Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

01.
arXiv (CS.CL) 2026-06-15

Characterizing Cultural Localization in AI-Generated Stories

The global use of artificial intelligence has increased interest in assessing the ability to generate culturally localized content, including stories. Cultural localization in stories often occurs through either templated localization – the use of cultural markers (e.g., names, locations) in a generic narrative – or holistic localization – the variation of plots, values, and themes, in addition to cultural markers. We propose a method to measure the degree to which content was generated through templated localization. Specifically, we identify the lexical tokens that distinguish stories across nationalities and measure the similarity of the narratives that remain after removing them. In stories generated by five models on 125 topics for 193 nationalities, our method is able to detect that only a small subset (9-17%) of the vocabulary accounts for the variation across nationalities and that the narratives that remain after removing them contain repeated multi-word sequences, suggesting the presence of a shared culturally-agnostic narrative template. Finally, we characterize the cultural markers for their stereotypicality and offensiveness, finding that markers from 19 countries, mostly located in the Global South, are on average offensive.

02.
arXiv (CS.CV) 2026-06-12

Goal2Pixel: Grounding Goals to Pixels for Vision-Language Navigation

Vision-language models (VLMs) have become a common foundation for vision-and-language navigation in continuous environments (VLN-CE). Yet most VLM-based methods cast navigation as low-level action prediction, an interface that is ambiguous, tied to short-horizon motion primitives, and inefficient due to repeated VLM querying. We propose Goal2Pixel, a pure pixel-based paradigm that reformulates VLN-CE as navigable pixel grounding. Rather than predicting actions, Goal2Pixel uses the image plane as a unified spatial interface between VLM reasoning and robot motion: the model predicts a visible navigable pixel to the agent, which is back-projected into a 3D waypoint for forward navigation. For non-forward actions, we append auxiliary directive regions to the image plane, where the left/right/bottom regions are interpreted as turning left, turning right, and stopping, respectively. To enable long-horizon navigation, we propose a visibility-aware keyframe memory for compact and informative history representation. To adapt pretrained VLMs to navigable pixel grounding, we introduce semantic embeddings and coordinate-aware auxiliary losses. Goal2Pixel achieves competitive state-of-the-art performance while requiring fewer VLM inference calls than prior methods. On R2R-CE Val-Unseen it achieves 54.1% SR and 52.5% SPL with just 7.75 VLM calls per episode, 6x fewer than the 46.62 required by direct action prediction at 32.9% SR. The same trend holds on RxR-CE.Project Page: https://baobao0926.github.io/Goal2Pixel/.

03.
medRxiv (Medicine) 2026-06-10

Documented clinical genetic testing among carriers of hereditary breast and ovarian cancer variants: Ancestry and socioeconomic disparities in the All of Us research program

Importance: Hereditary breast and ovarian cancer (HBOC) variant carriers benefit from risk-reducing interventions, but only if identified. The extent to which carriers are clinically recognized, and whether recognition is equitable across diverse populations, is poorly characterized in a single large U.S. cohort. Objective: To estimate P/LP HBOC carrier prevalence across genetic ancestry groups, quantify documented clinical genetic testing among carriers, and evaluate ancestry and socioeconomic disparities in testing. Design, Setting, and Participants: Cross-sectional analysis of the All of Us Research Program Controlled Tier (Curated Data Repository v8/C2024Q3R9), comprising participants with short-read whole genome sequencing and linked electronic health record (EHR) and survey data. Carriers were ascertained from research genomic data independent of clinical testing. Exposures: Genetically inferred ancestry (African [AFR], Admixed American [AMR], East Asian [EAS], European [EUR], Middle Eastern [MID], South Asian [SAS]); self-reported household income and educational attainment. Main Outcomes and Measures: (1) Carrier prevalence with Wilson 95% CIs; (2) documented clinical genetic testing (procedure codes) among carriers; (3) adjusted odds of documented testing among women, by ancestry, before and after socioeconomic adjustment, using multivariable logistic regression. Results: Among 414,830 participants, P/LP HBOC carrier prevalence was 1.42% (95% CI, 1.38-1.45) overall and similar across ancestry groups (AFR 1.24%, AMR 1.32%, EAS 1.19%, EUR 1.52%, MID 1.68%, SAS 1.33%; overlapping CIs). Among 250,071 women in the testing analysis, documented clinical genetic testing was rare: only 74 of 5,878 carriers overall (1.3%) and 59 of 3,572 European-ancestry carriers (1.7%) had a documented test, with counts below reportable thresholds in all other ancestry groups. African-ancestry women had lower adjusted odds of documented testing than European-ancestry women (Model 1 adjusted odds ratio [aOR], 0.32; 95% CI, 0.27-0.39), an association that attenuated but persisted after adjustment for income and education (Model 2 aOR, 0.48; 95% CI, 0.40-0.58; P < 0.001); Admixed American women also had reduced adjusted odds (aOR, 0.71; 95% CI, 0.61-0.84). Lower income and lower education were independently and dose-dependently associated with lower testing odds (income

04.
arXiv (CS.LG) 2026-06-19

Diffuse AI Control on Fuzzy Tasks

arXiv:2606.08892v2 Announce Type: replace Abstract: AI models deployed in critical domains, such as AI safety research, may subtly sabotage our efforts due to misalignment. Diffuse AI Control is a subfield of AI safety concerned with mitigating risks from AI sabotage distributed over long deployment horizons (diffuse threats). These risks are particularly pernicious on fuzzy tasks, i.e. tasks which are hard to grade or require intuition. To understand diffuse threats on fuzzy tasks, we introduce a framework that considers AI control as an adversarial game between a blue team and a red team. The blue team uses a weak trusted model to construct a weak score against which they would train a strong, potentially subversive model to remove the subversion propensity if it were present. The red team then tries to find model behaviors that are rated highly by the weak score, and thus might not be trained out, but actually correspond to poor performance. We test our framework on the task of writing experimental proposals for research questions from recent ML papers. We use a language model with access to the original paper as a proxy "ground-truth" scorer. Our red team discovers subversive behaviors using multi-objective evolutionary prompt optimization. We show that Opus~4.6 can write proposals that are worse according to the ground truth proxy than those of GPT-OSS-20B, while the weak scorer rates them as highly as the best proposals from Opus 4.6. We then propose an adversarial optimization algorithm for the blue team that discovers more robust prompts for the weak model. This algorithm produces a blue team prompt that our red team optimization fails to exploit.

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

Virtual Sensing to Enable Real-Time Monitoring of Inaccessible Locations & Unmeasurable Parameters

arXiv:2412.00107v2 Announce Type: replace-cross Abstract: Real-time monitoring of safety-critical interior states remains an open problem in energy systems where physical instrumentation is infeasible. Existing approaches rely on explicit governing equations, finite-dimensional state vectors, or per-instance retraining, which prevents mesh-independent, field-level inference at arbitrary interior coordinates under real-time constraints. We introduce operator-based virtual sensing for nuclear-grade thermal-fluid systems: we use the neural-operator framework to learn solution operators that map sparse boundary measurements to coupled internal fields in physically inaccessible regions, framing the problem class explicitly to distinguish it from classical state estimation and pointwise soft sensing. We instantiate this framework with MIMONet, a branch-trunk operator extended with three practical choices: multi-modal branch encoders for heterogeneous (scalar and function-valued) inputs; multiplicative branch fusion to preserve the bilinear PDE coupling structure; and shared-latent multi-field decoding with per-channel basis projections at the trunk's final layer. Evaluated across escalating complexity, from canonical lid-driven cavity flow to pressurized water reactor subchannels to fully coupled heat exchangers, MIMONet achieves below 5% relative errors and sub-millisecond inference on data-center accelerators (0.35 ms / 46 mJ per heat-exchanger inference on an NVIDIA H200, and sub-millisecond across the A40-H200-GH200 range), while remaining stable under 50% sensor noise. By staying accurate as geometric confinement and physics coupling intensify, MIMONet shows that operator-based virtual sensing can restore observability where physical instrumentation fails, establishing simulation-based feasibility within the evaluated operating envelopes as a step toward future experimental and cross-solver validation for safety-critical energy systems.

06.
medRxiv (Medicine) 2026-06-16

A Poisson Process Life Expectancy framework for optimising patient lifetime during chemotherapy

Cancer therapy balances between two competing objectives - treatment efficacy against the tumour and the risk of treatment related severe adverse events, including patient death. Most existing optimal control theory (OCT) formulations rely on optimising heuristic cost functionals that lack direct clinical interpretability. In clinical practice treatment efficacy and patient tolerability are primarily assessed through survival metrics and adverse event rates. Here we introduce the Continuous Lifetime Payoff (CLP), a novel OCT objective functional that directly links treatment decisions to patient survival. It explicitly incorporates tumour dynamics, tumour eradication, and patient mortality from tumour progression, drug-related toxicity and age. We fit age-related mortality from life tables and infer parameters from simulated survival data. The CLP provides a clinically grounded framework for optimising chemotherapy regimens.

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

LM-SPT: LM-Aligned Semantic Distillation for Speech Tokenization

With the rapid progress of speech language models (SLMs), discrete speech tokens have emerged as a core interface between speech and text, enabling unified modeling across modalities. Recent speech tokenization approaches aim to isolate semantic information from low-level acoustics to better align with language models (LMs). In particular, previous methods use self-supervised learning (SSL) teachers such as HuBERT to extract semantic representations, which are then distilled into a semantic quantizer to suppress acoustic redundancy as well as capture content-related latent structures. However, these tokenizers often operate at relatively high frame rates, producing token sequences significantly longer than their textual counterparts and hindering seamless integration with pretrained LMs. Although recent methods attempt to reduce the token rate by applying uniform average pooling to SSL features, this can over-smooth content-bearing regions and dilute the structural information, thereby potentially limiting the LM alignment. To address this, we propose LM-SPT, an LM-aligned speech tokenization method based on semantic speech-resynthesis distillation. Instead of directly matching teacher and student features via pooling, LM-SPT resynthesizes speech from semantic tokens only and minimizes the discrepancy between representations extracted from the original and resynthesized waveforms using a frozen, LM-aligned speech encoder. This indirect supervision avoids rigid temporal alignment and encourages dedicated semantic units that are more semantically aligned with LMs under reduced frame rates. Experimental results show that the proposed LM-SPT consistently outperforms previous semantic-enhanced speech tokenizers when applied to SLMs for the tasks of automatic speech recognition and text-to-speech, even without compromising the speech reconstruction fidelity at the codec level.

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

PermaVid: Consistent Video Generation Across Edits via Disentangled Context Memory

Consistent video generation under editing operations requires persistence: when edits modify scene appearance or layout, subsequent generations should remain coherent across time and viewpoints. However, existing memory designs struggle to maintain long-term consistency after such modifications, as stored contexts may become outdated or invalid. To address this, we propose PermaVid, a novel framework built upon a multi-modal context memory that disentangles spatial context into semantic appearance and geometric structure, together with an edit-aware memory update and retrieval strategy that keeps memory evolution aligned with subsequent observations. Specifically, we develop two complementary memory banks: an RGB context memory that captures appearance-aware observations while implicitly encoding geometry, and a depth context memory that preserves geometry-only structure disentangled from semantics. Building on this design, we introduce a memory-guided video generation model that performs multi-modal feature fusion under reference conditions drawn from mixed-modality memory contexts. Experiments demonstrate that our method maintains strong long-term semantic and structural consistency after edits, significantly outperforming state-of-the-art methods.

09.
arXiv (CS.CV) 2026-06-17

A Benchmark for Omni-Modal Reasoning in Long Videos

Long-form omni-modal video understanding requires integrating vision, speech, and ambient audio with coherent long-context reasoning. Existing video benchmarks often trade off temporal scale, modality coverage, open-ended interaction, and interpretable scoring. To address this gap, we introduce LongShOTBench, a long video understanding benchmark designed around three coupled goals: holistic omni-modal integration, intent-driven open-ended interaction, and rubric-level diagnosis. It builds single- and multi-turn questions from real viewing scenarios, with systematic tasks probing visual, speech, ambient-audio, temporal, and cross-modal reasoning. Each item includes a reference answer and a weighted criterion-level rubric, letting evaluation identify which perceptual facts, temporal links, modality-grounding requirements, and reasoning steps are satisfied or missed. All samples are manually verified to improve grounding, clarity, and rubric reliability. We also introduce LongShOTAgent, a training-free omni-modal evidence-seeking agent coupling full-video preprocessing with targeted retrieval, query-adaptive segment refinement, and explicit claim verification over visual, speech, and non-speech audio evidence. Its iterative search-refine-verify loop exposes intermediate evidence and lets modality-specific specialists re-analyze relevant moments before answering. We evaluate 105 video-capable models spanning open-source omni-modal models, vision-language systems, audio LLMs, agentic pipelines and closed-source APIs. Current MLLMs remain far from saturating LongShOTBench, while our LongShOTAgent is the strongest training-free system, reaching 66.64% overall. By releasing the benchmark, leaderboard, and method, we provide a shared, interpretable testbed for advancing long-form omni-modal video reasoning. Code, data, and the leaderboard are available at https://longshot.cvmbzuai.com/.

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

Can LLM Agents Infer World Models? Evidence from Agentic Automata Learning

We propose agentic automata learning to evaluate the extent to which tool-calling LLM agents can uncover hidden environments through interaction. In our setup, an agent should uncover a hidden deterministic finite automaton (DFA) by interacting with an oracle through (1) membership queries ("Does this string belong to the target language?") and (2) equivalence queries ("Is this the target DFA?"). This yields a scalable testbed with controlled task complexity, measurable interaction efficiency, and strong baselines (classic automata-learning algorithms). Evaluating state-of-the-art LLMs, we find that performance drops sharply as DFA size increases. Reasoning models are markedly stronger than non-reasoning models, yet trajectory analyses reveal recurring failures in query planning, evidence integration, and hypothesis construction. Overall, our results show that current LLM agents can sometimes perform non-trivial interactive discovery, but remain far less robust and efficient than classic algorithms for the task.

11.
medRxiv (Medicine) 2026-06-18

Guiding the development of climate counterfactuals for health impact attribution studies

Climate change detection and attribution (D&A) methods have become vital for quantifying the influence of anthropogenic forcing on the Earth's systems, including human health. Health impact attribution (HIA) studies seek to disentangle climate-driven health effects from natural variability yet are often constrained by the availability of accessible counterfactual climate scenarios. This tutorial paper presents a flexible, reproducible framework for developing counterfactual climates without reliance on computationally intensive global circulation models. We provide practical, R-based methodologies for constructing both trend-based (temperature and non-temperature) and event-based counterfactual, using a variety of techniques including model residual detrending, data-driven decomposition (e.g., Singular Spectrum Analysis and Empirical Mode Decomposition) and stochastic weather generators. The tutorial also explores the incorporation of greenhouse gas concentrations as forcing variables, rather than global mean temperature anomalies. By operationalising these methods through worked examples and an open code repository, this paper aims to build capacity within the HIA community, enhance methodological transparency, and foster interdisciplinary collaboration between climate and health researchers.

12.
arXiv (CS.LG) 2026-06-11

A Data-Centric Framework for Detecting and Correcting Corrupted Labels

arXiv:2606.11699v1 Announce Type: new Abstract: The performance of machine learning and deep learning models largely depends on the quality of the training data. However, the quality of the real-world datasets is often compromised by noisy labels, which can substantially degrade model accuracy and reliability. To address this challenge, we propose Relabeler, an end-to-end data-centric framework for detecting and correcting corrupted labels. For corrupted label detection, Relabeler jointly leverages both local and global relationships among data instances to identify potentially noisy samples. After detecting suspicious instances, Relabeler further performs label correction by estimating the most probable clean label for each instance based on both its input features and observed noisy label. Extensive experiments across multiple datasets, noise types, and noise rates demonstrate that Relabeler consistently outperforms state-of-the-art baselines, achieving up to 58% improvement in label correction precision and 6% improvement in downstream task performance.

13.
arXiv (math.PR) 2026-06-11

The Statistical Compass

arXiv:2606.11282v1 Announce Type: cross Abstract: This monograph develops probability and stochastic-process ideas as a translation language for statistics: from designed observations and data objects to targets, stability statements, inference, and use. The chapters move from motivating examples and randomization through probability measures, kernels, likelihoods, data objects, weak convergence, empirical fields, functional data, M- and Z-estimation, testing, local approximations, event-time processes, and prediction. Historical and biomedical examples are used to keep abstract objects tied to records, mechanisms, and decisions. The aim is to give readers a common grammar for classical probability, modern data structures, and statistical practice.

14.
arXiv (quant-ph) 2026-06-19

Benchmark of quantum algorithms for ground state preparation in the presence of noise

arXiv:2606.20551v1 Announce Type: new Abstract: We compare the performance of representative cooling, adiabatic, and optimization algorithms for ground-state preparation in the presence of noise. Using an exactly solvable family of quadratic fermionic Hamiltonians subject to depolarizing noise, we derive the scaling of the achievable relative energy as a function of the noise rate and support these results with numerical simulations. The Hamiltonian exhibits two phases, separated by a quantum phase transition. As expected, the performance of the different algorithms depends on the phase: adiabatic evolution is favorable in the trivial phase, while a multi-frequency cooling algorithm, as proposed in [1], becomes competitive or superior in the topological phase, where gap-closing limits adiabatic protocols. We further present numerical results for the quantum approximate optimization algorithm [2], showing that it performs competitively with cooling in the trivial phase but is typically outperformed in the topological regime. Finally, we show that for this model the cooling protocol exhibits enhanced robustness to parameter imperfections, highlighting its potential advantage for realistic implementations of noisy quantum state preparation. The analytical approach developed here, in conjunction with numerical validation, establishes an extendable approach to benchmarking ground-state preparation algorithms.

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

Blueprint First, Model Second: A Framework for Deterministic LLM Workflow

arXiv:2508.02721v2 Announce Type: replace-cross Abstract: While powerful, the inherent non-determinism of large language model (LLM) agents limits their application in structured operational environments where procedural fidelity and predictable execution are strict requirements. This limitation stems from current architectures that conflate probabilistic, high-level planning with low-level action execution within a single generative process. To address this, we introduce the \textsc{Source Code Agent} framework, a new paradigm built on the ``Blueprint First, Model Second'' philosophy that decouples workflow logic from the generative model. An expert-defined operational procedure is first codified into a source code-based Execution Blueprint, which is then executed by a deterministic engine. The LLM is strategically invoked as a specialized tool to handle bounded, complex sub-tasks within the workflow, but never to decide the workflow's path. We evaluate on the TravelPlanner benchmark for constraint-aware travel planning. The \textsc{Source Code Agent} achieves a 35.56\% final pass rate, a 97.6\% improvement over the state-of-the-art ATLAS baseline (18.00\%) on the same Claude-Sonnet-4 backbone. Critically, it reduces constraint violations by 96.0\% (11 vs 275) while improving execution efficiency by 27.1\% (10.2$\pm$0.7 steps vs 14.0). Two production incident-diagnosis deployments and additional results on ScienceWorld and ALFWorld confirm that the architecture transfers beyond travel planning to procedurally well-defined, constraint-intensive workflows. Our work enables the verifiable and reliable deployment of autonomous agents in applications governed by strict procedural logic.

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

PATCH: Action-Chunk-Conditioned Latent Patch Innovation Monitoring for Robot Manipulation

Learning-based manipulation policies have made substantial progress in real-world robot manipulation, particularly for short-horizon action generation. However, deployment in open workspaces remains fragile under unexpected local scene dynamics, such as moving objects, transient occlusions, or disturbances near the intended motion. Existing runtime monitors often rely on global observation anomalies, policy uncertainty, or frame-level visual changes, and struggle to distinguish task-relevant execution risk from benign visual variation. We introduce PATCH, an action-chunk-conditioned latent patch innovation monitor for deployment-time intervention. Given the active action chunk, PATCH defines a projected execution corridor, predicts latent patch evolution inside it, and accumulates persistent residuals unexplained by the robot's own motion. These residuals form a localized intervention signal that allows PATCH-Router to pause execution, select an available recovery source, and resume the original policy once localized innovation subsides. Experiments on real robot rollout data show that PATCH produces more stable and context-relevant triggers than competing runtime monitors. Real-robot deployment further demonstrates monitor-driven intervention and policy resumption for disturbance-aware manipulation. Project Page: https://yananzhou5555.github.io/PATCH/.

18.
arXiv (CS.LG) 2026-06-16

GauS: Differentiable Scheduling Optimization via Gaussian Reparameterization

arXiv:2602.20427v2 Announce Type: replace Abstract: Efficient operator scheduling is a fundamental challenge in software compilation and hardware synthesis. While recent differentiable approaches have sought to replace traditional ones like exact solvers or heuristics with gradient-based search, they typically rely on categorical distributions that fail to capture the ordinal nature of time and suffer from a parameter space that scales poorly. In this paper, we propose a novel differentiable framework, GauS, that models operator scheduling as a stochastic relaxation using Gaussian distributions, which fully utilize modern parallel computing devices like GPUs. By representing schedules as continuous Gaussian variables, we successfully capture the ordinal nature of time and reduce the optimization space by orders of magnitude. Our method is highly flexible to represent various objectives and constraints, which provides the first differentiable formulation for the complex pipelined scheduling problem. We evaluate our method on a range of benchmarks, demonstrating that Gaus achieves Pareto-optimal results.

19.
medRxiv (Medicine) 2026-06-18

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

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

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

Precision Is Not Faithfulness: Coverage-Aware Evaluation of Grounded Generation with a Complete Oracle

Reference-free faithfulness metrics verify each atomic claim a model makes against ground truth, and are increasingly used to evaluate grounded generation. We show they share a blind spot: they measure only precision – are the stated claims supported? – and therefore reward abstention, since a model can score near-perfect faithfulness by saying almost nothing. We make this measurable using Formula 1 telemetry, a domain where strategic ground truth is derived deterministically and, crucially, completely: for each decision we know the full set of facts that mattered. This completeness – absent in open-domain faithfulness benchmarks – lets us measure recall (coverage of the relevant facts) exactly, alongside precision. On a multilingual (EN/ES/PT) benchmark of 7,253 decision instances spanning 157 races, the most precise frontier model covers under half of the relevant facts and ranks last by F1, so requiring coverage reorders the systems; the same effect reappears in a second complete-oracle domain (NOAA weather forecasts). Fine-tuning small models (1B-7B) on the complete oracle closes the precision-recall gap entirely (F1 ~0.98), beating every zero-shot frontier system regardless of scale. We pair faithfulness with coverage into a single score, validate the metric (controlled perturbation; agreement across a model-free regex extractor and a cross-family LLM extractor, system-level Spearman 1.0), and give a verifier-guided generation method that improves precision and recall without references. We release the benchmark, structured annotations, metric, baselines, and an interactive demo.

21.
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.

22.
arXiv (quant-ph) 2026-06-12

Multiple Topological Haldane Phases for Symmetry-Protected Quantum Information Processing

arXiv:2606.12685v1 Announce Type: new Abstract: Symmetry-protected topological phases have attracted significant interest at the fundamental level and as a potential platform for quantum information processing, owing to their protected edge states and resilience to perturbations. Applying these features for practical and efficient quantum computation is highly desirable, but remains an open challenge. Here, we demonstrate the partitioning into multiple independent Haldane phase subsystems of a single spin-1/2 ladder system and propose this as a scalable architecture for gate-based quantum computation, which takes advantage of the symmetry-protected topological order. We encode qubits in the two topological states of the $S^{z}=0$ sector of each subsystem. Finite-size effects, typically viewed as detrimental, instead provide a controllable energy splitting that enables single-qubit rotations using only local magnetic fields. An Ising-type interaction between neighboring subsystem edges generates entangling gates, enabling universal quantum computation driven by two control parameters that are easily accessible experimentally. Our results demonstrate how symmetry-protected topological phases can be directly harnessed for circuit-model quantum computation in realistic systems.

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

An End-to-End Hybrid Framework for Rumour Detection in Low-Resources Algerian Dialect

The rapid growth of social media has intensified the spread of rumours. This issue is more challenging in the Algerian context due to the informal and code-switched nature of dialectal content, the scarcity of annotated resources, and the limited effectiveness of standard Arabic NLP tools on dialect text. This paper presents an end-to-end rumour detection hybrid framework for Algerian dialect social media content. We build a domain-specific annotated dataset by combining real social media posts, synthetic data, and the FASSILA corpus, with automatic labeling based on a similarity-based annotation process. A transliteration pipeline is also introduced to generate parallel datasets in Arabic script and Arabizi. We evaluate multiple approaches, including classical machine learning, deep learning, transformers, and hybrid models. Experimental results show that a hybrid approach combining transformer embeddings with a classical classifier achieves the best performance, reaching an F1-score of 0.84. We also find that domain-specific pre-training is more important than model size, with social media-trained models outperforming larger models trained on formal Arabic corpora. These results demonstrate the feasibility of rumour detection in low-resource Algerian dialect settings.

24.
medRxiv (Medicine) 2026-06-11

Neighborhood socioeconomic status associated with post-stroke cognitive impairment: a retrospective cohort study

Background: Late complications after stroke (LCAS), including cognitive symptoms, impact quality of life and recovery. It is not known if neighborhood-level measures of socioeconomic status (SES) influence LCAS. This study assessed associations between SES measures, including neighborhood income inequality (Gini) and area deprivation index (ADI), and cognitive symptoms after acute ischemic stroke (AIS) in a hospital leveraging active surveillance of LCAS. Methods: This retrospective cohort study included 512 patients hospitalized with AIS at Tufts Medical Center with subsequent follow-up (between zero and three months or between three and twelve months) in the Stroke Clinic from 1/1/2018 - 12/31/2022. Using ZIP code data, patients were characterized as low Gini (low inequality) and high ADI (high deprivation) (Gini = 5) by state medians. These variables were combined, indicating patients who were living in both a low Gini and high ADI neighborhood to evaluate the effects of living in a homogeneously deprived area. There were 206 and 281 patients in the low Gini and high ADI groups respectively. 140 patients lived in a low Gini and high ADI neighborhood. The multivariable logistic analysis assessed the likelihood of cognitive symptoms, adjusting for age, race, ethnicity, sex, NIH Stroke Scale (NIHSS), thrombolysis, active LCAS surveillance, poverty, and ADI-Gini combination. Results: There were no associations between high ADI (OR: 1.03, 95% CI: 0.67 ? 1.57) or low Gini (OR: 1.74, 95% CI: 0.98 ? 3.07) alone and cognitive symptoms after AIS. However, the combined variable demonstrated increased likelihood of cognitive symptoms in the high ADI-low Gini group (OR: 1.82, 95% CI: 1.08 ? 3.06). Conclusions: This study suggests that individuals living in homogeneously deprived neighborhoods report higher likelihood of cognitive symptoms after AIS. Further studies with increased power are needed to investigate the underlying causes of these disparities and to develop interventions to reduce these complications.

25.
PLOS Computational Biology 2026-06-18

scMagnifier: Resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering

Authors:

by Zhenhui He, Dong Kangning Resolving fine-grained cell subtypes in single-cell RNA sequencing (scRNA-seq) data remains challenging, as their subtle transcriptional differences are often obscured by technical noise and data sparsity. Here, we present scMagnifier, a consensus clustering framework that leverages gene regulatory network (GRN)-informed in silico perturbations to amplify subtle transcriptional differences and uncover latent cell subpopulations. scMagnifier perturbs candidate transcription factors (TFs), propagates perturbation effects through cluster-specific GRNs to simulate post-perturbation expression profiles, and integrates clustering results across multiple perturbations into stable subtype assignments. Additionally, scMagnifier introduces regulatory perturbation consensus UMAP (rpcUMAP), a perturbation-aware visualization that provides clearer separation between cell subtypes and guides the selection of the optimal number of clusters. In both single-batch and multi-batch benchmarks, scMagnifier consistently improves the resolution and accuracy of fine-grained cell type identification. Notably, when integrated with spatial clustering methods such as STAGATE, scMagnifier is compatible with spatial transcriptomics workflows and effectively reveals tumor cell subtypes and their spatial organization in ovarian cancer.