Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
arXiv (CS.AI) 2026-06-16

AgentLeak: A Benchmark for Internal-Channel Privacy Leakage in Multi-Agent LLM Systems

arXiv:2602.11510v3 Announce Type: replace Abstract: Multi-agent Large Language Model (LLM) systems create privacy risks that current output-only benchmarks cannot measure. When agents coordinate on tasks, sensitive data may pass through inter-agent messages, shared memory, and tool arguments, all pathways that final-output audits typically do not inspect. We introduce AgentLeak, a benchmark for evaluating internal-channel privacy leakage in multi-agent LLM systems. AgentLeak instruments seven privacy-relevant communication pathways and provides a large-scale empirical evaluation focused on final outputs, inter-agent messages, and shared memory. Across 1,000 scenarios spanning healthcare, finance, legal, and corporate domains, five production LLMs (GPT-4o, GPT-4o-mini, Claude 3.5 Sonnet, Mistral Large, and Llama 3.3 70B), and 4,979 validated execution traces, we find that multi-agent configurations reduce final-output leakage (C1: 27.2% vs 43.2% in single-agent mode) compared with single-agent baselines but introduce internal channels that raise total system exposure to 68.9% (aggregated across C1, C2, C5). Inter-agent messages (C2) leak at 68.8%, compared with 27.2% for final outputs (C1), meaning that output-only audits miss 41.7% of violations. Across all five models and four domains, the pattern C2 $\geq$ C1 holds consistently. These results suggest, within the evaluated coordinator-worker setting, that privacy risk in multi-agent systems is strongly shaped by architectural coordination channels rather than final-output behavior alone: it arises from internal channels that remain invisible to standard output-level defenses.

02.
medRxiv (Medicine) 2026-06-17

Determinants of non-utilization of insecticide-treated nets among children under five in Rwanda: analyses of the 2024 Rwanda malaria indicator survey

Background Insecticide-treated nets (ITNs) are effective for preventing malaria among children under five years, who bear a disproportionate burden of malaria. This study assessed the prevalence and determinants of ITN non-utilization among children under five in Rwanda using data from the 2024 Rwanda Malaria Indicator Survey (RMIS).Methodology This cross-sectional study utilized nationally representative data from the 2024 RMIS. Analyses were restricted to children under five residing in households that owned at least one ITN. The outcome was non-utilization of ITN, defined as not sleeping under an ITN the night preceding the survey. Survey-weighted descriptive statistics were used to estimate the prevalence of ITN non-utilization. Factors associated with non-utilization were identified using a survey-weighted Poisson regression model. Adjusted prevalence ratios (aPRs), 95% confidence intervals and p-values were reported.Results A total of 1,979 children were included in the study. The weighted prevalence of ITN non-utilization among children under five years was 20.11% (95% CI: 17.81 - 22.63). After adjusting for other factors, children aged 2 - 3 years were associated with an 83% higher prevalence of ITN non-utilization compared with those aged [&le;]1 year (aPR = 1.83, 95% CI: 1.423 - 2.352, p < 0.001). Compared with households that owned only one ITN, children in households with three or more ITNs were associated with a 76% lower prevalence of ITN non-utilization (aPR = 0.24, 95% CI: 0.171 - 0.332, p < 0.001). Children living in households with 5 - 7 members were associated with an 87% higher prevalence of ITN non-utilization compared with those in households with 1 - 4 members (aPR = 1.87, 95% CI: 1.476 - 2.358, p < 0.001).Conclusion The findings suggest that ITN utilization among children is influenced not only by household access to nets but also by household composition and dynamics that shape the allocation and use of available preventive resources.

03.
medRxiv (Medicine) 2026-06-15

Multidimensional nutritional assessment in Crohns disease: cross-sectional comparison of active disease and remission

Malnutrition is common in Crohns disease (CD), and its assessment requires multiple tools. Comprehensive evaluation of nutritional status in a population with CD, predominantly characterized by metabolic phenotype, was inadequately reported. This study evaluated the nutritional status of CD patients using anthropometric, clinical, and biochemical measures and compared patients with active disease with those in remission. This cross-sectional study included 127 adults with CD: 63 with active disease and 64 in remission. Disease activity was classified using the Crohns Disease Activity Index, the Simple Endoscopic Score for Crohns Disease, and magnetic resonance enterography. Nutritional assessment included body mass index (BMI), mid-upper arm circumference, calf circumference, triceps skinfold thickness, mid-arm muscle circumference, Mini Nutritional Assessment-Short Form (MNA-SF), and biochemical markers including hemoglobin, serum iron, folate, vitamin B12, albumin, and zinc. Malnutrition was defined using the Global Leadership Initiative on Malnutrition criteria. Overall, 47.2% of participants were malnourished. Malnutrition was significantly more frequent in active disease than in remission (81.0% vs. 14.1%, P

04.
arXiv (CS.CV) 2026-06-17

ProCUA-SFT Technical Report

Training computer-use agents (CUAs) – models that interact with graphical desktops through screenshots and keyboard/mouse actions – requires large-scale, diverse trajectory data collected in full desktop environments. The largest public resource, AgentNet (22.5K human trajectories), leads to negative transfer when used for supervised fine-tuning (SFT): continuing training UI-TARS 7B on AgentNet causes OSWorld success rate to fall from 26.3% to 8-10%. We present ProCUA-SFT, a dataset of 3.1M step-level SFT samples distilled from 93K synthetic trajectories across 2,484 application combinations. The dataset is produced by a fully automated pipeline that (i) synthesizes grounded tasks on live desktops seeded with real-world content – 912 spreadsheets from SpreadsheetBench, approximately 10K permissively-licensed presentations from Zenodo10K, and multi-application OSWorld configs – and (ii) verifies each task's feasibility through binary precondition checking before rollout. A single VLM (Kimi-K2.5) serves as goal generator, precondition judge, and trajectory executor, eliminating planner-actor capability gaps. Each trajectory is expanded into step-prefix samples that exactly reproduce the context layout seen at inference time. Fine-tuning UI-TARS 7B on ProCUA-SFT for one epoch yields 45.0% on OSWorld – an 18.7 percentage-point improvement over the base model and over 35% above AgentNet-trained counterparts. A subset of ProCUA was incorporated into the training data for the Nemotron 3 Nano Omni model, contributing to its computer-use capabilities.

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

SymQNet: Amortized Acquisition for Low-Latency Adaptive Hamiltonian Learning

arXiv:2606.12808v1 Announce Type: cross Abstract: Adaptive Hamiltonian learning is central to calibrating and characterizing quantum devices. In an adaptive controller, choosing the next experiment is itself a computation. Bayesian design rules are recomputed after every posterior update, and that step can take seconds. Across hundreds of shots, those seconds become a significant wall-clock cost for adaptivity. We introduce SymQNet, an amortized reinforcement-learning approach for low-latency adaptive Hamiltonian learning. SymQNet learns a posterior-conditioned acquisition policy offline, then uses a fast policy forward pass online while retaining Bayesian posterior feedback. On transverse-field Ising benchmarks, SymQNet substantially reduces acquisition latency relative to bounded Fisher-information search and bounded two-step Bayesian active learning by disagreement (BALD). At five qubits, it reduces acquisition-only decision latency by $47.1\times$ and $72.6\times$ relative to these online baselines; at twelve qubits, full simulated steps take $1.02$ s for SymQNet versus $13.27$ s for bounded two-step BALD. Overall, we show that learned acquisition can make adaptive Hamiltonian learning practical for repeated low-latency workloads.

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

Federated Foundation Language Model Post-Training Should Focus on Open-Source Models

arXiv:2505.23593v4 Announce Type: replace Abstract: Post-training of foundation language models has emerged as a promising research domain in federated learning (FL) with the goal to enable privacy-preserving model improvements and adaptations to user's downstream tasks. Recent advances in this area adopt centralized post-training approaches that build upon black-box foundation language models where there is no access to model weights and architecture details. Although the use of black-box models has been successful in centralized post-training, their blind replication in FL raises several concerns. Our opinion is that using black-box models in FL contradicts the core principles of federation such as data privacy and autonomy. In this paper, we critically analyze the usage of black-box models in federated post-training, and provide a detailed account of various aspects of openness and their implications for FL.

07.
medRxiv (Medicine) 2026-06-23

Post Hoc Localization of Beam F3 Stimulation Targets: An MRI-Derived Geodesic Approach for Refined TMS E-Field Simulations

Background: Transcranial magnetic stimulation (TMS) targeting the left dorsolateral prefrontal cortex (dlPFC) is an established treatment option in major depressive disorder. One of the most common approaches for targeting the dlPFC is the Beam F3 method, which determines the stimulation site (F3Beam) as a function of external cranial measurements. Precise knowledge of the individual stimulation site is essential for imaging-based analyses of TMS effects. However, due to the method's reliance on individual anatomy, retrospective identification of F3Beam targets across cohorts is challenging, limiting the analysis of existing datasets. We developed a scalable method to reconstruct subject-specific F3Beam target locations for e-field simulations based on structural imaging. Methods: High-resolution three-dimensional (3D) T1-weighted MRI was used to generate individual scalp meshes via the ''Simulation of Non-Invasive Brain Stimulation'' (SimNIBS) software. Subject-specific anatomical distances and coordinates of interest were measured geodesically using a Python-based script to reconstruct the individual F3Beam targets. Validation included a retrospective comparison between digital geodesic measurements and manual cranial measurements in 20 patients and a prospective comparison with MR-visible scalp markers in 2 healthy controls. To assess the impact of our targeting algorithm on e-field simulations, volumetric e-field maps based on three potential targets (F3Beam, F3MNI, F3Geo) were generated in SimNIBS and compared using voxel-wise statistics in SPM12. Results: Retrospective analysis revealed a systematic bias towards higher in vivo measurements compared to digital geodesic measurements, though deviations in the final distances determining F3Beam (xBeam and yBeam) were minimal ({Delta}xBeam: 0.11 {+/-} 0.08 cm; {Delta}yBeam: 0.14 {+/-} 0.21 cm). Prospective validation demonstrated that F3Beam coordinates better matched in vivo coil positions than group-template-derived targets (F3MNI). Group-level analysis showed method-dependent clustering of coil positions with corresponding voxel-wise e-field differences. Conclusions: Individualized geodesic measurements may enable accurate, scalable and retrospective identification of Beam F3 targets and coil orientations. This approach may yield more accurate e-field simulations than group-template based targeting and provides a practical method for retrospective analysis of existing TMS treatment cohorts. This could be leveraged to identify response predictors or imaging-based biomarkers of treatment response.

08.
arXiv (CS.LG) 2026-06-17

OmniPlan: An Adaptive Framework for Timely and Near-Optimal Network Planning Optimization

arXiv:2606.18105v1 Announce Type: cross Abstract: Network planning optimization is a fundamental problem across diverse domains, including transportation systems, communication networks, and power grids. It requires simultaneous optimization of multiple competing objectives under complex constraints. Existing network planning optimization frameworks rely on mixed integer programming (MIP) solvers, heuristics, and deep reinforcement learning (DRL) models to compute planning decisions. However, they lack effective adaptability to diverse and dynamic user intents, thus leading to the trade-off between execution time and optimality. In this paper, we propose OmniPlan, an adaptive framework that achieves both timeliness and near-optimality in network planning optimization. To achieve the adaptability lacking in existing solutions, OmniPlan employs a large language model (LLM)-based interpreter to convert heterogeneous natural-language intents into a unified and quantifiable user-preference vector. Then it employs a mixture-of-experts architecture that integrates MIP solvers, heuristics, and DRL models as specialized experts, where OmniPlan adapts to diverse intents by dynamically selecting timely and near-optimal experts. Finally, it incorporates a DRL-based expert configuration module that fine-tunes optimization objective weights to align planning decisions with user-specific preferences. We evaluate OmniPlan with a representative real-world workload, i.e., distributed machine learning (ML), where we leverage OmniPlan to offload a wide spectrum of ML inference tasks, e.g., decision trees, SVM, naive Bayes, XGBoost, and random forests, onto a network of hardware devices. Our experiments on a real-world testbed indicate that OmniPlan achieves near-optimal and low-execution-time offloading for real-world ML inference tasks, reducing latency by up to 97.8\% and network device resource consumption by up to 11.5\%.

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

Reframing AI Loss of Control: What It Is, How to Have It, How to Lose It

arXiv:2606.12442v1 Announce Type: cross Abstract: At present, loss of control risks have gained much prominence in public discussion, particularly in relation to AI, with extensive discourse present among academics, frontier labs, and even governments. However, in the existing literature, the concept seems to rest on surprisingly weak foundations, where even those that discuss loss of control extensively do not first establish what control is and what exactly is being lost. Our paper aims to address these gaps. We establish a working definition of control by anchoring it to the "setting and getting of goals". Then, we discuss various aspects of control, built on foundational concepts from related fields like cybernetics, management control, and control theory. This includes who (or what) can be in control, and the things they require to be in control, such as the ability to set goals, having a functional control loop, having requisite variety, and having sufficient goal alignment. Once a framework for control is established, we then discuss how control can be lost, how AIs can contribute to such loss of control, and offer relevant recommendations for how one can maintain control. One interesting consequence of our work is that humanity, as individuals and as groups, can lose varying degrees of control as a result of AI behaviour that is far below the level of superintelligence; the potential for loss of control scenarios (as we define them) already exist, and have existed for a long time.

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

A General Framework for Decision Trees via Bregman Divergences

arXiv:2606.13984v1 Announce Type: cross Abstract: Decision trees are one of the fundamental tools in statistical learning due to their interpretability, flexibility, and their ability to adapt to nonlinear structures. Among them, the Classification and Regression Trees, introduced by Breiman, Friedman, Olshen, and Stone in 1984, became one of the most influential algorithms and remains one of the most widely used methods for classification and regression problems. On the other hand, Bregman divergences, introduced by Lev Bregman in 1967 in the context of convex optimization, provide a broad family of loss functions that naturally generalize the squared Euclidean distance. This family includes, among others, the Kullback-Leibler divergence, the Poisson divergence, and the Itakura-Saito divergence, as well as several losses associated with distributions belonging to the exponential family. Moreover, Bregman divergences possess a rich geometric structure and deep connections with convex analysis and information geometry. In this work, we propose a generalization of the CART paradigm based on Bregman divergences, thereby obtaining a broader family of decision trees adapted to different statistical models and underlying geometries. Although algorithms such as CART or classical implementations such as rpart incorporate different impurity criteria, these are usually introduced in an ad hoc manner for each specific model. In contrast, the Bregman divergence approach provides a unified framework that allows these criteria to be derived and interpreted from common convex and geometric principles. Beyond the algorithmic construction, we also investigate theoretical properties of these trees. In particular, we study how properties of the generating convex function – such as strong convexity or smoothness – influence impurity gains between parent and child nodes, as well as stability and consistency properties of the estimator.

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

Building Social World Models with Large Language Models

Understanding and predicting how social beliefs evolve in response to events – from policy changes to scientific breakthroughs – remains a fundamental challenge in social science. Given LLMs' commonsense knowledge and social intelligence, we ask: Can LLMs model the dynamics of social beliefs following social events? In this work, we introduce the concept of the Social World Model (SWM), a general framework designed to capture how social beliefs evolve in response to major events. SWM learns state-transition functions for social beliefs by mining temporal patterns in social data and optimizing the evidence lower bound, without the need for explicit human annotations linking events to belief shifts, or for expensive census data. To evaluate SWM, we introduce a benchmark, SWM-bench, derived from real-world prediction markets, specifically Kalshi and Polymarket. SWM-bench includes over 12k data points for social belief prediction tasks spanning diverse domains such as politics, finance, and cryptocurrency. Our experimental results show that SWM significantly outperforms time-series foundation models, achieving state-of-the-art results on Kalshi data and demonstrating competitive performance on Polymarket data, while offering interpretable insights into the underlying mechanisms of social belief dynamics.

12.
arXiv (CS.AI) 2026-06-18

SAE Interventions are Unreliable: Post-Intervention Recovery of Suppressed Behavior

arXiv:2606.18322v1 Announce Type: cross Abstract: Sparse Autoencoders (SAEs) decompose residual-stream activations into interpretable features. Recent latent-space defenses increasingly rely on these decompositions, assuming that identified "unsafe" SAE features serve as actionable handles for monitoring and intervention. In this paradigm, clamping a specific harmful feature is expected to reliably prevent model misbehavior. However, we show that this success may hide a recoverable failure mode: the clamp may block one visible route to a behavior without eliminating the behavior itself. We formulate this vulnerability as post-intervention recovery, a constrained residual-space optimization problem. Starting from the post-intervention residual state, we optimize residual perturbations to recover the pre-intervention behavior while preserving the post-intervention values of the targeted SAE features. Even under a strong threat model where the intervention remains active throughout optimization and generation, recovery remains possible. To rule out that recovery simply undoes the intervention, we use encoder-orthogonal updates for single-layer interventions and the corresponding feature-map Jacobian in the cross-layer setting. Across TPP, unlearning, IOI, and refusal steering experiments, this stress test reveals recoverable behavior despite successful feature-level intervention. Especially in the safety-critical refusal-steering setting, we achieve a 95.8% recovery rate on valid samples while keeping defended-feature relative drift to 0.131, substantially below suffix-based baselines. A recovery-path attribution analysis further localizes this recovery to the SAE reconstruction residual, the component left unexplained by the SAE. These results expose a gap between feature-level control and behavioral completeness: SAE features can support causal intervention, but controlling them does not guarantee control over the underlying behavior.

13.
PLOS Medicine 2026-05-08

Optimal minimal residual disease threshold in pediatric acute myeloid leukemia: A retrospective cohort study based on the TARGET database

by Xiong-yu Liao, Hong Zheng, Jian-pei Fang, Dun-hua Zhou, Kun-yin Qiu Background Minimal residual disease (MRD) monitoring is a cornerstone of risk stratification in pediatric acute myeloid leukemia (AML), with a threshold of 0.1% conventionally defining positivity by flow cytometry. Advances in flow cytometric technologies, enabling detection of leukemic cells with higher sensitivity and specificity, warrant a reevaluation of whether a lower threshold improves prognostic accuracy. Methods and findings We conducted a retrospective cohort study using data from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)-AML initiative. The study population comprised 1,205 pediatric patients with de novo AML treated across Children’s Oncology Group (COG) clinical trial centers. Patients were enrolled between September 1996 and December 2016, with a median follow-up of 6.2 years (range: 0.5–20.1 years). The primary objective was to compare the prognostic performance of the traditional MRD threshold (≥0.1%) with a lower threshold (≥0.05%) after induction courses 1 and 2. The main outcome measure was 5-year event-free survival (EFS). Analyses included Kaplan−Meier survival estimates, Cox proportional hazards models to calculate hazard ratios (HR) with 95% confidence intervals (CI), receiver operating characteristic (ROC) curves, and net reclassification improvement (NRI). The optimal threshold for predicting 5-year EFS, determined by ROC analysis, was 0.05% after both induction course 1 (AUC: 0.840, 95%CI[0.76,0.88]) and course 2 (AUC: 0.854, 95%CI[0.78,0.89]). The 0.05% threshold demonstrated higher HR for the first event than the 0.1% threshold (after course 1: HR = 2.8, 95%CI[2.3,3.3]; P 

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

Comparing Human Gaze and Vision-Language Model Attention in Safety-Relevant Environments

Human visual attention plays an important role in how people perceive and respond to environments containing potential risks. This study investigates whether large vision-language models can identify the same regions of a scene that attract human attention in safety-relevant environments. Eye-tracking data were collected from ten participants viewing 33 scene images representing environments with varying levels of potential risk using Pupil Invisible wearable glasses. Gaze coordinates were mapped onto stimulus images to generate population-averaged human gaze heatmaps. In parallel, GPT-4o was prompted through the OpenAI Vision Application Programming Interface (API) to generate spatial predictions of visual attention, which were converted into saliency maps for comparison with human gaze patterns. Spatial alignment between human gaze heatmaps and model-generated saliency maps was evaluated using four complementary metrics: Pearson correlation (r = 0.515 +- 0.117), Normalised Scanpath Saliency (NSS = 0.988 +- 0.323), Kullback-Leibler divergence (KL = 1.766 +- 0.844), and Area Under the Receiver Operating Characteristic Curve using the Judd formulation (AUC-Judd = 0.806 +- 0.076). A cross-model comparison with Gemini Pro, Gemini Flash, and Claude showed that all models exceeded the AUC-Judd chance baseline of 0.5 and achieved positive NSS scores. Gemini Pro demonstrated the strongest spatial localisation according to three of the four metrics, whereas GPT-4o produced the closest distributional match to human attention as measured by KL divergence. These findings suggest that large vision-language models can identify regions that broadly correspond to where humans direct visual attention in safety-relevant scenes without requiring eye-tracking training data. The results highlight the potential of vision-language models as a scalable tool for approximating human attentional patterns.

15.
arXiv (CS.AI) 2026-06-12

TrajGenAgent: A Hierarchical LLM Agent for Human Mobility Trajectory Generation

arXiv:2606.12657v1 Announce Type: new Abstract: Human mobility data is important for transportation, urban planning, and epidemic control, but large-scale trajectory collection is often costly and privacy-constrained, motivating realistic synthetic trajectory generation. Existing LLM-based generators typically rely on either prompt engineering, which preserves zero-shot reasoning but lacks fine-grained spatiotemporal grounding, or trajectory-level fine-tuning, which improves statistical precision but incurs substantial computational cost and may weaken general reasoning. We propose TrajGenAgent, a semantic-aware hierarchical LLM-agent framework for human mobility trajectory generation without model fine-tuning. TrajGenAgent uses a two-stage orchestrator-worker design: an LLM first synthesizes an individual- and weekday-conditioned activity chain from historical evidence via in-context learning, and a deterministic workflow then grounds each activity into a complete visit using personalized POI retrieval, distance-aware location selection, kinematics-aware travel-time propagation, and LLM-based duration estimation. To evaluate realism beyond aggregate spatiotemporal statistics, we introduce an anomaly-detection-based evaluation framework using two complementary detectors to assess behavioral and semantic plausibility. Experiments on benchmark and large-scale simulation datasets show that TrajGenAgent improves spatiotemporal fidelity, semantic coherence, and individual-specific behavioral realism over representative neural and LLM-based baselines, while avoiding parameter updates.

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

MAPS: A Novel Multi-Axial Projective Sphere for Geometrically Visualizing Higher d-Valued Quantum State-Space of Qudits

arXiv:2606.15801v1 Announce Type: new Abstract: Visualizing the d-valued quantum state-space of quantum systems serves as a foundational pillar for the scientific research and practical applications in quantum computing and information science, where d >= 2. The 2-valued quantum states of a qubit are elegantly visualized on the three-dimensional Bloch sphere. In contrast, expanding this geometrical paradigm to visualize higher d-valued quantum states of a qudit (d >= 3), e.g., a qutrit (d=3), ququadit (d=4), and quintit (d=5), leads to severe structural and topological complexities. This paper introduces a new generalized three-dimensional framework to effectively visualize higher d-valued quantum states of a qudit, in the aspects of ease of illustration, structural simplicity, and natural representation for researchers and engineers. We called this new framework the "multi-axial projective sphere (MAPS)", which consists of n projectional intersecting spatial axes, where d-1

17.
bioRxiv (Bioinfo) 2026-06-11

Robust semi-supervised scRNA-seq integration from virtual adversarial learning

Single-cell RNA sequencing integration methods that rely solely on transcriptomic data often struggle to preserve fine-grained distinctions between closely related cell subtypes. As a result, cell populations that are separable in the raw data may become over-mixed after integration, reducing biological resolution and interpretability. Incorporating marker gene information can potentially address these issues; however, the variability and complexity of available marker sets limit their effective application. To address this, we introduce scCRAFT+, a semi-supervised integration model that innovatively incorporates marker gene information through Virtual Adversarial Training (VAT). By jointly optimizing marker-derived supervision and transcriptome-wide representations, VAT enforces local prediction smoothness among transcriptionally similar cells, improving robustness to noisy marker annotations while enhancing both integration quality and cell type auto-annotation. This targeted approach significantly enhances annotation accuracy and robustness, particularly when faced with incomplete or incorrect marker gene sets. Benchmarking shows that scCRAFT+ achieves consistently stronger performance than current unsupervised and supervised integration approaches, resulting in improved integration quality and biologically meaningful sub-cell type auto-annotations.

18.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

19.
arXiv (quant-ph) 2026-06-12

QuBE/Qubex: an integrated hardware-software system for superconducting qubit experiments with broadband control

arXiv:2606.13010v1 Announce Type: new Abstract: Achieving high-fidelity operation in large-scale superconducting qubit systems requires not only control hardware with broad frequency coverage, low crosstalk, and tight synchronization but also software that coordinates system configuration, experiment execution, and data analysis. Here we present an integrated qubit-control system that combines broadband microwave hardware with a pulse-level software stack for scalable superconducting qubit experiments. The hardware provides broadband microwave coverage, including an instantaneous span of up to 1.6 GHz from a control output, while the software reduces setup and calibration overhead through automated configuration and built-in experiment workflows. We validate the system on a 64-qubit fixed-frequency transmon chip through full-chip frequency identification and representative demonstrations, including multi-unit far-detuned cross-resonance calibration and benchmarking that yields a measured two-qubit gate fidelity of 98.34%, and multilevel readout beyond the computational subspace. By disclosing the hardware architecture and releasing the software stack as open source, this work provides an inspectable hardware-software foundation for scalable superconducting qubit control experiments.

20.
arXiv (CS.LG) 2026-06-18

Provable quantum speedups for computing persistence in topological data analysis

arXiv:2410.21258v2 Announce Type: replace-cross Abstract: Topological data analysis (TDA) aims to extract noise-robust features from a data set by examining the number and persistence of holes in its topology. We provide an efficient quantum algorithm for a computational problem closely related to a core task in TDA – determining whether a given hole persists across different length scales. Further, we prove the problem itself is $\mathsf{BQP}_1$-hard, implying that a classical solution is extremely unlikely; this stands in contrast to all previous quantum approaches to TDA, where the problems were also intractable for quantum computers, or where a rigorous proof of classical hardness still remains open. This result implies an {exponential} quantum speedup for this problem under standard complexity-theoretic assumptions. Our approach relies on encoding the persistence of a hole in a variant of the guided sparse Hamiltonian problem, where the guiding state is constructed from a harmonic representative of the hole.

21.
arXiv (CS.LG) 2026-06-17

Learning to Refine Hidden States for Reliable LLM Reasoning

arXiv:2606.17524v1 Announce Type: new Abstract: Large language models show strong reasoning ability, but their internal reasoning process can remain unstable in complex multi-step settings, where early hidden-state errors may propagate to incorrect predictions. We propose ReLAR, a reinforcement-guided latent refinement framework that iteratively updates hidden representations before decoding. ReLAR maintains a compact latent reasoning state and uses learned depth and action controllers to adaptively determine both the number and direction of refinement steps. The controllers are trained with a policy gradient objective based on step-wise likelihood improvement, enabling efficient input-dependent reasoning without explicit chain-of-thought generation. Experiments on medical, mathematical, multi-hop reasoning, and open-ended generation benchmarks show that ReLAR improves accuracy, generation quality, and reasoning stability with substantially lower inference overhead than explicit reasoning baselines.

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

SA-VIS: Sparse frame Annotations for training Video Instance Segmentation

Recent online video instance segmentation (VIS) methods have achieved impressive results, thus becoming the preferred approach to segment instances in videos. Despite the resurgence of impressive single image models, the online (or semi-online) VIS approaches outperform single-image models (e.g., based on SAM) by using long sequences of densely annotated frames during training. However,such a training setup of VIS is expensive in the sense of compute as well as dense annotations required. In order to solve these major flaws, we argue that the effective modeling of the instances and their evolution in videos do not require densely annotated frames. To that end, we propose a simple and effective module, called Past-frames Feature Propagation (PFP) which aggregates low-dimensional features from the image encoder of multiple frames. This simple low-compute module provides tremendous learning capability in using sparse video frame labels for end-to-end training. Combined with a light-weight frame-specific Instance Queries, our Sparse frame Annotation VIS (SA-VIS) significantly improves performance over its baseline. Most interestingly, our simple design that avoids complexities effectively bridges the gap in accuracy between training on sparsely and densely annotated video sequences. This translates to a mere 0.4% drop in performance of SA-VIS when using annotations for only 1/5 of the images in the dataset. Empirically, SA-VIS shows strong improvements over the baseline on YouTube-VIS 2019/2021/2022 and Occluded VIS (OVIS) and an over 1% improvement in AP on the state-of-the-art in a limited annotations scenario.

23.
arXiv (CS.AI) 2026-06-19

Token Factory: Efficiently Integrating Diverse Signals into Large Recommendation Models

arXiv:2606.19635v1 Announce Type: cross Abstract: Large Recommendation Models (LRMs) have demonstrated promising capabilities in industry-scale recommendation tasks. However, holistically integrating traditional signals into these transformer-based architectures effectively and efficiently remains a major challenge. Conventional approaches that "textualize" these signals directly or create discrete item representations often lead to excessively long prompts, substantial memory footprints, and high computational overhead. To overcome these limitations, we propose "Token Factory", a framework designed to transform traditional signals into "soft tokens" that can be directly processed by LRMs. This approach enables efficient integration and compression of heterogeneous input features, preventing prompt length explosion while enhancing model performance. We detail the architecture of Token Factory and present experimental results validating its effectiveness in a production-scale recommendation environment.

24.
Nature (Science) 2026-06-18

Daily briefing: The proteins that protect us from deadly mutations

作者:

Proteins that ‘buffer’ the effects of mutations could help to treat diseases such as cancers. Plus, goats can follow human voices and the battle over a key ocean observatory project in the United States. Proteins that ‘buffer’ the effects of mutations could help to treat diseases such as cancers. Plus, goats can follow human voices and the battle over a key ocean observatory project in the United States.

25.
arXiv (CS.AI) 2026-06-16

Artificial Intelligence Index Report 2026

arXiv:2606.15708v1 Announce Type: new Abstract: Welcome to the ninth edition of the AI Index report. As AI continues to advance rapidly, the question becomes whether the systems built around it can keep up. Governance frameworks, evaluation methods, education systems, and the data infrastructure needed to track AI's impact are struggling to match the pace of the technology itself. That gap between what AI can do and how prepared we are to manage it runs through every chapter of this year's report. New in this edition, the report tracks how AI is being tested more ambitiously across reasoning, safety, and real-world task execution, and why those measurements are increasingly difficult to rely on. It also features new estimates of generative AI's economic value alongside emerging evidence of its labor market effects, an analytical framework on AI sovereignty, and a science chapter developed in collaboration with Schmidt Sciences. For the first time, the report features standalone chapters on AI in science and AI in medicine, reflecting AI's growing impact across these two domains.