In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding complex biological processes. Key to this is the modeling and generation of hierarchical data that represents the intrinsic structure within datasets. Traditional methods face limitations in terms of computational cost, performance, generative capacity, and stability. Recent VAEs based approaches have made strides in addressing these challenges but still require specialized network modules for each tree branch, limiting their stability and ability to capture deep hierarchical relationships. To overcome these challenges, we introduce diffusion-based approach called HDTree. HDTree captures tree relationships within a hierarchical latent space using a unified hierarchical codebook and quantized diffusion processes to model tree node transitions. This method improves stability by eliminating branch-specific modules and enhancing generative capacity through gradual hierarchical changes simulated by the diffusion process. HDTree's effectiveness is demonstrated through comparisons on both general-purpose and single-cell datasets, where it outperforms existing methods in terms of accuracy and performance. These contributions provide a new tool for hierarchical lineage analysis, enabling more accurate and efficient modeling of cellular differentiation paths and offering insights for downstream biological tasks. The code of HDTree is available at anonymous link https://anonymous.4open.science/r/code_HDTree_review-A8DB.

Distributivity is a well-established and extensively studied notion in lattice theory. In the context of data analysis, particularly within Formal Concept Analysis (FCA), lattices are often observed to exhibit a high degree of distributivity. However, no standardized measure exists to quantify this property. In this paper, we introduce the notion of rises in (concept) lattices as a means to assess distributivity. Rises capture how the number of attributes or objects in covering concepts change within the concept lattice. We show that a lattice is distributive if and only if no non-unit rises occur. Furthermore, we relate rises to the classical notion of meet- and join distributivity. We observe that concept lattices from real-world data are to a high degree join-distributive, but much less meet-distributive. We additionally study how join-distributivity manifests on the level of ordered sets.

Simulation-based problems involving mixed-variable inputs frequently feature domains that are hierarchical, conditional, heterogeneous, or tree-structured. These characteristics pose challenges for data representation, modeling, and optimization. This paper reviews extensive literature on these structured input spaces and proposes a unified framework that generalizes existing approaches. In this framework, input variables may be continuous, integer, or categorical. A variable is described as meta if its value governs the presence of other decreed variables, enabling the modeling of conditional and hierarchical structures. We further introduce the concept of partially-decreed variables, whose activation depends on contextual conditions. To capture these inter-variable hierarchical relationships, we introduce design space graphs, combining principles from feature modeling and graph theory. This allows the definition of general hierarchical domains suitable for describing complex system architectures. The framework supports the use of surrogate models over such domains and integrates hierarchical kernels and distances for efficient modeling and optimization. The proposed methods are implemented in the open-source Surrogate Modeling Toolbox (SMT 2.0), and their capabilities are demonstrated through applications in Bayesian optimization for complex system design, including a case study in green aircraft architecture.

We conduct a systematic audit of three widely used reasoning benchmarks, SocialIQa, FauxPas-EAI, and ToMi, and uncover pervasive flaws in both benchmark items and evaluation methodology. Using five LLMs (GPT-{3, 3.5, 4, o1}, and LLaMA 3.1) as diagnostic tools, we identify structural, semantic, and pragmatic issues in benchmark design (e.g., duplicated items, ambiguous wording, and implausible answers), as well as scoring procedures that prioritize output form over reasoning process. Through systematic human annotation and re-evaluation on cleaned benchmark subsets, we find that model scores often improve not due to due to erratic surface wording variations and not to improved reasoning. Infact, further analyses show that model performance is highly sensitive to minor input variations such as context availability and phrasing, revealing that high scores may reflect alignment with format-specific cues rather than consistent inference based on the input. These findings challenge the validity of current benchmark-based claims about reasoning in LLMs, and highlight the need for evaluation protocols that assess reasoning as a process of drawing inference from available information, rather than as static output selection. We release audited data and evaluation tools to support more interpretable and diagnostic assessments of model reasoning.

We argue that viewing AI as a simple reduction in input costs overlooks two critical dynamics: (a) the inherent trade-offs among generality, accuracy, and simplicity, and (b) the redistribution of complexity across stakeholders. While LLMs appear to defy the traditional trade-off by offering high generality and accuracy through simple interfaces, this user-facing simplicity masks a significant shift of complexity to infrastructure, compliance, and specialized personnel. The GAS trade-off, therefore, does not disappear but is relocated from the user to the organization, creating new managerial challenges, particularly around accuracy in high-stakes applications. We contend that competitive advantage no longer stems from mere AI adoption, but from mastering this redistributed complexity through the design of abstraction layers, workflow alignment, and complementary expertise.

Real-world knowledge can take various forms, including structured, semi-structured, and unstructured data. Among these, knowledge graphs are a form of structured human knowledge that integrate heterogeneous data sources into structured representations but typically reduce complex n-ary relations to simple triples, thereby losing higher-order relational details. In contrast, hypergraphs naturally represent n-ary relations with hyperedges, which directly connect multiple entities together. Yet hypergraph representation learning often overlooks entity roles in hyperedges, limiting the finegrained semantic modelling. To address these issues, knowledge hypergraphs and hyper-relational knowledge graphs combine the advantages of knowledge graphs and hypergraphs to better capture the complex structures and role-specific semantics of real world knowledge. This survey provides a comprehensive review of methods handling n-ary relational data, covering both knowledge hypergraphs and hyper-relational knowledge graphs literatures. We propose a two-dimensional taxonomy: the first dimension categorises models based on their methodology, i.e., translation-based models, tensor factorisation-based models, deep neural network-based models, logic rules-based models, and hyperedge expansion-based models. The second dimension classifies models according to their awareness of entity roles and positions in n-ary relations, dividing them into aware-less, position-aware, and role-aware approaches. Finally, we discuss existing datasets, training settings and strategies, and outline open challenges to inspire future research.

This white paper discusses and explores the various points of intersection between quantum computing and artificial intelligence (AI). It describes how quantum computing could support the development of innovative AI solutions. It also examines use cases of classical AI that can empower research and development in quantum technologies, with a focus on quantum computing and quantum sensing. The purpose of this white paper is to provide a long-term research agenda aimed at addressing foundational questions about how AI and quantum computing interact and benefit one another. It concludes with a set of recommendations and challenges, including how to orchestrate the proposed theoretical work, align quantum AI developments with quantum hardware roadmaps, estimate both classical and quantum resources - especially with the goal of mitigating and optimizing energy consumption - advance this emerging hybrid software engineering discipline, and enhance European industrial competitiveness while considering societal implications.

Recent breakthroughs in artificial intelligence (AI) have brought about increasingly capable systems that demonstrate remarkable abilities in reasoning, language understanding, and problem-solving. These advancements have prompted a renewed examination of AI awareness not as a philosophical question of consciousness, but as a measurable, functional capacity. AI awareness is a double-edged sword: it improves general capabilities, i.e., reasoning, safety, while also raising concerns around misalignment and societal risks, demanding careful oversight as AI capabilities grow. In this review, we explore the emerging landscape of AI awareness, which includes metacognition (the ability to represent and reason about its own cognitive state), self-awareness (recognizing its own identity, knowledge, limitations, inter alia), social awareness (modeling the knowledge, intentions, and behaviors of other agents and social norms), and situational awareness (assessing and responding to the context in which it operates). First, we draw on insights from cognitive science, psychology, and computational theory to trace the theoretical foundations of awareness and examine how the four distinct forms of AI awareness manifest in state-of-the-art AI. Next, we systematically analyze current evaluation methods and empirical findings to better understand these manifestations. Building on this, we explore how AI awareness is closely linked to AI capabilities, demonstrating that more aware AI agents tend to exhibit higher levels of intelligent behaviors. Finally, we discuss the risks associated with AI awareness, including key topics in AI safety, alignment, and broader ethical concerns.

Reasoning plays a crucial role in advancing Multimodal Large Language Models (MLLMs) toward Artificial General Intelligence. However, existing MLLM benchmarks often fall short in precisely and comprehensively evaluating long-chain reasoning abilities from three key aspects: (1) lack of difficulty and diversity, (2) susceptibility to guessability and memorization, (3) inadequate assessment of intermediate reasoning steps. To fill this gap, we introduce MMReason, a new benchmark designed to precisely and comprehensively evaluate MLLM long-chain reasoning capability with diverse, open-ended, challenging questions. First, we curate challenging questions requiring multi-step reasoning from various fields (i.e., 6 disciplines) and multiple difficulty levels (i.e., from pre-university to university, and from foundational to competition tiers). Second, these questions are reformulated into an open-ended format and filtered using a multi-model voting technique to eliminate shortcut cases related to guessing and memorization, ensuring robust reasoning evaluations. Third, we annotate the questions with detailed step-by-step solutions, and design a reference-based ternary scoring mechanism to reliably assess intermediate reasoning steps. With MMReason, we benchmark popular leading MLLMs and provide an in-depth analysis of their reasoning capabilities. We hope MMReason will serve as a valuable resource for advancing MLLM reasoning research. Code will be available at https://github.com/HJYao00/MMReason.

The ability to process information from multiple modalities and to reason through it step-by-step remains a critical challenge in advancing artificial intelligence. However, existing reasoning benchmarks focus on text-only reasoning, or employ multimodal questions that can be answered by directly retrieving information from a non-text modality. Thus, complex reasoning remains poorly understood in multimodal domains. Here, we present MARBLE, a challenging multimodal reasoning benchmark that is designed to scrutinize multimodal language models (MLLMs) in their ability to carefully reason step-by-step through complex multimodal problems and environments. MARBLE is composed of two highly challenging tasks, M-Portal and M-Cube, that require the crafting and understanding of multistep plans under spatial, visual, and physical constraints. We find that current MLLMs perform poorly on MARBLE -- all the 12 advanced models obtain near-random performance on M-Portal and 0% accuracy on M-Cube. Only in simplified subtasks some models outperform the random baseline, indicating that complex reasoning is still a challenge for existing MLLMs. Moreover, we show that perception remains a bottleneck, where MLLMs occasionally fail to extract information from the visual inputs. By shedding a light on the limitations of MLLMs, we hope that MARBLE will spur the development of the next generation of models with the ability to reason and plan across many, multimodal reasoning steps.