Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: $3.6\%$ increase in drug response prediction correlation, $9.6\%$ improvement in single-cell drug classification AUC, and $1.1\%$ average gain in gene perturbation prediction accuracy.

Longitudinal network data are essential for analyzing political, economic, and social systems and processes. In political science, these datasets are often generated through human annotation or supervised machine learning applied to evolving corpora. However, as semantic contexts shift over time, inferring dynamic interaction types on emerging issues among a diverse set of entities poses significant challenges, particularly in maintaining timely and consistent annotations. This paper presents the Expert-Augmented LLM Annotation (EALA) approach, which leverages Large Language Models (LLMs) in combination with historically annotated data and expert-constructed codebooks to extrapolate and extend datasets into future periods. We evaluate the performance and reliability of EALA using a dataset of climate negotiations. Our findings demonstrate that EALA effectively predicts nuanced interactions between negotiation parties and captures the evolution of topics over time. At the same time, we identify several limitations inherent to LLM-based annotation, highlighting areas for further improvement. Given the wide availability of codebooks and annotated datasets, EALA holds substantial promise for advancing research in political science and beyond.

Commercial content moderation APIs are marketed as scalable solutions to combat online hate speech. However, the reliance on these APIs risks both silencing legitimate speech, called over-moderation, and failing to protect online platforms from harmful speech, known as under-moderation. To assess such risks, this paper introduces a framework for auditing black-box NLP systems. Using the framework, we systematically evaluate five widely used commercial content moderation APIs. Analyzing five million queries based on four datasets, we find that APIs frequently rely on group identity terms, such as ``black'', to predict hate speech. While OpenAI's and Amazon's services perform slightly better, all providers under-moderate implicit hate speech, which uses codified messages, especially against LGBTQIA+ individuals. Simultaneously, they over-moderate counter-speech, reclaimed slurs and content related to Black, LGBTQIA+, Jewish, and Muslim people. We recommend that API providers offer better guidance on API implementation and threshold setting and more transparency on their APIs' limitations. Warning: This paper contains offensive and hateful terms and concepts. We have chosen to reproduce these terms for reasons of transparency.

Multiple-choice exam questions with "None of the above" (NA) options have been extensively studied in educational testing, in which existing research suggests that they better assess true knowledge. However, their impact on Large Language Models (LLMs) evaluation remains underexplored. Through systematic experiments with 28 LLMs on the MMLU benchmark, we examine how NA options affect model performance and confidence calibration. Our analysis reveals that NA options, when used as the correct answer, lead to a consistent 30-50\% performance drop across models regardless of scale--suggesting that LLMs lack the meta-cognitive ability to systematically evaluate and reject all given options when none are correct. This degradation shows strong domain dependence, with minimal impact on mathematical reasoning (14.6\% drop) but severe effects on tasks requiring uncertainty handling like business ethics (48.1\% drop). Our results highlight important implications for benchmark design and raise questions about LLMs' ability to handle uncertainty in real-world applications.

We present a survey of methods for assessing and enhancing the quality of online discussions, focusing on the potential of Large Language Models (LLMs). While online discourses aim, at least in theory, to foster mutual understanding, they often devolve into harmful exchanges, such as hate speech, threatening social cohesion and democratic values. Recent advancements in LLMs enable facilitation agents that not only moderate content, but also actively improve the quality of interactions. Our survey synthesizes ideas from Natural Language Processing (NLP) and Social Sciences to provide (a) a new taxonomy on discussion quality evaluation, (b) an overview of intervention and facilitation strategies, along with a new taxonomy on conversation facilitation datasets, (c) an LLM-oriented roadmap of good practices and future research directions, from technological and societal perspectives.

The KM3NeT Collaboration is installing the ARCA and ORCA neutrino detectors at the bottom of the Mediterranean Sea. The focus of ARCA is neutrino astronomy, while ORCA is optimised for neutrino oscillation studies. Both detectors are already operational in their intermediate states and collect valuable data, including the measurements of the muons produced by cosmic ray interactions in the atmosphere. This work explores the potential of machine learning models for the reconstruction of muon bundles, which are multi-muon events. For this, data collected with intermediate detector configurations of ARCA and ORCA was used in addition to simulated data from the envisaged final configurations of those detectors. Prediction of the total number of muons in a bundle as well as their total energy and even the energy of the primary cosmic ray is presented.

The development of social media platforms has revolutionized the speed and manner in which information is disseminated, leading to both beneficial and detrimental effects on society. While these platforms facilitate rapid communication, they also accelerate the spread of rumors and extremist speech, impacting public perception and behavior significantly. This issue is particularly pronounced during election periods, where the influence of social media on election outcomes has become a matter of global concern. With the unprecedented number of elections in 2024, against this backdrop, the election ecosystem has encountered unprecedented challenges. This study addresses the urgent need for effective rumor detection on social media by proposing a novel method that combines semantic analysis with graph neural networks. We have meticulously collected a dataset from PolitiFact and Twitter, focusing on politically relevant rumors. Our approach involves semantic analysis using a fine-tuned BERT model to vectorize text content and construct a directed graph where tweets and comments are nodes, and interactions are edges. The core of our method is a graph neural network, SAGEWithEdgeAttention, which extends the GraphSAGE model by incorporating first-order differences as edge attributes and applying an attention mechanism to enhance feature aggregation. This innovative approach allows for the fine-grained analysis of the complex social network structure, improving rumor detection accuracy. The study concludes that our method significantly outperforms traditional content analysis and time-based models, offering a theoretically sound and practically efficient solution.

CognitiveDrone: A VLA Model and Evaluation Benchmark for Real-Time Cognitive T ask Solving and Reasoning in UA Vs Artem Lykov, V alerii Serpiva, Muhammad Haris Khan, Oleg Sautenkov, Artyom Myshlyaev, Grik Tadevosyan, Y asheerah Y aqoot, and Dzmitry Tsetserukou Abstract -- This paper introduces CognitiveDrone, a novel Vision-Language-Action (VLA) model tailored for complex Unmanned Aerial V ehicles (UA Vs) tasks that demand advanced cognitive abilities. Trained on a dataset comprising over 8,000 simulated flight trajectories across three key categories--Human Recognition, Symbol Understanding, and Reasoning--the model generates real-time 4D action commands based on first-person visual inputs and textual instructions. T o further enhance performance in intricate scenarios, we propose CognitiveDrone-R1, which integrates an additional Vision-Language Model (VLM) reasoning module to simplify task directives prior to high-frequency control. Experimental evaluations using our open-source benchmark, CognitiveDroneBench, reveal that while a racing-oriented model (RaceVLA) achieves an overall success rate of 31.3%, the base CognitiveDrone model reaches 59.6%, and CognitiveDrone-R1 attains a success rate of 77.2%. These results demonstrate improvements of up to 30% in critical cognitive tasks, underscoring the effectiveness of incorporating advanced reasoning capabilities into UA V control systems. Our contributions include the development of a state-of-the-art VLA model for UA V control and the introduction of the first dedicated benchmark for assessing cognitive tasks in drone operations.

This study examines ChatGPT-4's capability to replicate linguistic strategies used in political discourse, focusing on its potential for manipulative language generation. As large language models become increasingly popular for text generation, concerns have grown regarding their role in spreading fake news and propaganda. This research compares real political speeches with those generated by ChatGPT, emphasizing presuppositions (a rhetorical device that subtly influences audiences by packaging some content as already known at the moment of utterance, thus swaying opinions without explicit argumentation). Using a corpus-based pragmatic analysis, this study assesses how well ChatGPT can mimic these persuasive strategies. The findings reveal that although ChatGPT-generated texts contain many manipulative presuppositions, key differences emerge in their frequency, form, and function compared with those of politicians. For instance, ChatGPT often relies on change-of-state verbs used in fixed phrases, whereas politicians use presupposition triggers in more varied and creative ways. Such differences, however, are challenging to detect with the naked eye, underscoring the potential risks posed by large language models in political and public discourse.Using a corpus-based pragmatic analysis, this study assesses how well ChatGPT can mimic these persuasive strategies. The findings reveal that although ChatGPT-generated texts contain many manipulative presuppositions, key differences emerge in their frequency, form, and function compared with those of politicians. For instance, ChatGPT often relies on change-of-state verbs used in fixed phrases, whereas politicians use presupposition triggers in more varied and creative ways. Such differences, however, are challenging to detect with the naked eye, underscoring the potential risks posed by large language models in political and public discourse.

Enhancing Network Security Management in Water Systems using FM-based Attack Attribution Aleksandar Avdalovi c, Joseph Khoury, Ahmad Taha, Elias Bou-Harb Division of Computer Science and Engineering, Louisiana State University, USA Civil and Environmental Engineering, V anderbilt University, USA Abstract --Water systems are vital components of modern infrastructure, yet they are increasingly susceptible to sophisticated cyber attacks with potentially dire consequences on public health and safety. While state-of-the-art machine learning techniques effectively detect anomalies, contemporary model-agnostic attack attribution methods using LIME, SHAP, and LEMNA are deemed impractical for large-scale, interdependent water systems. This is due to the intricate interconnectivity and dynamic interactions that define these complex environments. Such methods primarily emphasize individual feature importance while falling short of addressing the crucial sensor-actuator interactions in water systems, which limits their effectiveness in identifying root cause attacks. T o this end, we propose a novel model-agnostic Factorization Machines (FM)-based approach that capitalizes on water system sensor-actuator interactions to provide granular explanations and attributions for cyber attacks. For instance, an anomaly in an actuator pump activity can be attributed to a top root cause attack candidates, a list of water pressure sensors, which is derived from the underlying linear and quadratic effects captured by our approach. In multi-feature cyber attack scenarios involving intricate sensor-actuator interactions, our FM-based attack attribution method effectively ranks attack root causes, achieving approximately 20% average improvement over SHAP and LEMNA. Additionally, our approach maintains strong performance in single-feature attack scenarios, demonstrating versatility across different types of cyber attacks. Notably, our approach maintains a low computational overhead equating to an O(n) time complexity, making it suitable for real-time applications in critical water system infrastructure. Our work underscores the importance of modeling feature interactions in water systems, offering a robust tool for operators to diagnose and mitigate root cause attacks more effectively. I NTRODUCTION W ATER systems at the physical layer comprise critical components such as flow and pressure sensors, and actuators, which are monitored and controlled by cyber layer systems to ensure a safe and reliable water supply for both communities and industries.