Transformer models have recently gained popularity in graph representation learning as they have the potential to learn complex relationships beyond the ones captured by regular graph neural networks.The main research question is how to inject the structural bias of graphs into the transformer architecture,and several proposals have been made for undirected molecular graphs and, recently, also for larger network graphs.In this paper, we study transformers over directed acyclic graphs (DAGs) and propose architecture adaptations tailored to DAGs: (1) An attention mechanism that is considerably more efficient than the regular quadratic complexity of transformers and at the same time faithfully captures the DAG structure, and (2) a positional encoding of the DAG's partial order, complementing the former.We rigorously evaluate our approach over various types of tasks, ranging from classifying source code graphs to nodes in citation networks, and show that it is effective in two important aspects: in making graph transformers generally outperform graph neural networks tailored to DAGs and in improving SOTA graph transformer performance in terms of both quality and efficiency.

Graph structured data are abundant in the real world. Among different graph types, directed acyclic graphs (DAGs) are of particular interest to machine learning researchers, as many machine learning models are realized as computations on DAGs, including neural networks and Bayesian networks. In this paper, we study deep generative models for DAGs, and propose a novel DAG variational autoencoder (D-VAE).

We developed a task-oriented dialogue framework structured as a Directed Acyclic Graph (DAG) of medical questions. The system integrates: (1) a systematic pipeline for transforming medical algorithms and guidelines into a clinical question corpus; (2) a cold-start mechanism based on hierarchical clustering to generate efficient initial questioning without prior patient information; (3) an expand-and-prune mechanism enabling adaptive branching and backtracking based on patient responses; (4) a termination logic to ensure interviews end once sufficient information is gathered; and (5) automated synthesis of doctor-friendly structured reports aligned with clinical workflows. Human-computer interaction principles guided the design of both the patient and physician applications. Preliminary evaluation involved five physicians using standardized instruments: NASA-TLX (cognitive workload), the System Usability Scale (SUS), and the Questionnaire for User Interface Satisfaction (QUIS). The patient application achieved low workload scores (NASA-TLX = 15.6), high usability (SUS = 86), and strong satisfaction (QUIS = 8.1/9), with particularly high ratings for ease of learning and interface design. The physician application yielded moderate workload (NASA-TLX = 26) and excellent usability (SUS = 88.5), with satisfaction scores of 8.3/9. Both applications demonstrated effective integration into clinical workflows, reducing cognitive demand and supporting efficient report generation. Limitations included occasional system latency and a small, non-diverse evaluation sample.

Artificial Intelligence has achieved remarkable advancements in recent years, yet much of its progress relies on identifying increasingly complex correlations. Enabling causality awareness in AI has the potential to enhance its performance by enabling a deeper understanding of the underlying mechanisms of the environment. In this paper, we introduce DODO, an algorithm defining how an Agent can autonomously learn the causal structure of its environment through repeated interventions. We assume a scenario where an Agent interacts with a world governed by a causal Directed Acyclic Graph (DAG), which dictates the system's dynamics but remains hidden from the Agent. The Agent's task is to accurately infer the causal DAG, even in the presence of noise. To achieve this, the Agent performs interventions, leveraging causal inference techniques to analyze the statistical significance of observed changes. Results show better performance for DODO, compared to observational approaches, in all but the most limited resource conditions. DODO is often able to reconstruct with as low as zero errors the structure of the causal graph. In the most challenging configuration, DODO outperforms the best baseline by +0.25 F1 points.

Bayesian causal discovery benefits from prior information elicited from domain experts, and in heterogeneous domains any prior knowledge would be badly needed. However, so far prior elicitation approaches have assumed a single causal graph and hence are not suited to heterogeneous domains. We propose a causal elicitation strategy for heterogeneous settings, based on Bayesian experimental design (BED) principles, and a variational mixture structure learning (VaMSL) method -- extending the earlier differentiable Bayesian structure learning (DiBS) method -- to iteratively infer mixtures of causal Bayesian networks (CBNs). We construct an informative graph prior incorporating elicited expert feedback in the inference of mixtures of CBNs. Our proposed method successfully produces a set of alternative causal models (mixture components or clusters), and achieves an improved structure learning performance on heterogeneous synthetic data when informed by a simulated expert. Finally, we demonstrate that our approach is capable of capturing complex distributions in a breast cancer database.

The increasing complexity of cascading risks in urban systems necessitates robust, data-driven frameworks to model interdependencies across multiple domains. This study presents a foundational Bayesian network-based approach for analyzing cross-domain risk propagation across key urban domains, including air, water, electricity, agriculture, health, infrastructure, weather, and climate. Directed Acyclic Graphs (DAGs) are constructed using Bayesian Belief Networks (BBNs), with structure learning guided by Hill-Climbing search optimized through Bayesian Information Criterion (BIC) and K2 scoring. The framework is trained on a hybrid dataset that combines real-world urban indicators with synthetically generated data from Generative Adversarial Networks (GANs), and is further balanced using the Synthetic Minority Over-sampling Technique (SMOTE). Conditional Probability Tables (CPTs) derived from the learned structures enable interpretable probabilistic reasoning and quantify the likelihood of cascading failures. The results identify key intra- and inter-domain risk factors and demonstrate the framework's utility for proactive urban resilience planning. This work establishes a scalable, interpretable foundation for cascading risk assessment and serves as a basis for future empirical research in this emerging interdisciplinary field.

Originality: The main architectural pieces (VAE, message passing) have been proposed previously, but the specific focus on directed graphs using these components is new to my knowledge. Quality: The proposal was technically sound, but the proposal has undesirable properties which were not addressed by the authors, and lacks sufficient empirical evaluation: 1. Does the proposal easily (from a practical implementation perspective) allow for batching? Instead of N steps with an RNN, the proposal's decoder uses N*(1 2 ... N-1) steps. This may limit the proposal to small graphs (the authors have only evaluated on a fixed, small graph size).

Although initial scores were mixed, after the rebuttal period reviewers all converged to acceptance. In this regard, some issues related to comparisons with existing work were adequately resolved. Beyond this, the demonstration of injectivity is also a nice analytical complement to the algorithmic and empirical contributions, and overall I enjoyed reading this work.

Transformer models have recently gained popularity in graph representation learning as they have the potential to learn complex relationships beyond the ones captured by regular graph neural networks.The main research question is how to inject the structural bias of graphs into the transformer architecture,and several proposals have been made for undirected molecular graphs and, recently, also for larger network graphs.In this paper, we study transformers over directed acyclic graphs (DAGs) and propose architecture adaptations tailored to DAGs: (1) An attention mechanism that is considerably more efficient than the regular quadratic complexity of transformers and at the same time faithfully captures the DAG structure, and (2) a positional encoding of the DAG's partial order, complementing the former.We rigorously evaluate our approach over various types of tasks, ranging from classifying source code graphs to nodes in citation networks, and show that it is effective in two important aspects: in making graph transformers generally outperform graph neural networks tailored to DAGs and in improving SOTA graph transformer performance in terms of both quality and efficiency.

We study the problem of reducing test-time acquisition costs in classification systems. Our goal is to learn decision rules that adaptively select sensors for each example as necessary to make a confident prediction. We model our system as a directed acyclic graph (DAG) where internal nodes correspond to sensor subsets and decision functions at each node choose whether to acquire a new sensor or classify using the available measurements. This problem can be naturally posed as an empirical risk minimization over training data. Rather than jointly optimizing such a highly coupled and non-convex problem over all decision nodes, we propose an efficient algorithm motivated by dynamic programming.