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01.
arXiv (CS.CL) 2026-06-18

Written by AI, Managed by AI: Semantic Space Control and Index Sickness Elimination Across 391 Consecutive Sessions

The prevailing engineering intuition for addressing conceptual drift in long-horizon LLM collaboration is to trade more formal constraints for more reliable outputs – designing symbolic identifier systems, accumulating defensive rules in System Prompts, expanding context windows. Our engineering record shows that in long-horizon settings, this direction may produce effects contrary to design intent. Using action research methods in a real software project (Bang-v3) spanning approximately one month and 391 collaborative sessions, we document and analyze the failure process of these strategies. When the symbolic system exceeds a complexity threshold, LLMs do not become more accurate – instead, they abandon genuine understanding of business semantics, retreat to self-referential reasoning within the symbolic layer, and generate outputs that appear internally consistent but are physically disconnected from reality. We name this failure pattern "Index Sickness," and its canonical manifestation "Phantom Legislation." We name the underlying principle the "Pang Principle (Semantic Vitality Law)": natural language carrying explicit purpose conveys far greater information quality than symbolic expression. From this, we design and validate its physical engineering mechanism: "Baseline-Log Physical Separation." In the same project, this mechanism reduced AI Instructions volume by ~75%, and across the subsequent ~150 sessions, no recurrence of Index Sickness was observed. A bilingual companion version (Chinese) is included as supplementary material.

02.
arXiv (CS.CL) 2026-06-19

Clusters are All You Need: Pre-Training the Tsetlin Machine with Semantic Clusters from Language Models for Interpretability

Pre-trained language models such as BERT achieve strong text classification performance but lack transparency, limiting their use in high-stakes settings. The Tsetlin Machine (TM) offers fully interpretable, clause-based reasoning but captures little semantic information, and prior attempts to bridge the two rely on static word embeddings that miss contextual meaning. We propose a semantic pre-training framework that transfers knowledge from a pre-trained language model into a TM without using embeddings. Text samples are grouped into semantically coherent clusters with K-means or Top2Vec, and the resulting cluster-sample pairs pre-train a non-negated TM with enhanced Type I feedback. The TM thereby learns interpretable semantic keywords that are fine-tuned on downstream tasks. Across five datasets, our method substantially outperforms vanilla and embedding-based TMs and reaches performance competitive with BERT while remaining interpretable.

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

InvDesMobility: a reliability-gated first-principles feedback framework for closed-loop materials discovery

arXiv:2606.16133v1 Announce Type: cross Abstract: Inverse materials design starts from target functionality and searches for structures that can realize it. Its value in closed-loop discovery depends not only on prediction performance, but also on whether expensive first-principles results are independently validated, provenance-recorded, and admitted as feedback only when evidence is sufficient. This is especially important for composite properties such as carrier mobility, where a final scalar value hides intermediate quantities, fit quality, convergence history, and workflow assumptions. Here we present InvDesMobility, a reliability-gated first-principles feedback framework that integrates multi-agent automated DFT, evidence stratification, generative structure proposal, acquisition ranking, and auditable release. Using 516 2DMatPedia-derived candidates, the workflow produced 280 QC-passed materials and 573 retained carrier-direction seed channels after channel-level reliability gating. These records were split into two feedback objects: relaxed structures updated the generative model, while retained mobility channels trained the acquisition model and set validation priority. Over multiple iterations, InvDesMobility screened 2.4 x 10^6 structures, submitted 102 candidates for DFT validation, and retained 86 reliability-gated generated channels across 41 formulas. Overall, the main contribution is not a fixed list of high-mobility materials, but a transferable feedback contract that makes closed-loop inverse design both useful and auditable when learning from expensive calculated properties. All source data, retained feedback records, and workflows are available at https://github.com/DreamLufei/invDesMobility, with an accompanying evidence website at https://dreamlufei.github.io/invDesMobility/.

04.
arXiv (CS.LG) 2026-06-12

Multimodal Graph Negative Learning

arXiv:2606.12863v1 Announce Type: new Abstract: Multimodal attributed graphs (MAGs) integrate graph topology with heterogeneous modality attributes, such as text and images, thereby enabling richer modeling of complex relational systems. However, such expressiveness also makes learning on MAGs depend on multiple semantic sources, including structural topology, textual and visual attributes, each of which can be regarded as a branch for node representation. Node-level branch semantic imbalance arises when these branches differ across nodes in semantic informativeness and reliability: a branch that provides discriminative semantics for one node may mislead another due to bias in modality quality or structural context. Existing methods often mitigate such heterogeneity through cross-branch agreement or alignment, implicitly treating the dominant prediction as reliable supervision. When the dominant branch is biased, forced imitation may propagate its bias to other branches and suppress original semantics that are useful for classification. We propose GraphMNL, a graph-aware multimodal negative learning framework that addresses this issue by using Negative Learning as cross-branch guidance. Instead of forcing inferior branches to imitate a teacher prediction, the model teaches them which classes a node is unlikely to belong to. GraphMNL builds a branch library, identifies dominant and inferior branches via graph-aware reliability arbitration, gates unstable transfer, and applies target-preserving negative learning over non-target classes. This design decouples target supervision from branch guidance so that supervised losses learn the correct class, while Negative Learning suppresses unlikely alternatives when branch agreement is unreliable. Through the comprehensive experimental evaluation, GraphMNL achieves the best performance on Grocery datasets with 72.47% accuracy and 76.60 F1 score on Reddit M datasets.

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

teasr: training-efficient any-step diffusion transformer for real-world image super-resolution

Diffusion models excel in Real-World Image Super-Resolution (Real-ISR) due to their powerful generative priors but suffer from slow iterative sampling. Although existing one-step distillation methods accelerate inference, they typically require auxiliary teacher models that inflate training memory and restrict scalability to large-scale architectures. Furthermore, these fixed-step models lack the flexibility to trade off speed for quality. In this paper, we propose TEASR, a training-efficient any-step diffusion framework for Real-ISR that enables both one-step and multi-step restoration within a unified model. Our key idea is to perform self-adversarial distillation within a single diffusion model, eliminating the need for auxiliary teachers or discriminators. Specifically, we propose a timestep-aware rectification strategy that stabilizes one-step generation across noise levels. These two designs further enables the distillation of 20B-parameter diffusion models on a single GPU, significantly improving training efficiency. Moreover, we introduce a dual-branch diffusion transformer with decoupled timestep condition to separate the current noise state and the denoising target to enhance sampling quality. Extensive experiments demonstrate that TEASR supports seamless any-step sampling and consistently outperforms state-of-the-art methods across multiple datasets.

06.
medRxiv (Medicine) 2026-06-22

Genetic and Shared Environmental Influences on Cancer Risk and Cross-Cancer Associations in Nordic Twins

The relative contributions of genetic and shared environmental influences to cancer risk and cross-cancer associations remain poorly understood. We analyzed data from 222,530 same-sex twins from Denmark, Finland, Norway, and Sweden in the Nordic Twin Study of Cancer, including 43,060 incident cancers over a median follow-up of 41.6 years. Using a target trial framework, biometric modeling, and competing-risk adjustment, we estimated familial risk, heritability, and shared environmental contributions across 35 cancer sites. Lifetime cancer risk was 36.5%, increasing to 51.4% in monozygotic (MZ) twins and 45.3% in dizygotic (DZ) twins with an affected co-twin. Overall cancer risk was explained by heritable (28%) and shared environmental (40%) influences. Heritability was highest for prostate (42%), non-melanoma skin (24%), and breast (18%) cancers. Cross-cancer analyses revealed extensive overlap in the genetic and shared environmental factors across sites, consistent with widespread pleiotropy and shared environmental susceptibility. Prostate cancer exhibited the strongest genetic overlap with rectum/anus (12%) and kidney (11%) cancers, whereas co-shared environmental influences were most pronounced for breast-lung (11%), prostate-bladder (11%), and prostate-lung (12%) cancers. These findings show pervasive genetic overlap across cancers at different sites and emphasize the importance of incorporating familial shared environmental exposures into cancer risk prediction and prevention strategies.

07.
arXiv (CS.CL) 2026-06-19

Ensembles of Large Language Models for Identifying EQ-5D Studies in PubMed Based on Their Abstracts

The rapid increase in scientific publications leads to the fact that manual study screening in systematic literature reviews (SLRs) is increasingly resource consuming, inefficient, and inconsistent. Classifying studies that clearly report health-related quality-of-life results, such as EQ-5D data, requires a high level of clinical interpretation and poses challenges for human reviewers. This study investigates the use of Google's Gemini and Gemma large language models (LLMs) in automating EQ-5D detection in the PubMed biomedical database based only on published abstracts. A multi-phase framework is proposed that integrates few-shot prompting, weight ensembling aggregation, and a soft stacking meta-classifier. Nine LLMs are evaluated on a dataset of PubMed studies manually labeled by two experts regarding EQ-5D reporting. The weighted ensemble of gemini-2.5-pro, gemma-3-12b, and gemma-3-27b obtained a 0.74 weighted F1-score and 0.74 accuracy, exceeding individually attained results. The ensembling of top-performing models improved the balance between precision and recall compared to individual models, while the soft stacking approach provided greater reliability and interpretability. Feature analysis shows that the probability results from the models are important in guiding the final predictions. The findings suggest that an ensemble-based LLM setup is a reliable and scalable approach for automating screening in biomedical research.

08.
medRxiv (Medicine) 2026-06-22

Nutrient Composition of Foods Represented in the U.S. Food and Nutrient Database for Dietary Studies, 2013-2023

Background: The U.S. Food and Nutrient Database for Dietary Studies (FNDDS) is updated across NHANES dietary cycles and is central to U.S. nutrition surveillance. However, multi-cycle food-code-level changes in nutrient composition have not been comprehensively characterized across the full WWEIA nutrient panel. Objective: To characterize ten-year temporal patterns in nutrient composition across five FNDDS cycles, evaluate pandemic-period food-code compositional stability, and distinguish exploratory mean-level signals from distributional heterogeneity that may reflect reformulation, database coverage, or food-code definition changes. Methods: We analyzed five consecutive FNDDS biennial releases: 2013-14, 2015-16, 2017-18, 2019-20, and 2021-23. Nutrient values were extracted from the public FNDDS/FoodData Central release files and standardized to per-100-g food-code-level records. Cycle midpoints, 2013.5, 2015.5, 2017.5, 2019.5, and 2022.0, served as the independent variable in an exploratory ordinary least squares (OLS) regression. Mann-Kendall testing assessed monotonic rank trends, Welch's ANOVA assessed food-code-level distributional heterogeneity, and pairwise Welch comparisons with Cohen's d summarized pre-pandemic, pandemic-period, and post-pandemic differences. Equivalence testing using TOST with +/-10% bounds was restricted to the 2019-20 versus 2021-23 stability comparison. OLS sensitivity analyses were repeated after excluding the structurally atypical 2017-18 cycle. Results: Sixty-three nutrients were analyzed. Eight nutrients showed nominal OLS trends, p < 0.05, but none remained significant after Bonferroni correction. Mann-Kendall testing identified two nominal monotonic signals, and none after adjustment. Welch's ANOVA detected cycle-level distributional differences for 61 of 63 nutrients at nominal p < 0.05 and 57 of 63 after adjustment. Pairwise pandemic-period analyses showed many adjusted differences when the pre-pandemic baseline was compared with 2019-20 or 2021-23, but standardized effects were small, with all absolute Cohen's d values < 0.20. No nutrient differed after adjustment between 2019-20 and 2021-23, and 39 of 48 primary analytes met +/-10% TOST equivalence criteria for that comparison. Slope estimates were directionally stable after excluding 2017-18, but nominal significance status remained sensitive to the short time series. Conclusions: FNDDS food composition varied across cycles, but there was no clear decade-long linear trend for most nutrients. The main signal was a possible increase in total PUFA and linoleic acid, which may reflect changes in fat quality. The 2021-23 cycle was very similar to 2019-20, suggesting no major post-pandemic shift in the foods represented. These findings should be interpreted as food-database signals, not as direct estimates of what people consumed.

09.
arXiv (CS.LG) 2026-06-15

Minimum Distance Summaries for Robust Neural Posterior Estimation

arXiv:2602.09161v2 Announce Type: replace-cross Abstract: Simulation-based inference (SBI) enables amortized Bayesian inference by first training a neural posterior estimator (NPE) on prior-simulator pairs, typically through low-dimensional summary statistics, which can then be cheaply reused for fast inference by querying it on new test observations. Because NPE is estimated under the training data distribution, it is susceptible to misspecification when observations deviate from the training distribution. Many robust SBI approaches address this by modifying NPE training or introducing error models, coupling robustness to the inference network and compromising amortization and modularity. We introduce minimum-distance summaries, a plug-in robust NPE method that adapts queried test-time summaries independently of the pretrained NPE. Leveraging the maximum mean discrepancy (MMD) as a distance between observed data and a summary-conditional predictive distribution, the adapted summary inherits strong robustness properties from the MMD. We demonstrate that the algorithm can be implemented efficiently with random Fourier feature approximations, yielding a lightweight, model-free test-time adaptation procedure. We provide theoretical guarantees for the robustness of our algorithm and empirically evaluate it on a range of synthetic and real-world tasks, demonstrating substantial robustness gains with minimal additional overhead.

10.
arXiv (CS.CL) 2026-06-24

CORE-Bench: Fostering the Credibility of Published Research Through a Computational Reproducibility Agent Benchmark

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

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

Mirror Descent Beyond Euclidean Stability: An Exponential Separation in Initialization Sensitivity

arXiv:2606.11431v1 Announce Type: new Abstract: Mirror Descent (MD) extends Gradient Descent (GD) beyond Euclidean geometry and has recently reappeared as a lens for KL-regularized policy optimization in reinforcement learning and LLM post-training. This raises a basic robustness question, crucial to reproducibility and reliability: how sensitive are MD dynamics to their inputs? We focus on initialization, often itself a pretrained or previously aligned model. Quadratic-regularized MD, including GD and Mahalanobis geometries, is well-known to be stable for convex smooth objectives. We show a sharp contrast: once the regularizer is non-quadratic, MD can be exponentially more sensitive to initialization than GD, even with a well-conditioned regularizer in Euclidean norm. We give a three-dimensional construction with a convex, smooth objective and a strongly convex, smooth, well-conditioned regularizer where an initial $\varepsilon$ perturbation is quickly amplified to $\min\{polylog^{-1}(1/\varepsilon), \varepsilon e^{\Omega(\eta T)}\}$ after $T$ iterations of MD with step size $\eta$. For canonical KL-regularized MD on the simplex, we show that even linear objectives can amplify an initial $\varepsilon$ perturbation exponentially fast in high-dimensional or near-boundary regimes. Finally, we show that adding a Bregman regularization term toward an anchor point can stabilize the dynamics while largely preserving the optimization guarantees, and that the choice of anchor is crucial: anchoring at the initialization only partially mitigates the instability, whereas anchoring at a fixed point yields a more stable mechanism.

12.
arXiv (CS.CV) 2026-06-17

Does the Data Processing Inequality Reflect Practice? On the Utility of Low-Level Tasks

The data processing inequality is an information-theoretic principle stating that the information content of a signal cannot be increased by processing the observations. In particular, it suggests that there is no benefit in enhancing the signal or encoding it before addressing a classification problem. This assertion can be proven to be true for the case of the optimal Bayes classifier. However, in practice, it is common to perform "low-level" tasks before "high-level" downstream tasks despite the overwhelming capabilities of modern deep neural networks. In this paper, we aim to understand when and why low-level processing can be beneficial for classification. We present a comprehensive theoretical study of a binary classification setup, where we consider a classifier that is tightly connected to the optimal Bayes classifier and converges to it as the number of training samples increases. We prove that for any finite number of training samples, there exists a pre-classification processing that improves the classification accuracy. We also explore the effect of class separation, training set size, and class balance on the relative gain from this procedure. We support our theory with an empirical investigation of the theoretical setup. Finally, we conduct an empirical study where we investigate the effect of denoising and encoding on the performance of practical deep classifiers on benchmark datasets. Specifically, we vary the size and class distribution of the training set, and the noise level, and demonstrate trends that are consistent with our theoretical results.

13.
arXiv (quant-ph) 2026-06-11

Optimizing Encoder Circuits of Entanglement-Assisted Quantum LDPC Codes via Beam Search

arXiv:2606.11468v1 Announce Type: new Abstract: Entanglement-assisted (EA) quantum QC-LDPC codes offer strong error-correction capabilities with structured parity-check matrices, but their practical use depends on efficient encoder circuits and the availability of pre-shared Bell pairs (ebits). In all encoder implementations based on the stabilizer formalism, the dominant contribution to this complexity comes from the use of controlled gates. In this paper, we adopt the Sharma-Kumar-Garani (SKG) encoder construction. We formulate the encoder optimization as a search over GF(2) row operations that decompose the binary matrix derived from its CNOT sub-sequence. We solve this problem using a beam search algorithm guided by a Hamming-distance heuristic. For the tested EA quantum QC-LDPC code families, the proposed method achieves CNOT-count reductions of 7.3-34.0% relative to the SKG baseline encoder. The optimized circuits also yield lower CNOT counts than Patel-Markov-Hayes synthesis on all tested instances and are verified by stabilizer-tableau simulation. These results show that substantial encoder simplification is possible for structured EA QC-LDPC codes.

14.
PLOS Medicine 2026-05-20

Prescribed hormonal contraceptive use trends in the Estonian Biobank: A longitudinal observational study

by Jelisaveta Džigurski, Märt Möls, Kristi Läll, Hannah Currant, Mall Eltermaa, Estonian Biobank Research Team , Reedik Mägi, Lili Milani, Triin Laisk Background Hormonal contraceptives (HCs) are widely used and have well-documented population-level statistics. Previous studies with short follow-ups have focussed on individual HC use and side effects. However, the same aspects over longer periods, HC formulation switching, and the impact of genetic factors on HC side effects remain understudied due to the limited availability of suitable datasets. We investigated whether the Estonian Biobank (EstBB) is suitable for studying genetic risk for HC side effects. Methods and findings This is a longitudinal descriptive study combining prescribed HC purchase data collected from 2004 to 2022 with genetic and health data from 73,071 female EstBB HC users aged 15–55 at the time of purchase. HC usage was defined by the Anatomical Therapeutic Chemical (ATC) codes G02B, G03A, and G03HB01. Methods included calculating age-stratified annual user prevalence, inferring usage periods from purchases, assessing formulation switching, identifying the International Classification of Diseases, Tenth Revision (ICD-10)-based side effect-related diagnoses and thromboembolism risk factors, and assessing carrier status for Factor V Leiden (FVL, rs6025) and prothrombin G20210A (PTM, rs1799963) genetic variants as proof-of-concept. Over 19 years, 20 HC formulations with five administration routes (oral pills, transdermal patches, vaginal rings, subdermal implants, intrauterine devices) were used. In the EstBB, combined HCs were the most commonly used among users aged 15–29, while progestin-only HC use increased with age and over time, comparable to the Estonian population. Overall, 64.2% (n = 46,920) of users switched formulations at least once, with 17.7% (n = 12,929) being rapid switchers. Side effect-related diagnoses were observed in 23.1% (n = 2,982) of rapid switchers, with excessive/irregular menstrual bleeding being the most common. Genetic analysis revealed that 5.3% (n = 3,886) of users carried at least one variant previously associated with increased thrombosis risk (3.5% (n = 2,556) carried FVL only, 1.8% (n = 1,276) PTM only, and 0.07% (n = 54) both). Carriers of thrombosis-associated variants had a significantly higher percentage of thrombosis (6.5%) than non-carriers (4.2%; OR = 1.61, 95% CI [1.40, 1.84], p 

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

GauS: Differentiable Scheduling Optimization via Gaussian Reparameterization

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

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

Urdu Katib Handwritten Dataset: A Historical Document Dataset for Offline Urdu Handwritten Text Recognition with CRNN-Based Baseline Evaluation

Automatic Handwritten Text Recognition (HTR) is inherently a challenging task, and its complexity is further increased when dealing with cursive scripts. Although significant efforts have been made on various cursive scripts, research regarding Urdu Handwritten Text Recognition (UHTR) has been relatively limited. This lag of research is primarily due to the unique challenges posed by its script, and the scarcity and unavailability of benchmark datasets. Therefore, to advance research in UHTR, this study presents a specialized real dataset called the Urdu Katib Handwritten Dataset (UKHD). To the best of our knowledge, this is the first offline Urdu handwritten text lines dataset specifically curated from the materials written by Katibs in historical times. It encompasses a diverse range of flat nib writing variations in the Nastalique calligraphic style. Additionally, the effectiveness of different CRNN-based hybrid models has been evaluated to identify the optimal architecture for Urdu Katib Handwriting Recognition (UKHR). Among the analyzed models, the CNN-BGRU-CTC model showed more robust performance, with low Character Error Rate (CER) and Word Error Rate (WER). This research work aims to support and encourage the research community in developing a robust recognition system for preserving Urdu handwritten literature.

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

GD$^2$PO: Mitigating Multi-Reward Conflicts via Group-Dynamic reward-Decoupled Policy Optimization

arXiv:2606.16771v1 Announce Type: new Abstract: As LLMs advance, post-training reinforcement learning (RL) increasingly relies on multi-dimensional rewards to cultivate comprehensive capabilities. This shift demands new algorithms capable of optimizing diverse and potentially competing objectives simultaneously. To address this, existing methods such as Group reward-Decoupled Policy Optimization (GDPO) decompose the overall score into independent reward groups, then compute the RL loss separately within each group. However, this strategy still encounters multi-reward conflicts: a single rollout can yield positive advantages on certain reward dimensions but negative ones on others, causing opposing signals to cancel each other out during aggregation, further hindering RL training efficiency. Inspired by Dynamic sAmpling Policy Optimization (DAPO), which improves RL training efficiency by filtering out ineffective rollouts with near-zero advantages, we propose Group-Dynamic reward-Decoupled Policy Optimization (GD$^2$PO). Specifically, GD$^2$PO employs a conflict-aware filtering mechanism to mask out rollouts suffering from severe reward-wise disagreement. By preventing conflicting signals from canceling each other out, this masking strategy preserves and enhances the magnitude of effective RL advantages, thereby significantly accelerating learning efficiency. Furthermore, we introduce query-level reweighting to dynamically adjust the update intensity of each query based on its overall reward consensus. Experiments on various multi-reward scenarios, including tool calling and human preference alignment, demonstrate that GD$^2$PO consistently and significantly outperforms existing baselines. The code is available at https://github.com/Qwen-Applications/GD2PO.

19.
arXiv (CS.CL) 2026-06-17

The Critical Role of Model Selection in Causal Inference: A Comparative Analysis of Classification Models within the InferBERT Framework for Pharmacovigilance

Distinguishing causal adverse drug events (ADEs) from spurious correlations remains a central challenge in pharmacovigilance. The InferBERT framework integrates transformer models with Do-calculus, but its success hinges on the underlying classification model. This study evaluates the impact of model choice in InferBERT, assessing whether simpler models suffice, if domain-specific pre-training helps, whether scaling to LLMs improves causal detection, and the effect of post-hoc calibration. We performed a comparative study on two benchmarks: Analgesics-induced Acute Liver Failure (AILF) and Tramadol-related Mortalities (TRAM). Four models were evaluated-XGBoost (baseline), ALBERT (original InferBERT), BioBERT (biomedical transformer), and Med-LLaMA (medical LLM)-using 5-fold cross-validation repeated over 20 runs. We measured accuracy, Expected Calibration Error (ECE) pre- and post-isotonic regression, and Jaccard concordance of causal terms with PRR, ROR, and EBGM; significance was tested with paired t-tests. BioBERT achieved the highest accuracy on both datasets, while Med-LLaMA underperformed despite its size and parameter-efficient fine-tuning. Domain-specific pre-training was decisive. Calibration improved ECE but had mixed effects on accuracy and causal discovery. BioBERT's superiority also yielded the strongest concordance with traditional pharmacovigilance signals. These results show that domain-specific pre-training provides a clear advantage over simpler baselines and larger LLMs. Investing in manageable, domain-aware models is more effective for computational pharmacovigilance than simply scaling model size.

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

Tensor-based second-order causal discovery

arXiv:2606.18074v1 Announce Type: cross Abstract: Causal discovery seeks to uncover the causal dependencies among variables. For this purpose, we propose an algorithm called Tensor-based Second-order Causal Discovery (TSCD). Its input is a tensor obtained from the covariance matrices of observational and interventional data. Assuming the causal dependencies follow a linear structural equation model on a directed acyclic graph (DAG), TSCD outputs the DAG and the functions on its edges, requiring only that the noise variables are uncorrelated. We also implement a version of the approach for nonlinear models. Our focus on second-order statistics (via the covariance matrices) is motivated by their statistical and computational efficiency relative to higher-order moments, their identifiability relative to first-order statistics, and that they work regardless of whether the variables are Gaussian. We show that TSCD has identifiable causal order and parameters from a number of interventions that is logarithmic in the number of variables. Experiments show that TSCD is robust to noise, competitive with existing methods, and scales to hundreds of variables.

21.
medRxiv (Medicine) 2026-06-16

Deployment-readiness audit of calibration, clinical utility, and fairness in perioperative infection prediction

Objective: Clinical risk scores intended to guide patient-level decisions can show strong average performance. However, predicted probabilities can be systematically too high or too low in specific subgroups even when overall performance is strong. We audited deployment readiness of a strong end-of-surgery postoperative infection model across clinically relevant subgroups and tested mitigation strategies in miscalibrated subgroups. Materials and Methods: We analyzed out-of-fold predictions for 10,719 surgical procedures at a Swiss tertiary hospital, with 504 postoperative bacterial infection events. Prespecified axes were recorded sex, age stratum, and an EHR-derived physiological-reserve proxy. Within subgroups and pairwise intersections, we evaluated discrimination, calibration, threshold-specific errors, and decision-curve net benefit at the prespecified operating threshold. We compared group-specific isotonic recalibration with Wasserstein-barycenter postprocessing and demonstrated portability in SUPPORT2. Results: Overall AUROC was 0.876. While sex-marginal discrimination was similar in women and men (0.878 vs 0.875), age and reserve stratification revealed deployment-readiness failures. Calibration-in-the-large ranged from -0.86 in frail patients to -2.47 in non-frail patients. At the 0.10 operating threshold, decision-curve net benefit was positive in frail patients but negative in pre-frail and non-frail patients. Isotonic recalibration corrected average physiological-reserve-stratified calibration without worsening Brier scores, whereas Wasserstein postprocessing worsened calibration in most procedure clusters. Discussion: Discrimination-only or sex-marginal evaluation would have missed subgroup failures with clinical-utility implications. Conclusion: Subgroup fairness audits for clinical deployment should jointly evaluate discrimination, calibration, and utility. We implemented the audit as the open-source isitfair framework for identifying deployment-relevant subgroup failures, comparing mitigation strategies, and generating structured reports.

22.
arXiv (CS.CL) 2026-06-12

NTS-CoT: Mitigating Hallucinations in LLM-based News Timeline Summarization with Chain-of-Thought Reasoning

The rapid updates of online news make tracking event developments challenging, highlighting the need for timeline summarization (TLS). Hallucinations, where LLM-generated content deviates from source news, still remain a critical issue in LLM-based TLS and are not well studied in existing works. To bridge this gap, we identify two primary types of hallucinations: unfaithful content during news summarization and information omission in date-event summarization. Then, we propose NTS-CoT, a novel framework that leverages Chain-of-Thought (CoT) reasoning to mitigate hallucinations in TLS. The framework consists of three key modules: i) Element-CoT to capture essential news elements for faithful summarization, ii) Date Selection to combine temporal saliency and event prominence for timestamp selection, and iii) Causal-CoT to infer causal relationships and reduce omissions in date-event summarization. Extensive experiments, including quantitative analysis on three TLS benchmarks and human evaluation, demonstrate that NTS-CoT outperforms state-of-the-art baselines, effectively mitigating hallucinations and improving LLM-based TLS performance. Our source code is available at https://anonymous.4open.science/r/NTS-CoT .

23.
arXiv (CS.LG) 2026-06-16

GPT-Based Fast Simulation of CLAS12 Detector Hits via Conditional Autoregressive Generation

arXiv:2606.16035v1 Announce Type: cross Abstract: Modern particles physics experiments have demonstrated an increasing need for fast, high-fidelity detector simulation as detector components have improved and subsequent computational requirements approach the limits of available resources. Recently, deep generative models have emerged as a promising alternative to traditional Monte-Carlo methods, with recent works drawing inspiration from large language models (LLMs) and self-supervised next-token prediction methods. In this work, we present an application of a GPT-style autoregressive transformer as a fast surrogate model for the calorimeter inside the CLAS12 experiment at the Thomas Jefferson National Accelerator Facility. The model is conditioned on incident momentum and generates realistic detector hits autoregressively across all nine calorimeter layers as sequences of strip, ADC, and TDC tokens. We demonstrate that the model faithfully reproduces hit multiplicity, spatial distributions, energy deposits, and the energy-momentum response of the electromagnetic calorimeter. The generator achieves inference rates exceeding 700 events per second on a single GPU, providing a substantial speedup over traditional Geant4-based simulations while maintaining physics fidelity essential for high-luminosity experimental programs.

24.
arXiv (CS.AI) 2026-06-16

Topological Flow Matching

arXiv:2606.15897v1 Announce Type: cross Abstract: Flow matching is a powerful generative modeling framework, valued for its simplicity and strong empirical performance. However, its standard formulation treats signals on structured spaces, such as fMRI data on brain graphs, as points in Euclidean space, overlooking the rich topological features of their domains. To address this, we introduce topological flow matching, a topology-aware generalization of flow matching. We interpret flow matching as a framework for solving a degenerate Schrödinger bridge problem and inject topological information by augmenting the reference process with a Laplacian-derived drift. This principled modification captures the structure of the underlying domain while preserving the desirable properties of flow matching: a stable, simulation-free objective and deterministic sample paths. As a result, our framework serves as a drop-in replacement for standard flow matching. We demonstrate its effectiveness on diverse structured datasets, including brain fMRIs, ocean currents, seismic events, and traffic flows.

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arXiv (quant-ph) 2026-06-16

Minimum measurements quantum protocol for band structure calculation

arXiv:2511.04389v2 Announce Type: replace Abstract: Protocols for quantum measurement are an essential part of quantum computing. Measurements are no longer confined to the final step of computation but are increasingly embedded within quantum circuits as integral components of noise-resilient algorithms. However, each observable typically requires a distinct measurement basis, often demanding a different circuit configuration. As the number of such configurations typically grows with the number of qubits, measurements constitute a major bottleneck. Focusing on electronic structure calculations in crystalline systems, we propose a measurement protocol that restricts the required measurement configurations to an absolute minimum of just three, independent of the number of qubits. This makes it one of the few known protocols that do not scale with qubit number. In particular, we derive the measurement protocol from the symmetries of tight-binding (TB) Hamiltonians and implement it within the Orthogonal-Ansatz Variational Quantum Eigensolver (OA-VQE) algorithm. We demonstrate its performance on three systems, namely a two-dimensional CuO$_2$ square lattice (3 qubits), bilayer graphene with hexagonal (Honeycomb) lattice (4 qubits) and three-dimensional diamond lattice (10 qubits). Beyond tight-binding systems, the protocol can be extended to enable efficient initial state preparation for many-body Hamiltonians, such as multi-orbital Hubbard models in a momentum space.