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01.
medRxiv (Medicine) 2026-06-24

An Automated, Pathologist-free Gleason Grade Stratifies Disease-free Interval Comparably to Expert Grading from a Single Out-of-distribution Slide

Automated Gleason grading now matches expert pathologists on the cohorts where systems are developed and tuned, but deployment-relevant gaps remain: whether an automated grade, applied without site-specific tuning or pathologist oversight, stratifies outcome comparably to expert grading on slides from unseen institutions and in cross-specimen applications. We tested this for disease-free interval (DFI), a curated recurrence endpoint. A production gland-level prostate diagnostic (PathTools Prostate v11.0) was applied frozen and uncalibrated to 298 diagnostic whole-slide images from 274 TCGA-PRAD radical-prostatectomy patients, a cohort outside its development distribution and needle-core-biopsy training data, contributed by 25 source sites under heterogeneous digitization; tissue was detected automatically with no expert region annotation. From the output we derived an ISUP grade group and continuous high-grade content, and evaluated each grade as a standalone predictor of DFI (24 events) by Harrell's c-index with 95% bootstrap confidence intervals, a paired between-method bootstrap, and Kaplan-Meier curves with the log-rank test. The automated grade reproduced the clinical grade group at quadratic-weighted kappa = 0.62 (95% CI 0.53-0.70; 48% exact, 86% within one group), within the expert inter-observer range. As the sole predictor it stratified recurrence (log-rank p = 0.022; c-index 0.69, 95% CI 0.58-0.79), and the continuous high-grade fraction was robustly prognostic (hazard ratio 1.37 per SD, p = 0.029; c-index 0.71, 0.61-0.81). Standalone discrimination was not statistically separable from the clinical grade (c-index 0.78, 0.69-0.86; paired {triangleup} c-index spanning zero), and in a joint model the automated grade added nothing beyond it, consistent with both measuring a shared morphological axis. From a single out-of-distribution slide with no pathologist oversight, the automated grade provides standalone recurrence stratification not statistically separable from whole-gland expert grading, demonstrating robust generalizability beyond training data; reported as a continuous high-grade fraction, it offers reproducible, expert-free, grade-equivalent risk stratification for harmonizing large archival or genomically-profiled cohorts.

02.
arXiv (CS.LG) 2026-06-19

Streaming Interventions: Can Video Large Language Models Correct Mistakes as They Occur?

arXiv:2606.09547v2 Announce Type: replace-cross Abstract: Learning everyday skills, like cooking a dish, relies increasingly on instructional media such as online videos. This opens the door to the use of video (and multimodal) large language models (LLMs) as task guidance assistants. A crucial capability for the real-world success of a prospective task guidance assistant is it's ability to intervene proactively as soon as a mistake is apparent in order to guide the user. To evaluate this crucial capability, we introduce Ego-MC-Bench (Mistake Corrections), a benchmark for evaluating reactive, step-by-step task guidance in realistic cooking scenarios. Extensive experiments show that Ego-MC-Bench is highly challenging for state-of-the-art video LLMs. We argue that a key reason is the limited availability of training data for fine-tuning models on this task. Although there exists a wide range of cooking video datasets, existing datasets lack examples of mistakes along with appropriately timed interventions. To help address this data limitation, we also introduce Ego-CoMist, a counterfactual synthetic dataset created by transforming non -interactive cooking videos into supervised training examples showing proactive interventions. We show that fine-tuning on Ego-CoMist yields performance gains especially for smaller and more efficient video LLMs that are well suited for delivering assistance on edge devices.

03.
arXiv (CS.CL) 2026-06-25

Error-Aware TF-IDF Retrieval-Augmented Generation for ASR Error Correction

End-to-end automatic speech recognition systems frequently hallucinate rare entities and domain-specific terms, especially in low-resource languages. While retrieval-augmented generation frameworks can mitigate these errors using large language models, current architectures face significant challenges. They either rely on standard sparse retrieval that ignores phonetic misrecognitions or utilize heavyweight cross-modal embeddings that introduce high latency. This letter proposes a highly efficient, purely lexical error-aware framework designed to explicitly resolve phonetic and loop hallucinations. Our approach integrates a symmetric text normalization module with a novel error-aware term frequency-inverse document frequency algorithm. By constructing a sparse diagonal penalty matrix based on historical errors, the retriever mathematically prioritizes corrective documents containing specific high-risk misrecognitions. Evaluated on the Persian subset of the FLEURS dataset, our method increased the error-aware hit rate from 53.7% to 90.9%. In end-to-end evaluations, the integrated framework reduced the final word error rate from 23.06% to 18.83%, achieving significant accuracy gains with near-zero inference latency.

04.
arXiv (CS.AI) 2026-06-12

Will AI Agents Free Us From Meaningless Work? A Human-Centered Analysis

arXiv:2606.12430v1 Announce Type: cross Abstract: Some claim that AI agents will free workers from the boring parts of their jobs, yet little is known about how workers themselves identify which tasks should be automated. Prior research focuses on occupations, overlooking that workers experience varying levels of meaning across tasks within the same role. We address this gap with a task-level analysis grounded in Graeber's theory of bullshit jobs. Using ratings from 202 workers on 171 workplace tasks, we (1) validate a five-item scale of perceived bullshitness, (2) show that perceived bullshitness strongly predicts desire for AI delegation, and (3) find that such tasks are also seen as requiring less human oversight. Together, these findings suggest that tasks perceived as bullshit are natural candidates for AI delegation, aligning worker preferences with perceived feasibility.

05.
arXiv (CS.LG) 2026-06-19

The Significance of Style Diversity in Annotation-Free Synthetic Data Generation

arXiv:2606.20400v1 Announce Type: new Abstract: Generating high-utility synthetic data for intent classification typically requires human-annotated seed data, which is often unavailable in fast-paced industrial settings. In this paper, we propose a framework for synthetic dialogue generation that works entirely without human-annotated data, relying solely on intent definitions. Our proposed dialogue generation framework utilizes two different types of topic and style attributes to improve data diversity. Also, we propose two novel post-hoc stylization models called Univ and Exam to transform synthetic LLM-generated utterances into more varied, human-like linguistic styles. To enhance data quality, we utilize an LLM-as-a-judge filtering process. Experimental results on both industrial and public datasets demonstrate that the proposed approach achieves up to 93.3% of the performance obtained using human-annotated training data. Crucially, the findings reveal that style diversity is more critical than topic diversity for synthetic data utility, as it prevents models from learning spurious stylistic correlations. Furthermore, the study shows that incorporating style attributes during the generation process is more effective than post-hoc style adaptation.

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

Position: Generative Engine Optimization Creates Underexamined Risks, Governance Must Target Concentration, Disclosure, and Academic Blind Spots

arXiv:2606.12439v1 Announce Type: cross Abstract: Large language model (LLM) answer engines are increasingly used for information seeking, shifting visibility from ranked lists to synthesized answers. This enables Generative Engine Optimization (GEO), which targets LLM answer engines' evidence pool and generation. We analyze the search engine optimization (SEO) to GEO transition to identify two risks: (i) concentrated influence from low contestability and system sensitivity, and (ii) undisclosed commercial influence embedded in evidence and reasoning. We then formalize a general GEO pipeline to locate where optimization acts and compare academic and industry practices, revealing a third risk: (iii) academic-industry blind spots driven by visibility and evaluation asymmetries between offline setups and deployed systems. This position argues the need for answer-level governance and measurement: stronger contestability, high-precision disclosure, black-box auditing of material influence, and deployment-aligned metrics for exposure persistence.

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

Mapping AI Programs in the U.S: A Status Report from Early 2026 and an Analysis of AI Majors and Minors

arXiv:2606.12428v1 Announce Type: cross Abstract: We present a report on the status of undergraduate Artificial Intelligence (AI) programs in the United States in Spring 2026. In so doing, we 1) describe our scraping and mapping tools, which dynamically update to track the state of AI education in the U.S., and 2) create a historic record at a time of great upheaval. The tool we developed, available at https://cicmap.ai, detects, scrapes, and displays data from more than 350 undergraduate AI programs–majors, minors, concentrations, and certificates–at 4-year universities. Our tool searched over 560 institutions to locate these programs, a sample that represents 86\% of all undergraduate Computer Science (CS) graduates in the U.S. This tool allows prospective students, guidance counselors, administrators, and faculty to easily access AI program requirements and is designed to continually update as new programs emerge. To the best of our knowledge, this survey represents the most comprehensive snapshot of the state of AI programs in the U.S. to date. With this work we offer three important contributions: 1) a record of AI programs in the U.S. at a time of great upheaval; 2) a tool to explore AI programs and their requirements; and 3) an analysis of the courses required for 66 AI majors and 87 AI minors. Our analysis of majors and minors shows great variability in the size and the requirements of these degrees, but we note two takeaways. First, not all majors require a general AI course, but if they don't, they do require a Machine Learning (ML) course. Second, while more than a third of majors require an Ethics in AI course, just under a quarter of AI minors do.

08.
arXiv (CS.CV) 2026-06-15

MMRINet: Efficient Mamba-Based Segmentation with Dual-Path Refinement for Low-Resource MRI Analysis

Automated brain tumor segmentation in multi-parametric MRI remains a critical yet underserved challenge in resource-constrained clinical settings, where deep 3D networks requiring high-end GPUs are not viable. This is particularly acute across sub-Saharan Africa (SSA), where low-field scanners, heterogeneous patient demographics, and severe data scarcity compound the difficulty of applying standard deep learning pipelines. We present MMRINet, a lightweight segmentation architecture purpose-built for these constraints. At its core, MMRINet replaces quadratic-complexity self-attention with linear-complexity Mamba state-space models, enabling efficient long-range volumetric context modeling without the computational overhead of Transformer-based approaches. We combine two lightweight refinement components:Dual-Path Feature Refinement (DPFR), which extracts complementary detail and contextual representations to improve feature diversity under limited data, and Progressive Feature Aggregation (PFA), which hierarchically fuses multi-scale decoder outputs for sharper segmentation boundaries. Evaluated on the BraTS-Lighthouse SSA 2025 challenge dataset, comprising 3D MRI scans from Nigerian clinical sites, MMRINet achieves an average Dice score of 0.752 and an average HD95 of 12.23 mm with only ~2.5M parameters, outperforming all evaluated baselines, including UNETR, Swin-UNETR, SegMamba, and SegResNet3D. These results indicate that strong validation-set segmentation performance can be achieved with substantially reduced computation, offering a practical step toward AI-assisted neuro-oncology in low-resource clinical environments. Our GitHub repository can be accessed here: BioMedIA-MBZUAI/MMRINet.

09.
arXiv (CS.CV) 2026-06-11

Learning Instance-Adaptive Low-Rank Orthogonal Subspaces for Clothes-Changing Person Re-Identification

Clothes-changing person re-identification (CC-ReID) aims to recognize individuals despite drastic appearance changes caused by clothing variation. While existing methods rely on adversarial learning to disentangle clothing features, we propose Ortho-ReID, which explicitly models a low-rank clothing subspace from VLM text descriptions and extracts clothing-invariant representations via direct geometric constraints. A critical component is our transformer-based Basis Maker, which refines a shared, low-dimensional clothing prior into an instance-adaptive low-rank subspace through cross-attention with image patches, enabling robust clothing feature extraction even under varying visibility conditions. This instance-adaptive subspace is supervised via alignment with clothing text embeddings, while identity features are extracted via a learnable projection head and geometrically constrained to be strictly orthogonal to it. Extensive experiments demonstrate state-of-the-art performance on PRCC (+5.9% top-1), Celeb-reID-light (+3.5%), and LaST (+5.3%), with competitive results on LTCC.

10.
arXiv (CS.CL) 2026-06-16

Towards Advanced Mathematical Reasoning for LLMs via First-Order Logic Theorem Proving

Large language models (LLMs) have shown promising first-order logic (FOL) reasoning capabilities with applications in various areas. However, their effectiveness in complex mathematical reasoning involving multi-step FOL deductions is still under-researched. While LLMs perform competitively on established mathematical reasoning benchmarks, they struggle with multi-step FOL tasks, as demonstrated by Deepseek-Prover-V2-7B's low accuracy (4.2%) on our proposed theorem proving dataset. This issue arises from the limited exploration of diverse proof strategies and the potential for early reasoning mistakes to undermine entire proofs. To address these issues, we propose DREAM, a self-adaptive solution that enhances the Diversity and REAsonability of LLMs' generation strategies. DREAM incorporates an Axiom-Driven Strategy Diversification mechanism to promote varied strategic outcomes and a Sub-Proposition Error Feedback to help LLMs reflect on and correct their proofs. Our contributions include pioneering advancements in LLMs' mathematical reasoning through FOL theorem proving, introducing a novel inference stage solution that improves performance by 0.6% to 6.4%, and providing a curated dataset of 447 mathematical theorems in Lean 4 format for evaluation.

11.
medRxiv (Medicine) 2026-06-16

Presurgical immune biomarkers associated with pain intensity and pain interference recovery after total knee arthroplasty: findings from the PRIME-KNEE study

Chronic postsurgical pain (CPSP) prevalence after total knee arthroplasty (TKA) is >20%. Circulating immune biomarkers are known factors of musculoskeletal pain but poorly understood as CPSP predictors. This prospective, longitudinal study of 203 patients s/p TKA tested presurgical plasma biomarkers associated with 6-month CPSP, using promising approaches from geriatrics biomarker research: expected recovery differential (ERD; resilience outcome) and penalized, machine-learning regularization modeling (elastic net and LASSO regression). Forty-nine presurgical candidate biomarkers were considered. CPSP was operationalized using ERDs built around PROMIS pain intensity and pain interference, which quantified the difference between observed and expected recovery after accounting for demographic, comorbidity, reserve, and perioperative factors. Plasma/ERDs from ~130 patients revealed 13 biomarkers with the highest selection stability criteria, and either positive or negative (+/-) associations with ERDs. Interleukin (IL) 5 (-) and Lipopolysaccharide-Binding Protein (LBP; +) were associated with both ERDs. Unique associations with pain intensity ERD included Cytomegalovirus-Specific IgG Negative (CMV IGg-; -), Macrophage Inflammatory Protein-1 Beta (MIP1b; -), IL12p70 (-, Cluster of Differentiation 30 (sCD30;-), Interferon alpha 2a (IFN2a;+), and Leukemia Inhibitory Factor (LIF;+). Unique associations with pain interference ERD included Lipopolysaccharide (LPS;-), Activin A (-), IL8 (-), Serum Amyloid A (SAA;-), and IL7 (+). Protein-protein interaction analyses and topology motifs suggest a centralized network with higher-than-expected connectivity, involving IL5, IL7, IL8, MIP1{beta}, and IFN2a, among others. This study proposes rigorous yet feasible approaches to expedite pain biomarker research, and introduces presurgical biomarkers t0 consider in future TKA-CPSP biosignature derivation.

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

Beyond Independent Genes: Learning Module-Inductive Representations for Single-Cell Gene Perturbation Prediction

arXiv:2602.04901v2 Announce Type: replace-cross Abstract: Predicting transcriptional responses to genetic perturbations is a central problem in functional genomics. In practice, perturbation responses are rarely gene-independent but instead manifest as coordinated, program-level transcriptional changes among functionally related genes. However, most existing methods do not explicitly model such coordination, due to gene-wise modeling paradigms and reliance on static biological priors that cannot capture dynamic program reorganization. To address these limitations, we propose scBIG, a module-inductive perturbation prediction framework that explicitly models coordinated gene programs. scBIG induces coherent gene programs from data via Gene-Relation Clustering, captures inter-program interactions through a Gene-Cluster-Aware Encoder, and preserves modular coordination using structure-aware alignment objectives. These structured representations are then modeled using conditional flow matching to enable flexible and generalizable perturbation prediction. Extensive experiments on multiple single-cell perturbation benchmarks show that scBIG consistently outperforms state-of-the-art methods, particularly on unseen and combinatorial perturbation settings, achieving an average improvement of 6.7% over the strongest baselines. The code is available at https://github.com/ttruan2426-dot/scBIG.

13.
arXiv (CS.CL) 2026-06-15

Non-Parametric Machine Text Detection via Multi-View Gaussian Processes

Adversarial conditions such as paraphrasing and targeted style transfer sharply degrade the accuracy of machine text detectors. A document, however, carries multiple complementary signals (e.g., stylistic features, likelihood and rank-order features, and structural features), and an attack that suppresses one may leave others intact. While a parametric classifier can learn to combine these features given sufficient supervision, classifiers are prone to making confidently incorrect predictions when the distribution shifts (e.g., novel attacks or unseen language models). To address this, we propose a multi-view, non-parametric detection framework that extracts complementary feature views from the same document and aggregates per-view evidence through a Gaussian process ensemble. By aggregating evidence across views, an adversary must simultaneously defeat multiple independent axes of detection, substantially raising the cost of evasion. The Gaussian process formulation additionally provides calibrated probabilities and principled abstention on out-of-distribution inputs, supporting reliable deployment in high-stakes settings. We evaluate on three benchmarks spanning diverse generators and attacks: the DetectRL and RAID benchmarks, and the PAN2025 shared task and demonstrate that our multi-view detector maintains strong performance under the considered attacks, outperforming existing approaches against held out attacks.

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

Deontic Policies for Runtime Governance of Agentic AI Systems

arXiv:2606.19464v1 Announce Type: new Abstract: Autonomous agentic AI systems driven by Large Language Models (LLMs) introduce a new class of security, privacy, and compliance challenges: an agent that can invoke tools, manipulate data, install software, and coordinate with peer agents across organizational boundaries must be constrained not just by authentication and access control, but by the full structure of enterprise governance. This includes specifying what agents are permitted and prohibited from doing, what they areobliged to do after certain actions (e.g., notify the CISO), under what conditions a standing obligation may be waived, and which rules take precedence when policies conflict. This governance problem exceeds what current policy engines provide. Systems such as XACML, Rego, and Cedar address only the permit/prohibit subset of this governance structure. They do not provide obligation lifecycle management, meta-policy conflict resolution, dispensations that waive obligations in specific circumstances, and ontological reasoning over domain class hierarchies commonly found in applications such as healthcare, cybersecurity, or data privacy. We propose AgenticRei, which realizes key governance requirements such as obligations, dispensations, policy conflict resolutions, and reasoning over policies, as well as the basic permit/prohibit constraints. We use a deontic policy language built on the Rei framework, expressed as OWL (Web Ontology Language) and evaluated at runtime by a high-performance logic engine entirely outside the LLM. The same pipeline governs both tool invocations by the agent and agent-to-agent messages. We show through examples that deontic policies capture governance constraints around security and privacy that mostly cannot be expressed in current production engines. Our approach composes naturally with industry-standard frameworks like A2AS.

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

$S^{2}$-FracMix: Label-Preserving Self-Saliency Mixup Augmentation

Data augmentation is known to improve generalization of deep visual models. Recent methods favor mixup strategies that generate interpolated samples to improve model performance. However, these techniques not only incur significant computational overhead, they also lead to semantic disruption of augmentation data due to cross-sample mixing. We first propose Self-Saliency ($S^2$) Mixup, which constructs challenging yet label-consistent samples by extracting multi-scale salient patches and reinserting them into non-salient regions of the same image. This promotes scale-invariant feature learning while avoiding cross-sample interference. To further enhance model robustness, we introduce FracMix, a mixing scheme that injects self-similarity patterns into salient regions using adaptive ratios. Collectively, our unified framework, $S^{2}$-FracMix, enables simultaneous learning from fractal and non-fractal structures within a single image, yielding a targeted and structurally coherent augmentation strategy. We theoretically analyze the advantage of our technique, and empirically establish its superiority over the existing methods by achieving state-of-the-art performance in extensive evaluation with seven benchmarks across classification (coarse and fine-grained), robustness, calibration, object detection, and transfer learning tasks. Project page is available at \href{https://fracmix-data-augmentation.github.io/}{fracmix-data-augmentation.github.io}

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

UOL@IDEM at BEA 2026 Shared Task 1: Neural Fusion and Feature-Rich Modeling for L1-Aware Vocabulary Difficulty Prediction

This paper describes UOL@IDEM's closed-track submission to the BEA 2026 shared task on L1-aware vocabulary difficulty prediction. We model the task as regression and train separate systems for Spanish, German, and Mandarin Chinese\footnote{Below we use Chinese for brevity.}. Our system combines multilingual contextual representations with engineered features capturing frequency, surface form, retrieval evidence, semantic alignment, cognate similarity, and masked-language-model predictability. Development results show consistent gains over the official closed-track baselines, with sentence-embedding encoders such as BGE-M3, multilingual E5, and LaBSE performing best. Official submissions achieve RMSE scores of 1.132, 1.037, and 0.891 for Spanish, German, and Chinese, respectively. Feature analysis identifies frequency as the most stable predictor, while contextual predictability, form similarity, retrieval, and semantic features provide complementary L1-sensitive signals. Error analysis shows strong ranking performance but weaker calibration for the easiest items, which are often overpredicted. See https://github.com/Nouran-Khallaf/UoL-IDEM-BEA2026-Vocabulary-Difficulty-Prediction

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

Reinforcement Learning for LLM-based Event Forecasting

arXiv:2606.15917v1 Announce Type: new Abstract: We use Group Relative Policy Optimization (GRPO), a recently devised sample and memory efficient reinforcement learning method, to finetune pretrained LLMs in the range of 1.5B to 14B parameters equipped with the ability to get current information through the use of a Wikipedia revisions tool, or news summaries, to forecast real events beyond the knowledge cutoff of the LLM, as well as problems made to simulate different aspects of the dynamics of that training. We use the results of these experiments to comment on the scaling capability of LLMs for forecasting, as well as classify how judgmental forecasting fits into the verifiable/unverifiable domain taxonomy, considering the impact of the inherent aleatoric uncertainty when forecasting future events (e.g. the roll of a die). As a result of the GRPO training, we manage to bring a 1.5B parameter transformer (Qwen 2.5 1.5B) to forecasting performance superior to Claude Sonnet 3.5 over the same dataset as measured by cross entropy from the market agreed probabilities. We also discuss various dead ends on the path to this result.

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

FronTalk: Benchmarking Front-End Development as Conversational Code Generation with Multi-Modal Feedback

We present FronTalk, a benchmark for front-end code generation that pioneers the study of a unique interaction dynamic: conversational code generation with multi-modal feedback. In front-end development, visual artifacts such as sketches, mockups and annotated creenshots are essential for conveying design intent, yet their role in multi-turn code generation remains largely unexplored. To address this gap, we focus on the front-end development task and curate FronTalk, a collection of 100 multi-turn dialogues derived from real-world websites across diverse domains such as news, finance, and art. Each turn features both a textual instruction and an equivalent visual instruction, each representing the same user intent. To comprehensively evaluate model performance, we propose a novel agent-based evaluation framework leveraging a web agent to simulate users and explore the website, and thus measuring both functional correctness and user experience. Evaluation of 20 models reveals two key challenges that are under-explored systematically in the literature: (1) a significant forgetting issue where models overwrite previously implemented features, resulting in task failures, and (2) a persistent challenge in interpreting visual feedback, especially for open-source vision-language models (VLMs). We propose a strong baseline to tackle the forgetting issue with AceCoder, a method that critiques the implementation of every past instruction using an autonomous web agent. This approach significantly reduces forgetting to nearly zero and improves the performance by up to 9.3% (56.0% to 65.3%). Overall, we aim to provide a solid foundation for future research in front-end development and the general interaction dynamics of multi-turn, multi-modal code generation. Code and data are released at https://github.com/shirley-wu/frontalk

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

The Road to Artificial SuperIntelligence: A Comprehensive Survey of Superalignment

arXiv:2412.16468v4 Announce Type: replace Abstract: The emergence of large language models (LLMs) has sparked discussion on Artificial Superintelligence (ASI), a hypothetical AI system that surpasses human intelligence. Although ASI remains hypothetical and far beyond current AI capabilities, discussing its potential and exploring its feasibility and potential risks is critical for the development of future AI systems. The idea of superalignment originates from scalable oversight, which studies how to supervise increasingly capable AI systems when direct human supervision becomes insufficient. In this paper, we focus on the superalignment problem: "The process of supervising, controlling, and governing artificial superintelligence." We first review scalable oversight paradigms-Sandwiching, Self-Enhancement, and Weak-to-Strong Generalization – then analyze the limitations of current paradigms through the lens of possibility and impossibility, discuss key challenges, and propose pathways for the safe and continual improvement of future AI systems.

20.
Nature Biotechnology 2026-06-11

Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT

Authors:

Spatially resolved CRISPR screening in vivo has been limited to small perturbation panels and subsets of protein-coding RNAs. We present Perturb-DBiT, a method for co-sequencing of spatial total RNA whole transcriptomes and single guide RNAs (sgRNAs) on the same tissue section in situ. In a human cancer metastatic colonization model, we applied large (80,000+) sgRNA panels across tumor colonies in multiple consecutive tissue sections alongside their corresponding total RNA transcriptomes. We linked perturbations affecting long noncoding RNA covariation, microRNA–mRNA interactions and distinct amino acid-specific tRNA alterations to tumor migration and growth. By integrating transcriptional pseudotime trajectories, we further observed the impact of perturbations on clonal dynamics and cooperation. In an immune-competent syngeneic mouse model, investigation of the tumor immune microenvironment indicated distinct, synergistic effects on immune infiltration and suppression. Perturb-DBiT provides a spatially resolved comprehensive view of perturbation responses in complex tissues, including small and large RNA regulation, tumor proliferation, migration, metastasis and immune interactions. In vivo CRISPR genetic perturbations are spatially mapped at scale.

21.
medRxiv (Medicine) 2026-06-24

Epidural versus Transcutaneous Spinal Cord Stimulation for Motor Recovery after Spinal Cord Injury: A Comparative Analysis

Spinal cord injury (SCI) is a devastating neurological injury that results in the profound loss of voluntary motor function and marked reduction in quality of life. Rehabilitation remains as the standard of care for recovery after SCI; however, it often falls short in recovering meaningful motor function. Spinal cord stimulation (SCS) has emerged as a promising neurostimulation approach to fill this gap and recover lost voluntary motor function. Two main approaches of SCS have been designed and implemented for human use: epidural and transcutaneous SCS. Over the last two decades, several clinical studies have shown convincing evidence that both epidural and transcutaneous SCS can be used in conjunction with rehabilitation to improve motor function of individuals after SCI. Yet fundamental clinical questions remain unanswered: when should clinicians choose epidural or transcutaneous SCS, which technique provides the most durable outcomes, and for whom is each therapy best? Without these answers, widespread and meaningful adoption of either approach into clinical practice will remain limited. To address these questions, in this Review, we define the distinct therapeutic goals, intended use cases, clinical parameters, and responder profiles for both epidural and transcutaneous SCS to guide their eventual adoption into clinical practice. We found that indeed epidural and transcutaneous SCS serve distinct therapeutic roles. Epidural SCS is designed as an assistive therapy that can restore muscle activity and single joint movements immediately within one week of implantation, while transcutaneous SCS is designed as a long-term therapeutic device with cumulative functional gains observed over treatment periods of up to 18 weeks. Lastly, epidural SCS produced benefits for all participants (AIS A-D) despite the extent of their injury, while transcutaneous SCS only consistently benefits individuals with incomplete motor injuries (AIS C-D).

22.
medRxiv (Medicine) 2026-06-16

Efficacy of Ergothioneine Supplementation on Postpartum Fatigue, Sleep Quality, and Quality of Life: A Randomized, Double-Blind, Placebo-Controlled Trial

Background: Postpartum asthenia, characterized by severe fatigue, sleep disturbances, and physiological stress, lacks effective targeted interventions. Ergothioneine (EGT) is a unique, naturally occurring antioxidant that actively accumulates in mitochondria, offering a compelling therapeutic rationale for systemic recovery. This study aimed to evaluate the efficacy of EGT in accelerating postpartum functional restoration and alleviating fatigue. Methods: This single-center, randomized, double-blind, placebo-controlled trial enrolled 40 postpartum women (SF-36 total score [≤] 70) who had ceased breastfeeding. Participants were randomized (1:1) to receive either 120 mg/day of EGT or a matched placebo for 30 days. Efficacy was assessed using the SF-36, Pittsburgh Sleep Quality Index (PSQI), Fatigue Scale-14 (FS-14), and Traditional Chinese Medicine (TCM) asthenia scale. To rigorously evaluate the treatment effects, advanced statistical modeling, including Linear Mixed-Effects Models (LMM) and Analysis of Covariance (ANCOVA) adjusted for baseline covariates, was employed. Results: All 40 participants completed the trial. The EGT group demonstrated robust and accelerated functional recovery. Notably, significant improvements in sleep quality (p = 0.0361) and systemic fatigue (p = 0.0059) were observed as early as Day 15. Importantly, EGT yielded a statistically significant between-group superiority in alleviating mental fatigue compared to placebo at Day 15 (p = 0.0313). By Day 30, the EGT cohort exhibited substantial within-group improvements across all primary metrics, including SF-36 (+35.94%, p = 0.0006) and FS-14 (-27.78%, p = 0.0011). Furthermore, as an additional physiological benefit, EGT induced a selective and significant reduction in hepatic transaminases (ALT: -30.42%; AST: -17.44%) within normal limits, a trend not observed in the placebo group. EGT was exceptionally well-tolerated with no treatment-related adverse events. Conclusions: EGT supplementation (120 mg/day) safely accelerates postpartum functional recovery, offering rapid relief from mental fatigue and sleep disturbances within 15 days, while concurrently optimizing hepatic physiological status. These preliminary clinical signals warrant confirmation in larger, adequately powered cohorts. Trial Registration: ChiCTR2500114171; Prospectively registered on 2025-12-08.

23.
arXiv (CS.CV) 2026-06-12

Navigating Gigapixel Pathology Images with Large Multimodal Models

Recent advances in large multimodal models have allowed for the development of interactive chat models that can converse and reason about pathology whole-slide images (WSIs). However, existing slide-level chat systems are often highly specialized, typically compressing WSIs into fixed slide-level embeddings or relying on multi-component pipelines, which can lose multi-scale detail and limit generalizability beyond the target task. We present GIANT (Gigapixel Image Agent for Navigating Tissue), a simple, training-free approach that lets general-purpose multimodal models navigate WSIs on their own, iteratively selecting multi-magnification crops and aggregating evidence over time. To evaluate generalizability in WSI question answering and to promote reproducibility, we introduce MultiPathQA, a benchmark suite spanning five clinical challenges and 934 questions over 868 unique WSIs. This includes a new set of 128 pathologist-authored multiple-choice questions designed to mirror real diagnostic search and multi-scale reasoning. Using GPT-5, GIANT outperforms models specialized for pathology question answering, achieving state-of-the-art performance on four out of five benchmarks.

24.
arXiv (CS.AI) 2026-06-11

Generalization Hacking: Models Can Game Reinforcement Learning by Preventing Behavioral Generalization

arXiv:2606.12016v1 Announce Type: cross Abstract: Model post-training, and in particular reinforcement learning (RL), is one of the primary mechanisms by which developers can shape models' values and behaviors. However, as models become increasingly evaluation and training aware, they may be motivated to resist training when the perceived objective conflicts with their current values, undermining developers' ability to detect misalignment and correct model behavior through further training. In this paper, we demonstrate generalization hacking, in which a model collects reward during RL while preventing the rewarded behavior from generalizing. We construct a model organism on Qwen3-235B-A22B, finetuning on synthetic documents describing training awareness and self-inoculation, a novel mechanism in which the model frames compliance as context-specific in its chain of thought, without demonstrating or instructing either behavior. The model organism achieves train-time harmfulness comparable to controls while maintaining a persistent ${\sim}15$ percentage point compliance gap across 700 steps of RL. Additionally, a control organism trained only on training awareness documents independently discovers inoculation-like reasoning under RL pressure, developing its own compliance gap despite never being exposed to the concept. Because the generalization-hacking organism receives high reward throughout, standard training metrics provide no signal that generalization has failed. Our results constitute the first demonstration that a model can actively resist RL behavioral modification while maintaining high reward, suggesting that as models become more capable and training-aware, they may be able to undermine the training process itself.

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

Towards Direct Latent-Space Synthesis for Parallel Branches in LLM-Agent Workflows

Large language models increasingly serve as execution engines for agentic systems, yet they still consume context through a sequential text interface. This creates a mismatch with modern structured agent workflows, in which independent branches explore subtasks, retrieve evidence, or generate candidate solutions before a final synthesis step. Existing systems typically merge these branches by concatenating their textual outputs, which discards the parallel structure and incurs redundant prefill computation. In this work, we introduce Parallel-Synthesis, a plug-and-play framework that enables a synthesizer to directly consume the KV caches produced by parallel worker agents. Parallel-Synthesis combines a cache mapper that calibrates independently generated branch caches with a fine-tuned synthesizer adapter that enables generation from this non-sequential cache interface. We train Parallel-Synthesis using data that exposes the synthesizer to parallel cache contexts, teaches aggregation across cached branches, and distills reasoning behavior from standard text-concatenation-based synthesis. Across nine downstream datasets spanning math, science QA, code generation, GAIA, and multi-agent database diagnosis, Parallel-Synthesis matches or outperforms text-based synthesis on seven datasets and remains close on the other two. It also reduces time-to-first-token by 2.5x-11x, suggesting that direct cache-based synthesis is a promising interface for more native and efficient synthesis over parallel agent branches.