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01.
arXiv (CS.LG) 2026-06-19

When to Trust, How to Distill: Multi-Foundation Model Guidance for Lightweight, Robust Scientific Time Series Forecasting

arXiv:2606.19363v1 Announce Type: new Abstract: The deployment of Time-Series Foundation Models (TSFMs) in physical sciences is hindered by a critical trade-off: while these models encode rich, universal temporal dynamics, they suffer from severe distributional misalignment when applied zero-shot to specific scientific domains, and their computational cost prohibits deployment in edge-computing sensor networks. We address a fundamental challenge: How can we extract latent structural knowledge from misaligned foundation models (FM) to train lightweight, specialized forecasters? We propose Gated Uncertainty-Aware Routing for Distillation (Guard), a novel framework that reframes multiteacher distillation as an instance-wise decision process with two adaptive mechanisms: (1) a Contextual Router that dynamically selects the most relevant teacher based on local input statistics, exploiting complementarity across diverse foundation models; and (2) an Uncertainty-Gated Temperature mechanism that acts as a "circuit-breaker," automatically attenuating distillation strength when teacher confidence diverges from domain reality. We evaluate our proposed lightweight framework on four climate-critical domains: meteorology, ecosystem carbon flux, soil moisture, and energy grids. Our method significantly reduces RMSE relative to a fixed-weight multi-teacher distillation baseline, successfully distilling knowledge from pretrained FMs (teachers) even when they exhibit suboptimal zero-shot accuracy due to distribution shift between the original and target data domains. We demonstrate that these domain-misaligned teachers can still serve as critical correctives, outperforming the globally superior FMs on 28.5% of the hardest instances. Ultimately, this enables high-precision scientific forecasting suitable for resource-constrained edge deployment. Code is available at https://github.com/RupasreeDey/GUARD-KDD2026.

02.
arXiv (math.PR) 2026-06-11

Hierarchical Random Measures without Tables

arXiv:2505.02653v2 Announce Type: replace-cross Abstract: The hierarchical Dirichlet process is the cornerstone of Bayesian nonparametric multilevel models. Its generative model can be described through a set of latent variables, commonly referred to as tables within the popular restaurant franchise metaphor. The latent tables simplify the expression of the posterior and allow for the implementation of Gibbs sampling algorithms to approximately draw posterior samples. However, managing their assignments can become computationally expensive, especially as the size of the dataset and the number of levels increase. In this work, we identify a prior for the concentration parameter of the hierarchical Dirichlet process that (i) induces a quasi-conjugate posterior distribution, and (ii) removes the need for tables, leading to more interpretable expressions for the posterior, with both a scalable and an exact algorithm to sample from it. Remarkably, this construction extends beyond the Dirichlet process, leading to a new framework for defining normalized hierarchical random measures and a new class of algorithms to sample from their posteriors. The key analytical tool is the independence of multivariate increments, that is, their representation as completely random vectors.

03.
medRxiv (Medicine) 2026-06-16

Diurnal variation in brain-derived tau and five other blood-based biomarkers for dementia and their association with cognitive performance

Blood-based biomarkers of dementia are a promising scalable tool for early diagnosis, tracking disease progression, and evaluating therapeutic efficacy. Utility of these biomarkers will not only be dependent on the reliability of their association with pathology but also contingent on their ability to track cognitive status. Previously, we demonstrated diurnal variation in several biomarkers (amyloid beta (A{beta}) 42 and 40, 42/40 ratio, glial fibrillary acidic protein (GFAP), neurofilament light (NfL), and phosphorylated-Tau 217 (p-Tau217)) which has implications for their reliability. Here, we extend these observations to a larger cohort, include brain-derived tau (BD-Tau), which is assumed to be produced exclusively in the brain, and report endocrine measures of circadian rhythmicity. We not only assessed whether these biomarkers vary with time of day, but also whether they associate with daytime function and whether these associations vary with cognitive domain and number of repeated assessments. Data collected in 20 PLWA (72.4{+/-}5.9 years, mean{+/-}SD) and 19 controls (68.9{+/-}9.8 years) were analysed. Participants completed 14 days of home monitoring and one laboratory assessment of sleep and daytime function: mood, daytime sleepiness, reaction time, immediate and delayed memory recall, everyday memory errors. During the 27-hour residential laboratory session, 3-hourly blood samples were collected and analysed for the six blood-based biomarkers of dementia as well as melatonin and cortisol. Rhythmicity of melatonin and cortisol did not differ between groups. P-Tau217 and GFAP (p

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

Do we have the knowledge we need? Rethinking human-AI decision-making in corporations

arXiv:2606.15575v1 Announce Type: new Abstract: Organizational knowledge is fragmented across a variety of software systems, tacit expertise, and manual documents that have traditionally been designed for human consumption. As AI systems are increasingly deployed and granted decision-making roles, they require access to this knowledge. This raises two questions: how should organizations store and maintain knowledge so that it remains accessible to both humans and future AI systems, and how should agency be allocated between humans and AI across tasks with different risks and levels of uncertainty? In this position paper, we describe how organizational knowledge evolves and contribute a framework that maps task attributes and knowledge availability to recommended agency allocations and control mechanisms. We illustrate the applicability of the framework on two different manufacturing tasks: a routine operation (visual quality inspection) and a one-off strategic decision (factory location), and conclude with opportunities for future research.

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

Intelligence as Managed Autonomy: Failure, Escalation, and Governance for Agentic AI Systems

arXiv:2605.27628v2 Announce Type: replace Abstract: As autonomous and agentic AI systems scale in robotic and human-machine environments, managing hallucination and persistent but unjustified action remains an open challenge. Rather than attributing these failures solely to model or alignment limitations, this paper explores the architectural vulnerability of unbounded autonomy - the presumption that an agent should continue operating regardless of rising uncertainty. It introduces a theory of managed autonomy that defines intelligent behavior through the formal capacity to detect epistemic drift, suspend reasoning, attempt recovery, and ultimately surrender control when reliability diminishes. We instantiate this theory via the SMARt (Self-Managing Multi-tier Autonomous Reasoning with Regulated/Revoked transitions) model, a four-layer framework featuring Stable, Meta-cognitive, Assisted, and Regulated states. By developing a timed, guarded Petri net formulation, we establish theoretically bounded properties for the system, demonstrating how architecture can formally mandate escalation, constrain invalid outputs, and ensure governance reachability under specified conditions. We further analyze how incorporating domain-specific trigger sets across varied operational settings (e.g., healthcare, robotics, etc.) can systematically preserve safety, assuming completeness and soundness criteria are met. Because these triggers are designed to be adaptive, the SMARt model accommodates the safe, controlled expansion of an agent's operational scope over time. We conclude that formalizing failure management within the autonomy lifecycle is a crucial step toward realizing reliable and governed artificial intelligence.

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

AIGS-Net: Compact Illumination Field Modeling via 2D Gaussian Splatting for Fast Low-Light Image Enhancement

Existing low-light image enhancement methods often face a bottleneck between the representation capacity of illumination-field modeling and computational complexity. To address this issue, this paper proposes an Adaptive Illumination Gaussian Splatting Network (AIGS-Net), an ultra-lightweight architecture for fast low-light enhancement. Unlike conventional static priors, AIGS-Net constructs an input-adaptive 2D Gaussian Splatting illumination field. The opacity of Gaussian basis functions is dynamically modulated by relative luminance statistics of the input image, and spatially varying illumination compensation is rendered through ordered alpha compositing. To guide adaptive illumination compensation efficiently, a zero-parameter nonlinear multiscale contextual encoding module is introduced to extract low-frequency structures and local contrast cues without additional convolutional weights. To suppress noise amplification and sensor-induced color bias, AIGS-Net integrates noise-mask estimation, locked single-channel Gamma mapping, cross-channel consistency regularization, and target color-alignment constraints. Experiments on LOL and LSRW benchmarks show that AIGS-Net improves detail recovery and color fidelity while requiring only approximately 40 learnable parameters, achieving an effective trade-off between enhancement quality and extreme inference efficiency.

07.
arXiv (quant-ph) 2026-06-16

Scalable Graph State Generation with O(1) Local Feedforward in Quantum Networks

arXiv:2606.16375v1 Announce Type: new Abstract: The development of quantum networks faces a key challenge: the contradiction between probabilistic long-range entanglement generation and finite coherence time. Existing routing protocols typically focus on global state computation or path optimization. As the network scales up, classical delays accumulate and exacerbate decoherence, leading to a decrease in entanglement fidelity. To reduce routing decision delays to levels far below the coherence time of qubits, we propose a protocol based on local measurement and classical feedforward. This protocol reduces the local decision complexity to amortized O(1) level, ensuring that the decision delay is always much smaller than the coherence time of qubits. We map this protocol onto a dual-species trapped-ion platform and perform hybrid simulations. The results show that the proposed protocol performs well in terms of both resource efficiency and time feasibility. Noise analysis indicates that readout fidelity is the main bottleneck of this protocol, but noise suppression can be achieved by employing an erasure transformation in the dual-species architecture, combined with spatial multiplexing and branch independence, thereby ensuring the generation of high-fidelity star subgraphs. This protocol provides a clear path to achieving high-fidelity star subgraphs. These subgraphs can serve as general modules, merging to construct arbitrary subgraphs, providing a feasible solution for future fault-tolerant distributed quantum computing.

08.
arXiv (quant-ph) 2026-06-19

Complexity of detecting large coefficients in the Pauli basis

arXiv:2606.19545v1 Announce Type: new Abstract: We study the problem of deciding, given a mechanism to prepare a quantum state $\rho$ and a value $\varepsilon > 0$, whether there is some non-identity Pauli matrix $P$ such that $|Tr(P \rho)| \geq \varepsilon$. We consider that the state $\rho$ is described as the result of tracing out some of the qubits of a pure state prepared by a circuit $C$, and we assume the promise that either there is a Pauli matrix satisfying the stated condition or, instead, that for all non-identity Pauli matrices $P$ it is the case that $|Tr(P\rho)|\leq \varepsilon/2$. The problem is in $QCMA$, and we prove that if it belongs to $BQP$ then $NP \subseteq BQP$. The result is obtained through a reduction from the minimum-weight code problem, and it holds even when $\rho$ is assumed to be a pure state (i.e. when no qubits are discarded) and $\varepsilon$ is constant. This resolves an open question regarding the existence of efficient tomographic procedures to find the largest coefficients of a quantum state in the Pauli basis: namely, they do not exist under the standard hypothesis $NP \nsubseteq BQP$.

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

CogCanvas: A Benchmark for Evaluating Multi-Subject Reference-Based Image Generation

Multi-subject reference-based image generation requires jointly preserving multiple human identities, binding per-person objects and fashion items, and respecting a specified background scene, a regime where current diffusion models remain brittle. Existing benchmarks evaluate only one axis at a time and none jointly captures multi-identity composition with human-object interaction, background grounding, and spatial plausibility. We introduce CogCanvas, a benchmark of 1,952 curated reference images spanning 100 celebrity identities, 115 distinctive objects and fashion items, and 29 real-world background scenes including landmarks, from which we construct 1,361 compositional prompts covering 2-5 person group sizes. The curation pipeline combines DINOv2-based deduplication, two-stage aesthetic filtering, and automated derivation of structured interaction and position graphs that serve as ground-truth supervision. CogCanvas supports three tasks, reference-based multi-human-object generation (primary), text-to-image compositional generation, and reference retrieval, under a unified six-axis evaluation protocol. We introduce two metrics tailored to the multi-reference setting: BG-Sim, which scores background fidelity on SAM 3-masked regions via DINOv3 feature similarity, and Attr-VQA, which uses a multimodal LLM to verify per-subject attribute binding and inter-person interactions against the structured graphs. Benchmarking five SOTA methods reveals that every model degrades substantially as group size grows from 2 to 5, with near-complete failure on object/fashion binding beyond three subjects.

10.
medRxiv (Medicine) 2026-06-15

Prevalence and Clinical Impact of Pathogenic Variants in Cardiomyopathy Genes Among Individuals with Cardiac Conduction Disorders

Importance: Cardiac conduction disorders have traditionally been regarded as a secondary manifestation of underlying structural heart diseases. However, isolated conduction disorders may precede the onset of heart failure (HF) suggesting shared mechanisms. Objective: To evaluate the prevalence and clinical significance of pathogenic/likely pathogenic (P/LP) rare variants in cardiomyopathy genes among individuals with conduction disorders. Design, Setting, and Participants: Biobank analysis of 192,834 participants with whole genome sequence data from Vanderbilt's BioVU and 353,092 participants from the All of Us Research Program (AoU). Participants with primary conduction disorder (left bundle branch block [LBBB], right bundle branch block [RBBB], high-grade atrioventricular block [AVB]) were identified after excluding secondary causes. Exposures: P/LP variants in cardiomyopathy genes. Main Outcomes and Measures: Primary outcome was P/LP carrier status by age and HF status. Secondary outcomes included incident HF and composite ventricular arrhythmias/sudden cardiac death/mortality (VA/SCD/mortality). Results: Among 16,959 participants with conduction disorders in BioVU and 13,442 in AoU, 432 (2.6%) and 206 (1.5%) were P/LP carriers, respectively. Conduction disorder was independently associated with carrier status (BioVU p

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

Moving Beyond Diffusion: Hierarchy-to-Hierarchy Autoregression for fMRI-to-Image Reconstruction

Reconstructing visual stimuli from fMRI signals is a central challenge bridging machine learning and neuroscience. Recent diffusion-based methods typically map fMRI activity to a single neural embedding, using it as static guidance throughout the entire generation process. However, this fixed guidance collapses hierarchical neural information and is misaligned with the stage-dependent demands of image reconstruction. In response, we propose MindHier, a coarse-to-fine fMRI-to-image reconstruction framework built on scale-wise autoregressive modeling. MindHier introduces three components: a Hierarchical fMRI Encoder to extract multi-level neural embeddings, a Hierarchy-to-Hierarchy Alignment scheme to enforce layer-wise correspondence with CLIP features, and a Scale-Aware Coarse-to-Fine Neural Guidance strategy to inject these embeddings into autoregression at matching scales. These designs make MindHier an efficient and cognitively aligned alternative to diffusion-based methods by enabling a hierarchical reconstruction process that synthesizes global semantics before refining local details, akin to human visual perception. Extensive experiments on the NSD dataset show that MindHier achieves superior semantic fidelity, 4.67$\times$ faster inference, and more deterministic results than the diffusion-based baselines.

12.
Science (Express) 2026-05-07

TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution | Science

作者: 未知作者

Single-cell transcriptomics is revolutionizing our understanding of cellular diversity, yet comparing transcriptional programs across the tree of life remains challenging. We developed TranscriptFormer, a family of generative foundation models trained on up to 112 million cells spanning 1.53 billion years of evolution across 12 species. We demonstrate state-of-the-art performance on cell type classification, even for species separated over 685 million years of evolution, and zero-shot disease state identification in human cells. Developmental trajectories, phylogenetic relationships and cellular hierarchies emerge naturally in TranscriptFormer’s representations without any explicit training on these annotations. This work establishes a powerful framework for quantitative single-cell analysis and comparative cellular biology, thus demonstrating that universal principles of cellular organization can be learned and predicted across the tree of life.

13.
medRxiv (Medicine) 2026-06-15

Investigation of Intra-Fraction Stability and Inter-Fraction Reproducibility of Deep Inspiration Breath-Hold Across Two Hypofractionated Radiotherapy Regimens in the HYPORT Adjuvant Study.

Background: Deep Inspiration Breath Hold (DIBH) is a widely used respiratory motion management technique for minimizing cardiac dose in left-sided breast radiotherapy. In the Breast HYPORT Adjuvant study, DIBH was employed for cardiac sparing in patients without nodal irradiation using a standardized institutional protocol with the Varian Real-time Position Management (RPM) system. Both moderate-hypofractionation (control arm - 40Gy in 15 fractions) and one-week hypofractionation (experimental arm - 26 Gy in 5 fractions) regimens were delivered using this protocol. This study aimed to evaluate the robustness of DIBH by analyzing intra-fraction stability and inter-fraction reproducibility of breath-hold amplitude across the two treatment regimens. Methods: Respiratory waveforms acquired during each treatment session were analyzed to determine the median breath-hold amplitude and its standard deviation during beam delivery. Intra-fraction stability was assessed from vari- ations within individual treatment sessions, while inter-fraction reproducibility was evaluated relative to the simula- tion waveform amplitude across all treatment sessions. These parameters were compared between the two HYPORT regimens to examine breath-hold consistency during treatment delivery. Moreover, an additional comparison was made between the one-week hypofractionation regimen and the first five fractions of the moderate-hypofractionation regimen to evaluate the effect of treatment duration . Lung volumes from free-breathing and DIBH CT scans were analyzed to assess the effectiveness of patient breath-hold training. Results: Both arms demonstrated an average 1.7-fold increase of air volume in lung during the breath-hold position, confirming the effective implementation of DIBH during treatment planning and delivery. Structured training resulted in increased breath-hold amplitudes, with gains of 22.87% and 24.16% with respect to the first trial session in the experimental and control arms, respectively. Both regimens receive equivalent doses for approximately the same air volume in lung . Despite the different prescription doses in the two arms (26 Gy vs. 40 Gy), the experimental arm achieved an equivalent mean heart dose of 2.91% (75.6 cGy) compared with 2.95% (118.51 cGy) in the control arm, suggesting a similar cardiac preservation protocol adopted during treatment planning. Intra-fraction stability was similar between the control arm and the experimental arm, with median amplitude variations of 1.006 mm (95% CI: [0.998-1.015]) and 1.079 mm (95% CI: [1.067-1.097]), respectively. In contrast, inter-fraction reproducibility improved in the experimental arm, with lower deviation from simulation amplitude (0.44 {+/-} 0.24 mm vs. 0.66 {+/-} 0.25 mm) for the entire treatment schedule. The stability and reproducibility of experimental arm were further compared with the first five fractions of the control arm. The results were similar to those of the experimental arm. Conclusion: In this study, we compared two treatment regimens in terms of intra-fraction stability and inter-fraction reproducibility during DIBH radiotherapy. Both regimens demonstrated comparable intra-fraction stability, indicating effective motion management irrespective of treatment duration. However, the experimental arm showed better inter- fraction reproducibility, suggesting more consistent breath-hold performance throughout the treatment course. Based on stability and reproducibility, a reasonable narrowing of the DIBH gating window may be implemented with minor changes to the institutional protocol. The observed trend highlights the potential for improved consistency with the experimental approach and supports further investigation to better understand the underlying factors and strengthen these findings in future studies.

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

EvoMemBench: Benchmarking Agent Memory from a Self-Evolving Perspective

Recent benchmarks for Large Language Model (LLM) agents mainly evaluate reasoning, planning, and execution. However, memory is also essential for agents, as it enables them to store, update, and retrieve information over time. This ability remains under-evaluated, largely because existing benchmarks do not provide a systematic way to assess memory mechanisms. In this paper, we study agent memory from a self-evolving perspective and introduce EvoMemBench, a unified benchmark organized along two axes: memory scope (in-episode vs. cross-episode) and memory content (knowledge-oriented vs. execution-oriented). We compare 15 representative memory methods with strong long-context baselines under a standardized protocol. Results show that current memory systems are still far from a general solution: long-context baselines remain highly competitive, memory helps most when the current context is insufficient or tasks are difficult, and no single memory form works consistently across all settings. Retrieval-based methods remain strong for knowledge-intensive settings, whereas procedural and long-term memory methods are more effective for execution-oriented tasks when their stored experience matches the task structure. We hope EvoMemBench facilitates future research on more effective memory systems for LLM-based agents. Our code is available at https://github.com/DSAIL-Memory/EvoMemBench.

15.
arXiv (CS.CL) 2026-06-16

SHARD: Safe and Helpful Alignment via Self-Reframing Distillation

Large language models often struggle with sensitive prompts. They may refuse outright, provide generic safety boilerplate, or fail to address the user's legitimate informational needs that can be answered safely. We introduce SHARD, a self-reframing distillation method to improve safe-helpfulness. It first rewrites sensitive prompts to surface benign intent using philosophical guidelines, then reframes its original responses into safe, more helpful ones, and finally fine-tunes the model on its self-reframed responses. Across DNA and the English subset of LINGUASAFE, SHARD improves helpfulness for most model families while preserving safety. It also remains competitive with distillation from a larger teacher model, suggesting that models can internalize safe and helpful behavior elicited from their own. Warning: This paper contains content that may be offensive or harmful.

16.
arXiv (CS.AI) 2026-06-12

Mining Architectural Quality Under Agentic AI Adoption: A Causal Study of Java Repositories

arXiv:2606.13298v1 Announce Type: cross Abstract: AI coding tools are now used by a majority of developers, and agentic use of these tools has popularized the practice colloquially called "vibe coding". Yet causal evidence on their effect on software architecture is scarce. Prior causal work has measured code-level outcomes (complexity, static analysis warnings); whether such degradation propagates to architecture-level outcomes remains unknown. We mine 151 open-source Java repositories, 74 with detectable agentic AI adoption (identified via configuration files and Co-Authored-By commit trailers) and 77 propensity-matched controls, across a 13-month per-repository window yielding 1,811 monthly Arcan snapshots. We estimate the causal effect of adoption on architectural smell density (ASD) with a staggered difference-in-differences design and the Borusyak imputation estimator, applying a causal design recently used for code-level metrics to the architecture level. Total smell counts are essentially unchanged (+1.1%, p = 0.82) while lines of code grow +12.8% (p = 0.003); the resulting 6.7% ASD decline (p = 0.004) is therefore a denominator effect rather than an architectural improvement. Per-type estimates and robustness checks (wild cluster bootstrap, Lee bounds, stale-observation sensitivity) corroborate the pattern; pre-trends are flat (Wald p = 0.90), consistent with parallel trends. Density-normalized outcomes can mislead when treatment affects system size: raw counts and explicit decomposition are required for causal mining studies of AI tool adoption. The complete replication package, including the curated 151-repository monthly panel, is publicly available.

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

PreLort: Prefix-Nested LoRA for Federated Fine-Tuning under Rank Heterogeneity

Federated fine-tuning of large language models using parameter-efficient methods such as LoRA enables privacy-preserving adaptation of foundation models. Heterogeneous hardware resources introduce challenges, as clients with different adapter ranks cannot be directly aggregated. While existing methods enable aggregation under heterogeneous ranks, they fail to control how information is distributed across rank dimensions, leading to suboptimal use of shared low-rank representations. Instead, we propose PreLort: a nested low-rank formulation for federated LoRA that organizes adapter dimensions into a prefix hierarchy. Our approach ensures that lower-rank dimensions encode task-relevant information, while higher-rank dimensions capture additional capacity. Building on this, we introduce (i) a segment-wise aggregation rule that averages only over clients contributing to each rank segment, avoiding dilution from zero-padded lower-rank clients, and (ii) a prefix-nested training strategy that optimizes each adapter under multiple rank truncations, encouraging useful signal to concentrate in low-rank prefix dimensions. Together, these components encourage a consistent low-rank prefix capturing the most task-relevant information, while higher-rank dimensions learn additional capacity. This allows low-rank clients to benefit from richer information contributed by higher-rank clients, as prefix dimensions are consistently learned and aggregated. Experiments demonstrate that our method consistently outperforms prior heterogeneous federated LoRA methods in accuracy and ROUGE-L, while achieving lower or comparable perplexity across multiple base models.

18.
bioRxiv (Bioinfo) 2026-06-19

HTS-Oracle v2: Prospective AI-Guided Discovery and Experimental Validation of Small Molecule Modulators Across Multiple Targets

High-throughput screening (HTS) remains the cornerstone of early-phase small molecule discovery yet consistently underperforms against immunotherapy targets, yielding validated hit rates below 0.1%. Here we introduce HTS-Oracle v2, which features rigorous cross-validation that ensures honest performance estimates. HTS-Oracle v2 was trained and validated across four clinically significant immune checkpoint targets (CD28, ICOS, LAG-3, and TIGIT) achieving ROC-AUC values of 0.968, 0.969, 0.875, 0.928 respectively under rigorous cross-validation. For prospective experimental validation, HTS-Oracle v2 was applied to an 8,960-compound Enamine Protein Mimetic Library, selecting only 25 compounds per target for experimental testing using temperature-related intensity change (TRIC) technology, a 99.7% reduction in screening burden. HTS-Oracle v2 identified 4, 5, 4, and 6 validated binders from 25 prospectively selected compounds per target, corresponding to validated hit rates of 16%, 20%, 16%, and 24%, respectively. Notably, 67-80% of all experimentally confirmed hits across the full 8,960-compound library were captured within just 25 model-selected compounds per target. For CD28, this represents a 28-fold improvement over HTS-Oracle v1 (239x versus 8.4x), establishing HTS-Oracle v2 as an efficient platform for AI-guided prospective hit discovery across immunotherapy targets.

19.
arXiv (CS.CL) 2026-06-12

When Iterative RAG Beats Ideal Evidence: A Diagnostic Study in Scientific Multi-hop Question Answering

Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains with multi-hop reasoning, sparse domain knowledge, and heterogeneous evidence. We provide the first controlled, mechanism-level diagnostic study of whether synchronized iterative retrieval and reasoning can surpass an idealized static upper bound (Gold Context) RAG. We benchmark eleven state-of-the-art LLMs under three regimes: (i) No Context, measuring reliance on parametric memory; (ii) Gold Context, where all oracle evidence is supplied at once; and (iii) Iterative RAG, a training-free controller that alternates retrieval, hypothesis refinement, and evidence-aware stopping. Using the chemistry-focused ChemKGMultiHopQA dataset, we isolate questions requiring genuine retrieval and analyze behavior with diagnostics spanning retrieval coverage gaps, anchor-carry drop, query quality, composition fidelity, and control calibration. Across models, Iterative RAG consistently outperforms Gold Context, with gains up to 25.6 percentage points, especially for non-reasoning fine-tuned models. Staged retrieval reduces late-hop failures, mitigates context overload, and enables dynamic correction of early hypothesis drift, but remaining failure modes include incomplete hop coverage, distractor latch trajectories, early stopping miscalibration, and high composition failure rates even with perfect retrieval. Overall, staged retrieval is often more influential than the mere presence of ideal evidence; we provide practical guidance for deploying and diagnosing RAG systems in specialized scientific settings and a foundation for more reliable, controllable iterative retrieval-reasoning frameworks.

20.
bioRxiv (Bioinfo) 2026-06-11

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele- and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

21.
arXiv (CS.CV) 2026-06-16

RealityBridge: Bridging Editable 3D Gaussian Splatting Driving Simulations and Real-World Videos

Long-tail hazardous scenarios are essential for safety-oriented autonomous driving, yet they are difficult to collect and reproduce at scale. Editable 3D Gaussian Splatting (3DGS) simulation offers a promising alternative by reconstructing real driving scenes and supporting controllable scene editing. However, edited 3DGS-rendered videos still suffer from a significant Sim-to-Real gap, including rendering artifacts, degraded foreground assets, inconsistent illumination, and temporal flickering. Existing restoration and video generation methods are insufficient for this task, as they often fail to jointly repair 3DGS-specific artifacts, improve visual realism, and ensure temporal consistency. To fill this gap, we propose RealityBridge, a structure-preserving and asset-aware Sim-to-Real framework for edited 3DGS driving videos. RealityBridge uses multimodal controls, including rendered videos, foreground masks, edge maps, and semantic masks, together with a lightweight GateNet for adaptive condition allocation across backbone layers. We further construct targeted training data and introduce autoregressive long-video training with reward-guided post-training to improve restoration quality, temporal stability, and hallucination suppression. Extensive experiments on internal and public driving datasets show that RealityBridge outperforms existing methods in artifact removal, illumination harmonization, and long-sequence temporal consistency.

22.
arXiv (math.PR) 2026-06-12

Scaling limits of the single-curve interface and outermost loops in the planar random field Ising model

arXiv:2606.13147v1 Announce Type: new Abstract: We prove that the interface separating $+1$ and $-1$ spins in the near-critical planar random field Ising model (RFIM) with Dobrushin boundary conditions has a scaling limit, whose law is conformally covariant and almost surely absolutely continuous with respect to SLE$_3$. The limiting curve can be seen as a massive version of SLE$_3$ in the sense of Makarov and Smirnov, but in a random environment. We then show that the outermost spin loops of the near-critical planar RFIM with $+1$ boundary conditions have subsequential limits and that any of these limits is almost surely singular with respect to CLE$_3$. This dichotomy between absolute continuity of the single interface and singularity of the outermost loops reflects the fact that a single interface does not explore enough of the magnetization field of the near-critical RFIM to detect the singularity of this field with respect to the critical Ising magnetization field, whereas the outermost spin loops do.

23.
arXiv (CS.AI) 2026-06-18

Efficient Zeroth-Order Federated Finetuning of Language Models on Resource-Constrained Devices

arXiv:2502.10239v3 Announce Type: replace-cross Abstract: Federated Learning (FL) is a promising paradigm for finetuning Large Language Models (LLMs) across distributed data sources while preserving data privacy. However, finetuning such large models is challenging on edge devices due to its high resource demand. Zeroth-order Optimization (ZO) estimates gradients through finite-difference approximations, which rely on function evaluations under random perturbations of the model parameters. Consequently, ZO with task alignment provides a potential solution, allowing finetuning using only forward passes with inference-level memory requirements and low communication overhead, but it suffers from slow convergence and higher computational demand. In this paper, we propose a new ZO-based method that applies a more efficient technique to reduce the computational demand associated with using a large number of perturbations while preserving their convergence benefits. This is achieved by splitting the model into consecutive blocks and allocating a higher number of perturbations to the second block, enabling efficient reuse of intermediate activations to update the full network with fewer forward evaluations. Our evaluation on RoBERTa-large, OPT1.3B, LLaMa-3-3.2B models shows up to $3\times$ reduction in computation compared to the other ZO-based techniques, while retaining the memory and communication benefits over first-order federated learning techniques.

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

Evaluating Factual Density in Multi-Source RAG: A Study in Medical AI Accuracy

Retrieval-Augmented Generation (RAG) is the current industry standard for grounding AI in real-world facts. Traditional retrieval methods rely on keyword matching and topic proximity, ranking content based on how closely it sounds like the user's query. What they do not measure is how many verified facts the content actually contains. This structural gap, termed the Expert Blindness Effect, causes standard RAG pipelines to consistently bury high-density factual evidence in favor of lexically dominant text on the same topic. To address this gap, this paper introduces Factual Density (FD*), a novel retrieval optimization signal that measures the proportion of verified atomic claims relative to total token count. Using the NexusAgentics Ghost Audit preprocessing pipeline, raw text is scored for factual specificity using probabilistic factuality analysis to filter content before corpus ingestion. An initial formulation introduced a severe document-length confound (Pearson R = -0.8636, p = 2.27e-07). Implementing Z-score normalization within length bins resolved this bias, validating FD* as a length-independent density signal (p = 0.0749). Evaluated against the HealthFC benchmark (750 health claims labeled Supported, Refuted, or No Evidence by medical experts), FD*-optimized retrieval was the only condition to achieve 100% systematic review saturation in top-5 results, surfacing Cochrane evidence that standard cosine similarity ranked outside the top ten. Ground truth verification confirmed 25 mappings across seven HealthFC-supported claims. While full statistical validation across n=50 queries remains future work due to constraints on corpus-benchmark alignment, these findings establish factual density reranking as a low-cost, high-impact intervention for improving factual precision in health RAG architectures.

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arXiv (math.PR) 2026-06-12

Conditional means, vector pricings, amenability and fixed points in cones

arXiv:2512.13829v4 Announce Type: replace Abstract: We develop a generalization of conditional probability for arbitrary ordered vector spaces. A related problem is that of assigning a numerical value to one vector relative to another. We characterize the groups for which these generalized probabilities can be stationary, respectively invariant. Our results deviate from the setting of classical probability and lead to a new criterion for amenability and for fixed points in cones.