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

SHARD: Safe and Helpful Alignment via Self-Reframing Distillation

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

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

The Linguistics Olympiads: Towards a New Corpus for Linguistics Research?

Linguistics olympiad problems (LOPs) are a category of self-sufficient puzzles consisting of a scaled-down corpus representative of certain linguistic phenomena, from which the solver must deduce a primitive set of rules of the language and then translate a new set of elements. The linguistics olympiads (LOs) have become a worldwide phenomenon with 43 different territories taking part in the International Linguistics Olympiad (IOL) 2025. While the typology and solving strategies of LOPs have been analysed, their scientific facet and connections to academic linguistics have yet to be explored. LOPs are directly connected to many linguistic fields, e.g., linguistic typology, linguistic relativity, and linguistics fieldwork. Recently, LOPs have become a research focus as benchmarks for large language models, thus highlighting their usefulness in computational linguistics. Nevertheless, they have not yet been integrated into mainstream linguistics research. This paper attempts to open new directions of including this particular type of puzzle in academic research by offering a structured evaluation of LOPs as linguistic data sources and proposes criteria for their responsible use in academic research. Starting from a set of over 1800 LOPs, this study critically examines the potential of LOPs as a novel corpus for linguistics research by discussing their strengths and limitations as tools, as well as the areas of linguistics into which these problems could fit. This work forms the foundation for a broader initiative aimed at bridging the gap between LOs and academic linguistics, by establishing a robust theoretical framework for LOPs.

03.
bioRxiv (Bioinfo) 2026-06-18

Deciphering shared and divergent tissue architectures from cross-species spatial transcriptomics

作者:

The integration of spatial transcriptomics (ST) data across species is essential for cross-species and translational studies, but remains challenging due to molecular divergence and anatomical differences between organisms. We present STACAME, a graph attention autoencoder-based framework to decipher shared and divergent tissue architectures from cross-species ST data by explicitly modeling both orthologous and species-specific genes. STACAME aligns ST slices in a spatially aware manner, identifies homologous and species-specific domains, and enables a suite of downstream comparative analyses. We demonstrate its utility by integrating ST datasets from diverse tissues, including hippocampus, isocortex, embryo, breast, liver, and cerebellum, across multiple species such as human, macaque, marmoset, mouse, and zebrafish. STACAME supports cross-species spatial domain alignment, the detection of shared and divergent spatially variable genes, development alignment and comparison, and the 3D integration of tissue architecture. This flexible approach facilitates the translation of findings from model organisms to humans, providing a unified computational platform for cross-species spatial transcriptomics.

04.
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.

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

Polynomial-Time Mistake-Bounded Language Generation

arXiv:2606.16077v1 Announce Type: cross Abstract: In this note, we introduce a polynomial-time version of the mistake-bounded language generation (MBLG) framework due to Kleinberg, Peale, and Reingold (2026). We observe that the family of parities of variables, and the family of conjunctions of literals, are polynomial-time MBLG. Our main result states that the family of monotone Boolean functions with polynomially-many maxterms is polynomial-time MBLG. This family includes all monotone Boolean functions, computable by polynomial-size decision trees. Our technique can be presented as a new combinatorial game about writing numbers on a board.

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

My Chemical Harness: Evolutionary Molecular Design over Synthetic Pathways with Large Language Model Agents

arXiv:2606.11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes. We introduce My Chemical Harness, a route-native evolutionary framework for goal-directed molecular design in which the search population consists of executable synthetic pathways rather than isolated molecular graphs. Each route is built from purchasable building blocks and reaction templates, executed by deterministic chemistry tools, and scored through task-specific molecular oracles. Large language models (LLMs) are used only as strategy controllers that select high-level preferences over route length, move type, reaction families, motifs, and exploration pressure, while local code performs route construction, validation, deduplication, scoring, selection, and memory updates. This separation lets the LLM guide exploration without allowing it to introduce hallucinated products or unsupported reaction steps. On a soluble epoxide hydrolase proxy task, our LLM agent improves over single pass LLM and deterministic controllers, reaching state-of-the-art performance across the sEH score, synthetic accessibility score, and AiZynthFinder success rate metrics. These results suggest that constrained LLM agents can play a significant role in molecular discovery without requiring training, fine-tuning, or dedicated generative models.

07.
arXiv (CS.AI) 2026-06-24

LLM-MINE: Large Language Model based Alzheimer's Disease and Related Dementias Phenotypes Mining from Clinical Notes

arXiv:2603.13673v2 Announce Type: replace Abstract: Accurate extraction of Alzheimer's Disease and Related Dementias (ADRD) phenotypes from electronic health records (EHR) is critical for early-stage detection and disease staging. However, this information is usually embedded in unstructured textual data rather than tabular data, making it difficult to be extracted accurately. We therefore propose LLM-MINE, a Large Language Model-based phenotype mining framework for automatic extraction of ADRD phenotypes from clinical notes. Using two expert-defined phenotype lists, we evaluate the extracted phenotypes by examining their statistical significance across cohorts and their utility for unsupervised disease staging. Chi-square analyses confirm statistically significant phenotype differences across cohorts, with memory impairment being the strongest discriminator. Few-shot prompting with the combined phenotype lists achieves the best clustering performance (ARI=0.290, NMI=0.232), substantially outperforming biomedical NER and dictionary-based baselines. Our results demonstrate that LLM-based phenotype extraction is a promising tool for discovering clinically meaningful ADRD signals from unstructured notes.

08.
arXiv (CS.AI) 2026-06-12

Fantastic Scientific Agents and How to Build Them: AgentBuild for Rietveld Refinement

arXiv:2606.12834v1 Announce Type: new Abstract: As scientific workflows shift from deterministic executables to LLM-based agents, the development practices on offer, such as fine-tuning, reinforcement learning, and prompt-and-go, bury the scientist's judgment. We propose treating agent construction as a workflow stage and introduce AgentBuild, which builds a scientific agent from a contract the scientist authors. The contract is a version-controlled rubric, a difficulty-graded curriculum, and a curated external knowledge base. A rubric-driven judge gates a meta-optimizer coding agent that edits the agent within a declared boundary, so the build compiles the agent, not the scientist's judgment. We instantiate this for Rietveld refinement of X-ray diffraction data through GSAS-II behind MCP and A2A, where a blank-harness construction run progresses through a lithium lanthanum zirconium oxide (LLZO) signal-to-noise ladder, reaches the 4 hour scan as a frontier case, and exposes the workflow-scope limits that remain. The same rubric that rewards credible fits also scores trajectory scope, making the frontier a contract failure rather than a pattern-fitting failure. As base models evolve, re-running AgentBuild is a re-tune, not a rebuild, and the scientist's authored contract remains the durable asset.

09.
arXiv (CS.LG) 2026-06-11

Deep Learning of Solver-Aware Turbulence Closures from Nudged LES Dynamics

arXiv:2604.23874v3 Announce Type: replace-cross Abstract: The differentiable physics paradigm may be leveraged as an a-posteriori approach for discovering turbulence closure models by embedding a neural network parameterization directly inside the solver and optimizing it given potentially sparse target data. This addresses a key limitation of a-priori learning where direct numerical simulation (DNS) data is used to approximate the subgrid stress with the assumption of a low-pass filter. Closures trained in this a-priori manner frequently lead to unstable deployments due to the mismatch between the assumed filter and the effect of numerical discretizations and coarse-graining. In comparison, while typically stable during deployment, a-posteriori learning incurs high computational costs due to the need to backpropagate through a large eddy simulation (LES) solver. Furthermore, a-posteriori methods are challenging to apply broadly since they require significant modification of existing solvers. Finally, both approaches are limited when generalization is desired across different numerical schemes with their implicit filtering characteristics. In this work, we present a deep-learning approach for turbulence closure modeling built on the continuous data assimilation framework. Our approach enables the a-priori training of closures using sparsely observed DNS data without modifying or differentiating through the LES solver, while preserving stability during deployment for the recovery of invariant statistics. We focus on the model's ability to adapt to different discretizations by explicitly conditioning it on the numerical scheme. We use two- and three-dimensional canonical cases to test our framework and show that the learned correction systematically tracks the discretization error of the coarse solver.

10.
arXiv (CS.AI) 2026-06-16

RAID: Semantic Graph Diffusion for True Cold-Start and Cross-Lingual Forecasting

arXiv:2606.16925v1 Announce Type: new Abstract: Time-series foundation models show strong transfer performance when given a non-empty history window. However, true cold-start scenarios, where a new item has no prior observations, violate this assumption. We propose RAID (Retrieval-Augmented Iterative Diffusion) a framework, which replaces history-based correlation learning with metadata-driven semantic retrieval and graph-conditioned diffusion. RAID maps textual metadata into a shared semantic space using a frozen multilingual embedding model and constructs an inductive retrieval graph that extends naturally to unseen items. It first forms a base forecast by aggregating information from semantically related neighbors, then refines this forecast with a gated diffusion module to model residual uncertainty. Under a strict true cold-start protocol, RAID outperforms strong foundation models and competitive baselines on both forecasting accuracy and prediction interval coverage, while reducing inference latency by an order of magnitude through non-autoregressive decoding. The shared semantic space also enables zero-shot cross-lingual transfer, allowing a model trained on English descriptions to generalize to items described in other languages without direct supervision.

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

DOG-DPO:Dynamic Optimization in Geometry for Safety Alignment

arXiv:2606.07678v2 Announce Type: replace-cross Abstract: Safety alignment for large language models relies on preference data, but current pipelines often train on large, redundant datasets. Existing data selection methods typically score each preference pair independently, collapsing directional preference information into scalar quality or diversity scores. This sample-centric view is especially limiting in multi-dataset settings, where shared safety directions coexist with dataset-specific residual risks. We propose DOG-DPO, a training-free data selection framework that treats preference pairs as structured geometric signals. DOG-DPO first represents each preference pair as a direction in model representation space. It then decomposes multi-dataset preference geometry into a global anchor subspace and dataset-specific residual subspaces. Finally, it selects subsets by maximizing diversity-based coverage, encouraging broad, non-redundant coverage of alignment directions before DPO training. Across six safety benchmarks and two model backbones, DOG-DPO achieves a strong utility-robustness trade-off using only 11% of the preference pairs. It recovers most of the safety gains of full-data training while remaining entirely teacher-free, training-free, and substantially faster than representative selection baselines.

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

Nemotron 3 Ultra: Open, Efficient Mixture-of-Experts Hybrid Mamba-Transformer Model for Agentic Reasoning

We introduce Nemotron 3 Ultra, a 550 billion total and 55 billion active parameter Mixture-of-Experts Hybrid Mamba-Attention language model. We pre-trained Nemotron 3 Ultra on 20 trillion text tokens, then extended the context length to 1M tokens, and post-trained using Supervised Fine Tuning (SFT), Reinforcement Learning (RL), and Multi-teacher On-Policy Distillation (MOPD). Nemotron 3 Ultra is our most capable model yet, employing multiple key technologies - LatentMoE, Multi Token Prediction (MTP), NVFP4 pre-training, multi-environment RLVR, MOPD, and reasoning budget control. Nemotron 3 Ultra achieves up to ~6x higher inference throughput as compared to state-of-the-art publicly available LLMs while attaining on-par accuracy. The state-of-the-art accuracy, high inference throughput, and 1M token context length make Nemotron 3 Ultra ideal for long-running autonomous agentic tasks. We open-source the base, post-trained, and quantized checkpoints, along with the training data and recipe on HuggingFace.

13.
medRxiv (Medicine) 2026-06-24

SWI and T2*-GRE Microhemorrhage Counts in Anti-Amyloid Therapy Eligibility: A Real-World-Calibrated Simulation Study

INTRODUCTION: Anti-amyloid therapy eligibility excludes patients with five or more cerebral microhemorrhages (CMHs), but current guidance allows either T2*-GRE or the more sensitive SWI. This may create sequence-dependent differences in eligibility classification. METHODS: We fitted a Bayesian right-censored zero-inflated Poisson model to single-center real-world SWI-based CMH counts from 130 memory clinic patients. We then simulated T2*-GRE counts under a directional binomial detection model across a range of relative detection probabilities and estimated two metrics: P(T2*

14.
medRxiv (Medicine) 2026-06-22

Biopsychosocial determinants of HPV vaccine perception in university students of both sexes in Cucuta, Colombia, 2024: a cross-sectional study

Colombia has been internationally recognised as a paradigmatic case of vaccine confidence crisis since the 2014 Carmen de Bolivar event, and national HPV vaccination coverage remains far below the World Health Organization 2030 target. Most published evidence focuses on female adolescents and on cervical cancer; the perception of the HPV vaccine in university-age populations of both sexes–and across the broader spectrum of HPV-attributable disease–remains comparatively understudied. We aimed to describe the influence of biopsychosocial determinants on HPV vaccine perception among university students of both sexes in Cucuta, Norte de Santander, Colombia. We conducted a cross-sectional study with a mixed quantitative-qualitative approach in 2024 among four universities (Universidad de Santander, Universidad Francisco de Paula Santander, Universidad de Pamplona and Universidad Libre; combined enrolment 21,033 students). Using convenience sampling stratified by institution, 750 actively enrolled undergraduate students of both sexes (18-60 years) completed a structured online questionnaire adapted from previously validated instruments. The instrument captured sociodemographic information, HPV knowledge and HPV vaccine perception. Data were analysed using Students t-test, one-way analysis of variance, Tukey post-hoc tests, effect sizes and 95% confidence intervals, with a 0.05 significance threshold. Of 750 respondents, 54.2% were women, 61.3% were under 20 years of age, and 75.1% attended public universities. HPV knowledge was high in 39.2%, intermediate in 42.4% and low in 18.4%; women and students aged 26 years or older displayed higher knowledge. Although 91.2% had heard of HPV and 82.5% knew that both sexes could acquire it, recognition of clinical manifestations and complications was uneven: cervical cancer 51.7%, penile cancer 30.5%, vaginal warts 45.9% and warts in the penis, larynx, anus or rectum 34.0%. Vaccine-specific knowledge was low in 77.1%, with men disproportionately represented (85.9% versus 69.5% in women). Overall positive perception of HPV vaccination was 66.6%, slightly higher in women (68.8%) than men (63.9%), in students aged 26 years or older (70.1%) and in students from private universities (68.1% versus 65.9%). Inferential analysis identified sex (Cohens d = -0.357), type of university (d = 0.189) and HPV knowledge (partial eta-squared = 0.096) as the only significant determinants. Age, socioeconomic stratum, age at sexual debut and vaccine-specific knowledge did not reach meaningful significance. HPV vaccine perception was predominantly positive but conditioned by three biopsychosocial determinants, with HPV knowledge as the primary driver. The persistent gender gap reflects historical anchoring of HPV messaging in cervical disease and female-targeted campaigns. Public-health strategies should adopt comprehensive, gender-inclusive educational interventions that explicitly visibilise non-cervical HPV-related cancers and address both sexes from a common evidence base.

15.
arXiv (CS.AI) 2026-06-19

QMFOL: Benchmarking Large Language Model Reasoning via Quantifiable Monadic First-Order Logic Test Case Generation

arXiv:2606.20227v1 Announce Type: new Abstract: Large Language Models (LLMs) have made significant progress in reasoning, particularly in deductive reasoning, which is crucial for high-stakes decision-making. As models improve, evaluation benchmarks should evolve to keep pace. However, existing benchmarks lack fine-grained control over logical complexity and struggle to balance semantic diversity with logical consistency. To address these issues, we propose QMFOL, an automated framework for generating monadic first-order logic reasoning tasks with quantifiable and controllable complexity. It constructs formal logical structures using conjunction and disjunction patterns, enabling precise control over reasoning depth, width, label types, and distractors. These structures are then translated into natural language via LLMs, with logical consistency ensured through round-trip verification using an external prover. Based on our framework, we build QMFOLBench, a benchmark comprising 2880 instances with 960 configurations across diverse logical and semantic dimensions. Evaluations on six large reasoning models (LRMs) and two LLMs show that performance degrades and computational overhead increases with rising logical complexity. Models perform better on True-labeled tasks than on False or Unknown ones, and exhibit sensitivity to semantic variation. Overall, QMFOL offers a scalable and reliable approach for constructing deductive reasoning benchmarks with controllable complexity, enabling more precise evaluation of reasoning capabilities in modern language models.

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

uva-irlab-conv at SemEval-2026 Task 8: Multi-Turn RAG with Learned Sparse Retrieval and Listwise Reranking

This report describes our participation in SemEval-2026 Task 8 on multi-turn retrieval and question answering. The task evaluates conversational systems across four domains (finance, cloud documentation, government, Wikipedia), and includes unanswerable queries where the available collection does not contain sufficient evidence to produce a complete response. We propose a multi-turn retrieval-augmented generation pipeline that combines learned sparse retrieval with LLM-based reranking and generation. Using sparse retrieval as the primary retrieval method, we leverage its strong generalization across domains. In addition, we make use of the long-context capabilities of LLMs for conversational query rewriting, pointwise and listwise reranking, and generating the final response, each conditioned on the full conversational history. This multi-step design enables effective integration of conversational context throughout retrieval and generation, improving robustness across domains.

17.
arXiv (CS.LG) 2026-06-24

Low-rank Updates in Slowly Time-varying Graphs for Spatial-Temporal Signal Interpolation

arXiv:2606.24011v1 Announce Type: cross Abstract: A crucial assumption in graph signal processing (GSP) is the existence of an underlying graph that captures the pairwise similarities between nodes, allowing filters to be designed based on this graph for tasks such as denoising. For spatial-temporal data in which node-to-node similarities evolve over time, a static spatial graph is insufficient. In this paper, to represent slowly time-varying pairwise relationships, we model the graph changes in two consecutive adjacency matrices $P = W^{(2)} - W^{(1)}$ across time as a low-rank matrix. % Specifically, given an initial adjacency matrix $W^{(1)}$ at time $t=1$, we jointly interpolate a signal $x_2$ and estimate $W^{(2)}$ at $t=2$ using both a graph signal smoothness prior for $x_2$ and a low-rank prior on $\P$. We alternate optimization steps. With $W^{(2)}$ fixed, $x_2$ is interpolated by solving a linear system. Alternatively, holding $x_2$ fixed, $W^{(2)}$ is updated via proximal gradient descent (PGD). The proximal mapping of the rank term $Gamma(W^{(2)} - W^{(1)})$ is approximated in linear time using a fast orthogonal matching pursuit (OMP) algorithm that selects a sparse combination of atoms from a dictionary $cR$ formed by the outer products of $W^{(1)}$'s eigenvectors. We unroll iterations of our algorithm into layers to build a lightweight neural network for limited data-driven parameter tuning. Experiments show that our joint optimization achieves better signal interpolation compared to existing time-varying graph models.

18.
arXiv (math.PR) 2026-06-17

Poisson approximation by coupling

arXiv:2605.01894v2 Announce Type: replace Abstract: It is well known that a binomial $(n,p)$ can be approximated by a Poisson distribution with parameter $np$. The typical approach in undergraduate probability texts is to show a convergence result for the distribution of the binomial as $n$ goes to infinity and $np$ converges to some $\lambda$. In this note we use instead the coupling technique to show a much more general result. Moreover, we only use elementary results from probability.

19.
arXiv (CS.AI) 2026-06-16

UrbanWell: Benchmarking Multimodal Large Language Models for Spatio-Temporal Urban Wellbeing Analytics

arXiv:2606.15890v1 Announce Type: new Abstract: Understanding urban wellbeing from multimodal data requires integrating heterogeneous spatial and temporal signals, posing significant challenges for current multimodal large language models (MLLMs). We introduce UrbanWell, a large-scale benchmark designed to systematically evaluate the spatio-temporal reasoning capabilities of MLLMs for urban wellbeing analytics through joint modeling of satellite and street view imagery. UrbanWell spans 38 cities across multiple years and includes diverse indicators covering (1) environmental conditions (CO$_2$, NO$_2$, PM${2.5}$, and Normalized Difference Vegetation Index), (2) spatial accessibility (minimum distance to supermarkets and restaurants), (3) urban form (road length, road density, and land use), (4) urban vitality (population, economic activity diversity, and land use diversity), and (5) subjective perception attributes (e.g., safety, beauty, liveliness, wealth, and quietness). All indicators are aligned at grid level to enable standardized evaluation. Beyond static prediction, UrbanWell defines temporal reasoning tasks, including future value forecasting from historical observations and temporal trend classification. We benchmark 15 state-of-the-art representative MLLMs in a zero-shot setting, providing a comprehensive comparative evaluation across spatial and temporal dimensions. Experimental results indicate that while MLLMs capture salient spatial and perceptual cues, their performance varies substantially across heterogeneous urban indicators spanning environment and subjective perception. UrbanWell serves as a unified benchmark for evaluating multimodal spatial and temporal reasoning in urban wellbeing analytics, offering a standardized testbed for systematic assessment and future research on multimodal urban intelligence. Our codes and datasets are accessible via https://github.com/axin1301/UrbanWell-Benchmark.

20.
arXiv (CS.LG) 2026-06-12

Robust State-Conditional Feature-Weighted Jump Models for Temporal Clustering

arXiv:2606.13146v1 Announce Type: cross Abstract: We propose a robust feature-weighted jump model for time-dependent clustering. A penalty is used to encourage smoothness of transitions over time, while robustness is achieved through the use of a Tukey's biweight loss function. An additional parameter controls the variability of feature weights across states, allowing the model to assign state-specific relevance to each feature. We illustrate in simulation how the method accurately recovers the true cluster sequence and reliably identifies relevant features, outperforming competing approaches, particularly in the presence of outliers. We conclude with two empirical applications, one on the number of conflict-related homicides in Kosovo in the period 1998-2000, and another on macroeconomic performance of twelve European countries in the period 1949-2024.

21.
bioRxiv (Bioinfo) 2026-06-15

Multiple Fault Analysis and Drug Therapy on Signaling Pathways Using Dynamic Bayesian Network-based Model

Cell growth is an intricate biological phenomenon that is closely regulated by the interplay between various growth factors and transcription factors. Signaling pathways are the main mediators in this event, which provide the driving force for mitosis or sometimes meiosis. However, when malfunctions occur within the biological network, they can cause uncontrolled cell division, regardless of external stimuli. By employing Dynamic Bayesian Networks (DBNs), these malfunctions can be explicitly simulated, offering insights into their effects on cellular behavior and growth regulation. To a significant extent, the resultant outcomes can be mitigated through the use of reduced drug combinations. This study delves into the intricacies of signaling pathway behavior under the influence of concurrent malfunctions. Initially, we replicate the effects of these dysfunctions within DBNs. Subsequently, drug therapy is applied to alleviate their impact. Our methodology introduces a parameter known as efficiency_score, enabling the identification of optimized drug combinations without prior knowledge of specific dysfunctions. Particularly relevant in the context of realistic cancer conditions, these tailored drug inhibition points demonstrate enhanced efficacy compared to conventional treatments. Leveraging GPU acceleration throughout the modeling process accelerates the analysis of multiple faults within the biological networks, rendering our approach notably faster and more efficient.

22.
arXiv (CS.LG) 2026-06-24

Stabilizing Physics-Informed Consistency Models via Structure-Preserving Training

arXiv:2602.09303v2 Announce Type: replace Abstract: We propose a physics-informed consistency modeling framework for solving partial differential equations (PDEs) via fast, few-step generative inference. We identify a key stability challenge in physics-constrained consistency training, where PDE residuals can drive the model toward trivial or degenerate solutions, degrading the learned data distribution. To address this, we introduce a structure-preserving two-stage training strategy that decouples distribution learning from physics enforcement by freezing the coefficient decoder during physics-informed fine-tuning. We further propose a two-step residual objective that enforces physical consistency on refined, structurally valid generative trajectories rather than noisy single-step predictions. The resulting framework enables stable, high-fidelity inference for both unconditional generation and forward problems. We demonstrate that forward solutions can be obtained via a projection-based zero-shot inpainting procedure, achieving consistent accuracy of diffusion baselines with orders of magnitude reduction in computational cost.

23.
arXiv (CS.CL) 2026-06-24

Sentence-Level Contextual Entrainment in Large Language Models

Contextual entrainment, which is a newly discovered phenomenon in large language models (LLMs), refers to the tendency of a model to assign higher probabilities to tokens that appear in its context. In this work, we extend this phenomenon from the token level to the sentence level by examining the per-token mean log-probability of a sentence instead of the probabilities of individual tokens. We investigate sentence-level contextual entrainment across 26 LLMs from seven families and two datasets, which cover both subjective and objective tasks. We find that sentence-level contextual entrainment exists. This means that the sentences in the prompt (even if they are counterfactual statements) can significantly increase their probability during model inference time. As the model size increases, contextual entrainment gradually decreases. We also find that contextual entrainment is controlled by 2% to 4% of the attention heads. Turning off these attention heads can effectively mitigate contextual entrainment without hurting the model's performance.

24.
arXiv (CS.CV) 2026-06-19

Efficiently Linking Real Scenes with Synthetic Data Generation for AI-based Cognitive Robotics and Computer Vision Applications

AI vision models are a driving factor for the potential use case scenarios of cognitive robotics within in the industry and household applications. A large array of methods from semantic environment analysis towards 6D and grasping pose estimation have been proposed based on the latest AI achievements. However, such advancements require further strong and efficient methods w.r.t. training data and AI-architectures, which are capable in synergy to tackle current challenges, precision limits, and scalability beyond domain gaps. In this paper, we discuss these current limits and trends in the related state-of-the-art which are challenging those. Further we discuss our current work in progress on bridging the domain gap between simulations and real world applications by linking those in the training data generation.

25.
arXiv (CS.LG) 2026-06-18

Exponentially many initializations to avoid barren plateaus

arXiv:2606.18515v1 Announce Type: cross Abstract: Barren plateaus are stated as an average-case phenomenon: pick an ansatz, initialize it naively, and concentration follows. This has led to the common view that a potential cure for barren plateaus is simply to initialize the parameters more carefully. Here we show that the situation is subtler. We introduce a first-moment framework that gives a simple operator-level diagnostic for when an initialization may escape the fully concentrated barren-plateau fixed point, and for comparing the biases induced by different initialization strategies. Our framework recovers several known initialization schemes such as identity and Gaussian initialization, but also shows that barren-plateau avoidance is highly non-unique. Indeed, many shifted, biased, and non-symmetric parameter distributions can avoid concentration, and these choices need not be equivalent. In fact, our results show that one can generate exponentially many families of inequivalent initialization strategies. Then, our numerics indicate that different first-moment-distinct initializations can lead to different attained minima, suggesting that avoiding barren plateaus via smart initializations can trade the exponential concentration problem for the challenge of selecting the right trainable pocket amongst many options.