The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

Federated Learning (FL) marks a transformative approach to distributed model training by combining locally optimized models from various clients into a unified global model. While FL preserves data privacy by eliminating centralized storage, it encounters significant challenges such as performance degradation, slower convergence, and reduced robustness of the global model due to the heterogeneity in client data distributions. Among the various forms of data heterogeneity, label skew emerges as a particularly formidable and prevalent issue, especially in domains such as image classification. To address these challenges, we begin with comprehensive experiments to pinpoint the underlying issues in the FL training process. Based on our findings, we then introduce an innovative dual-strategy approach designed to effectively resolve these issues. First, we introduce an adaptive loss function for client-side training, meticulously crafted to preserve previously acquired knowledge while maintaining an optimal equilibrium between local optimization and global model coherence. Secondly, we develop a dynamic aggregation strategy for aggregating client models at the server. This approach adapts to each client's unique learning patterns, effectively addressing the challenges of diverse data across the network. Our comprehensive evaluation, conducted across three diverse real-world datasets, coupled with theoretical convergence guarantees, demonstrates the superior efficacy of our method compared to several established state-of-the-art approaches.

Intelligent autonomous agents hold much potential for the domain of cyber security. However, due to many state-of-the-art approaches relying on uninterpretable black-box models, there is growing demand for methods that offer stakeholders clear and actionable insights into their latent beliefs and motivations. To address this, we evaluate Theory of Mind (ToM) approaches for Autonomous Cyber Operations. Upon learning a robust prior, ToM models can predict an agent's goals, behaviours, and contextual beliefs given only a handful of past behaviour observations. In this paper, we introduce a novel Graph Neural Network (GNN)-based ToM architecture tailored for cyber-defence, Graph-In, Graph-Out (GIGO)-ToM, which can accurately predict both the targets and attack trajectories of adversarial cyber agents over arbitrary computer network topologies. To evaluate the latter, we propose a novel extension of the Wasserstein distance for measuring the similarity of graph-based probability distributions. Whereas the standard Wasserstein distance lacks a fixed reference scale, we introduce a graph-theoretic normalization factor that enables a standardized comparison between networks of different sizes. We furnish this metric, which we term the Network Transport Distance (NTD), with a weighting function that emphasizes predictions according to custom node features, allowing network operators to explore arbitrary strategic considerations. Benchmarked against a Graph-In, Dense-Out (GIDO)-ToM architecture in an abstract cyber-defence environment, our empirical evaluations show that GIGO-ToM can accurately predict the goals and behaviours of various unseen cyber-attacking agents across a range of network topologies, as well as learn embeddings that can effectively characterize their policies.

As the strength of Large Language Models (LLMs) has grown over recent years, so too has interest in their use as the underlying models for autonomous agents. Although LLMs demonstrate emergent abilities and broad expertise across natural language domains, their inherent unpredictability makes the implementation of LLM agents challenging, resulting in a gap between related research and the real-world implementation of such systems. To bridge this gap, this paper frames actionable insights and considerations from the research community in the context of established application paradigms to enable the construction and facilitate the informed deployment of robust LLM agents. Namely, we position relevant research findings into four broad categories--Planning, Memory, Tools, and Control Flow--based on common practices in application-focused literature and highlight practical considerations to make when designing agentic LLMs for real-world applications, such as handling stochasticity and managing resources efficiently. While we do not conduct empirical evaluations, we do provide the necessary background for discussing critical aspects of agentic LLM designs, both in academia and industry.

Recent advances in deep learning and natural language generation have significantly improved image captioning, enabling automated, human-like descriptions for visual content. In this work, we apply these captioning techniques to generate clinician-like interpretations of ECG data. This study leverages existing ECG datasets accompanied by free-text reports authored by healthcare professionals (HCPs) as training data. These reports, while often inconsistent, provide a valuable foundation for automated learning. We introduce an encoder-decoder-based method that uses these reports to train models to generate detailed descriptions of ECG episodes. This represents a significant advancement in ECG analysis automation, with potential applications in zero-shot classification and automated clinical decision support. The model is tested on various datasets, including both 1- and 12-lead ECGs. It significantly outperforms the state-of-the-art reference model by Qiu et al., achieving a METEOR score of 55.53% compared to 24.51% achieved by the reference model. Furthermore, several key design choices are discussed, providing a comprehensive overview of current challenges and innovations in this domain. The source codes for this research are publicly available in our Git repository https://git.zib.de/ableich/ecg-comment-generation-public

The rapid development of Artificial Intelligence (AI) has led to the creation of powerful text generation models, such as large language models (LLMs), which are widely used for diverse applications. However, concerns surrounding AI-generated content, including issues of originality, bias, misinformation, and accountability, have become increasingly prominent. This paper offers a comprehensive overview of AI text generators (AITGs), focusing on their evolution, capabilities, and ethical implications. This paper also introduces Retrieval-Augmented Generation (RAG), a recent approach that improves the contextual relevance and accuracy of text generation by integrating dynamic information retrieval. RAG addresses key limitations of traditional models, including their reliance on static knowledge and potential inaccuracies in handling real-world data. Additionally, the paper reviews detection tools that help differentiate AI-generated text from human-written content and discusses the ethical challenges these technologies pose. The paper explores future directions for improving detection accuracy, supporting ethical AI development, and increasing accessibility. The paper contributes to a more responsible and reliable use of AI in content creation through these discussions.

Game-theoretic scenarios have become pivotal in evaluating the social intelligence of Large Language Model (LLM)-based social agents. While numerous studies have explored these agents in such settings, there is a lack of a comprehensive survey summarizing the current progress. To address this gap, we systematically review existing research on LLM-based social agents within game-theoretic scenarios. Our survey organizes the findings into three core components: Game Framework, Social Agent, and Evaluation Protocol. The game framework encompasses diverse game scenarios, ranging from choice-focusing to communication-focusing games. The social agent part explores agents' preferences, beliefs, and reasoning abilities. The evaluation protocol covers both game-agnostic and game-specific metrics for assessing agent performance. By reflecting on the current research and identifying future research directions, this survey provides insights to advance the development and evaluation of social agents in game-theoretic scenarios.

The rapid advancement of deep learning has resulted in substantial advancements in AI-driven applications; however, the "black box" characteristic of these models frequently constrains their interpretability, transparency, and reliability. Explainable artificial intelligence (XAI) seeks to elucidate AI decision-making processes, guaranteeing that explanations faithfully represent the model's rationale and correspond with human comprehension. Despite comprehensive research in XAI, a significant gap persists in standardized procedures for assessing the efficacy and transparency of XAI techniques across many real-world applications. This study presents a unified XAI evaluation framework incorporating extensive quantitative and qualitative criteria to systematically evaluate the correctness, interpretability, robustness, fairness, and completeness of explanations generated by AI models. The framework prioritizes user-centric and domain-specific adaptations, hence improving the usability and reliability of AI models in essential domains. To address deficiencies in existing evaluation processes, we suggest defined benchmarks and a systematic evaluation pipeline that includes data loading, explanation development, and thorough method assessment. The suggested framework's relevance and variety are evidenced by case studies in healthcare, finance, agriculture, and autonomous systems. These provide a solid basis for the equitable and dependable assessment of XAI methodologies. This paradigm enhances XAI research by offering a systematic, flexible, and pragmatic method to guarantee transparency and accountability in AI systems across many real-world contexts.

Recent efforts in fine-tuning language models often rely on automatic data selection, commonly using Nearest Neighbors retrieval from large datasets. However, we theoretically show that this approach tends to select redundant data, limiting its effectiveness or even hurting performance. To address this, we introduce SIFT, a data selection algorithm designed to reduce uncertainty about the model's response given a prompt, which unifies ideas from retrieval and active learning. Whereas Nearest Neighbor retrieval typically fails in the presence of information duplication, SIFT accounts for information duplication and optimizes the overall information gain of the selected examples. We focus our evaluations on fine-tuning at test-time for prompt-specific language modeling on the Pile dataset, and show that SIFT consistently outperforms Nearest Neighbor retrieval, with minimal computational overhead. Moreover, we show that our uncertainty estimates can predict the performance gain of test-time fine-tuning, and use this to develop an adaptive algorithm that invests test-time compute proportional to realized performance gains. We provide the $\texttt{activeft}$ (Active Fine-Tuning) library which can be used as a drop-in replacement for Nearest Neighbor retrieval.

Graphs are ubiquitous in real-world applications, ranging from social networks to biological systems, and have inspired the development of Graph Neural Networks (GNNs) for learning expressive representations. While most research has centered on static graphs, many real-world scenarios involve dynamic, temporally evolving graphs, motivating the need for Continuous-Time Dynamic Graph (CTDG) models. This paper provides a comprehensive review of Graph Representation Learning (GRL) on CTDGs with a focus on Self-Supervised Representation Learning (SSRL). We introduce a novel theoretical framework that analyzes the expressivity of CTDG models through an Information-Flow (IF) lens, quantifying their ability to propagate and encode temporal and structural information. Leveraging this framework, we categorize existing CTDG methods based on their suitability for different graph types and application scenarios. Within the same scope, we examine the design of SSRL methods tailored to CTDGs, such as predictive and contrastive approaches, highlighting their potential to mitigate the reliance on labeled data. Empirical evaluations on synthetic and real-world datasets validate our theoretical insights, demonstrating the strengths and limitations of various methods across long-range, bi-partite and community-based graphs. This work offers both a theoretical foundation and practical guidance for selecting and developing CTDG models, advancing the understanding of GRL in dynamic settings.