Systematic reviews (SRs) - the librarian-assisted literature survey of scholarly articles takes time and requires significant human resources. Given the ever-increasing volume of published studies, applying existing computing and informatics technology can decrease this time and resource burden. Due to the revolutionary advances in (1) Generative AI such as ChatGPT, and (2) External knowledge-augmented information extraction efforts such as Retrieval-Augmented Generation, In this work, we explore the use of techniques from (1) and (2) for SR. We demonstrate a system that takes user queries, performs query expansion to obtain enriched context (includes additional terms and definitions by querying language models and knowledge graphs), and uses this context to search for articles on scholarly databases to retrieve articles. We perform qualitative evaluations of our system through comparison against sentinel (ground truth) articles provided by an in-house librarian. The demo can be found at: https://youtu.be/zMdP56GJ9mU.
Using machine learning (ML) techniques to predict material properties is a crucial research topic. These properties depend on numerical data and semantic factors. Due to the limitations of small-sample datasets, existing methods typically adopt ML algorithms to regress numerical properties or transfer other pre-trained knowledge graphs (KGs) to the material. However, these methods cannot simultaneously handle semantic and numerical information. In this paper, we propose a numerical reasoning method for material KGs (NR-KG), which constructs a cross-modal KG using semantic nodes and numerical proxy nodes. It captures both types of information by projecting KG into a canonical KG and utilizes a graph neural network to predict material properties. In this process, a novel projection prediction loss is proposed to extract semantic features from numerical information. NR-KG facilitates end-to-end processing of cross-modal data, mining relationships and cross-modal information in small-sample datasets, and fully utilizes valuable experimental data to enhance material prediction. We further propose two new High-Entropy Alloys (HEA) property datasets with semantic descriptions. NR-KG outperforms state-of-the-art (SOTA) methods, achieving relative improvements of 25.9% and 16.1% on two material datasets. Besides, NR-KG surpasses SOTA methods on two public physical chemistry molecular datasets, showing improvements of 22.2% and 54.3%, highlighting its potential application and generalizability. We hope the proposed datasets, algorithms, and pre-trained models can facilitate the communities of KG and AI for materials.
Trajectory prediction in traffic scenes involves accurately forecasting the behaviour of surrounding vehicles. To achieve this objective it is crucial to consider contextual information, including the driving path of vehicles, road topology, lane dividers, and traffic rules. Although studies demonstrated the potential of leveraging heterogeneous context for improving trajectory prediction, state-of-the-art deep learning approaches still rely on a limited subset of this information. This is mainly due to the limited availability of comprehensive representations. This paper presents an approach that utilizes knowledge graphs to model the diverse entities and their semantic connections within traffic scenes. Further, we present nuScenes Knowledge Graph (nSKG), a knowledge graph for the nuScenes dataset, that models explicitly all scene participants and road elements, as well as their semantic and spatial relationships. To facilitate the usage of the nSKG via graph neural networks for trajectory prediction, we provide the data in a format, ready-to-use by the PyG library. All artefacts can be found here: https://github.com/boschresearch/nuScenes_Knowledge_Graph
Reasoning with knowledge graphs (KGs) has primarily focused on triple-shaped facts. Recent advancements have been explored to enhance the semantics of these facts by incorporating more potent representations, such as hyper-relational facts. However, these approaches are limited to \emph{atomic facts}, which describe a single piece of information. This paper extends beyond \emph{atomic facts} and delves into \emph{nested facts}, represented by quoted triples where subjects and objects are triples themselves (e.g., ((\emph{BarackObama}, \emph{holds\_position}, \emph{President}), \emph{succeed\_by}, (\emph{DonaldTrump}, \emph{holds\_position}, \emph{President}))). These nested facts enable the expression of complex semantics like \emph{situations} over time and \emph{logical patterns} over entities and relations. In response, we introduce NestE, a novel KG embedding approach that captures the semantics of both atomic and nested factual knowledge. NestE represents each atomic fact as a $1\times3$ matrix, and each nested relation is modeled as a $3\times3$ matrix that rotates the $1\times3$ atomic fact matrix through matrix multiplication. Each element of the matrix is represented as a complex number in the generalized 4D hypercomplex space, including (spherical) quaternions, hyperbolic quaternions, and split-quaternions. Through thorough analysis, we demonstrate the embedding's efficacy in capturing diverse logical patterns over nested facts, surpassing the confines of first-order logic-like expressions. Our experimental results showcase NestE's significant performance gains over current baselines in triple prediction and conditional link prediction. The code and pre-trained models are open available at https://github.com/xiongbo010/NestE.
Objective: Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a lack of knowledge, previous contrastive learning models trained with Unified Medical Language System (UMLS) synonyms struggle at clustering difficult terms and do not generalize well beyond UMLS terms. In this work, we leverage the world knowledge from Large Language Models (LLMs) and propose Contrastive Learning for Representing Terms via Explanations (CoRTEx) to enhance term representation and significantly improves term clustering. Materials and Methods: The model training involves generating explanations for a cleaned subset of UMLS terms using ChatGPT. We employ contrastive learning, considering term and explanation embeddings simultaneously, and progressively introduce hard negative samples. Additionally, a ChatGPT-assisted BIRCH algorithm is designed for efficient clustering of a new ontology. Results: We established a clustering test set and a hard negative test set, where our model consistently achieves the highest F1 score. With CoRTEx embeddings and the modified BIRCH algorithm, we grouped 35,580,932 terms from the Biomedical Informatics Ontology System (BIOS) into 22,104,559 clusters with O(N) queries to ChatGPT. Case studies highlight the model's efficacy in handling challenging samples, aided by information from explanations. Conclusion: By aligning terms to their explanations, CoRTEx demonstrates superior accuracy over benchmark models and robustness beyond its training set, and it is suitable for clustering terms for large-scale biomedical ontologies.
Knowledge-grounded dialogue is a task of generating an informative response based on both the dialogue history and external knowledge source. In general, there are two forms of knowledge: manually annotated knowledge graphs and knowledge text from website. From various evaluation viewpoints, each type of knowledge has advantages and downsides. To further distinguish the principles and determinants from the intricate factors, we conduct a thorough experiment and study on the task to answer three essential questions. The questions involve the choice of appropriate knowledge form, the degree of mutual effects between knowledge and the model selection, and the few-shot performance of knowledge. Supported by statistical shreds of evidence, we offer conclusive solutions and sensible suggestions for directions and standards of future research.
Knowledge graphs generally suffer from incompleteness, which can be alleviated by completing the missing information. Deep knowledge convolutional embedding models based on neural networks are currently popular methods for knowledge graph completion. However, most existing methods use external convolution kernels and traditional plain convolution processes, which limits the feature interaction capability of the model. In this paper, we propose a novel dynamic convolutional embedding model ConvD for knowledge graph completion, which directly reshapes the relation embeddings into multiple internal convolution kernels to improve the external convolution kernels of the traditional convolutional embedding model. The internal convolution kernels can effectively augment the feature interaction between the relation embeddings and entity embeddings, thus enhancing the model embedding performance. Moreover, we design a priori knowledge-optimized attention mechanism, which can assign different contribution weight coefficients to multiple relation convolution kernels for dynamic convolution to improve the expressiveness of the model further. Extensive experiments on various datasets show that our proposed model consistently outperforms the state-of-the-art baseline methods, with average improvements ranging from 11.30\% to 16.92\% across all model evaluation metrics. Ablation experiments verify the effectiveness of each component module of the ConvD model.
Molecular interaction prediction plays a crucial role in forecasting unknown interactions between molecules, such as drug-target interaction (DTI) and drug-drug interaction (DDI), which are essential in the field of drug discovery and therapeutics. Although previous prediction methods have yielded promising results by leveraging the rich semantics and topological structure of biomedical knowledge graphs (KGs), they have primarily focused on enhancing predictive performance without addressing the presence of inevitable noise and inconsistent semantics. This limitation has hindered the advancement of KG-based prediction methods. To address this limitation, we propose BioKDN (Biomedical Knowledge Graph Denoising Network) for robust molecular interaction prediction. BioKDN refines the reliable structure of local subgraphs by denoising noisy links in a learnable manner, providing a general module for extracting task-relevant interactions. To enhance the reliability of the refined structure, BioKDN maintains consistent and robust semantics by smoothing relations around the target interaction. By maximizing the mutual information between reliable structure and smoothed relations, BioKDN emphasizes informative semantics to enable precise predictions. Experimental results on real-world datasets show that BioKDN surpasses state-of-the-art models in DTI and DDI prediction tasks, confirming the effectiveness and robustness of BioKDN in denoising unreliable interactions within contaminated KGs
Natural language artefact descriptions are primary carriers of engineering design knowledge, whose retrieval, representation, and reuse are fundamental to supporting knowledge-intensive tasks in the design process. In this paper, we explicate design knowledge from patented artefact descriptions as knowledge graphs and examine these to understand the linguistic and structural basis. The purpose of our work is to advance the traditional and ontological perspectives of design knowledge and to guide Large-Language Models (LLMs) on how to articulate natural language responses that reflect knowledge that is valuable in a design environment. We populate 33,881 knowledge graphs from a sample of patents stratified according to technology classes. For linguistic basis, we conduct Zipf distribution analyses on the frequencies of unique entities and relationships to identify 64 and 37 generalisable linguistic syntaxes respectively. The relationships largely represent attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'). For structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node subgraph patterns that could be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Based on these results, we suggest concretisation strategies for entities and relationships and explicating hierarchical structures, potentially aiding the construction and modularisation of design knowledge.
Prediction of vehicle lane change maneuvers has gained a lot of momentum in the last few years. Some recent works focus on predicting a vehicle's intention by predicting its trajectory first. This is not enough, as it ignores the context of the scene and the state of the surrounding vehicles (as they might be risky to the target vehicle). Other works assessed the risk made by the surrounding vehicles only by considering their existence around the target vehicle, or by considering the distance and relative velocities between them and the target vehicle as two separate numerical features. In this work, we propose a solution that leverages Knowledge Graphs (KGs) to anticipate lane changes based on linguistic contextual information in a way that goes well beyond the capabilities of current perception systems. Our solution takes the Time To Collision (TTC) with surrounding vehicles as input to assess the risk on the target vehicle. Moreover, our KG is trained on the HighD dataset using the TransE model to obtain the Knowledge Graph Embeddings (KGE). Then, we apply Bayesian inference on top of the KG using the embeddings learned during training. Finally, the model can predict lane changes two seconds ahead with 97.95% f1-score, which surpassed the state of the art, and three seconds before changing lanes with 93.60% f1-score.
Large Language Models (LLMs) have demonstrated remarkable capabilities in many real-world applications. Nonetheless, LLMs are often criticized for their tendency to produce hallucinations, wherein the models fabricate incorrect statements on tasks beyond their knowledge and perception. To alleviate this issue, researchers have explored leveraging the factual knowledge in knowledge graphs (KGs) to ground the LLM's responses in established facts and principles. However, most state-of-the-art LLMs are closed-source, making it challenging to develop a prompting framework that can efficiently and effectively integrate KGs into LLMs with hard prompts only. Generally, existing KG-enhanced LLMs usually suffer from three critical issues, including huge search space, high API costs, and laborious prompt engineering, that impede their widespread application in practice. To this end, we introduce a novel Knowledge Graph based PrompTing framework, namely KnowGPT, to enhance LLMs with domain knowledge. KnowGPT contains a knowledge extraction module to extract the most informative knowledge from KGs, and a context-aware prompt construction module to automatically convert extracted knowledge into effective prompts. Experiments on three benchmarks demonstrate that KnowGPT significantly outperforms all competitors. Notably, KnowGPT achieves a 92.6% accuracy on OpenbookQA leaderboard, comparable to human-level performance.
Entity alignment (EA) seeks identical entities in different knowledge graphs, which is a long-standing task in the database research. Recent work leverages deep learning to embed entities in vector space and align them via nearest neighbor search. Although embedding-based EA has gained marked success in recent years, it lacks explanations for alignment decisions. In this paper, we present the first framework that can generate explanations for understanding and repairing embedding-based EA results. Given an EA pair produced by an embedding model, we first compare its neighbor entities and relations to build a matching subgraph as a local explanation. We then construct an alignment dependency graph to understand the pair from an abstract perspective. Finally, we repair the pair by resolving three types of alignment conflicts based on dependency graphs. Experiments on a variety of EA datasets demonstrate the effectiveness, generalization, and robustness of our framework in explaining and repairing embedding-based EA results.
Knowledge graphs (KGs) comprise entities interconnected by relations of different semantic meanings. KGs are being used in a wide range of applications. However, they inherently suffer from incompleteness, i.e. entities or facts about entities are missing. Consequently, a larger body of works focuses on the completion of missing information in KGs, which is commonly referred to as link prediction (LP). This task has traditionally and extensively been studied in the transductive setting, where all entities and relations in the testing set are observed during training. Recently, several works have tackled the LP task under more challenging settings, where entities and relations in the test set may be unobserved during training, or appear in only a few facts. These works are known as inductive, few-shot, and zero-shot link prediction. In this work, we conduct a systematic review of existing works in this area. A thorough analysis leads us to point out the undesirable existence of diverging terminologies and task definitions for the aforementioned settings, which further limits the possibility of comparison between recent works. We consequently aim at dissecting each setting thoroughly, attempting to reveal its intrinsic characteristics. A unifying nomenclature is ultimately proposed to refer to each of them in a simple and consistent manner.
Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the context of knowledge graphs. Our goal is to provide a systematic understanding of the landscape of graph neural networks for knowledge graphs pertaining to the prominent task of link prediction. Our analysis entails a unifying perspective on seemingly unrelated models and unlocks a series of other models. The expressive power of various models is characterized via a corresponding relational Weisfeiler-Leman algorithm. This analysis is extended to provide a precise logical characterization of the class of functions captured by a class of graph neural networks. The theoretical findings presented in this paper explain the benefits of some widely employed practical design choices, which are validated empirically.
Real-world knowledge can be represented as a graph consisting of entities and relationships between the entities. The need for efficient and scalable solutions arises when dealing with vast genomic data, like RNA-sequencing. Knowledge graphs offer a powerful approach for various tasks in such large-scale genomic data, such as analysis and inference. In this work, variant-level information extracted from the RNA-sequences of vaccine-na\"ive COVID-19 patients have been represented as a unified, large knowledge graph. Variant call format (VCF) files containing the variant-level information were annotated to include further information for each variant. The data records in the annotated files were then converted to Resource Description Framework (RDF) triples. Each VCF file obtained had an associated CADD scores file that contained the raw and Phred-scaled scores for each variant. An ontology was defined for the VCF and CADD scores files. Using this ontology and the extracted information, a large, scalable knowledge graph was created. Available graph storage was then leveraged to query and create datasets for further downstream tasks. We also present a case study using the knowledge graph and perform a classification task using graph machine learning. We also draw comparisons between different Graph Neural Networks (GNNs) for the case study.
The term "Reversal Curse" refers to the scenario where auto-regressive decoder large language models (LLMs), such as ChatGPT, trained on "A is B" fail to learn "B is A," assuming that B and A are distinct and can be uniquely identified from each other, demonstrating a basic failure of logical deduction. This raises a red flag in the use of GPT models for certain general tasks such as constructing knowledge graphs, considering their adherence to this symmetric principle. In our study, we examined a bidirectional LLM, BERT, and found that it is immune to the reversal curse. Driven by ongoing efforts to construct biomedical knowledge graphs with LLMs, we also embarked on evaluating more complex but essential deductive reasoning capabilities. This process included first training encoder and decoder language models to master the intersection and union operations on two sets and then moving on to assess their capability to infer different combinations of union and intersection operations on three newly created sets. The findings showed that while both encoder and decoder language models, trained for tasks involving two sets (union/intersection), were proficient in such scenarios, they encountered difficulties when dealing with operations that included three sets (various combinations of union and intersection). Our research highlights the distinct characteristics of encoder and decoder models in simple and complex logical reasoning. In practice, the choice between BERT and GPT should be guided by the specific requirements and nature of the task at hand, leveraging their respective strengths in bidirectional context comprehension and sequence prediction.
This paper presents a novel benchmarking framework Dyport for evaluating biomedical hypothesis generation systems. Utilizing curated datasets, our approach tests these systems under realistic conditions, enhancing the relevance of our evaluations. We integrate knowledge from the curated databases into a dynamic graph, accompanied by a method to quantify discovery importance. This not only assesses hypothesis accuracy but also their potential impact in biomedical research which significantly extends traditional link prediction benchmarks. Applicability of our benchmarking process is demonstrated on several link prediction systems applied on biomedical semantic knowledge graphs. Being flexible, our benchmarking system is designed for broad application in hypothesis generation quality verification, aiming to expand the scope of scientific discovery within the biomedical research community. Availability and implementation: Dyport framework is fully open-source. All code and datasets are available at: https://github.com/IlyaTyagin/Dyport
Querying knowledge graphs (KGs) using deep learning approaches can naturally leverage the reasoning and generalization ability to learn to infer better answers. Traditional neural complex query answering (CQA) approaches mostly work on entity-centric KGs. However, in the real world, we also need to make logical inferences about events, states, and activities (i.e., eventualities or situations) to push learning systems from System I to System II, as proposed by Yoshua Bengio. Querying logically from an EVentuality-centric KG (EVKG) can naturally provide references to such kind of intuitive and logical inference. Thus, in this paper, we propose a new framework to leverage neural methods to answer complex logical queries based on an EVKG, which can satisfy not only traditional first-order logic constraints but also implicit logical constraints over eventualities concerning their occurrences and orders. For instance, if we know that "Food is bad" happens before "PersonX adds soy sauce", then "PersonX adds soy sauce" is unlikely to be the cause of "Food is bad" due to implicit temporal constraint. To facilitate consistent reasoning on EVKGs, we propose Complex Eventuality Query Answering (CEQA), a more rigorous definition of CQA that considers the implicit logical constraints governing the temporal order and occurrence of eventualities. In this manner, we propose to leverage theorem provers for constructing benchmark datasets to ensure the answers satisfy implicit logical constraints. We also propose a Memory-Enhanced Query Encoding (MEQE) approach to significantly improve the performance of state-of-the-art neural query encoders on the CEQA task.
Most current methods for multi-hop question answering (QA) over knowledge graphs (KGs) only provide final conclusive answers without explanations, such as a set of KG entities that is difficult for normal users to review and comprehend. This issue severely limits the application of KG-based QA in real-world scenarios. However, it is non-trivial to solve due to two challenges: First, annotations of reasoning chains of multi-hop questions, which could serve as supervision for explanation generation, are usually lacking. Second, it is difficult to maintain high efficiency when explicit KG triples need to be retrieved to generate explanations. In this paper, we propose a novel Graph Neural Network-based Two-Step Reasoning model (GNN2R) to solve this issue. GNN2R can provide both final answers and reasoning subgraphs as a rationale behind final answers efficiently with only weak supervision that is available through question-final answer pairs. We extensively evaluated GNN2R with detailed analyses in experiments. The results demonstrate that, in terms of effectiveness, efficiency, and quality of generated explanations, GNN2R outperforms existing state-of-the-art methods that are applicable to this task. Our code and pre-trained models are available at https://github.com/ruijie-wang-uzh/GNN2R.
Humankind's understanding of the world is fundamentally linked to our perception and cognition, with \emph{human languages} serving as one of the major carriers of \emph{world knowledge}. In this vein, \emph{Large Language Models} (LLMs) like ChatGPT epitomize the pre-training of extensive, sequence-based world knowledge into neural networks, facilitating the processing and manipulation of this knowledge in a parametric space. This article explores large models through the lens of "knowledge". We initially investigate the role of symbolic knowledge such as Knowledge Graphs (KGs) in enhancing LLMs, covering aspects like knowledge-augmented language model, structure-inducing pre-training, knowledgeable prompts, structured CoT, knowledge editing, semantic tools for LLM and knowledgeable AI agents. Subsequently, we examine how LLMs can boost traditional symbolic knowledge bases, encompassing aspects like using LLM as KG builder and controller, structured knowledge pretraining, and LLM-enhanced symbolic reasoning. Considering the intricate nature of human knowledge, we advocate for the creation of \emph{Large Knowledge Models} (LKM), specifically engineered to manage diversified spectrum of knowledge structures. This promising undertaking would entail several key challenges, such as disentangling knowledge base from language models, cognitive alignment with human knowledge, integration of perception and cognition, and building large commonsense models for interacting with physical world, among others. We finally propose a five-"A" principle to distinguish the concept of LKM.