This paper proposes a knowledge-enhanced disease diagnosis method based on a prompt learning framework. The method retrieves structured knowledge from external knowledge graphs related to clinical cases, encodes it, and injects it into the prompt templates to enhance the language model's understanding and reasoning capabilities for the task.We conducted experiments on three public datasets: CHIP-CTC, IMCS-V2-NER, and KUAKE-QTR. The results show that the proposed method significantly outperforms existing models across multiple evaluation metrics, with an F1 score improvement of 2.4% on the CHIP-CTC dataset, 3.1% on the IMCS-V2-NER dataset,and 4.2% on the KUAKE-QTR dataset. Additionally,ablation studies confirmed the critical role of the knowledge injection module,as the removal of this module resulted in a significant drop in F1 score. The experimental results demonstrate that the proposed method not only effectively improves the accuracy of disease diagnosis but also enhances the interpretability of the predictions, providing more reliable support and evidence for clinical diagnosis.
The Knowledge Graph-to-Text Generation task aims to convert structured knowledge graphs into coherent and human-readable natural language text. Recent efforts in this field have focused on enhancing pre-trained language models (PLMs) by incorporating graph structure information to capture the intricate structure details of knowledge graphs. However, most of these approaches tend to capture only single-granularity structure information, concentrating either on the relationships between entities within the original graph or on the relationships between words within the same entity or across different entities. This narrow focus results in a significant limitation: models that concentrate solely on entity-level structure fail to capture the nuanced semantic relationships between words, while those that focus only on word-level structure overlook the broader relationships between original entire entities. To overcome these limitations, this paper introduces the Multi-granularity Graph Structure Attention (MGSA), which is based on PLMs. The encoder of the model architecture features an entity-level structure encoding module, a word-level structure encoding module, and an aggregation module that synthesizes information from both structure. This multi-granularity structure encoding approach allows the model to simultaneously capture both entity-level and word-level structure information, providing a more comprehensive understanding of the knowledge graph's structure information, thereby significantly improving the quality of the generated text. We conducted extensive evaluations of the MGSA model using two widely recognized KG-to-Text Generation benchmark datasets, WebNLG and EventNarrative, where it consistently outperformed models that rely solely on single-granularity structure information, demonstrating the effectiveness of our approach.
Domain-specific Named Entity Recognition (NER), whose goal is to recognize domain-specific entities and their categories, provides an important support for constructing domain knowledge graphs. Currently, deep learning-based methods are widely used and effective in NER tasks, but due to the reliance on large-scale labeled data. As a result, the scarcity of labeled data in a specific domain will limit its application.Therefore, many researches started to introduce few-shot methods and achieved some results. However, the entity structures in specific domains are often complex, and the current few-shot methods are difficult to adapt to NER tasks with complex features.Taking the Chinese coal chemical industry domain as an example,there exists a complex structure of multiple entities sharing a single entity, as well as multiple relationships for the same pair of entities, which affects the NER task under the sample less condition.In this paper, we propose a Large Language Models (LLMs)-based entity recognition framework LLM-DER for the domain-specific entity recognition problem in Chinese, which enriches the entity information by generating a list of relationships containing entity types through LLMs, and designing a plausibility and consistency evaluation method to remove misrecognized entities, which can effectively solve the complex structural entity recognition problem in a specific domain.The experimental results of this paper on the Resume dataset and the self-constructed coal chemical dataset Coal show that LLM-DER performs outstandingly in domain-specific entity recognition, not only outperforming the existing GPT-3.5-turbo baseline, but also exceeding the fully-supervised baseline, verifying its effectiveness in entity recognition.
Competency question (CQ) formulation is central to several ontology development and evaluation methodologies. Traditionally, the task of crafting these competency questions heavily relies on the effort of domain experts and knowledge engineers which is often time-consuming and labor-intensive. With the emergence of Large Language Models (LLMs), there arises the possibility to automate and enhance this process. Unlike other similar works which use existing ontologies or knowledge graphs as input to LLMs, we present a retrieval-augmented generation (RAG) approach that uses LLMs for the automatic generation of CQs given a set of scientific papers considered to be a domain knowledge base. We investigate its performance and specifically, we study the impact of different number of papers to the RAG and different temperature setting of the LLM. We conduct experiments using GPT-4 on two domain ontology engineering tasks and compare results against ground-truth CQs constructed by domain experts. Empirical assessments on the results, utilizing evaluation metrics (precision and consistency), reveal that compared to zero-shot prompting, adding relevant domain knowledge to the RAG improves the performance of LLMs on generating CQs for concrete ontology engineering tasks.
Scholarly communication is a rapid growing field containing a wealth of knowledge. However, due to its unstructured and document format, it is challenging to extract useful information from them through conventional document retrieval methods. Scholarly knowledge graphs solve this problem, by representing the documents in a semantic network, providing, hidden insights, summaries and ease of accessibility through queries. Naturally, question answering for scholarly graphs expands the accessibility to a wider audience. But some of the knowledge in this domain is still presented as unstructured text, thus requiring a hybrid solution for question answering systems. In this paper, we present a two step solution using open source Large Language Model(LLM): Llama3.1 for Scholarly-QALD dataset. Firstly, we extract the context pertaining to the question from different structured and unstructured data sources: DBLP, SemOpenAlex knowledge graphs and Wikipedia text. Secondly, we implement prompt engineering to improve the information retrieval performance of the LLM. Our approach achieved an F1 score of 40% and also observed some anomalous responses from the LLM, that are discussed in the final part of the paper.
In process mining, a log exploration step allows making sense of the event traces; e.g., identifying event patterns and illogical traces, and gaining insight into their variability. To support expressive log exploration, the event log can be converted into a Knowledge Graph (KG), which can then be queried using general-purpose languages. We explore the creation of semantic KG using the Resource Description Framework (RDF) as a data model, combined with the general-purpose Notation3 (N3) rule language for querying. We show how typical trace querying constraints, inspired by the state of the art, can be implemented in N3. We convert case- and object-centric event logs into a trace-based semantic KG; OCEL2 logs are hereby "flattened" into traces based on object paths through the KG. This solution offers (a) expressivity, as queries can instantiate constraints in multiple ways and arbitrarily constrain attributes and relations (e.g., actors, resources); (b) flexibility, as OCEL2 event logs can be serialized as traces in arbitrary ways based on the KG; and (c) extensibility, as others can extend our library by leveraging the same implementation patterns.
Advances in information extraction have enabled the automatic construction of large knowledge graphs (e.g., Yago, Wikidata or Google KG), which are widely used in many applications like semantic search or data analytics. However, due to their semi-automatic construction, KGs are often incomplete. Rule learning methods, concerned with the extraction of frequent patterns from KGs and casting them into rules, can be applied to predict potentially missing facts. A crucial step in this process is rule ranking. Ranking of rules is especially challenging over highly incomplete or biased KGs (e.g., KGs predominantly storing facts about famous people), as in this case biased rules might fit the data best and be ranked at the top based on standard statistical metrics like rule confidence. To address this issue, prior works proposed to rank rules not only relying on the original KG but also facts predicted by a KG embedding model. At the same time, with the recent rise of Language Models (LMs), several works have claimed that LMs can be used as alternative means for KG completion. In this work, our goal is to verify to which extent the exploitation of LMs is helpful for improving the quality of rule learning systems.
This article presents a method for verifying RDF triples using LLMs, with an emphasis on providing traceable arguments. Because the LLMs cannot currently reliably identify the origin of the information used to construct the response to the user query, our approach is to avoid using internal LLM factual knowledge altogether. Instead, verified RDF statements are compared to chunks of external documents retrieved through a web search or Wikipedia. To assess the possible application of this workflow on biosciences content, we evaluated 1,719 positive statements from the BioRED dataset and the same number of newly generated negative statements. The resulting precision is 88%, and recall is 44%. This indicates that the method requires human oversight. We demonstrate the method on Wikidata, where a SPARQL query is used to automatically retrieve statements needing verification. Overall, the results suggest that LLMs could be used for large-scale verification of statements in KGs, a task previously unfeasible due to human annotation costs.
Knowledge representation has been a central aim of AI since its inception. Symbolic Knowledge Graphs (KGs) and neural Large Language Models (LLMs) can both represent knowledge. KGs provide highly accurate and explicit knowledge representation, but face scalability issue; while LLMs offer expansive coverage of knowledge, but incur significant training costs and struggle with precise and reliable knowledge manipulation. To this end, we introduce OneEdit, a neural-symbolic prototype system for collaborative knowledge editing using natural language, which facilitates easy-to-use knowledge management with KG and LLM. OneEdit consists of three modules: 1) The Interpreter serves for user interaction with natural language; 2) The Controller manages editing requests from various users, leveraging the KG with rollbacks to handle knowledge conflicts and prevent toxic knowledge attacks; 3) The Editor utilizes the knowledge from the Controller to edit KG and LLM. We conduct experiments on two new datasets with KGs which demonstrate that OneEdit can achieve superior performance.
Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.
The increasing amount of published scholarly articles, exceeding 2.5 million yearly, raises the challenge for researchers in following scientific progress. Integrating the contributions from scholarly articles into a novel type of cognitive knowledge graph (CKG) will be a crucial element for accessing and organizing scholarly knowledge, surpassing the insights provided by titles and abstracts. This research focuses on effectively conveying structured scholarly knowledge by utilizing large language models (LLMs) to categorize scholarly articles and describe their contributions in a structured and comparable manner. While previous studies explored language models within specific research domains, the extensive domain-independent knowledge captured by LLMs offers a substantial opportunity for generating structured contribution descriptions as CKGs. Additionally, LLMs offer customizable pathways through prompt engineering or fine-tuning, thus facilitating to leveraging of smaller LLMs known for their efficiency, cost-effectiveness, and environmental considerations. Our methodology involves harnessing LLM knowledge, and complementing it with domain expert-verified scholarly data sourced from a CKG. This strategic fusion significantly enhances LLM performance, especially in tasks like scholarly article categorization and predicate recommendation. Our method involves fine-tuning LLMs with CKG knowledge and additionally injecting knowledge from a CKG with a novel prompting technique significantly increasing the accuracy of scholarly knowledge extraction. We integrated our approach in the Open Research Knowledge Graph (ORKG), thus enabling precise access to organized scholarly knowledge, crucially benefiting domain-independent scholarly knowledge exchange and dissemination among policymakers, industrial practitioners, and the general public.
We consider fact-checking approaches that aim to predict the veracity of assertions in knowledge graphs. Five main categories of fact-checking approaches for knowledge graphs have been proposed in the recent literature, of which each is subject to partially overlapping limitations. In particular, current text-based approaches are limited by manual feature engineering. Path-based and rule-based approaches are limited by their exclusive use of knowledge graphs as background knowledge, and embedding-based approaches suffer from low accuracy scores on current fact-checking tasks. We propose a hybrid approach -- dubbed HybridFC -- that exploits the diversity of existing categories of fact-checking approaches within an ensemble learning setting to achieve a significantly better prediction performance. In particular, our approach outperforms the state of the art by 0.14 to 0.27 in terms of Area Under the Receiver Operating Characteristic curve on the FactBench dataset. Our code is open-source and can be found at https://github.com/dice-group/HybridFC.
The integration of Large Language Models (LLMs) with Knowledge Graphs (KGs) offers significant synergistic potential for knowledge-driven applications. One possible integration is the interpretation and generation of formal languages, such as those used in the Semantic Web, with SPARQL being a core technology for accessing KGs. In this paper, we focus on measuring out-of-the box capabilities of LLMs to work with SPARQL and more specifically with SPARQL SELECT queries applying a quantitative approach. We implemented various benchmarking tasks in the LLM-KG-Bench framework for automated execution and evaluation with several LLMs. The tasks assess capabilities along the dimensions of syntax, semantic read, semantic create, and the role of knowledge graph prompt inclusion. With this new benchmarking tasks, we evaluated a selection of GPT, Gemini, and Claude models. Our findings indicate that working with SPARQL SELECT queries is still challenging for LLMs and heavily depends on the specific LLM as well as the complexity of the task. While fixing basic syntax errors seems to pose no problems for the best of the current LLMs evaluated, creating semantically correct SPARQL SELECT queries is difficult in several cases.
Knowledge graphs (KGs) have recently been used for many tools and applications, making them rich resources in structured format. However, in the real world, KGs grow due to the additions of new knowledge in the form of entities and relations, making these KGs dynamic. This chapter formally defines several types of dynamic KGs and summarizes how these KGs can be represented. Additionally, many neurosymbolic methods have been proposed for learning representations over static KGs for several tasks such as KG completion and entity alignment. This chapter further focuses on neurosymbolic methods for dynamic KGs with or without temporal information. More specifically, it provides an insight into neurosymbolic methods for dynamic (temporal or non-temporal) KG completion and entity alignment tasks. It further discusses the challenges of current approaches and provides some future directions.
A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.
Advancements in natural language processing have revolutionized the way we can interact with digital information systems, such as databases, making them more accessible. However, challenges persist, especially when accuracy is critical, as in the biomedical domain. A key issue is the hallucination problem, where models generate information unsupported by the underlying data, potentially leading to dangerous misinformation. This paper presents a novel approach designed to bridge this gap by combining Large Language Models (LLM) and Knowledge Graphs (KG) to improve the accuracy and reliability of question-answering systems, on the example of a biomedical KG. Built on the LangChain framework, our method incorporates a query checker that ensures the syntactical and semantic validity of LLM-generated queries, which are then used to extract information from a Knowledge Graph, substantially reducing errors like hallucinations. We evaluated the overall performance using a new benchmark dataset of 50 biomedical questions, testing several LLMs, including GPT-4 Turbo and llama3:70b. Our results indicate that while GPT-4 Turbo outperforms other models in generating accurate queries, open-source models like llama3:70b show promise with appropriate prompt engineering. To make this approach accessible, a user-friendly web-based interface has been developed, allowing users to input natural language queries, view generated and corrected Cypher queries, and verify the resulting paths for accuracy. Overall, this hybrid approach effectively addresses common issues such as data gaps and hallucinations, offering a reliable and intuitive solution for question answering systems. The source code for generating the results of this paper and for the user-interface can be found in our Git repository: https://git.zib.de/lpusch/cyphergenkg-gui
While large multimodal models (LMMs) have obtained strong performance on many multimodal tasks, they may still hallucinate while generating text. Their performance on detecting salient features from visual data is also unclear. In this paper, we develop a framework to generate faithful and salient text from mixed-modal data, which includes images and structured data ( represented in knowledge graphs or tables). Specifically, we train a small vision critic model to identify hallucinated and non-salient features from the image modality. The critic model also generates a list of salient image features. This information is used in the post editing step to improve the generation quality. Experiments on two datasets show that our framework improves LMMs' generation quality on both faithfulness and saliency, outperforming recent techniques aimed at reducing hallucination.
Knowledge Graph Completion has been increasingly adopted as a useful method for several tasks in biomedical research, like drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models has been proposed over the years. However, little is known about the properties that render a dataset useful for a given task and, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. We conduct a comprehensive investigation into the topological properties of publicly available biomedical Knowledge Graphs and establish links to the accuracy observed in real-world applications. By releasing all model predictions and a new suite of analysis tools we invite the community to build upon our work and continue improving the understanding of these crucial applications.
To protect patient safety, modern pharmaceutical complexity demands strict prescription verification. We offer a new approach - Rx Strategist - that makes use of knowledge graphs and different search strategies to enhance the power of Large Language Models (LLMs) inside an agentic framework. This multifaceted technique allows for a multi-stage LLM pipeline and reliable information retrieval from a custom-built active ingredient database. Different facets of prescription verification, such as indication, dose, and possible drug interactions, are covered in each stage of the pipeline. We alleviate the drawbacks of monolithic LLM techniques by spreading reasoning over these stages, improving correctness and reliability while reducing memory demands. Our findings demonstrate that Rx Strategist surpasses many current LLMs, achieving performance comparable to that of a highly experienced clinical pharmacist. In the complicated world of modern medications, this combination of LLMs with organized knowledge and sophisticated search methods presents a viable avenue for reducing prescription errors and enhancing patient outcomes.
Large Language Models (LLMs) may suffer from hallucinations in real-world applications due to the lack of relevant knowledge. In contrast, knowledge graphs encompass extensive, multi-relational structures that store a vast array of symbolic facts. Consequently, integrating LLMs with knowledge graphs has been extensively explored, with Knowledge Graph Question Answering (KGQA) serving as a critical touchstone for the integration. This task requires LLMs to answer natural language questions by retrieving relevant triples from knowledge graphs. However, existing methods face two significant challenges: \textit{excessively long reasoning paths distracting from the answer generation}, and \textit{false-positive relations hindering the path refinement}. In this paper, we propose an iterative interactive KGQA framework that leverages the interactive learning capabilities of LLMs to perform reasoning and Debating over Graphs (DoG). Specifically, DoG employs a subgraph-focusing mechanism, allowing LLMs to perform answer trying after each reasoning step, thereby mitigating the impact of lengthy reasoning paths. On the other hand, DoG utilizes a multi-role debate team to gradually simplify complex questions, reducing the influence of false-positive relations. This debate mechanism ensures the reliability of the reasoning process. Experimental results on five public datasets demonstrate the effectiveness and superiority of our architecture. Notably, DoG outperforms the state-of-the-art method ToG by 23.7\% and 9.1\% in accuracy on WebQuestions and GrailQA, respectively. Furthermore, the integration experiments with various LLMs on the mentioned datasets highlight the flexibility of DoG. Code is available at \url{https://github.com/reml-group/DoG}.