Drug repositioning-a promising strategy for discovering new therapeutic uses for existing drugs-has been increasingly explored in the computational science literature using biomedical databases. However, the technological potential of drug repositioning candidates has often been overlooked. This study presents a novel protocol to comprehensively analyse various sources such as pharmaceutical patents and biomedical databases, and identify drug repositioning candidates with both technological potential and scientific evidence. To this end, first, we constructed a scientific biomedical knowledge graph (s-BKG) comprising relationships between drugs, diseases, and genes derived from biomedical databases. Our protocol involves identifying drugs that exhibit limited association with the target disease but are closely located in the s-BKG, as potential drug candidates. We constructed a patent-informed biomedical knowledge graph (p-BKG) by adding pharmaceutical patent information. Finally, we developed a graph embedding protocol to ascertain the structure of the p-BKG, thereby calculating the relevance scores of those candidates with target disease-related patents to evaluate their technological potential. Our case study on Alzheimer's disease demonstrates its efficacy and feasibility, while the quantitative outcomes and systematic methods are expected to bridge the gap between computational discoveries and successful market applications in drug repositioning research.
Predicting vehicle trajectories is crucial for ensuring automated vehicle operation efficiency and safety, particularly on congested multi-lane highways. In such dynamic environments, a vehicle's motion is determined by its historical behaviors as well as interactions with surrounding vehicles. These intricate interactions arise from unpredictable motion patterns, leading to a wide range of driving behaviors that warrant in-depth investigation. This study presents the Graph-based Interaction-aware Multi-modal Trajectory Prediction (GIMTP) framework, designed to probabilistically predict future vehicle trajectories by effectively capturing these interactions. Within this framework, vehicles' motions are conceptualized as nodes in a time-varying graph, and the traffic interactions are represented by a dynamic adjacency matrix. To holistically capture both spatial and temporal dependencies embedded in this dynamic adjacency matrix, the methodology incorporates the Diffusion Graph Convolutional Network (DGCN), thereby providing a graph embedding of both historical states and future states. Furthermore, we employ a driving intention-specific feature fusion, enabling the adaptive integration of historical and future embeddings for enhanced intention recognition and trajectory prediction. This model gives two-dimensional predictions for each mode of longitudinal and lateral driving behaviors and offers probabilistic future paths with corresponding probabilities, addressing the challenges of complex vehicle interactions and multi-modality of driving behaviors. Validation using real-world trajectory datasets demonstrates the efficiency and potential.
Many downstream inference tasks for knowledge graphs, such as relation prediction, have been handled successfully by knowledge graph embedding techniques in the transductive setting. To address the inductive setting wherein new entities are introduced into the knowledge graph at inference time, more recent work opts for models which learn implicit representations of the knowledge graph through a complex function of a network's subgraph structure, often parametrized by graph neural network architectures. These come at the cost of increased parametrization, reduced interpretability and limited generalization to other downstream inference tasks. In this work, we bridge the gap between traditional transductive knowledge graph embedding approaches and more recent inductive relation prediction models by introducing a generalized form of harmonic extension which leverages representations learned through transductive embedding methods to infer representations of new entities introduced at inference time as in the inductive setting. This harmonic extension technique provides the best such approximation, can be implemented via an efficient iterative scheme, and can be employed to answer a family of conjunctive logical queries over the knowledge graph, further expanding the capabilities of transductive embedding methods. In experiments on a number of large-scale knowledge graph embedding benchmarks, we find that this approach for extending the functionality of transductive knowledge graph embedding models to perform knowledge graph completion and answer logical queries in the inductive setting is competitive with--and in some scenarios outperforms--several state-of-the-art models derived explicitly for such inductive tasks.
We present a method for balancing between the Local and Global Structures (LGS) in graph embedding, via a tunable parameter. Some embedding methods aim to capture global structures, while others attempt to preserve local neighborhoods. Few methods attempt to do both, and it is not always possible to capture well both local and global information in two dimensions, which is where most graph drawing live. The choice of using a local or a global embedding for visualization depends not only on the task but also on the structure of the underlying data, which may not be known in advance. For a given graph, LGS aims to find a good balance between the local and global structure to preserve. We evaluate the performance of LGS with synthetic and real-world datasets and our results indicate that it is competitive with the state-of-the-art methods, using established quality metrics such as stress and neighborhood preservation. We introduce a novel quality metric, cluster distance preservation, to assess intermediate structure capture. All source-code, datasets, experiments and analysis are available online.
Temporal Interaction Graphs (TIGs) are widely employed to model intricate real-world systems such as financial systems and social networks. To capture the dynamism and interdependencies of nodes, existing TIG embedding models need to process edges sequentially and chronologically. However, this requirement prevents it from being processed in parallel and struggle to accommodate burgeoning data volumes to GPU. Consequently, many large-scale temporal interaction graphs are confined to CPU processing. Furthermore, a generalized GPU scaling and acceleration approach remains unavailable. To facilitate large-scale TIGs' implementation on GPUs for acceleration, we introduce a novel training approach namely Streaming Edge Partitioning and Parallel Acceleration for Temporal Interaction Graph Embedding (SPEED). The SPEED is comprised of a Streaming Edge Partitioning Component (SEP) which addresses space overhead issue by assigning fewer nodes to each GPU, and a Parallel Acceleration Component (PAC) which enables simultaneous training of different sub-graphs, addressing time overhead issue. Our method can achieve a good balance in computing resources, computing time, and downstream task performance. Empirical validation across 7 real-world datasets demonstrates the potential to expedite training speeds by a factor of up to 19.29x. Simultaneously, resource consumption of a single-GPU can be diminished by up to 69%, thus enabling the multiple GPU-based training and acceleration encompassing millions of nodes and billions of edges. Furthermore, our approach also maintains its competitiveness in downstream tasks.
Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.
Influence estimation aims to predict the total influence spread in social networks and has received surged attention in recent years. Most current studies focus on estimating the total number of influenced users in a social network, and neglect susceptibility estimation that aims to predict the probability of each user being influenced from the individual perspective. As a more fine-grained estimation task, susceptibility estimation is full of attractiveness and practical value. Based on the significance of susceptibility estimation and dynamic properties of social networks, we propose a task, called susceptibility estimation in dynamic social networks, which is even more realistic and valuable in real-world applications. Susceptibility estimation in dynamic networks has yet to be explored so far and is computationally intractable to naively adopt Monte Carlo simulation to obtain the results. To this end, we propose a novel end-to-end framework DySuse based on dynamic graph embedding technology. Specifically, we leverage a structural feature module to independently capture the structural information of influence diffusion on each single graph snapshot. Besides, {we propose the progressive mechanism according to the property of influence diffusion,} to couple the structural and temporal information during diffusion tightly. Moreover, a self-attention block {is designed to} further capture temporal dependency by flexibly weighting historical timestamps. Experimental results show that our framework is superior to the existing dynamic graph embedding models and has satisfactory prediction performance in multiple influence diffusion models.
Pain is a complex concept that can interconnect with other concepts such as a disorder that might cause pain, a medication that might relieve pain, and so on. To fully understand the context of pain experienced by either an individual or across a population, we may need to examine all concepts related to pain and the relationships between them. This is especially useful when modeling pain that has been recorded in electronic health records. Knowledge graphs represent concepts and their relations by an interlinked network, enabling semantic and context-based reasoning in a computationally tractable form. These graphs can, however, be too large for efficient computation. Knowledge graph embeddings help to resolve this by representing the graphs in a low-dimensional vector space. These embeddings can then be used in various downstream tasks such as classification and link prediction. The various relations associated with pain which are required to construct such a knowledge graph can be obtained from external medical knowledge bases such as SNOMED CT, a hierarchical systematic nomenclature of medical terms. A knowledge graph built in this way could be further enriched with real-world examples of pain and its relations extracted from electronic health records. This paper describes the construction of such knowledge graph embedding models of pain concepts, extracted from the unstructured text of mental health electronic health records, combined with external knowledge created from relations described in SNOMED CT, and their evaluation on a subject-object link prediction task. The performance of the models was compared with other baseline models.
Learning graph embeddings is a crucial task in graph mining tasks. An effective graph embedding model can learn low-dimensional representations from graph-structured data for data publishing benefiting various downstream applications such as node classification, link prediction, etc. However, recent studies have revealed that graph embeddings are susceptible to attribute inference attacks, which allow attackers to infer private node attributes from the learned graph embeddings. To address these concerns, privacy-preserving graph embedding methods have emerged, aiming to simultaneously consider primary learning and privacy protection through adversarial learning. However, most existing methods assume that representation models have access to all sensitive attributes in advance during the training stage, which is not always the case due to diverse privacy preferences. Furthermore, the commonly used adversarial learning technique in privacy-preserving representation learning suffers from unstable training issues. In this paper, we propose a novel approach called Private Variational Graph AutoEncoders (PVGAE) with the aid of independent distribution penalty as a regularization term. Specifically, we split the original variational graph autoencoder (VGAE) to learn sensitive and non-sensitive latent representations using two sets of encoders. Additionally, we introduce a novel regularization to enforce the independence of the encoders. We prove the theoretical effectiveness of regularization from the perspective of mutual information. Experimental results on three real-world datasets demonstrate that PVGAE outperforms other baselines in private embedding learning regarding utility performance and privacy protection.
Continual graph learning (CGL) studies the problem of learning from an infinite stream of graph data, consolidating historical knowledge, and generalizing it to the future task. At once, only current graph data are available. Although some recent attempts have been made to handle this task, we still face two potential challenges: 1) most of existing works only manipulate on the intermediate graph embedding and ignore intrinsic properties of graphs. It is non-trivial to differentiate the transferred information across graphs. 2) recent attempts take a parameter-sharing policy to transfer knowledge across time steps or progressively expand new architecture given shifted graph distribution. Learning a single model could loss discriminative information for each graph task while the model expansion scheme suffers from high model complexity. In this paper, we point out that latent relations behind graph edges can be attributed as an invariant factor for the evolving graphs and the statistical information of latent relations evolves. Motivated by this, we design a relation-aware adaptive model, dubbed as RAM-CG, that consists of a relation-discovery modular to explore latent relations behind edges and a task-awareness masking classifier to accounts for the shifted. Extensive experiments show that RAM-CG provides significant 2.2%, 6.9% and 6.6% accuracy improvements over the state-of-the-art results on CitationNet, OGBN-arxiv and TWITCH dataset, respective.
Knowledge Graph Embedding (KGE) has proven to be an effective approach to solving the Knowledge Graph Completion (KGC) task. Relational patterns which refer to relations with specific semantics exhibiting graph patterns are an important factor in the performance of KGE models. Though KGE models' capabilities are analyzed over different relational patterns in theory and a rough connection between better relational patterns modeling and better performance of KGC has been built, a comprehensive quantitative analysis on KGE models over relational patterns remains absent so it is uncertain how the theoretical support of KGE to a relational pattern contributes to the performance of triples associated to such a relational pattern. To address this challenge, we evaluate the performance of 7 KGE models over 4 common relational patterns on 2 benchmarks, then conduct an analysis in theory, entity frequency, and part-to-whole three aspects and get some counterintuitive conclusions. Finally, we introduce a training-free method Score-based Patterns Adaptation (SPA) to enhance KGE models' performance over various relational patterns. This approach is simple yet effective and can be applied to KGE models without additional training. Our experimental results demonstrate that our method generally enhances performance over specific relational patterns. Our source code is available from GitHub at https://github.com/zjukg/Comprehensive-Study-over-Relational-Patterns.
This study aims to validate whether the research performance of scholars correlates with how the scholars work together. Although the most straightforward approaches are centrality measurements or community detection, scholars mostly participate in multiple research groups and have different roles in each group. Thus, we concentrate on the subgraphs of co-authorship networks rooted in each scholar that cover (i) overlapping of the research groups on the scholar and (ii) roles of the scholar in the groups. This study calls the subgraphs “collaboration patterns” and applies subgraph embedding methods to discover and represent the collaboration patterns. Based on embedding the collaboration patterns, we have clustered scholars according to their collaboration styles. Then, we have examined whether scholars in each cluster have similar research performance, using the quantitative indicators. The coherence of the indicators cannot be solid proofs for validating the correlation between collaboration and performance. Nevertheless, the examination for clusters has exhibited that the collaboration patterns can reflect research styles of scholars. This information will enable us to predict the research performance more accurately since the research styles are more consistent and sustainable features of scholars than a few high-impact publications.
Over the past two decades, recommendation systems (RSs) have used machine learning (ML) solutions to recommend items, e.g., movies, books, and restaurants, to clients of a business or an online platform. Recipe recommendation, however, has not yet received much attention compared to those applications. We introduce RECipe as a multi-purpose recipe recommendation framework with a multi-modal knowledge graph (MMKG) backbone. The motivation behind RECipe is to go beyond (deep) neural collaborative filtering (NCF) by recommending recipes to users when they query in natural language or by providing an image. RECipe consists of 3 subsystems: (1) behavior-based recommender, (2) review-based recommender, and (3) image-based recommender. Each subsystem relies on the embedding representations of entities and relations in the graph. We first obtain (pre-trained) embedding representations of textual entities, such as reviews or ingredients, from a fine-tuned model of Microsoft's MPNet. We initialize the weights of the entities with these embeddings to train our knowledge graph embedding (KGE) model. For the visual component, i.e., recipe images, we develop a KGE-Guided variational autoencoder (KG-VAE) to learn the distribution of images and their latent representations. Once KGE and KG-VAE models are fully trained, we use them as a multi-purpose recommendation framework. For benchmarking, we created two knowledge graphs (KGs) from public datasets on Kaggle for recipe recommendation. Our experiments show that the KGE models have comparable performance to the neural solutions. We also present pre-trained NLP embeddings to address important applications such as zero-shot inference for new users (or the cold start problem) and conditional recommendation with respect to recipe categories. We eventually demonstrate the application of RECipe in a multi-purpose recommendation setting.
A knowledge graph is a powerful representation of real-world entities and their relations. The vast majority of these relations are defined as positive statements, but the importance of negative statements is increasingly recognized, especially under an Open World Assumption. Explicitly considering negative statements has been shown to improve performance on tasks such as entity summarization and question answering or domain-specific tasks such as protein function prediction. However, no attention has been given to the exploration of negative statements by knowledge graph embedding approaches despite the potential of negative statements to produce more accurate representations of entities in a knowledge graph. We propose a novel approach, TrueWalks, to incorporate negative statements into the knowledge graph representation learning process. In particular, we present a novel walk-generation method that is able to not only differentiate between positive and negative statements but also take into account the semantic implications of negation in ontology-rich knowledge graphs. This is of particular importance for applications in the biomedical domain, where the inadequacy of embedding approaches regarding negative statements at the ontology level has been identified as a crucial limitation. We evaluate TrueWalks in ontology-rich biomedical knowledge graphs in two different predictive tasks based on KG embeddings: protein-protein interaction prediction and gene-disease association prediction. We conduct an extensive analysis over established benchmarks and demonstrate that our method is able to improve the performance of knowledge graph embeddings on all tasks.
Recently there has been a series of studies in knowledge graph embedding (KGE), which attempts to learn the embeddings of the entities and relations as numerical vectors and mathematical mappings via machine learning (ML). However, there has been limited research that applies KGE for industrial problems in manufacturing. This paper investigates whether and to what extent KGE can be used for an important problem: quality monitoring for welding in manufacturing industry, which is an impactful process accounting for production of millions of cars annually. The work is in line with Bosch research of data-driven solutions that intends to replace the traditional way of destroying cars, which is extremely costly and produces waste. The paper tackles two very challenging questions simultaneously: how large the welding spot diameter is; and to which car body the welded spot belongs to. The problem setting is difficult for traditional ML because there exist a high number of car bodies that should be assigned as class labels. We formulate the problem as link prediction, and experimented popular KGE methods on real industry data, with consideration of literals. Our results reveal both limitations and promising aspects of adapted KGE methods.
Online reviews play a crucial role in shaping consumer decisions, especially in the context of e-commerce. However, the quality and reliability of these reviews can vary significantly. Some reviews contain misleading or unhelpful information, such as advertisements, fake content, or irrelevant details. These issues pose significant challenges for recommendation systems, which rely on user-generated reviews to provide personalized suggestions. This article introduces a recommendation system based on Passer Learning Optimization-enhanced Bi-LSTM classifier applicable to e-commerce recommendation systems with improved accuracy and efficiency compared to state-of-the-art models. It achieves as low as 1.24% MSE on the baby dataset. This lifts it as high as 88.58%. Besides, there is also robust performance of the system on digital music and patio lawn garden datasets at F1 of 88.46% and 92.51%, correspondingly. These results, made possible by advanced graph embedding for effective knowledge extraction and fine-tuning of classifier parameters, establish the suitability of the proposed model in various e-commerce environments.
Accurate online transient stability prediction is critical for ensuring power system stability when facing disturbances. While traditional transient stablity analysis replies on the time domain simulations can not be quickly adapted to the power grid toplogy change. In order to vectorize high-dimensional power grid topological structure information into low-dimensional node-based graph embedding streaming data, graph embedding dynamic feature (GEDF) has been proposed. The transient stability GEDF-based supervised contrastive learning (GEDF-SCL) model uses supervised contrastive learning to predict transient stability with GEDFs, considering power grid topology information. To evaluate the performance of the proposed GEDF-SCL model, power grids of varying topologies were generated based on the IEEE 39-bus system model. Transient operational data was obtained by simulating N-1 and N-$\bm{m}$-1 contingencies on these generated power system topologies. Test result demonstrated that the GEDF-SCL model can achieve high accuracy in transient stability prediction and adapt well to changing power grid topologies.
Deep learning has achieved remarkable results in fingerprint embedding, which plays a critical role in modern Automated Fingerprint Identification Systems. However, previous works including CNN-based and Transformer-based approaches fail to exploit the nonstructural data, such as topology and correlation in fingerprints, which is essential to facilitate the identifiability and robustness of embedding. To address this challenge, we propose a novel paradigm for fingerprint embedding, called Minutiae Relation-Aware model over Graph Neural Network (MRA-GNN). Our proposed approach incorporates a GNN-based framework in fingerprint embedding to encode the topology and correlation of fingerprints into descriptive features, achieving fingerprint representation in the form of graph embedding. Specifically, we reinterpret fingerprint data and their relative connections as vertices and edges respectively, and introduce a minutia graph and fingerprint graph to represent the topological relations and correlation structures of fingerprints. We equip MRA-GNN with a Topological relation Reasoning Module (TRM) and Correlation-Aware Module (CAM) to learn the fingerprint embedding from these graphs successfully. To tackle the over-smoothing problem in GNN models, we incorporate Feed-Forward Module and graph residual connections into proposed modules. The experimental results demonstrate that our proposed approach outperforms state-of-the-art methods on various fingerprint datasets, indicating the effectiveness of our approach in exploiting nonstructural information of fingerprints.
The paper introduces the application of information geometry to describe the ground states of Ising models by utilizing parity-check matrices of cyclic and quasi-cyclic codes on toric and spherical topologies. The approach establishes a connection between machine learning and error-correcting coding. This proposed approach has implications for the development of new embedding methods based on trapping sets. Statistical physics and number geometry applied for optimize error-correcting codes, leading to these embedding and sparse factorization methods. The paper establishes a direct connection between DNN architecture and error-correcting coding by demonstrating how state-of-the-art architectures (ChordMixer, Mega, Mega-chunk, CDIL, ...) from the long-range arena can be equivalent to of block and convolutional LDPC codes (Cage-graph, Repeat Accumulate). QC codes correspond to certain types of chemical elements, with the carbon element being represented by the mixed automorphism Shu-Lin-Fossorier QC-LDPC code. The connections between Belief Propagation and the Permanent, Bethe-Permanent, Nishimori Temperature, and Bethe-Hessian Matrix are elaborated upon in detail. The Quantum Approximate Optimization Algorithm (QAOA) used in the Sherrington-Kirkpatrick Ising model can be seen as analogous to the back-propagation loss function landscape in training DNNs. This similarity creates a comparable problem with TS pseudo-codeword, resembling the belief propagation method. Additionally, the layer depth in QAOA correlates to the number of decoding belief propagation iterations in the Wiberg decoding tree. Overall, this work has the potential to advance multiple fields, from Information Theory, DNN architecture design (sparse and structured prior graph topology), efficient hardware design for Quantum and Classical DPU/TPU (graph, quantize and shift register architect.) to Materials Science and beyond.
Graphs are a representation of structured data that captures the relationships between sets of objects. With the ubiquity of available network data, there is increasing industrial and academic need to quickly analyze graphs with billions of nodes and trillions of edges. A common first step for network understanding is Graph Embedding, the process of creating a continuous representation of nodes in a graph. A continuous representation is often more amenable, especially at scale, for solving downstream machine learning tasks such as classification, link prediction, and clustering. A high-performance graph embedding architecture leveraging Tensor Processing Units (TPUs) with configurable amounts of high-bandwidth memory is presented that simplifies the graph embedding problem and can scale to graphs with billions of nodes and trillions of edges. We verify the embedding space quality on real and synthetic large-scale datasets.