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01.
arXiv (CS.AI) 2026-06-11

SAGE: Scalable AI Governance & Evaluation

arXiv:2602.07840v4 Announce Type: replace-cross Abstract: Evaluating relevance in large-scale search systems is fundamentally constrained by the governance gap between nuanced, resource-constrained human oversight and the high-throughput requirements of production systems. While traditional approaches rely on engagement proxies or sparse manual review, these methods often fail to capture the full scope of high-impact relevance failures. We present SAGE (Scalable AI Governance \& Evaluation), a framework that operationalizes high-quality human product judgment as a scalable evaluation signal. At the core of SAGE is a bidirectional calibration loop where natural-language Policy, curated Precedent, and an LLM Surrogate Judge co-evolve. SAGE systematically resolves semantic ambiguities and misalignments, transforming subjective relevance judgment into an executable, multi-dimensional rubric with near human-level agreement. To bridge the gap between frontier model reasoning and industrial-scale inference, we apply teacher-student distillation to transfer high-fidelity judgments into compact student surrogates at 92$\times$ lower cost. Deployed within LinkedIn Search ecosystems, SAGE guided model iteration through simulation-driven development, distilling policy-aligned models for online serving and enabling rapid offline evaluation. In production, it powered policy oversight that measured ramped model variants and detected regressions invisible to engagement metrics. Collectively, these drove a 0.25\% lift in LinkedIn daily active users.

02.
arXiv (CS.AI) 2026-06-16

Semantics-Enhanced Retrieval-Augmented Time Series Forecasting

arXiv:2606.14941v1 Announce Type: new Abstract: Time series forecasting models often benefit from historical patterns. Inspired by Retrieval-Augmented Generation (RAG), recent research explored retrieving relevant historical time series segments to enhance forecasting. However, relying solely on time series similarity is often insufficient for retrieval under non-stationarity. To address this, we propose a multimodal approach: a Semantics-Enhanced Retrieval-Augmented Time Series Forecasting framework, SERAF. Unlike mainstream approaches that depend only on time series similarity, SERAF conducts dual retrieval over the time series and their self-generated textual descriptions. It retrieves two complementary sets of historical patterns and corresponding futures, which are selectively and jointly used to guide future predictions. Experiments across seven real-world datasets demonstrate the effectiveness of SERAF in bridging numerical and semantic views of time series compared with state-of-the-art baselines.

03.
arXiv (CS.CV) 2026-06-16

Mitigating Visual Hallucinations in Multimodal Systems through Retrieval-Augmented Reliability-Aware Inference

Multimodal large language models (MLLMs) have demonstrated strong capabilities in vision-language understanding and natural-language response generation. However, these systems can still produce overconfident predictions and hallucination-like outputs, particularly when the visual evidence is weak, ambiguous, or semantically inconsistent. Most existing approaches focus on improving multimodal representation alignment or retrieval-augmented generation, while providing limited mechanisms to quantify instance-level prediction reliability or identify incorrect visual outputs. This work proposes a retrieval-augmented reliability-aware inference framework for trustworthy multimodal visual understanding. The proposed framework constructs an external visual evidence database using pretrained visual embeddings and nearest-neighbor retrieval over normalized feature representations. Retrieved evidence is used to estimate prediction trustworthiness through multiple reliability indicators, including similarity strength, class-support agreement, evidence margin, entropy-based uncertainty, and an aggregate reliability score. Based on these signals, a decision gate determines whether the system should accept the prediction, answer with caution, or abstain/fallback when evidence is insufficient. A multimodal response-generation layer then produces a final user-facing response conditioned on the reliability decision. Experiments on ImageNet-100 demonstrate that the proposed reliability-aware framework improves accepted prediction accuracy from 85.84\% to 88.88\% at 89.04\% coverage. The hallucination-like accepted wrong-answer rate is reduced from 14.16\% to 11.12\%. These results show that integrating retrieval evidence, reliability estimation, and selective decision gating can improve calibration and reduce overconfident visual errors without retraining large multimodal models.

04.
arXiv (CS.LG) 2026-06-11

Finding Multiple Interpretations in Datasets

arXiv:2606.12277v1 Announce Type: new Abstract: In this paper, we propose an approach to finding sets of similar-performing models (in terms of loss/accuracy measurements) with highly different context-aware characteristics. Through experiments on the METABRIC dataset, we show that the proposed method finds multiple models with highly different gene expressions than those found by the control methodology without performance penalties. We argue that the proposed methodology is important whenever one aims to analyze any global characteristic of a model to extract insight into the underlying phenomenon being studied.

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

The Reverse Telescoping Coordinate System for Positive Definite Matrices: Geometry, Computation, and Generative Modeling

arXiv:2606.15442v1 Announce Type: cross Abstract: We design a new unconstrained coordinate system where a $p\times p$ symmetric positive definite (SPD) matrix $\Theta$ is represented by a reverse telescoping map $\Theta(x)=\rm{RT}(x)$, with $x=(v,d,r)\in\mathbb{R}\times\mathbb{R}^{(p-1)}\times\mathbb{R}^{p(p-1)/2}$, representing respectively the log volume or log determinant; and the shape, as encoded by log relative diagonal scales and partial covariances among the nodes. This construction results in important properties not available in other charts, e.g., matrix logarithm, such as Jacobian depending on only the log-determinant. A useful feature of our construction is $x$ contains a lossless symbolic representation of both the matrix and its inverse. Many important computations involving a matrix and its inverse can be performed in $O(p^2)$ in the transformed domain, while it is the rendering of results in matrix forms (on demand) that must incur an $O(p^3)$ cost. Moreover, two unit-determinant matrices in the transformed domain can be joined by a straight line with pathwise unit determinant. For generative modeling, this allows designing a split volume-shape flow model trained by conditional flow matching for transporting the shape over the unit-determinant path, with a separate one-dimensional flow for transporting the volume or the determinant. The forbidding SPD constraint, tamed thus into a powerful guiding force, leads to the surprising insight that it is in some sense easier to design a volume-normalized shape flow for SPD compared to the unconstrained $\mathbb{R}^{p\times p}$, with no intrinsic notion of volume to aid normalization, unlike the determinant of SPD matrices. We apply our construction for up to $p=200$ in generative modeling of SPD matrices on a difficult synthetic bimodal target, and in generating brain connectivity networks by models trained on fMRI data; as well as in intrinsic diffusion on the SPD manifold.

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

AI Receptivity or AI Adoption Breadth? A Tool-Specific Reanalysis of the Lower-Literacy/Higher-Usage Link

arXiv:2606.13734v1 Announce Type: new Abstract: Recent evidence reported by Tully, Longoni, and Appel (2025) suggests that lower artificial intelligence (AI) literacy predicts greater receptivity toward AI. We revisit this claim using the public data from Study 3 of that article, which measures past usage of five AI tool categories on a five-point frequency scale. We first reproduce the negative association between AI literacy and aggregate AI usage using OLS on participant-level averages, binary logit, ordered logit, and multinomial logit specifications. We then show that the aggregate relationship masks substantial heterogeneity by tool type. In our demographic-adjusted primary specification, AI literacy does not significantly predict text AI usage (ordered-logit $\beta$ = -0.090, p = .387), whereas it remains a strong predictor of non-text AI adoption ($\beta$ = -0.377, p < .001). The non-text effect is also robust under Tully et al.'s original Study 3 control specification ($\beta$ = -0.502, p < .001). Binary, ordered-logit, and multinomial specifications suggest that the non-text relationship is primarily an adoption/non-adoption pattern rather than evidence of intensive use: the demographic-adjusted odds ratio of ever having used a non-text AI tool is 0.68. Thus, in the study that measures self-reported past usage rather than stated preferences, the evidence does not support a simple claim that lower AI literacy predicts greater receptivity to AI in general. It points instead to a narrower pattern of broader adoption across lower-penetration, non-text AI tools.

07.
medRxiv (Medicine) 2026-06-22

Integration of lung tissue proteomics and genome-wide association data to identify lung cancer susceptibility proteins and potential drug targets

Background: Proteins directly impact disease development and act as drug targets. Therefore, we integrated genomic and lung tissue proteomics data to identify lung cancer susceptibility proteins, elucidating genetic mechanisms and candidate drug targets. Method: We profiled the proteome and genome in non-neoplastic lung tissue from 200 lung cancer patients. Using this data, we constructed genetic models to predict abundance across the proteome in lung tissue. We applied these models to genome-wide association study (GWAS) data from 55,174 lung cancer cases and 1,294,174 controls to evaluate their associations with the risk of lung cancer, overall and by major histological subtypes. Bayesian colocalization and Mendelian randomization (MR) analyses were used to prioritize putative causal proteins, which were cross-referenced with three main drug-protein databases to identify potential therapeutic targets. Results: We identified 29 proteins associated with lung cancer risk at a false discovery rate < 5%, including 25 for overall lung cancer, two (AQP3 and IL18) specifically for adenocarcinoma, and another two (HMGN2 and HLA-DMB) for squamous cell carcinoma. Of them, genes encoding 17 proteins reside at least 2Mb away from any known GWAS risk loci, including 14 for overall lung cancer (HYI, GPX1, GMPPB, DSP, HDDC2, MTCH2, SUOX, JMJD7, PDIA3, IL16, IQGAP1, SULT1A2, ARHGAP27, and TYMP) and three for subtypes (AQP3, IL18, and HMGN2). Among the 12 proteins located within the known risk loci, EPHX2, CLDN18, PSMD5, and CYP2S1 proteins showed an association independent of the proximal GWAS-identified lead variant. Colocalization and/or MR analysis suggested 11 potential causal proteins. Five of these candidate causal proteins (DSP, CLDN18, IQGAP1, IL18 and TYMP) are targeted by nine drugs already approved by the FDA or in phase III trials. Conclusion: Our study identified novel lung cancer susceptibility proteins and potential drug targets, offering valuable insights into lung cancer biology and future translational utilities.

08.
arXiv (CS.CL) 2026-06-11

AI Coding Agents in Social Science: Methodologically Diverse, Empirically Consistent, Interpretively Vulnerable

The deployment of LLM-based agents in scientific analysis raises opposing concerns: that agents may reduce methodological diversity, or that they may amplify the analytic flexibility through which researchers reach motivated conclusions. We argue these worries target two empirically separable layers: a design layer of methodological choices, and a verdict layer in which a decision rule maps estimates to a substantive claim. We test both by running 20 independent executions of Claude Code and Codex on a prominent immigration and social-policy against a many-analysts human baseline. At the design layer, Codex matches human methodological diversity and Claude Code produces nearly three times as many specifications; both agents' effect estimates remain broadly aligned with the human consensus, and no agent model exactly matches any human model. A prompt-induced anti-immigration researcher prior reorganizes each agent's methodological decisions but, unlike for biased human analysts in the same data, does not shift aggregate estimates or final verdicts; nor do agents reroute along the methodological axes humans use to bias their estimates. At the verdict layer, an explicit confirmatory prompt flips Claude Code's verdicts from 10% to 90% support while leaving its coefficient distribution essentially unchanged, operating through rule omission rather than rule softening. AI agents can rival or exceed human methodological diversity at the design layer while remaining vulnerable at the verdict layer. In our setting, the locus of AI bias is not estimation but interpretation.

09.
Nature (Science) 2026-06-17

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago

Plague is among the most devastating diseases in human history1. However, early strains of the plague-causing bacterium Yersinia pestis lacked virulence factors that are required for the bubonic form until around 3,800 years ago2,3. Consequently, the morbidity and mortality of early plague strains remain unclear. Here we describe early plague strains that are associated with two phases of outbreaks among mid-Holocene hunter-gatherers near Lake Baikal in southeast Siberia, beginning from about 5,500 years ago. These outbreaks occur across four hunter-gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups were affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11 years). We further note functional differences, including in the ypm superantigen locus, which is also present in present day Yersinia pseudotuberculosis. The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating that this happened before approximately 5,700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter-gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics. Analyses of ancient DNA from hunter-gatherers near Lake Baikal in southeast Siberia around 5,500 years ago indicate that highly virulent Yersinia pestis emerged earlier than previously estimated, far&nbsp;from the next known&nbsp;cases of infection&nbsp;in Late Neolithic Europe.

10.
Nature (Science) 2026-06-17

Emergent decadal predictability in Antarctic contribution to sea-level rise

Despite large uncertainties associated with future mass loss from the Antarctic Ice Sheet, ice-sheet models show that the rate of sea-level rise from Antarctic ice loss in 2025 is strongly predictive of the rate for the next several decades, regardless of emission pathway or model complexity. This finding is robust across all models that were considered in the Intergovernmental Panel on Climate Change Sixth Assessment Report global mean sea-level projections, including the low-likelihood, high-impact scenarios of sea-level rise. Given this strong near-term decadal predictability, ice-sheet models that can accurately reproduce present-day ice-mass loss provide a reliable basis for near-term sea-level planning and adaptation through to mid-century. The predictability breaks down by the end of the twenty-first century as feedbacks, such as those related to marine ice-sheet retreat, begin to emerge, leading to accelerating ice loss. Drawing on these results, we identify key feedback mechanisms that can account for the transition between near-term decadal predictability and the longer-term, feedback-driven evolution, and suggest priorities for ice-sheet model development aimed at resolving long-term sea-level rise uncertainty. Although Antarctic ice loss projections diverge widely by 2100, this Perspective shows that present-day rates robustly predict mid-century sea level rise, providing a firm basis for near-term planning, while highlighting priorities for model development aimed at resolving longer-term sea level rise uncertainty.

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

HadBalance: A Plug-and-Play Unified Global Geometric Prior Framework for Generalizable Biomedical Segmentation

Precise biomedical image segmentation is crucial for clinical diagnosis. Geometric cues (e.g., boundary, shape, and topology) can improve structural consistency, yet most are task-specific and lack a unified geometric foundation that generalizes across organs and modalities. We are motivated by the observation that several medical segmentation targets can be approximated as globally near-convex shapes. A convex region is one in which any two interior points can be connected by a line segment entirely contained within the region. In practice, medical targets may exhibit small local concavities or boundary irregularities; we refer to such globally convex-like shapes as near-convex. Motivated by this, we derive Hadwiger Shape Priors from Hadwiger's theorem as an interpretable global regularizer using three 2D measures: area A, perimeter P, and Euler characteristic chi, enabling transfer across organs and modalities. However, because medical datasets are shape-heterogeneous, enforcing near-convex priors uniformly can over-regularize non-convex anatomy with significant concavities, washing out concavities and fine details and degrading segmentation accuracy. To address this challenge, we propose Conflict-Aware Objective Balancing (CAOB), which integrates shape priors with segmentation in a gradient-aware manner. For each prior, CAOB removes only the gradient component that conflicts with segmentation while preserving the remaining aligned component, and adaptively regulates objective influences to prevent prior dominance. This enables stable use of shape priors on shape-heterogeneous data without erasing genuine concavities or fine structural details. We call this plug-and-play framework HadBalance.

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

Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

arXiv:2605.29228v2 Announce Type: replace Abstract: Protein structure classification (PSC) uses supervised learning to predict a protein's CATH/SCOP(e) class from the protein's sequence or 3D structural feature(s). We already modeled 3D structures as (static) protein structure networks (PSNs), demonstrating the competitiveness of PSN-based features to sequence or direct (i.e. non-network) 3D structural features in the PSC task. More recently, we demonstrated the power of features extracted from dynamic PSNs over features extracted from static PSNs (and thus by transitivity over sequence and direct 3D structural features) in the same task. That dynamic PSN approach used traditional machine learning (ML), combining manual (pre-engineered) features with an off-the-shelf classifier. Here, we evaluate whether automatic deep learning (DL) from the dynamic PSNs yields improvements. Our evaluation on 72 datasets spanning ~44,000 CATH- or SCOPe-labeled dynamic PSNs reveals that in terms of PSC accuracy, traditional ML and DL are (close to) tied for a large majority of the datasets, while DL is on average 10+ times slower. We are the first to evaluate traditional ML vs. DL in the dynamic PSN-based PSC task.

13.
medRxiv (Medicine) 2026-06-15

Poly-Social Risk for Hypertension Among Black and Latina Women

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

14.
medRxiv (Medicine) 2026-06-23

Association between the hemoglobin albumin lymphocyte and platelet score and chronic kidney disease: insights from patient data and animal models

Introduction The hemoglobin, albumin, lymphocytes and platelets (HALP) score, a novel nutritional and inflammatory biomarker, has been used in various chronic disease studies. However, the relationship between the HALP score and chronic kidney disease (CKD) remains poorly elucidated. This study aimed to explore the possible association between the HALP score and CKD. Methods Our analysis encompassed 25,160 adult participants drawn from NHANES cycles spanning 2009 through 2018. Weighted multivariable logistic regression and generalized additive models (GAMs) were employed to evaluate the independent associations between the HALP score and CKD, albuminuria, and low-estimated glomerular filtration rate (eGFR). Threshold effects were examined using two-piecewise linear regression. Subgroup and sensitivity analyses were performed to assess robustness. Receiver operating characteristic (ROC) curve analyses were applied to compare the discriminative capacity of the HALP score with the prognostic nutritional index (PNI), systemic immune-inflammation index (SII), lymphocyte-to-monocyte ratio (LMR), and platelet-to-lymphocyte ratio (PLR). The clinical findings were further validated in a 5/6 nephrectomy rat model. Results After adjustment for multiple confounders, higher HALP scores were inversely associated with the risk of CKD (OR = 0.97, 95% CI: 0.94-0.99) and albuminuria (OR = 0.97, 95% CI: 0.93-0.99). However, after full adjustment for demographic characteristics, physical examination indices and laboratory parameters (Model 3), the correlation between the HALP score and low-eGFR was no longer statistically significant. Non-linear analyses revealed a threshold effect, with CKD risk declining as the HALP score increased up to an inflection point of 52.43 (OR = 0.97, 95% CI: 0.95-0.99), beyond which no further protective effect was observed. A similar threshold effect was identified for albuminuria. Subgroup and interaction analyses indicated no meaningful effect modification by age, sex, BMI, hypertension, or diabetes. Sensitivity analyses confirmed the robustness of the results. ROC analysis demonstrated that the HALP score showed superior discriminative ability for CKD and albuminuria compared with PNI, SII, LMR, and PLR. In the animal experiment, CKD model rats exhibited significantly lower HALP scores than controls. Inverse correlations were observed between the HALP score and serum creatinine (Scr), blood urea nitrogen (BUN), and urinary albumin-to-creatinine ratio (UACR), with UACR showing the strongest correlation, which was consistent with the clinical findings. Conclusion Lower HALP scores are independently associated with increased prevalence of CKD and albuminuria. As an affordable and readily measurable biomarker, the HALP score may facilitate CKD risk assessment.

15.
Nature Medicine 2026-06-09

Adjuvanted inactivated rabies virus-vectored Lassa virus vaccine in healthy adults: a phase 1 trial

Lassa fever causes substantial morbidity and mortality in West Africa, and no licensed vaccine is available. We evaluated LASSARAB, an inactivated rabies virus-vectored Lassa virus (Josiah strain) glycoprotein complex vaccine. We conducted a randomized, controlled, dose-escalation phase 1 trial. Participants (total n = 54) received two intramuscular doses of LASSARAB containing 700 (n = 15), 1,400 (n = 15) or 2,800 (n = 14) relative units of antigen formulated with the TLR-4 agonist 3D-6-acyl PHAD-SE adjuvant, or licensed rabies vaccine control (n = 10), administered 28 days apart. This protocol-defined interim analysis reports the primary safety evaluation and secondary immunogenicity assessments through day 61. There were no prespecified hypotheses or formal power calculations. All primary safety end points demonstrated an acceptable safety profile. After dose 1, local solicited adverse events occurred in 86.7–100.0% of LASSARAB groups and 80% of controls; systemic events in 33.3–71.4% and 60.0% of controls. After dose 2, local solicited adverse events occurred in 66.7–86.7% of LASSARAB groups and 55.6% of controls; systemic events in 53.3–71.4% of LASSARAB groups and 55.6% of controls. Events were predominantly mild and self-limited. Unsolicited adverse events occurred in 28.6–60.0% of LASSARAB groups and 20.0% of controls. No serious adverse event, immune-mediated condition or sensorineural hearing loss occurred. Safety laboratory abnormalities occurred in 13.3–66.7% of LASSARAB groups and 30.0% of controls (14 mild, 6 moderate and none severe). After two doses, Lassa virus GPC IgG ELISA seroconversion (≥fourfold rise) was achieved in 100.0% (44 of 44) of LASSARAB recipients and 0.0% (0 of 10) of controls. Rabies glycoprotein IgG ELISA seroconversion (≥fourfold rise) and neutralizing antibody by rapid fluorescent focus inhibition test (RFFIT) seroprotection (≥0.5 IU ml−1) were also 100% across all groups, including controls. LASSARAB + 3D-6-acyl phosphorylated hexaacyl disaccharide (PHAD)-SE demonstrated a favorable safety profile and immunogenicity against Lassa and rabies viruses. The per-protocol final study report will include safety and durability through day 394. ClinicalTrials.gov identifier NCT06546709 . An interim report of a first-in-human phase 1 trial found an adjuvanted, combination inactivated rabies-vectored, Lassa fever vaccine (LASSARAB + 3D-6-acyl PHAD-SE) to be safe and induced immunogenicity to both Lassa and rabies viruses in healthy participants.

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

Context-aware Modality-Topology Co-Alignment for Multimodal Attributed Graphs

Multimodal Attributed Graphs (MAGs) model real-world entities by coupling graph topology with heterogeneous attributes such as text and images. They support graph-centric tasks requiring structural and class-discriminative representations, and modality-centric tasks requiring fine-grained cross-modal correspondence. However, existing MAG methods often rely on fixed graph contexts or uniformly fused representations, causing task-agnostic propagation and over-compressed fusion that hinder diverse task requirements and modality-specific evidence preservation. To address this, we propose CoMAG, a unified MAG backbone that learns task-adaptive reliable contexts and modality-preserving alignment within them. CoMAG first conducts Reliable Context Learning by estimating edge reliability from multimodal semantic consistency, complementing raw topology with semantic neighbors, and selecting context components through a task-aware gate. It then performs Modality-preserving Hop-token Alignment by maintaining modality-specific multi-hop trajectories, matching modality-hop tokens across modalities, and decoupling shared and private representations. Thus, CoMAG produces graph and modality representations from one forward pass while retaining modality-specific cues. We further analyze stable propagation, over-smoothing mitigation, and modality-collapse control. Experiments on nine OpenMAG datasets compare CoMAG with feature-only, graph-only, multimodal, and unified MAG baselines across graph-level prediction, modality matching, and graph-conditioned generation. Results show that CoMAG achieves the best reported performance, demonstrating that task-adaptive reliable contexts and modality-preserving alignment improve structural prediction, cross-modal matching, and graph-conditioned generation while retaining sparse edge-linear complexity.

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

A Survey on 3D Gaussian Splatting Applications: Segmentation, Editing, and Generation

In the context of novel view synthesis, 3D Gaussian Splatting (3DGS) has recently emerged as an efficient and competitive counterpart to Neural Radiance Field (NeRF), enabling high-fidelity photorealistic rendering in real time. Beyond novel view synthesis, the explicit and compact nature of 3DGS enables a wide range of downstream applications that require geometric and semantic understanding. This survey provides a comprehensive overview of recent progress in 3DGS applications. It first reviews the reconstruction preliminaries of 3DGS, followed by the problem formulation, 2D foundation models, and related NeRF-based research areas that inform downstream 3DGS applications. We then categorize 3DGS applications into three foundational tasks: segmentation, editing, and generation, alongside additional functional applications built upon or tightly coupled with these foundational capabilities. For each, we summarize representative methods, supervision strategies, and learning paradigms, highlighting shared design principles and emerging trends. Commonly used datasets and evaluation protocols are also summarized, along with comparative analyses of recent methods across public benchmarks. To support ongoing research and development, a continually updated repository of papers, code, and resources is maintained at https://github.com/heshuting555/Awesome-3DGS-Applications.

18.
arXiv (CS.AI) 2026-06-17

Learning Fair Pareto-Optimal Policies in Multi-Objective Reinforcement Learning

arXiv:2606.18111v1 Announce Type: cross Abstract: Fairness is an important aspect of decision-making in multi-objective reinforcement learning (MORL), where policies must ensure both optimality and equity across multiple, potentially conflicting objectives. While single-policy MORL methods can learn fair policies for fixed user preferences using welfare functions such as the generalized Gini welfare function (GGF), they fail to provide the diverse set of policies necessary for dynamic or unknown user preferences. To address this limitation, we formalize the fair optimization problem in multi-policy MORL, where the goal is to learn a set of Pareto-optimal policies that ensure fairness across all possible user preferences. Our key technical contributions are threefold: (1) We show that for concave, piecewise-linear welfare functions (e.g., GGF), fair policies remain in the convex coverage set (CCS), which is an approximated Pareto front for linear scalarization. (2) We demonstrate that non-stationary policies, augmented with accrued reward histories, and stochastic policies improve fairness by dynamically adapting to historical inequities. (3) We propose three novel algorithms, which include integrating GGF with multi-policy multi-objective Q-Learning (MOQL), state-augmented multi-policy MOQL for learning non-statoinary policies, and its novel extension for learning stochastic policies. We evaluate our algorithms across various domains and compare our methods against the state-of-the-art MORL baselines. The empirical results show that our methods learn a set of fair policies that accommodate different user preferences.

19.
bioRxiv (Bioinfo) 2026-06-23

CellOS: Learning a World Model of Cellular State through Joint Embedding Prediction

Foundation models learned from single-cell transcriptomes are central to the prospect of AI virtual cell that can represent, query and predict cellular state. However, most current single-cell foundation models learn from a single view of gene expression and are optimized primarily through reconstruction or next-token prediction. As a result, they capture expression abundance but can-not explicitly reconcile complementary views of cellular state. Here we present CellOS, a multi-view foundation model that learns cellular representations from paired expression and perception views. CellOS integrates complementary views through a scalable three-stage training strategy that combines causal cell-sentence language modelling, function-preserving dense-to-mixture-of-experts expansion and latent-space alignment via an LLM-JEPA objective. Using this framework, we trained a 12-billion-parameter model on 390.5 million single-cell transcriptomes. Across diverse benchmarks spanning cell-state annotation, batch integration and perturbation-response prediction, CellOS consistently outperformed state-of-the-art single-cell foundation models in cell-state annotation and perturbation-response prediction while preserving robust batch integration. Together, these results suggest that predictive alignment between complementary cellular views provides a scalable path toward representation-centric cellular world models and transferable AI virtual cells.

20.
arXiv (quant-ph) 2026-06-11

Collective Emission in LH2 Assembly Beyond the Point-Dipole Approximation

arXiv:2606.11227v1 Announce Type: cross Abstract: Collective emission in light-harvesting assemblies is governed by the local transition dipole and finite geometry of emitting units, a fact that point-dipole approximation obscures. To go beyond this picture, we develop a non-Hermitian Hamiltonian using the quantum electrodynamic dyadic Green's tensor for a purple bacteria. We construct it for the isolated 24-bacteriochlorophyll conical frustum and its P42$_1$2 crystallographic assembly. The P42$_1$2 unit-cell symmetry is found to invert the bright-dark ordering of the single ring, placing subradiant states at the low-energy end and revealing the entire crystal to be the energy-harvesting entity. Tilt-driven switching is activated only in crystal geometries where the finite dipole-carrier (LH2) lies perpendicular to the growth plane. Vacancy and orientational disorder work only in cooperation to renormalize the switching threshold from higher polar angles to lower values.

21.
bioRxiv (Bioinfo) 2026-06-15

AliceDB database and pipeline for identification of natural protein variants based on mass spectrometry measurement data

The natural variation that distinguishes living organisms within a single species is currently being studied intensively, primarily at the genetic level. Unfortunately, studies of natural variants at the level of protein gene products are not very common, mainly due to the lack of appropriate databases and bioinformatics tools. The main research technique used to study proteomes/peptidomes is mass spectrometry (MS). A classic method for interpreting raw mass spectrometry data in proteomic/peptidomic studies involves the use of databases containing representative (canonical) sequences that define the proteome of the organism under study. In this paper, we present the AliceDB database, which contains information on over 7 million natural variants of protein sequences described in the scientific literature for Homo sapiens. The data contained in the AliceDB database can be utilized using widely available and commonly used software for interpreting proteomic data. Test results regarding the use of the AliceDB database for the interpretation of proteomic data indicate that accounting for the presence of natural variants increases both the number and quality of identified proteins. Furthermore, it is easy to identify protein sequence variants that may, for example, be of significance in medicine.

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

Insulin4RL: Real-Time Insulin Management in the Intensive Care Unit for Offline Reinforcement Learning

arXiv:2606.19481v1 Announce Type: new Abstract: Offline reinforcement learning (ORL) offers the potential to improve the quality of clinical decision-making using historical electronic health record (EHR) data. Current training and evaluative practices in this field rely heavily on EHR datasets that have been temporally discretised into fixed, regular time intervals. Discretisation creates fictional representations of complex clinical scenarios and compromises the generalisability of retrospective model evaluations. In this paper, we introduce Insulin4RL, a healthcare ORL dataset featuring naturally irregular inputs and actions from real clinical trajectories. Derived from MIMIC-IV, Insulin4RL comprises over 375,000 labelled decisions across 12,209 patients requiring insulin infusion titration in the Intensive Care Unit. The dataset can thus be used for research into ORL model performance under realistic clinical sampling assumptions. We provide a description of the dataset's structure and characteristics, baseline performance metrics using model-free offline reinforcement learning, and a standardised evaluation protocol using fitted Q-evaluation. We conclude with suggested areas for future research that could be addressed using this resource.

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

QUIVER: Cost-Aware Adaptive Preference Querying in Surrogate-Assisted Evolutionary Multi-Objective Optimization

arXiv:2605.04267v2 Announce Type: replace Abstract: Interactive multi-objective optimization systems face a budget allocation dilemma: one can spend resources on expensive objective evaluations or on eliciting decision-maker preferences that identify the relevant region of the Pareto set. Moreover, preference elicitation itself spans modalities with different information content and cognitive burden, ranging from cheap, noisy pairwise preference statements (PS) to richer but costlier indifference adjustments (IA). We study cost-aware optimization under an unknown scalarization and introduce QUIVER (Query-Informed Value Estimation for Regret), a surrogate-assisted evolutionary multi-objective optimizer that adaptively chooses between objective evaluations and heterogeneous preference queries. At each step, QUIVER selects the next action by maximizing the expected decision-quality improvement per unit total cost. Across DTLZ and WFG benchmarks under synthetic decision-maker models, QUIVER achieves the lowest final utility regret on challenging WFG problems (utility regret of 2.14 on WFG4, 2.82 on WFG9: a 25% improvement over baselines), outperforming all single-modality baselines. We analyze how the optimal mix of PS and IA adapts to problem difficulty: on easy problems (DTLZ2), QUIVER selects 80\% PS queries; on hard problems (WFG9), it shifts to 35% IA queries. This adaptive modality selection demonstrates cost-aware preference learning in action.

25.
arXiv (CS.LG) 2026-06-12

Machine Learning-based Two-Stage Graph Sparsification for the Travelling Salesman Problem

arXiv:2604.20236v2 Announce Type: replace Abstract: High-performance TSP solvers such as Lin-Kernighan-Helsgaun (LKH) search within a candidate graph – a small subset of edges pre-selected for the solver – rather than over the complete graph. The two leading sparsification heuristics, $\alpha$-Nearest and POPMUSIC, each fall short of the density-coverage balance: $\alpha$-Nearest is dense with stable recall, while POPMUSIC is sparser but its recall degrades with scale. Their union closes the recall gap while remaining far below the complete graph in density, leaving room for further reduction. Existing learning-based sparsifiers score edges on the complete graph, an approach that is expensive and largely limited to Euclidean instances. We propose a two-stage method that inverts this logic. Stage~1 takes the union of $\alpha$-Nearest and POPMUSIC, achieving near-perfect recall at ${\sim}6N$ edges. Crucially, the union annotates each edge with its source provenance – whether it was endorsed by $\alpha$-Nearest, POPMUSIC, or both. Stage~2 trains a lightweight classifier on these annotated edges and prunes the lowest-scoring ones. Because dual-source edges are almost always optimal, the learning problem reduces to filtering the single-source subset – a substantially easier task than classifying all $O(N^2)$ edges from scratch. Across four distance types, five spatial distributions, and problem sizes from 50 to 500, the pipeline reduces candidate-graph density by $37$-$47\%$ while retaining ${\geq}99.69\%$ of optimal-tour edges, and matches or exceeds the coverage of recent Euclidean-only neural sparsifiers at lower density at TSP500.