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01.
arXiv (quant-ph) 2026-06-19

Operator Learning for efficient Quantum Computation

arXiv:2606.20184v1 Announce Type: new Abstract: An efficient implementation of quantum algorithms is often hindered by the lack of efficient primitives for operators and state preparation. This limits both the ability of near-term quantum hardware to simulate complex problems and the potential of fault-tolerant algorithms to achieve practical quantum advantage. To address this, we propose a full-stack variational framework that transforms arbitrary operators to compact quantum circuits. The resulting variational circuits can be tailored to the connectivity and long-range interaction of the target hardware. The learning process employs backpropagation together with a cost function that efficiently optimizes unitary operators and non-unitary – dense or sparse – operators using only a single ancilla qubit for block encoding. Additionally, we introduce a regularization term that reduces the approximation error. The approach is validated for both quantum mechanical and engineering applications. In the former case, we learn propagators that arise in native quantum problems – such as quantum simulation and quantum chemistry – and achieve improved resource scaling in comparison to standard Suzuki-Trotter expansions. In the latter case, we demonstrate the approach's ability to implement the second-order central finite difference approximation of the Laplace operator – relevant for solving partial differential equations – while improving upon current error metrics. The final example deals with learning a dense, non-unitary operator that arises in the analysis of inviscid potential flow around an airfoil. This universality of the framework opens the door for solving general problems beyond prototypical engineering and quantum applications.

02.
arXiv (CS.AI) 2026-06-15

Recovering Stranded Discrimination in Knowledge Tracing: Per-Item Bias Correction via Empirical-Bayes Shrinkage

arXiv:2606.14123v1 Announce Type: cross Abstract: Deployed knowledge-tracing models are typically frozen after training, yet systematic per-item logit bias arises, from limited per-item expressivity in backbone architectures and from post-deployment shifts in item properties, degrading prediction quality. Global post-hoc calibrators such as Platt scaling, temperature scaling, and isotonic regression improve probability estimates but leave discriminative ability, as measured by AUC, unchanged. This AUC invariance is a structural consequence of monotone score-only transforms; recovering the stranded discrimination requires conditioning on item identity. We propose SLC (State-space Logit Correction), which converts binary observations to Gaussian pseudo-observations via Laplace/IRLS, applies empirical-Bayes shrinkage through a Kalman smoother, and fits an offset-Platt link. The state-space formulation also yields a detectability bound that characterizes the Bernoulli information floor, explaining why temporal tracking provides no benefit at current data densities. Across four datasets, five backbones, and three seeds, SLC improves AUC on all four datasets and NLL on three, with the advantage concentrating on sparse items. Cross-domain controls suggest that the same phenomenon can arise beyond education when the deployed backbone leaves entity-level bias.

03.
arXiv (CS.CL) 2026-06-17

PARSE: Provenance-Aware Retrieval Sanitization for Professional Domain LLM Agents

作者:

Prompt injection defenses evaluated on synthetic benchmarks do not generalize to real enterprise documents, which are longer, denser, and interleave legitimate authority language with factual content. We demonstrate this gap with a real-document benchmark of 122 tasks across five professional domains (financial, legal, medical, scientific, DevOps) using actual SEC filings, Federal Register rules, PubMed abstracts, arXiv papers, and GitHub postmortems. Paraphrasing, the strongest defense on synthetic benchmarks, shows no statistically significant attack success rate reduction on real documents (p=0.500) while degrading utility from 91.8% to 82.8%. We introduce PARSE (Provenance-Aware Retrieval Sanitization), a domain-aware, fact-preserving sanitization pipeline that classifies each sentence by injection likelihood, extracts structured facts before rewriting, and verifies fact preservation via a consistency-checking loop. A directiveness gate routes 59% of real enterprise documents to a lightweight path, concentrating computational cost on high-risk documents. PARSE achieves 15.6% attack success rate – a 38% reduction versus the 25.4% baseline – at 86.9% utility, the only condition that is both statistically significant (p=0.014, adequately powered) and maintains near-baseline utility. Practitioners should evaluate defenses on domain-matched real documents, not synthetic proxies.

04.
medRxiv (Medicine) 2026-06-23

Food Colorings in Child-Targeted Ultra-Processed Foods in Brazil: Market Prevalence and Parental Perceptions

Child-targeted marketing on packaged foods can shape children's food preferences and parents' purchasing decisions, yet many products with child-targeted marketing are ultra-processed foods (UPFs) and contain cosmetic additives such as food colorings, which have raised concerns about adverse effects on children's health and behavior. This mixed-methods study examined the prevalence of food colorings in child-directed UPFs and explored parents' perceptions and knowledge of these additives in beverages commonly consumed by children. Quantitative data were obtained from the Mintel Global New Products Database to identify child-directed products launched in Brazil between 2018 and 2021, measured as having at least one child-targeted marketing strategy in the food package, and whether they contained food colorings. Qualitative data came from seven focus groups with parents of children aged 2-5 and 6-11 years in Brazil, alongside a brief survey assessing participants' ability to identify food colorings on product labels. Among 5,078 UPFs launched during the study period, 23.0% contained child-targeted marketing, and 40.3% of these had food colorings. The highest prevalence was observed in carbonated beverages, candies, and ice creams, in which more than half of products contained food colorings. Parents generally understood that food colorings are used to make products more attractive to children and associated them with potential health risks, but reported difficulties avoiding them. These findings highlight the widespread presence of food colorings in child-targeted UPFs in Brazil and underscore the need for stronger regulatory measures to restrict the use of food colorings and improve labelling on food packages.

05.
arXiv (CS.AI) 2026-06-25

Surrogate models for Rock-Fluid Interaction: A Grid-Size-Invariant Approach

arXiv:2602.22188v2 Announce Type: replace-cross Abstract: Modelling rock-fluid interaction requires solving a set of partial differential equations (PDEs) to predict the flow behaviour and the reactions of the fluid with the rock on the interfaces. Conventional high-fidelity numerical models require a high resolution to obtain reliable results, resulting in huge computational expense. This restricts the applicability of these models for multi-query problems, such as uncertainty quantification and optimisation, which require running numerous scenarios. As a cheaper alternative to high-fidelity models, this work develops eight surrogate models for predicting the fluid flow in porous media. Four of these are reduced-order models (ROM) based on one neural network for compression and another for prediction. The other four are single neural networks with the property of grid-size invariance; a term which we use to refer to image-to-image models that are capable of inferring on computational domains that are larger than those used during training. In addition to the novel grid-size-invariant framework for surrogate models, we compare the predictive performance of UNet and UNet++ architectures, and demonstrate that UNet++ outperforms UNet for surrogate models. Furthermore, we show that the grid-size-invariant approach is a reliable way to reduce memory consumption during training, resulting in good correlation between predicted and ground-truth values and outperforming the ROMs analysed. The application analysed is particularly challenging because fluid-induced rock dissolution results in a non-static solid field and, consequently, it cannot be used to help in adjustments of the future prediction.

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

Automating Low-Risk Code Review at Meta: RADAR, Risk Calibration, and Review Efficiency

arXiv:2605.30208v2 Announce Type: replace-cross Abstract: AI-assisted coding tools have altered software production. At Meta, significant lines of code per human-landed diff grew by 105.9% year over year and per-developer diff volume rose 51%, with agentic AI responsible for over 80% of that growth. Meanwhile, the share of diffs receiving timely review has declined, exposing a widening gap between code supply and reviewer bandwidth. We ask three questions that progress from feasibility through calibration to impact: (1) can risk-stratified automation operate at scale across diverse organizations, (2) how does tuning the risk threshold affect the trade-off between automation yield and safety, and (3) to what extent does automated review reduce end-to-end latency for AI-generated changes? We deployed RADAR (Risk Aware Diff Auto Review), a multi-stage funnel that classifies each diff by authorship and source type, applies eligibility gates, static heuristics, a machine-learned Diff Risk Score, LLM-based Automated Code Review, and deterministic validation before landing qualifying changes. We evaluate RADAR through telemetry covering 535K+ RADAR-reviewed diffs, observational before-after comparisons for policy changes, and difference-in-differences analysis of efficiency outcomes. RADAR has reviewed 535K+ diffs and landed 331K+. Relaxing the Diff Risk Score threshold from the 25th to the 50th percentile increased the approve rate to 60.31%. The revert rate for RADAR-reviewed diffs is 1/3 that of non-RADAR diffs, and the Production Incident rate is 1/50 that of non-RADAR diffs. RADAR reduces median time to close by over 330% and median diff review wall time by 35%. Risk-aware layered automation can materially reduce review bottlenecks created by AI-driven code growth without compromising production safety.

07.
arXiv (math.PR) 2026-06-17

A Tanaka-Type Formula for Compact Sets and Equilibrium Measures of L\'{e}vy Processes

arXiv:2606.17472v1 Announce Type: new Abstract: Tanaka's formula is a classical identity for Brownian motion, and Tsukada (2018) extended it to L\'{e}vy processes not necessarily symmetric. From a potential-theoretic point of view, this formula shows that the invariant function for the process killed upon hitting a singleton can be decomposed into the sum of a martingale part and a local time. In this paper, we generalize this singleton setting and derive a Tanaka-type formula for a compact set $B$. To this end, we introduce the equilibrium measure, defined as the rescaled limit of the $q$-capacity measures, and show that the invariant function for the process killed upon hitting $B$ can be represented as the integral, with respect to the equilibrium measure, of the invariant functions associated with processes killed upon hitting singletons, up to an additive constant called the Robin constant. Moreover, when $B$ is an interval, we obtain explicit representations of the equilibrium measure, the Robin constant, and the martingale part for recurrent stable processes as well as for recurrent spectrally negative L\'{e}vy processes. Finally, we discuss how an analogous Tanaka-type formula can also be established for transient L\'{e}vy processes.

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

Reload-Mamba: Hierarchical Anti-Dilution State-Space Modeling for Multi-Class Semantic Segmentation

Mamba-based state space models offer linear-time long-range modeling for high-resolution dense prediction, but sequential state-space propagation can attenuate boundary-sensitive and detail-sensitive responses that are critical in multi-class semantic segmentation. We propose Reload-Mamba, a semantic segmentation framework that addresses this propagation-induced response dilution through three segmentation-specific designs: (i) a boundary-supervised local detail prior that is explicitly trained with ground-truth boundary masks to identify regions requiring response restoration; (ii) a class-uncertainty-aware Reload Gate that incorporates per-pixel class entropy from a pre-reload auxiliary head as an additional gating signal, a formulation that is informative only under multi-class dense prediction; and (iii) a hierarchical multi-level Reload mechanism that applies anti-dilution refinement at three decoder levels and fuses the restored representations top-down. Built upon a ConvNeXt-Tiny encoder with a multi-scale decoder and four-directional Mamba scanning with pixel-wise directional attention, Reload-Mamba achieves 47.9% single-scale (48.9% multi-scale) mIoU on ADE20K and 83.2% single-scale mIoU on Cityscapes. With ResNet-101 + COCO pre-training under the standard DeepLab-style protocol, Reload-Mamba reaches 87.8% mIoU on PASCAL VOC 2012 val. Controlled ablations show that each of the three segmentation-specific designs contributes beyond a direct port of the prior anti-dilution architecture proposed for binarization, cumulatively improving over the direct-port baseline by +2.2 mIoU on ADE20K.

09.
arXiv (CS.AI) 2026-06-19

Policy-aware Vector Search: A Vision for Fine Grained Access Control in Vector Databases

arXiv:2606.19803v1 Announce Type: cross Abstract: Vector databases are increasingly used in security sensitive contexts with Retrieval Augmented Generation and organizational AI pipelines; however, their security capabilities remain limited. Specifically, Fine-grained Access Control (FGAC) which is required to ensure that data access adheres to user-specific policies is not fully supported in modern vector databases. Unlike relational databases, vector databases combine structured and unstructured attributes to provide semantic, approximate query results, which complicates FGAC implementation. This creates an inherent tension between enforcing FGAC policies correctly, achieving high ANN search recall and maintaining low query latency. In this paper, we present a vision for Policy-aware Vector Search by formalizing the FGAC policy model in vector databases as well as the enforcement problem. We compare various enforcement strategies, present preliminary findings, and identify key open challenges for future research in policy-aware vector search.

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

When Language Representations Interact: Separability and Cross-Lingual Effects in LLMs

arXiv:2606.14347v1 Announce Type: new Abstract: Large language models exhibit strong multilingual capabilities, however, their internal representations are difficult to interpret. Understanding these interactions is important for ensuring reliable behavior in multilingual systems. Recent work has shown that causal-geometric structure can explain how certain concepts are encoded as approximately linear and separable directions, but whether this framework extends to multilingual models, where language identity is correlated and hierarchical, is underexplored. We apply causal-geometric analysis to multilingual LLMs, studying 28 bilingual contrasts across three models, allowing us to analyze when languages behave as approximately independent factors and when structured dependencies persist. We find evidence that language concepts admit stable linear representations that are largely separable under a covariance-adjusted (causal) inner product, with structured deviations reflecting linguistic similarity. Moreover, languages within the same family (such as Germanic or Romance) exhibit a simplex-like geometric structure, suggesting hierarchical organization. These results extend causal-geometric interpretability to multilingual settings and provide insight into how separability and similarity may exist in multilingual LLM representations, motivating interpretability analyses that diagnose when and how structured dependencies between concepts can be anticipated. This has implications for trustworthy deployment, as residual structure between languages may lead to unintended cross-lingual effects when models are monitored or intervened upon.

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

AL-GNN: Privacy-Preserving and Replay-Free Continual Graph Learning via Analytic Learning

arXiv:2512.18295v2 Announce Type: replace-cross Abstract: Continual graph learning (CGL) aims to enable graph neural networks to incrementally learn from a stream of graph structured data without forgetting previously acquired knowledge. Existing methods particularly those based on experience replay typically store and revisit past graph data to mitigate catastrophic forgetting. However, these approaches pose significant limitations, including privacy concerns, inefficiency. In this work, we propose AL GNN, a novel framework for continual graph learning that eliminates the need for backpropagation and replay buffers. Instead, AL GNN leverages principles from analytic learning theory to formulate learning as a recursive least squares optimization process. It maintains and updates model knowledge analytically through closed form classifier updates and a regularized feature autocorrelation matrix. This design enables efficient one pass training for each task, and inherently preserves data privacy by avoiding historical sample storage. Extensive experiments on multiple dynamic graph classification benchmarks demonstrate that AL GNN achieves competitive or superior performance compared to existing methods. For instance, it improves average performance by 10% on CoraFull and reduces forgetting by over 30% on Reddit, while also reducing training time by nearly 50% due to its backpropagation free design.

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

Beyond Reward Engineering: A Data Recipe for Long-Context Reinforcement Learning

Long-context reasoning is an essential capability for large language models, particularly when they are deployed as autonomous agents that must reason over lengthy trajectories. Reinforcement learning (RL) has recently emerged as a dominant paradigm for improving this ability, yet existing work largely focuses on reward engineering while diverse training data remains scarce. We revisit this problem from a data-centric perspective and show that a simple yet effective data recipe alone, paired with a minimal outcome-based GRPO setup, suffices to substantially improve long-context reasoning. Our recipe targets three complementary task families – retrieval, multi-evidence synthesis, and reasoning – for which we construct and curate eight datasets totaling ~14K examples. Experiments on three models (Qwen3-4B/8B/30B-A3B) yield average gains of +7.2/+3.2/+6.4 points across seven long-context benchmarks, surpassing prior RL training sets. We further demonstrate that these gains transfer to agentic tasks, where continuing RL training on an agent-tuned model with our data recipe improves GAIA by +4.8 and BrowseComp by +7.0 points. We will release our datasets to facilitate future research.

13.
arXiv (CS.AI) 2026-06-16

Benign in Isolation, Harmful in Composition: Security Risks in Agent Skill Ecosystems

arXiv:2606.15242v1 Announce Type: cross Abstract: Skills are becoming the capability layer through which LLM agents turn plans into actions, but their use introduces security risks such as data leakage, unauthorized operations, and tool misuse. Existing vetting usually evaluates each skill in isolation, while real agent tasks often invoke multiple skills in a shared execution context. This creates Skill Composition Risk (SCR): a skill that appears benign alone can become harmful when its outputs, trust signals, authorization cues, or side effects influence later invocations along an activated path. We introduce SCR-Bench to evaluate this risk in controlled, sandboxed skill environments. Rather than relying only on textual intent or surface behavior, SCR-Bench records downstream state changes and path-level outcomes across composed skill executions. It contains three sub-benchmarks: SCR-CapFlow for capability-flow composition, SCR-TrustLift for trust-transfer composition, and SCR-AuthBlur for authorization-confusion composition. Across SCR-Bench, composed paths expose risks that are largely absent under isolated evaluation. In SCR-CapFlow, attack success rate reaches 33.6 percent under composition, compared with near-zero isolated baselines. In SCR-TrustLift, attack success rate exceeds 96.5 percent on four of five backends. In SCR-AuthBlur, the risky-approval rate increases by 71.8 percent relative to the L0 isolated baseline under the L1 context setting. These results show that agent skill security should be assessed at the level of activated paths rather than isolated artifacts. SCR and SCR-Bench provide a foundation for path-aware risk evaluation and defense in LLM agent skill ecosystems. Benchmark: https://github.com/saint-viperx/SCR_Bench.

14.
arXiv (quant-ph) 2026-06-24

Discovery of connectivity-trainability trade-off of IQP Circuits for Hamiltonian Optimization

arXiv:2606.24264v1 Announce Type: cross Abstract: Instantaneous Quantum Polynomial-time (IQP) circuits are promising candidates for near-term quantum advantage due to the conjectured classical hardness of their sampling task. However, their capabilities for optimization remain largely unexplored. We present a systematic investigation of the performance and trainability of IQP circuits for Hamiltonian optimization. Our results reveal a trade-off between optimization performance and circuit connectivity, demonstrating that the circuit structure plays a key role in determining the ability of IQP circuits to reach low-energy states.

15.
arXiv (math.PR) 2026-06-17

Convergence rate of Euler–Maruyama scheme to the invariant probability measure under total variation distance for the SDEs

arXiv:2505.04218v3 Announce Type: replace Abstract: This article shows the geometric decay rate of Euler-Maruyama scheme for one-dimensional stochastic differential equation towards its invariant probability measure under total variation distance. Firstly, the existence and uniqueness of invariant probability measure and the uniform geometric ergodicity of the chain are studied through introduction of non-atomic Markov chains. Secondly, the equivalent conditions for uniform geometric ergodicity of the chain are discovered, by constructing a split Markov chain based on the original Euler-Maruyama scheme.

16.
arXiv (math.PR) 2026-06-17

Time-dependent averages of a critical long-range stochastic heat equation

arXiv:2411.09058v2 Announce Type: replace Abstract: We study the time-dependent spatial averages of a critical stochastic partial differential equation, namely the stochastic heat equation in dimension $d\geq 3$ with noise white in time and colored in space with covariance kernel $\|\cdot\|^{-2}$. The solution to this SPDE is a singular measure and was constructed by Mueller and Tribe in [MT04]. We show that the time-dependent spatial averages of this SPDE over a ball of radius $R$ at time $t$ have different limits under different space-time scales. In particular, when $t\ll R^2$, the central limit theorem holds; when $t=R^2$, the spatial average is a non-Gaussian random variable; when $t\gg R^2$, the spatial average becomes extinct.

17.
arXiv (math.PR) 2026-06-16

Probabilities

arXiv:2601.18853v4 Announce Type: replace-cross Abstract: Probabilities is the English translation of the book Probabilités Tome 1 and Tome 2. The mathematic content is authored by Prof. Jean-Yves Ouvrard. The English version has been done by his eldest son Dr. Xavier Ouvrard. This probability theory book covers not only an introduction to this field, but also advanced concepts based on measure theory. The first part introduces the fundamentals of probability theory across 7 chapters, targeting bachelor level, including event algebras, random variables, independence, conditional probabilities, moments of discrete and continuous random variables, generating functions, and limit theorems. The second part contains 10 chapters and corresponds to master level. Following a brief introduction to measure theory, this part develops more advanced topics: probability measures and their complements, distributions and moments of random variables, modes of convergence, laws of large numbers, conditional expectation, Fourier transforms and characteristic functions, Gaussian random variables, convergence of measures, convergence in distribution, discrete-time stochastic processes, martingales, and Markov chains. The reader's work is greatly facilitated by the inclusion, in every chapter, of numerous exercises, all accompanied by detailed solutions that often provide substantial extensions to the theoretical material.

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

From Prompts to Tokens: Internalizing Causal Supervision in Vision-Language Model for Multi-Image Causal Reasoning

Visual causal reasoning is essential for understanding and intervening in the physical world, requiring identification of causal variables from visual inputs and reasoning over intervention effects. Despite recent progress, large vision–language models (VLMs) remain brittle at such tasks, especially for interventional and counterfactual queries over multi-image inputs. Most existing explorations inject causal knowledge via textual prompts, leaving causal mechanisms external to model execution and limiting reliable control during inference. To address this problem, we propose BridgeVLM, which internalizes visual causal reasoning by inducing a causal graph from multi-image inputs and converting it into structured Causal Tokens executed by RAMP layers injected into the LLM decoder for causal message passing. We further introduce a unified training interface M3S for fine-grained causal supervision from different granularities (local/global level). BridgeVLM achieves 54.4% accuracy on intervention tasks on CausalVLBench (vs. 33.2% with prompt-level supervision), improves results on Causal3D from 43.6% to 49.0%, and substantially improves causal structure learning on CausalVLBench ($F_1$: 33.4% $\rightarrow$ 75.1%).

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

Perceive, Interact, Reason: Building Tool-Augmented Visual Agents for Spatial Reasoning

While recent vision-language models (VLMs) demonstrate strong multimodal understanding, they remain limited in spatial reasoning tasks that require active evidence acquisition and multi-step visual interaction. This limitation suggests that relying solely on implicit visual representations from vision encoders is insufficient for recovering fine-grained spatial evidence. We introduce PERception-Interaction-reason Agent (PERIA), a tool-augmented visual agent for spatial reasoning tasks across map reasoning, visual probing, and vision reconstruction. PERIA uses two lightweight tool families: vision perception tools for exposing textual, symbolic, and spatial evidence, and vision interaction tools for manipulating visual context, tracing paths, and verifying spatial relations. To train PERIA, we develop a unified recipe that combines supervised tool-use trajectory synthesis, composite rewards, and Observation-Relaxed Group-in-Group Policy Optimization (OR-GIGPO) for effective multi-tool behavior. Experiments on 13 benchmarks from 8 datasets show that PERIA-8B improves over the Qwen3-8B backbone by 10.0% on in-distribution benchmarks and 4.4% on out-of-distribution benchmarks, while outperforming previous state-of-the-art baselines of similar size by 7.0%-14.8%. It also achieves performance comparable to much larger models such as Qwen3-VL-235B-A22B-Thinking and GPT-5, demonstrating the effectiveness of PERIA in enhancing spatial reasoning capabilities.

20.
medRxiv (Medicine) 2026-06-11

Malaria Risk among Internally Mobile Individuals and Heterogeneous Mobility Patterns in Two Hypoendemic Communities: Implications for Malaria Elimination in the Peruvian Amazon.

Background: Human mobility is increasingly recognized as a key factor influencing malaria transmission dynamics, particularly in low-transmission settings approaching elimination. This study aimed to assess mobility patterns and their association with malaria risk in two hypoendemic communities in the Peruvian Amazon. Method: A longitudinal study was conducted in the communities of Libertad and Urcomirano (Mazan River basin). Monthly population screenings were combined with weekly active and passive case detection. A total of 678 individuals were enrolled. Mobility patterns were assessed through structured questionnaires, and social network analysis was used to characterize travel connections. Log-binomial regression analysis was applied to identify risk factors associated with malaria infection. Result: Internally, mobile individuals in Libertad showed a higher malaria incidence (>32.47 cases per 1,000 person-months) than those in Urcomirano (

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

Learning Survival Models with Right-Censored Reporting Delays

arXiv:2510.04421v3 Announce Type: replace-cross Abstract: Survival analysis provides statistical methods to model the time until an event occurs. Reporting delays arise when event times are not observed at their occurrence but are only revealed upon reporting. This issue is particularly critical for timely risk evaluation when the observation window is short due to administrative censoring. In this study, we incorporate right-censored reporting delays by jointly modeling parametric hazards for the event and reporting processes. We then construct a consistent estimator for the model parameters and develop a Monte Carlo expectation-maximization algorithm to compute it. To address the challenges posed by administrative censoring, we leverage these findings and propose a transfer-learning procedure. Experimental results demonstrate that our method improves the accuracy of timely risk evaluation under administrative censoring.

22.
arXiv (CS.CV) 2026-06-25

Spatial Transcriptomics as Images for Large-Scale Pretraining

Spatial Transcriptomics (ST) profiles thousands of gene expression values at discrete spots with precise coordinates on tissue sections, preserving spatial context essential for clinical and pathological studies. With rising sequencing throughput and advancing platforms, the expanding data volumes motivate large-scale ST pretraining. However, the fundamental unit for pretraining, i.e., what constitutes a single training sample, remains ill-posed. Existing choices fall into two camps: (1) treating each spot as an independent sample, which discards spatial dependencies and collapses ST into single-cell transcriptomics; and (2) treating an entire slide as a single sample, which produces prohibitively large inputs and drastically fewer training examples, undermining effective pretraining. To address this gap, we propose treating spatial transcriptomics as croppable images. Specifically, we define a multi-channel image representation with fixed spatial size by cropping patches from raw slides, thereby preserving spatial context while substantially increasing the number of training samples. Along the channel dimension, we define gene subset selection rules to control input dimensionality and improve pretraining stability. Extensive experiments show that the proposed image-like dataset construction for ST pretraining consistently improves downstream performance, outperforming conventional pretraining schemes. Ablation studies verify that both spatial patching and channel design are necessary, establishing a unified, practical paradigm for organizing ST data and enabling large-scale pretraining.

23.
arXiv (CS.CL) 2026-06-11

VietMed-MCQ: A Consistency-Filtered Data Synthesis Framework for Vietnamese Traditional Medicine Evaluation

Large Language Models (LLMs) have demonstrated remarkable proficiency in general medical domains. However, their performance significantly degrades in specialized, culturally specific domains such as Vietnamese Traditional Medicine (VTM), primarily due to the scarcity of high-quality, structured benchmarks. In this paper, we introduce VietMed-MCQ, a novel multiple-choice question dataset generated via a Retrieval-Augmented Generation (RAG) pipeline with an automated consistency check mechanism. Unlike previous synthetic datasets, our framework incorporates a dual-model validation approach to ensure reasoning consistency through independent answer verification, though the substring-based evidence checking has known limitations. The complete dataset of 3,190 questions spans three difficulty levels and underwent validation by one medical expert and four students, achieving 94.2 percent approval with substantial inter-rater agreement (Fleiss' kappa = 0.82). We benchmark seven open-source models on VietMed-MCQ. Results reveal that general-purpose models with strong Chinese priors outperform Vietnamese-centric models, highlighting cross-lingual conceptual transfer, while all models still struggle with complex diagnostic reasoning. Our code and dataset are publicly available to foster research in low-resource medical domains.

24.
bioRxiv (Bioinfo) 2026-06-19

Nickel-Driven Dynamics of Urease in Sporosarcina pasteurii: Integrated Computational and Experimental Insights

Urease is a nickel-dependent enzyme that plays an important role in urea hydrolysis and in a process named as microbial-induced calcium carbonate precipitation (MICP), which is widely used in sustainable environmental biotechnology. Despite its ecological importance, urease powers Biogrout (biocementation), a promising green technology for soil stabilization and infrastructure repair. Yet, the relationship between nickel availability, enzyme activation, and bacterial fitness remains poorly understood. In this study, we reveal a striking dual effect of nickel on Sporosarcina pasteurii: while high Ni2+ concentrations strongly inhibit growth (IC50 {approx} 637.7 {micro}M), they simultaneously boost specific urease activity up to six-fold. This uncoupling between biomass and enzymatic efficiency highlights a previously overlooked adaptive strategy under metal stress. Using structural bioinformatics and molecular docking, we show that Ure1–the catalytic subunit–exhibits the strongest nickel affinity (-4.3 kcal{middle dot}mol-1), supported by highly conserved active-site residues, whereas accessory proteins UreE and UreG display moderate and weak binding, consistent with their roles in metal delivery and GTP-dependent maturation. In addition, microscopic observations confirmed that calcium carbonate precipitation was most pronounced at intermediate nickel concentrations (approximately 400-1000 {micro}M), whereas higher concentrations ([≥]1000-1300 {micro}M) led to reduced mineral formation due to loss viable cells. Taken together, these results indicates that nickel availability controls both urease activation and bacterial fitness, and that an optimal balance is required to maximize biomenerilization efficiency in environmental applications, particularly in biocementation technology.

25.
arXiv (CS.LG) 2026-06-17

Physics-Constrained Neural Networks for Improved Short-Term Weather Forecasting: A Case Study over the South Pacific

arXiv:2606.17659v1 Announce Type: new Abstract: This study introduces enhancements to physics-constrained neural networks (PCNNs) that improve the accuracy and stability of hybrid short-term weather forecasting models. Building on the WeatherGFT architecture, three innovations are proposed. First, an upgraded numerical solver, combining a fifth-order weighted essentially non-oscillatory scheme (WENO-5), a beta-plane approximation, and subgrid-scale viscosity, permits a fourfold increase in the integration time step to 1200 s while reducing the daily mean squared error by up to 26%. Second, a unified autoregressive hybrid block replaces the original chain of 24 specialised modules, eliminating overfitting to specific lead times. Third, the physical core is integrated with two state-of-the-art neural backbones, resulting in PI-PredFormer and PI-IAM4VP. Evaluation on the WeatherBench South Pacific subset from 2000 to 2004 shows that these hybrids reduce root mean squared error at 1-12 h lead times by 8-22% compared to purely neural counterparts, while better preserving physical consistency. These results demonstrate that incremental refinement of hybrid components offers a practical route toward more accurate and efficient short-range weather forecasting.