Knowledge graphs (KGs) have become the standard technology for the representation of factual information in applications such as recommendation engines, search, and question-answering systems. However, the continual updating of KGs, as well as the integration of KGs from different domains and KGs in different languages, remains to be a major challenge. What we suggest here is that by a reification of abstract objects and by acknowledging the ontological distinction between concepts and types, we arrive at an ontologically grounded and language-agnostic representation that can alleviate the difficulties in KG integration.
Knowledge graphs, represented in RDF, are able to model entities and their relations by means of ontologies. The use of knowledge graphs for information modeling has attracted interest in recent years. In recommender systems, items and users can be mapped and integrated into the knowledge graph, which can represent more links and relationships between users and items. Constraint-based recommender systems are based on the idea of explicitly exploiting deep recommendation knowledge through constraints to identify relevant recommendations. When combined with knowledge graphs, a constraint-based recommender system gains several benefits in terms of constraint sets. In this paper, we investigate and propose the construction of a constraint-based recommender system via RDF knowledge graphs applied to the vehicle purchase/sale domain. The results of our experiments show that the proposed approach is able to efficiently identify recommendations in accordance with user preferences.
Knowledge graphs have proven to be effective for modeling entities and their relationships through the use of ontologies. The recent emergence in interest for using knowledge graphs as a form of information modeling has led to their increased adoption in recommender systems. By incorporating users and items into the knowledge graph, these systems can better capture the implicit connections between them and provide more accurate recommendations. In this paper, we investigate and propose the construction of a personalized recommender system via knowledge graphs embedding applied to the vehicle purchase/sale domain. The results of our experimentation demonstrate the efficacy of the proposed method in providing relevant recommendations that are consistent with individual users.
Conversational recommender systems (CRS) aim to timely trace the dynamic interests of users through dialogues and generate relevant responses for item recommendations. Recently, various external knowledge bases (especially knowledge graphs) are incorporated into CRS to enhance the understanding of conversation contexts. However, recent reasoning-based models heavily rely on simplified structures such as linear structures or fixed-hierarchical structures for causality reasoning, hence they cannot fully figure out sophisticated relationships among utterances with external knowledge. To address this, we propose a novel Tree structure Reasoning schEmA named TREA. TREA constructs a multi-hierarchical scalable tree as the reasoning structure to clarify the causal relationships between mentioned entities, and fully utilizes historical conversations to generate more reasonable and suitable responses for recommended results. Extensive experiments on two public CRS datasets have demonstrated the effectiveness of our approach.
Stemming from traditional knowledge graphs (KGs), hyper-relational KGs (HKGs) provide additional key-value pairs (i.e., qualifiers) for each KG fact that help to better restrict the fact validity. In recent years, there has been an increasing interest in studying graph reasoning over HKGs. Meanwhile, as discussed in recent works that focus on temporal KGs (TKGs), world knowledge is ever-evolving, making it important to reason over temporal facts in KGs. Previous mainstream benchmark HKGs do not explicitly specify temporal information for each HKG fact. Therefore, almost all existing HKG reasoning approaches do not devise any module specifically for temporal reasoning. To better study temporal fact reasoning over HKGs, we propose a new type of data structure named hyper-relational TKG (HTKG). Every fact in an HTKG is coupled with a timestamp explicitly indicating its time validity. We develop two new benchmark HTKG datasets, i.e., Wiki-hy and YAGO-hy, and propose an HTKG reasoning model that efficiently models hyper-relational temporal facts. To support future research on this topic, we open-source our datasets and model.
Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.
Although large language models (LLMs) have achieved significant success in various tasks, they often struggle with hallucination problems, especially in scenarios requiring deep and responsible reasoning. These issues could be partially addressed by introducing external knowledge graphs (KG) in LLM reasoning. In this paper, we propose a new LLM-KG integrating paradigm ``$\hbox{LLM}\otimes\hbox{KG}$'' which treats the LLM as an agent to interactively explore related entities and relations on KGs and perform reasoning based on the retrieved knowledge. We further implement this paradigm by introducing a new approach called Think-on-Graph (ToG), in which the LLM agent iteratively executes beam search on KG, discovers the most promising reasoning paths, and returns the most likely reasoning results. We use a number of well-designed experiments to examine and illustrate the following advantages of ToG: 1) compared with LLMs, ToG has better deep reasoning power; 2) ToG has the ability of knowledge traceability and knowledge correctability by leveraging LLMs reasoning and expert feedback; 3) ToG provides a flexible plug-and-play framework for different LLMs, KGs and prompting strategies without any additional training cost; 4) the performance of ToG with small LLM models could exceed large LLM such as GPT-4 in certain scenarios and this reduces the cost of LLM deployment and application. As a training-free method with lower computational cost and better generality, ToG achieves overall SOTA in 6 out of 9 datasets where most previous SOTAs rely on additional training.
Biomedical datasets are often modeled as knowledge graphs (KGs) because they capture the multi-relational, heterogeneous, and dynamic natures of biomedical systems. KG completion (KGC), can, therefore, help researchers make predictions to inform tasks like drug repositioning. While previous approaches for KGC were either rule-based or embedding-based, hybrid approaches based on neurosymbolic artificial intelligence are becoming more popular. Many of these methods possess unique characteristics which make them even better suited toward biomedical challenges. Here, we survey such approaches with an emphasis on their utilities and prospective benefits for biomedicine.
Bayesian inference has many advantages in robotic motion planning over four perspectives: The uncertainty quantification of the policy, safety (risk-aware) and optimum guarantees of robot motions, data-efficiency in training of reinforcement learning, and reducing the sim2real gap when the robot is applied to real-world tasks. However, the application of Bayesian inference in robotic motion planning is lagging behind the comprehensive theory of Bayesian inference. Further, there are no comprehensive reviews to summarize the progress of Bayesian inference to give researchers a systematic understanding in robotic motion planning. This paper first provides the probabilistic theories of Bayesian inference which are the preliminary of Bayesian inference for complex cases. Second, the Bayesian estimation is given to estimate the posterior of policies or unknown functions which are used to compute the policy. Third, the classical model-based Bayesian RL and model-free Bayesian RL algorithms for robotic motion planning are summarized, while these algorithms in complex cases are also analyzed. Fourth, the analysis of Bayesian inference in inverse RL is given to infer the reward functions in a data-efficient manner. Fifth, we systematically present the hybridization of Bayesian inference and RL which is a promising direction to improve the convergence of RL for better motion planning. Sixth, given the Bayesian inference, we present the interpretable and safe robotic motion plannings which are the hot research topic recently. Finally, all algorithms reviewed in this paper are summarized analytically as the knowledge graphs, and the future of Bayesian inference for robotic motion planning is also discussed, to pave the way for data-efficient, explainable, and safe robotic motion planning strategies for practical applications.
Explainable AI (XAI) is an increasingly important area of machine learning research, which aims to make black-box models transparent and interpretable. In this paper, we propose a novel approach to XAI that uses the so-called counterfactual paths generated by conditional permutations of features. The algorithm measures feature importance by identifying sequential permutations of features that most influence changes in model predictions. It is particularly suitable for generating explanations based on counterfactual paths in knowledge graphs incorporating domain knowledge. Counterfactual paths introduce an additional graph dimension to current XAI methods in both explaining and visualizing black-box models. Experiments with synthetic and medical data demonstrate the practical applicability of our approach.
In any system that uses structured knowledge graph (KG) data as its underlying knowledge representation, KG-to-text generation is a useful tool for turning parts of the graph data into text that can be understood by humans. Recent work has shown that models that make use of pretraining on large amounts of text data can perform well on the KG-to-text task even with relatively small sets of training data on the specific graph-to-text task. In this paper, we build on this concept by using large language models to perform zero-shot generation based on nothing but the model's understanding of the triple structure from what it can read. We show that ChatGPT achieves near state-of-the-art performance on some measures of the WebNLG 2020 challenge, but falls behind on others. Additionally, we compare factual, counter-factual and fictional statements, and show that there is a significant connection between what the LLM already knows about the data it is parsing and the quality of the output text.
Aiming to support Retrieval Augmented Generation (RAG) in the design process, we present a method to identify explicit, engineering design facts - {head entity :: relationship :: tail entity} from patented artefact descriptions. Given a sentence with a pair of entities (based on noun phrases) marked in a unique manner, our method extracts the relationship that is explicitly communicated in the sentence. For this task, we create a dataset of 375,084 examples and fine-tune language models for relation identification (token classification) and elicitation (sequence-to-sequence). The token classification approach achieves up to 99.7% accuracy. Upon applying the method to a domain of 4,870 fan system patents, we populate a knowledge base of over 2.93 million facts. Using this knowledge base, we demonstrate how Large Language Models (LLMs) are guided by explicit facts to synthesise knowledge and generate technical and cohesive responses when sought out for knowledge retrieval tasks in the design process.
Knowledge Graphs (KG) provide us with a structured, flexible, transparent, cross-system, and collaborative way of organizing our knowledge and data across various domains in society and industrial as well as scientific disciplines. KGs surpass any other form of representation in terms of effectiveness. However, Knowledge Graph Engineering (KGE) requires in-depth experiences of graph structures, web technologies, existing models and vocabularies, rule sets, logic, as well as best practices. It also demands a significant amount of work. Considering the advancements in large language models (LLMs) and their interfaces and applications in recent years, we have conducted comprehensive experiments with ChatGPT to explore its potential in supporting KGE. In this paper, we present a selection of these experiments and their results to demonstrate how ChatGPT can assist us in the development and management of KGs.
Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.
Knowledge graph completion (KGC) is the task of inferencing missing facts from any given knowledge graphs (KG). Previous KGC methods typically represent knowledge graph entities and relations as trainable continuous embeddings and fuse the embeddings of the entity $h$ (or $t$) and relation $r$ into hidden representations of query $(h, r, ?)$ (or $(?, r, t$)) to approximate the missing entities. To achieve this, they either use shallow linear transformations or deep convolutional modules. However, the linear transformations suffer from the expressiveness issue while the deep convolutional modules introduce unnecessary inductive bias, which could potentially degrade the model performance. Thus, we propose a novel Transformer-based Patch Refinement Model (PatReFormer) for KGC. PatReFormer first segments the embedding into a sequence of patches and then employs cross-attention modules to allow bi-directional embedding feature interaction between the entities and relations, leading to a better understanding of the underlying KG. We conduct experiments on four popular KGC benchmarks, WN18RR, FB15k-237, YAGO37 and DB100K. The experimental results show significant performance improvement from existing KGC methods on standard KGC evaluation metrics, e.g., MRR and H@n. Our analysis first verifies the effectiveness of our model design choices in PatReFormer. We then find that PatReFormer can better capture KG information from a large relation embedding dimension. Finally, we demonstrate that the strength of PatReFormer is at complex relation types, compared to other KGC models
Entity alignment (EA) aims to find the equivalent entity pairs between different knowledge graphs (KGs), which is crucial to promote knowledge fusion. With the wide use of temporal knowledge graphs (TKGs), time-aware EA (TEA) methods appear to enhance EA. Existing TEA models are based on Graph Neural Networks (GNN) and achieve state-of-the-art (SOTA) performance, but it is difficult to transfer them to large-scale TKGs due to the scalability issue of GNN. In this paper, we propose an effective and efficient non-neural EA framework between TKGs, namely LightTEA, which consists of four essential components: (1) Two-aspect Three-view Label Propagation, (2) Sparse Similarity with Temporal Constraints, (3) Sinkhorn Operator, and (4) Temporal Iterative Learning. All of these modules work together to improve the performance of EA while reducing the time consumption of the model. Extensive experiments on public datasets indicate that our proposed model significantly outperforms the SOTA methods for EA between TKGs, and the time consumed by LightTEA is only dozens of seconds at most, no more than 10% of the most efficient TEA method.
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.
Digital twin technology has is anticipated to transform healthcare, enabling personalized medicines and support, earlier diagnoses, simulated treatment outcomes, and optimized surgical plans. Digital twins are readily gaining traction in industries like manufacturing, supply chain logistics, and civil infrastructure. Not in patient care, however. The challenge of modeling complex diseases with multimodal patient data and the computational complexities of analyzing it have stifled digital twin adoption in the biomedical vertical. Yet, these major obstacles can potentially be handled by approaching these models in a different way. This paper proposes a novel framework for addressing the barriers to clinical twin modeling created by computational costs and modeling complexities. We propose structuring patient health data as a knowledge graph and using closed-form continuous-time liquid neural networks, for real-time analytics. By synthesizing multimodal patient data and leveraging the flexibility and efficiency of closed form continuous time networks and knowledge graph ontologies, our approach enables real time insights, personalized medicine, early diagnosis and intervention, and optimal surgical planning. This novel approach provides a comprehensive and adaptable view of patient health along with real-time analytics, paving the way for digital twin simulations and other anticipated benefits in healthcare.
Personalized recommender systems play a crucial role in direct marketing, particularly in financial services, where delivering relevant content can enhance customer engagement and promote informed decision-making. This study explores interpretable knowledge graph (KG)-based recommender systems by proposing two distinct approaches for personalized article recommendations within a multinational financial services firm. The first approach leverages Reinforcement Learning (RL) to traverse a KG constructed from both structured (tabular) and unstructured (textual) data, enabling interpretability through Path Directed Reasoning (PDR). The second approach employs the XGBoost algorithm, with post-hoc explainability techniques such as SHAP and ELI5 to enhance transparency. By integrating machine learning with automatically generated KGs, our methods not only improve recommendation accuracy but also provide interpretable insights, facilitating more informed decision-making in customer relationship management.
Clinicians are increasingly looking towards machine learning to gain insights about patient evolutions. We propose a novel approach named Multi-Modal UMLS Graph Learning (MMUGL) for learning meaningful representations of medical concepts using graph neural networks over knowledge graphs based on the unified medical language system. These representations are aggregated to represent entire patient visits and then fed into a sequence model to perform predictions at the granularity of multiple hospital visits of a patient. We improve performance by incorporating prior medical knowledge and considering multiple modalities. We compare our method to existing architectures proposed to learn representations at different granularities on the MIMIC-III dataset and show that our approach outperforms these methods. The results demonstrate the significance of multi-modal medical concept representations based on prior medical knowledge.