Parviainen et al. (2014) adopted an anytime integer linear programming (ILP) Otherwise it returns a sub-optimal DAG with bounded treewidth. Nie et al. (2014) proposed an efficient anytime ILP approach with a polynomial number of constraints Nie et al. (2015) proposed the method S2.

We present a method for learning Bayesian networks from data sets containing thousands of variables without the need for structure constraints. Our approach is made of two parts. The first is a novel algorithm that effectively explores the space of possible parent sets of a node. It guides the exploration towards the most promising parent sets on the basis of an approximated score function that is computed in constant time. The second part is an improvement of an existing ordering-based algorithm for structure optimization. The new algorithm provably achieves a higher score compared to its original formulation. Our novel approach consistently outperforms the state of the art on very large data sets.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

This article presents MCTS-BN, an adaptation of the Monte Carlo Tree Search (MCTS) algorithm for the structural learning of Bayesian Networks (BNs). Initially designed for game tree exploration, MCTS has been repurposed to address the challenge of learning BN structures by exploring the search space of potential ancestral orders in Bayesian Networks. Then, it employs Hill Climbing (HC) to derive a Bayesian Network structure from each order. In large BNs, where the search space for variable orders becomes vast, using completely random orders during the rollout phase is often unreliable and impractical. We adopt a semi-randomized approach to address this challenge by incorporating variable orders obtained from other heuristic search algorithms such as Greedy Equivalent Search (GES), PC, or HC itself. This hybrid strategy mitigates the computational burden and enhances the reliability of the rollout process. Experimental evaluations demonstrate the effectiveness of MCTS-BN in improving BNs generated by traditional structural learning algorithms, exhibiting robust performance even when base algorithm orders are suboptimal and surpassing the gold standard when provided with favorable orders.

A deep understanding of the intricate interactions between particles within a system is a key approach to revealing the essential characteristics of the system, whether it is an in-depth analysis of molecular properties in the field of chemistry or the design of new materials for specific performance requirements in materials science. To this end, we propose Graph Attention Hamiltonian Neural Network (GAHN), a neural network method that can understand the underlying structure of lattice Hamiltonian systems solely through the dynamic trajectories of particles. We can determine which particles in the system interact with each other, the proportion of interactions between different particles, and whether the potential energy of interactions between particles exhibits even symmetry or not. The obtained structure helps the neural network model to continue predicting the trajectory of the system and further understand the dynamic properties of the system. In addition to understanding the underlying structure of the system, it can be used for detecting lattice structural abnormalities, such as link defects, abnormal interactions, etc. These insights benefit system optimization, design, and detection of aging or damage. Moreover, this approach can integrate other components to deduce the link structure needed for specific parts, showcasing its scalability and potential. We tested it on a challenging molecular dynamics dataset, and the results proved its ability to accurately infer molecular bond connectivity, highlighting its scientific research potential.

We present a method for learning Bayesian networks from data sets containing thousands of variables without the need for structure constraints. Our approach is made of two parts. The first is a novel algorithm that effectively explores the space of possible parent sets of a node. It guides the exploration towards the most promising parent sets on the basis of an approximated score function that is computed in constant time. The second part is an improvement of an existing ordering-based algorithm for structure optimization. The new algorithm provably achieves a higher score compared to its original formulation. Our novel approach consistently outperforms the state of the art on very large data sets.

We present a method for learning treewidth-bounded Bayesian networks from data sets containing thousands of variables. Bounding the treewidth of a Bayesian network greatly reduces the complexity of inferences. Yet, being a global property of the graph, it considerably increases the difficulty of the learning process. Our novel algorithm accomplishes this task, scaling both to large domains and to large treewidths. Our novel approach consistently outperforms the state of the art on experiments with up to thousands of variables.

The surging demand for high-definition video streaming services and large neural network models (e.g., Generative Pre-trained Transformer, GPT) implies a tremendous explosion of Internet traffic. To mitigate the traffic pressure, architectures with in-network storage have been proposed to cache popular contents at devices in closer proximity to users. Correspondingly, in order to maximize caching utilization, it becomes essential to devise an effective popularity prediction method. In that regard, predicting popularity with dynamic graph neural network (DGNN) models achieve remarkable performance. However, DGNN models still suffer from tackling sparse datasets where most users are inactive. Therefore, we propose a reformative temporal graph network, named semantics-enhanced temporal graph network (STGN), which attaches extra semantic information into the user-content bipartite graph and could better leverage implicit relationships behind the superficial topology structure. On top of that, we customize its temporal and structural learning modules to further boost the prediction performance. Specifically, in order to efficiently aggregate the diversified semantics that a content might possess, we design a user-specific attention (UsAttn) mechanism for temporal learning module. Unlike the attention mechanism that only analyzes the influence of genres on content, UsAttn also considers the attraction of semantic information to a specific user. Meanwhile, as for the structural learning, we introduce the concept of positional encoding into our attention-based graph learning and adopt a semantic positional encoding (SPE) function to facilitate the analysis of content-oriented user-association analysis. Finally, extensive simulations verify the superiority of our STGN models and demonstrate the effectiveness in content caching.

Learning a Bayesian network is an NP-hard problem and with an increase in the number of nodes, classical algorithms for learning the structure of Bayesian networks become inefficient. In recent years, some methods and algorithms for learning Bayesian networks with a high number of nodes (more than 50) were developed. But these solutions have their disadvantages, for instance, they only operate one type of data (discrete or continuous) or their algorithm has been created to meet a specific nature of data (medical, social, etc.). The article presents a BigBraveBN algorithm for learning large Bayesian Networks with a high number of nodes (over 100). The algorithm utilizes the Brave coefficient that measures the mutual occurrence of instances in several groups. To form these groups, we use the method of nearest neighbours based on the Mutual information (MI) measure. In the experimental part of the article, we compare the performance of BigBraveBN to other existing solutions on multiple data sets both discrete and continuous. The experimental part also represents tests on real data. The aforementioned experimental results demonstrate the efficiency of the BigBraveBN algorithm in structure learning of Bayesian Networks.

Probabilistic sentential decision diagrams are a class of structured-decomposable probabilistic circuits especially designed to embed logical constraints. To adapt the classical LearnSPN scheme to learn the structure of these models, we propose a new scheme based on a partial closed-world assumption: data implicitly provide the logical base of the circuit. Sum nodes are thus learned by recursively clustering batches in the initial data base, while the partitioning of the variables obeys a given input vtree. Preliminary experiments show that the proposed approach might properly fit training data, and generalize well to test data, provided that these remain consistent with the underlying logical base, that is a relaxation of the training data base.