasets: Limits of Persona-Based Localization via Nationality and Language

作者:
Yunkai Xu↗Saeed Abdullah↗

AI and large language models (LLMs) have emerged as promising tools to address global mental health challenges. Despite the global nature of these challenges, there remains a critical shortage of high-quality datasets for training and evaluating such systems. To mitigate this gap, researchers increasingly generate synthetic clinical personas to simulate user data and test digital mental health support systems. However, most validated personas rely on English-centric contexts. This paper investigates whether similar persona-based methods can be used to generate multilingual mental health datasets. We modified nationality and language parameters in personas to generate clinical dialogues in Mandarin, Bengali, and Hindi. We then examined how different LLMs perform when evaluating the depression severity of these generated multilingual datasets against the baseline in English. Our findings indicate that just adding nationality and language parameters in personas might not be adequate, as it can introduce clinical inconsistency across languages. LLM judge models often exhibit inaccuracies in assessing depression severity in non-English texts, with performance varying across different models. This exposes the systemic limitations of applying English-centric personas to multilingual contexts. Ultimately, our work highlights the urgent need for culturally responsive data generation to ensure equitable mental health systems globally.

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15.
Science (Express) 2026-05-28

A Hormone Cell Atlas maps the human endocrine system at cellular resolution | Science

作者: 未知作者

Hormones act across tissues and organs to coordinate physiological functions. Drawing inspiration from the Human Cell Atlas, we analyzed expression of 379 hormone and receptor genes in a transcriptomic dataset comprising 14 million single cells and nuclei across 47 human tissues. Using hormone2cell, we mapped putative hormone-producing and hormone-receiving cell types, defining tissue-specific and cross-tissue endocrine signatures. We predicted non-classical sites of hormone expression, including secretin in plasmacytoid dendritic cells, inferred convergent hormone action and endocrine feedback loops, and implicated cell populations in monogenic endocrine disorders. In a cross-tissue integration of adipocyte datasets, we uncovered dynamic endocrine programs across depots, within adipocyte subtypes and through adipogenic differentiation. Cumulatively, the Hormone Cell Atlas ( hormonecellatlas.org.uk ) provides a comprehensive framework for dissecting hormonal impact on health and disease.

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

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

作者:
Zhuoyi Peng↗Jingzhou Jiang↗Hanlin Gu↗Lixin Fan↗Yi Yang↗

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

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17.
medRxiv (Medicine) 2026-06-15

Automated AI-Based Ventricular Subcompartment Segmentation and Volumetry in Idiopathic Normal Pressure Hydrocephalus

作者:
Mutke↗M. A↗Griot↗S. A↗Wasserthal↗Indrakanti↗A. K↗Vishwanathan↗Mahmutoglu↗D'Antonoli↗T. A↗Bach↗…

Purpose In idiopathic normal pressure hydrocephalus (iNPH), longitudinal monitoring of ventricular size is important for diagnosis and treatment follow-up. This study aimed to validate a fully automated AI model for CT ventricular volumetry with subcompartments and to compare AI-derived volume changes with routine radiology assessments. Methods This retrospective, single-center study included 88 patients with iNPH and 456 non-contrast-enhanced head CT examinations. The model was trained on 38 manually labeled CT scans with 12 ventricular subcompartments. Outcomes included segmentation accuracy, correspondence between AI-derived longitudinal ventricular volume changes and radiology report categories (decreased, unchanged, increased), radiologist detection thresholds for ventricular change, and paired pre- and postoperative volume changes in 22 patients with ventriculoperitoneal shunt. Results Mean segmentation accuracy was high (Dice, 0.83). 91% of 100 segmentations were rated as excellent by an expert neuroradiologist. AI-derived ventricular volume changes corresponded well to radiology report categories (median total ventricular volume changes of -17% in cases reported as decreased, 0% in unchanged cases, and +22% in increased cases; all p < 0.001). Radiologists reported ventricular volume change in 50% of cases at an AI-measured relative volume change of +/-6%, and in 90% of cases at +21% for enlargement and -18% for decrease. After shunt placement, ventricular volume decreased by -8% (median), with the largest relative reductions observed in the right temporal and occipital horns. Conclusions Automated AI-based ventricular segmentation on CT enables accurate and reproducible assessment of ventricular volume changes in iNPH and complements routine radiological evaluation for longitudinal and postoperative monitoring.

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18.
bioRxiv (Bioinfo) 2026-06-19

StickForStats: automated statistical assumption validation for reproducible computational biology

作者:
Bharti↗Chakraborty↗

Reproducible computational biology depends on statistical decisions that routine workflows often skip: verifying that a differential-expression test's assumptions hold across all genes, that a strategy-comparison ANOVA is robust to non-normality, or that a meta-analysis is not distorted by publication bias. Surveys consistently find that fewer than 20% of published biomedical studies report checking these assumptions, and existing statistical software leaves validation to the analyst as an optional step. We present StickForStats, an open-source web platform that reframes assumption validation as a default precondition for every analysis. Its Guardian system–a middleware pipeline of eight validators (normality, variance homogeneity, independence, outliers, sample size, modality, linearity, homoscedasticity)–checks assumptions before execution and, on critical violations, reroutes to an appropriate nonparametric alternative with a documented decision trail. At genome scale, applying Guardian to a 91-sample synovial-sarcoma RNA-seq study (GSE271517) cascaded 90.6% of 27,221 genes to a rank-based test and flipped the differential-expression verdict for 553 genes–479 rescued from an under-powered t-test and 74 outlier-driven false positives rejected–materially changing the gene list a biologist would act on. The same automatic validation generalizes across domains: a CRISPR editing-strategy comparison (ANOVA F = 1122, with Guardian recommending Kruskal-Wallis H = 36.6), an ordinal correlation (Pearson r = 0.476 corrected to Spearman {rho} = 0.479), and a sixteen-trial clinical meta-analysis revealing severe publication bias (Egger's t = -5.78, p < 0.001); a complementary module extends the same validators to published manuscripts, checking claims against CONSORT, STROBE, ICH-E9, and JARS-Quant reporting standards. By making assumption validation automatic and transparent, StickForStats targets a tractable, under-served contributor to irreproducibility. The platform is MIT-licensed, validated against SciPy and R, and freely available at https://github.com/visvikbharti/stickforstats_new.

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19.
arXiv (math.PR) 2026-06-11

Unbiased Derivative Estimation for Stationary Mean of Parameterized Markov chains

作者:
Jeffrey Wang↗Chang-han Rhee↗

arXiv:2606.11487v1 Announce Type: cross Abstract: We propose a new approach to unbiased estimation of the gradients of the stationary means associated with parametrized families of Markov chains. Our estimators are particularly efficient when the Markov chains have slow mixing rate. Our approach does not require a specific parametrization except for an oracle to evaluate the transition density and its gradient at a given data point without any additional knowledge about the density function itself. It makes our estimator suitable for parametrizations associated with neural networks. The estimator can potentially achieve large improvement in terms of efficiency. Numerical experiments confirm the good performance predicted by the theory.

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20.
arXiv (CS.AI) 2026-06-17

ARVO: Atlas of Reproducible Vulnerabilities for Open-Source Software

作者:
Xiang Mei↗Jordi Del Castillo↗Pulkit Singh Singaria↗Haoran Xi↗Abdelouahab Benchikh↗Tiffany Bao↗Ruoyu Wang↗Yan Shoshitaishvili↗Adam Doup\'e↗Hammond Pearce↗Brendan Dolan-Gavitt↗

arXiv:2606.17283v1 Announce Type: cross Abstract: Achieving reproducibility, quantity, and diversity in vulnerability datasets has long been viewed as an inherent three-way trade-off, where improving one dimension often comes at the cost of the others. In practice, reproducibility has been the dimension most often neglected. This has limited what can be automatically extracted from historical bug datasets, and has reduced their utility for downstream security research. In this work, we propose a method to produce a new security dataset which ensures reproducibility for diverse vulnerabilities at scale by identifying the key obstacles to large-scale bug reproduction and addressing them with general solutions. Using this method, we introduce full reproducibility to the largest open source software vulnerability dataset (OSS-Fuzz) and construct the ARVO dataset (an Atlas of Reproducible Vulnerabilities in Open-source software). ARVO is a large-scale dataset consisting of over 6,100 real-world vulnerabilities across 311 projects. Focusing on reproducibility, ARVO differs from existing datasets by providing each vulnerability in a form that can be consistently rebuilt, triggered, and analyzed across versions. Reproducibility also enables automatic identification of the corresponding patch for each vulnerability and supports direct interaction with vulnerabilities after code changes, capabilities that existing large-scale datasets do not provide. In our evaluation, ARVO successfully reproduces 81% of vulnerabilities and achieves 89.4% accuracy on the located patches. We also discuss ARVO's influence on both upstream practices and downstream security research.

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21.
arXiv (quant-ph) 2026-06-16

Interaction and non-Hermiticity controlled transmission in extended Su-Schrieffer-Heeger models

作者:
Syeda Rafisa Rahaman↗Shreekantha Sil↗Nilanjan Bondyopadhaya↗

arXiv:2606.15245v1 Announce Type: cross Abstract: We study the transport characteristics of an extended version of the Su-Schrieffer-Heeger (SSH) model with next-nearest-neighbor (NNN) interactions and non-Hermitian onsite energies. We observed that transport in such a system is significantly modified by the NNN interaction and the non-Hermitian terms. The transmission coefficient exhibits oscillatory behavior as the strength of the NNN interaction varies in a fixed-length chain. Moreover, the transmission coefficient also shows oscillation with system size for a fixed strength of the NNN interaction. We find that novel oscillatory behavior of the transmission coefficient, arising form the NNN interaction, is a unique feature of such a model and has not been reported previously. The presence of the non-Hermitian terms also enhances/reduces the transmission coefficient depending on the values of the other system parameters like intra-, inter- and NNN hopping. It appears from our study that both the NNN interaction and the non-Hermiticity introduce significant changes in the transport properties of the extended SSH chain, which are not observed in the standard Hermitian nearest-neighbour variant of the SSH model.

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

Limited Marginal Benefit of Reasoning-Heavy LLM Deployment in ESG Narrative Scoring: A 4-Model Consensus Study on Japanese Listed Firms

作者:
Hiroyuki Kokubu↗

arXiv:2606.13693v1 Announce Type: cross Abstract: Automated scoring of ESG narrative disclosures with large language models (LLMs) is gaining traction, yet whether reasoning-heavy frontier models add value commensurate with their cost remains empirically unsettled. We evaluate this question on a corpus of ten Japanese listed firms across three rubric axes – quantitative targets, progress-tracking infrastructure, and external-standard alignment – using a four-model consensus design that combines a reasoning-on frontier model with three reasoning-off contemporaries. Across 120 firm x axis x model scores, the pooled mean absolute deviation between the reasoning-on model and each reasoning-off counterpart is 0.38 on a 5-point scale; only 2% of pairwise comparisons reach a two-point deviation, and none exceeds two points. Per-firm cost accounting shows the reasoning-on arm alone costs roughly 5.6x as much as the three-provider reasoning-off ensemble, for outcomes that differ only within small margins. We conclude that in span-based ESG narrative scoring, reasoning-heavy deployment does not materially improve outcomes relative to reasoning-off consensus, while substantially increasing operational cost. We discuss implications for cost-effective ESG auto-scoring pipelines and LLM deployment governance in applied accountability settings. An earlier version of this work is available on SSRN (Abstract ID 6683303).

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23.
bioRxiv (Bioinfo) 2026-06-11

Tumour evolution as ground truth for cancer whole-genome sequencing

作者:
Valeriani↗Gandolfi↗Buscaroli↗Davydzenka↗Santacatterina↗Antonello↗Sadr↗A. H↗Gazziero↗V. A↗Milite↗Rivaroli↗…

Cancer genomes are shaped by evolutionary processes that couple mutagenesis, clonal selection, chromosomal instability, spatial growth and treatment response into structured genomic patterns, yet current benchmarking strategies largely ignore this evolutionary dependency. Here, we present SCOUT, a large-scale synthetic whole-genome sequencing resource of over 200 samples, designed for systematic benchmarking of tumour genomic analysis and evolutionary inference under controlled evolutionary ground truth. Unlike conventional task-specific simulations, SCOUT models tumour evolution as a latent generative process that simultaneously shapes mutations, copy-number alterations, variant allele frequencies, mutational signatures and clonal architectures. SCOUT recapitulates key features of solid and haematological malignancies, including driver mutations, chromosomal instability, intratumour heterogeneity, spatial sampling and treatment-associated evolutionary dynamics in tumour and matched-normal longitudinal and multi-region sequencing designs. Using SCOUT, we benchmarked widely used methods for somatic variant detection, copy-number analysis, mutational signature inference and tumour evolutionary reconstruction. Across analytical tasks, performance deteriorated in low-purity, highly subclonal and structurally complex tumours, while spatial sampling bias and hypermutation generated spurious evolutionary signals that confounded tumour interpretation across multiple inference layers. Evolutionary simulations further distinguished lineage-restricted genetic bottlenecks from multi-lineage resistance dynamics associated with tumour plasticity. Tumour purity consistently exerted a stronger effect on inference accuracy than sequencing depth. Together, our results establish evolutionary ground truth as a prerequisite for reproducible benchmarking and biologically interpretable analysis of cancer whole-genome sequencing data.

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24.
arXiv (CS.AI) 2026-06-12

A Mathematical Forum Platform for Collaborative Problem Solving and Dataset Generation for AI Reasoning

作者:
Akbar Erkinov↗Nurmukhammad Abdurasulov↗

arXiv:2606.12976v1 Announce Type: new Abstract: Sharing mathematical content in online forums remains a significant friction point for students and educators: writing raw LATEX is error-prone, standalone optical character recognition tools require platform switching, and current forum software offers no integrated path from a photograph of a formula to a rendered post. We present a unified system that eliminates this friction by embedding an image to LATEX conversion pipeline directly inside a forum posting interface. A user uploads or captures an image of a mathematical expression; the system routes it through the Mathpix OCR API, detects whether the returned output is LATEX or plain text containing inline math, applies the appropriate delimiter normalisation, and renders a live preview in either LATEX or Markdown mode before the post is committed to the database. The architecture is organized in three loosely coupled layers: image processing, rendering, and storage, and supports both desktop and mobile clients. A provisional US patent application has been filed covering the core methods. We describe the full system design, each component in detail, the data schema, and the key technical innovations, and we position the work against existing standalone tools and forum platforms to demonstrate the practical gap it closes. Beyond immediate usability, we argue that a deployed platform of this kind constitutes a continuously growing, community-validated dataset of mathematical problems and step-by-step solutions, a resource that can be used to train and benchmark AI systems for accurate mathematical reasoning

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25.
arXiv (CS.LG) 2026-06-18

Automated Byzantine-Resilient Clustered Decentralized Federated Learning for Battery Intelligence in Connected EVs

作者:
Mouhamed Amine Bouchiha↗Abdelaziz Amara Korba↗Yacine Ghamri-Doudane↗

arXiv:2605.21115v2 Announce Type: replace-cross Abstract: Federated learning (FL) has emerged as a promising paradigm for managing electric vehicle (EV) battery data in intelligent transportation systems (ITS), enabling privacy-preserving tasks such as anomaly detection and capacity estimation. However, most existing frameworks rely on centralized aggregation schemes, which pose critical limitations in terms of security and trust. To address these challenges, we propose ABC-DFL, an automated Byzantine-resilient clustered decentralized federated learning (C-DFL) framework for connected EVs. The proposed incentive-driven C-DFL system replaces the central server with an open-permissioned blockchain, featuring a new dynamic Quorum Byzantine Fault Tolerance (QBFT) protocol and an oracle-based aggregation layer, to enhance trust, security, and automation. At the core of ABC-DFL lies FLECA (Filtered Layered Enhanced Clustering Aggregation), a robust hierarchical aggregation protocol that mitigates Byzantine attacks by having each EV filter malicious updates using an adaptive threshold based on deviations from its reference model update. Oracle nodes, responsible for inter-group aggregation, employ robust clustering to isolate and aggregate model updates from trustworthy EV groups. Comprehensive experimental evaluations demonstrate that FLECA matches FedProx convergence under benign conditions and significantly outperforms existing defenses with attack impact scores below 0.10 in adaptive adversarial scenarios. Furthermore, several learning experiments with multitask models confirm the effectiveness and fairness of the incentive mechanism. Finally, on-chain and off-chain benchmarks validate the practicality of ABC-DFL.

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