Unified Structured Knowledge Reasoning (USKR) aims to answer natural language questions (NLQs) by using structured sources such as tables, databases, and knowledge graphs in a unified way. Existing USKR methods either rely on employing task-specific strategies or custom-defined representations, which struggle to leverage the knowledge transfer between different SKR tasks or align with the prior of LLMs, thereby limiting their performance. This paper proposes a novel USKR framework named \textsc{Pandora}, which takes advantage of \textsc{Python}'s \textsc{Pandas} API to construct a unified knowledge representation for alignment with LLM pre-training. It employs an LLM to generate textual reasoning steps and executable Python code for each question. Demonstrations are drawn from a memory of training examples that cover various SKR tasks, facilitating knowledge transfer. Extensive experiments on four benchmarks involving three SKR tasks demonstrate that \textsc{Pandora} outperforms existing unified frameworks and competes effectively with task-specific methods.
High-stakes domains like cyber operations need responsible and trustworthy AI methods. While large language models (LLMs) are becoming increasingly popular in these domains, they still suffer from hallucinations. This research paper provides learning outcomes from a case study with LinkQ, an open-source natural language interface that was developed to combat hallucinations by forcing an LLM to query a knowledge graph (KG) for ground-truth data during question-answering (QA). We conduct a quantitative evaluation of LinkQ using a well-known KGQA dataset, showing that the system outperforms GPT-4 but still struggles with certain question categories - suggesting that alternative query construction strategies will need to be investigated in future LLM querying systems. We discuss a qualitative study of LinkQ with two domain experts using a real-world cybersecurity KG, outlining these experts' feedback, suggestions, perceived limitations, and future opportunities for systems like LinkQ.
This chapter investigates the concept of mutual understanding between humans and systems, positing that Neuro-symbolic Artificial Intelligence (NeSy AI) methods can significantly enhance this mutual understanding by leveraging explicit symbolic knowledge representations with data-driven learning models. We start by introducing three critical dimensions to characterize mutual understanding: sharing knowledge, exchanging knowledge, and governing knowledge. Sharing knowledge involves aligning the conceptual models of different agents to enable a shared understanding of the domain of interest. Exchanging knowledge relates to ensuring the effective and accurate communication between agents. Governing knowledge concerns establishing rules and processes to regulate the interaction between agents. Then, we present several different use case scenarios that demonstrate the application of NeSy AI and Knowledge Graphs to aid meaningful exchanges between human, artificial, and robotic agents. These scenarios highlight both the potential and the challenges of combining top-down symbolic reasoning with bottom-up neural learning, guiding the discussion of the coverage provided by current solutions along the dimensions of sharing, exchanging, and governing knowledge. Concurrently, this analysis facilitates the identification of gaps and less developed aspects in mutual understanding to address in future research.
Recent advances in Large Language Models have demonstrated their capabilities across a variety of tasks. However, automatically extracting implicit knowledge from natural language remains a significant challenge, as machines lack active experience with the physical world. Given this scenario, semantic knowledge graphs can serve as conceptual spaces that guide the automated text generation reasoning process to achieve more efficient and explainable results. In this paper, we apply a logic-augmented generation (LAG) framework that leverages the explicit representation of a text through a semantic knowledge graph and applies it in combination with prompt heuristics to elicit implicit analogical connections. This method generates extended knowledge graph triples representing implicit meaning, enabling systems to reason on unlabeled multimodal data regardless of the domain. We validate our work through three metaphor detection and understanding tasks across four datasets, as they require deep analogical reasoning capabilities. The results show that this integrated approach surpasses current baselines, performs better than humans in understanding visual metaphors, and enables more explainable reasoning processes, though still has inherent limitations in metaphor understanding, especially for domain-specific metaphors. Furthermore, we propose a thorough error analysis, discussing issues with metaphorical annotations and current evaluation methods.
Time series analysis is crucial in fields like finance, transportation, and industry. However, traditional models often focus solely on temporal features, limiting their ability to capture underlying information. This paper proposes a novel time series multitask framework, called LTM, which integrates temporal features with textual descriptions to enhance analytical and predictive capabilities. LTM combines pre-trained time series model, large language model (LLM), and knowledge graph to tackle time series tasks, including forecasting, imputation, and anomaly detection. LTM achieves improved performance with a few trainable parameters. It is very efficient and practical. LTM encodes time series data into patches and enriches user-provided prompts using knowledge graphs to generate enhanced prompts. A novel feature fusion method embeds prompts into each patch encoding, which is processed by a frozen LLM, followed by a feature enhancement module and a time decoder module. During fine-tuning stage, cosine similarity between prompts and temporal patches is integrated into the loss function to boost performance. Experiments on benchmark datasets show that LTM significantly outperforms existing methods. It provides a robust and versatile solution for time series tasks.
Discovery gene-disease links is important in biology and medicine areas, enabling disease identification and drug repurposing. Machine learning approaches accelerate this process by leveraging biological knowledge represented in ontologies and the structure of knowledge graphs. Still, many existing works overlook ontologies explicitly representing diseases, missing causal and semantic relationships between them. The gene-disease association problem naturally frames itself as a link prediction task, where embedding algorithms directly predict associations by exploring the structure and properties of the knowledge graph. Some works frame it as a node-pair classification task, combining embedding algorithms with traditional machine learning algorithms. This strategy aligns with the logic of a machine learning pipeline. However, the use of negative examples and the lack of validated gene-disease associations to train embedding models may constrain its effectiveness. This work introduces a novel framework for comparing the performance of link prediction versus node-pair classification tasks, analyses the performance of state of the art gene-disease association approaches, and compares the different order-based formalizations of gene-disease association prediction. It also evaluates the impact of the semantic richness through a disease-specific ontology and additional links between ontologies. The framework involves five steps: data splitting, knowledge graph integration, embedding, modeling and prediction, and method evaluation. Results show that enriching the semantic representation of diseases slightly improves performance, while additional links generate a greater impact. Link prediction methods better explore the semantic richness encoded in knowledge graphs. Although node-pair classification methods identify all true positives, link prediction methods outperform overall.
Retrieval over knowledge graphs is usually performed using dedicated, complex query languages like SPARQL. We propose a novel system, Ontology and Semantic Exploration Toolkit (OnSET) that allows non-expert users to easily build queries with visual user guidance provided by topic modelling and semantic search throughout the application. OnSET allows users without any prior information about the ontology or networked knowledge to start exploring topics of interest over knowledge graphs, including the retrieval and detailed exploration of prototypical sub-graphs and their instances. Existing systems either focus on direct graph explorations or do not foster further exploration of the result set. We, however, provide a node-based editor that can extend on these missing properties of existing systems to support the search over big ontologies with sub-graph instances. Furthermore, OnSET combines efficient and open platforms to deploy the system on commodity hardware.
Investigative workflows require interactive exploratory analysis on large heterogeneous knowledge graphs. Current databases show limitations in enabling such task. This paper discusses the architecture of Siren Federate, a system that efficiently supports exploratory graph analysis by bridging document-oriented, relational and graph models. Technical contributions include distributed join algorithms, adaptive query planning, query plan folding, semantic caching, and semi-join decomposition for path query. Semi-join decomposition addresses the exponential growth of intermediate results in path-based queries. Experiments show that Siren Federate exhibits low latency and scales well with the amount of data, the number of users, and the number of computing nodes.
Retrieval Augmented Generation (RAG) has enjoyed increased attention in the recent past and recent advancements in Large Language Models (LLMs) have highlighted the importance of integrating world knowledge into these systems. Current RAG methodologies often modify the internal architecture of pre-trained language models (PLMs) or rely on textifying knowledge graphs (KGs), which is inefficient in terms of token usage. This paper introduces ConceptFormer, a new approach to augment LLMs with structured knowledge from KGs, such as Wikidata, without altering their internal structure or relying on textual input of KGs. ConceptFormer operates in the LLM embedding vector space, creating and injecting \emph{concept vectors} that encapsulate the information of the KG nodes directly. Trained in conjunction with a frozen LLM, ConceptFormer generates a comprehensive lookup table that maps KG nodes to their respective concept vectors. The approach aims to enhance the factual recall capabilities of LLMs by enabling them to process these concept vectors natively, thus enriching them with structured world knowledge in an efficient and scalable manner. Our experiments demonstrate that the addition of concept vectors to GPT-2 0.1B substantially increases its factual recall ability (Hit@10) by up to 272\% when tested on sentences from Wikipedia and up to 348\% on synthetically generated sentences. Even injecting only a single concept vector into the prompt increases factual recall ability (Hit@10) by up to 213\% on Wikipedia sentences, significantly outperforming RAG with graph textification while consuming 130x fewer input tokens.
Coreference resolution across multiple documents poses a significant challenge in natural language processing, particularly within the domain of knowledge graphs. This study introduces an innovative method aimed at identifying and resolving references to the same entities that appear across differing texts, thus enhancing the coherence and collaboration of information. Our method employs a dynamic linking mechanism that associates entities in the knowledge graph with their corresponding textual mentions. By utilizing contextual embeddings along with graph-based inference strategies, we effectively capture the relationships and interactions among entities, thereby improving the accuracy of coreference resolution. Rigorous evaluations on various benchmark datasets highlight notable advancements in our approach over traditional methodologies. The results showcase how the contextual information derived from knowledge graphs enhances the understanding of complex relationships across documents, leading to better entity linking and information extraction capabilities in applications driven by knowledge. Our technique demonstrates substantial improvements in both precision and recall, underscoring its effectiveness in the area of cross-document coreference resolution.
Large Language Models (LLMs) have demonstrated remarkable capabilities across a wide range of tasks requiring complex reasoning. However, the effects of scaling on their reasoning abilities remain insufficiently understood. In this paper, we introduce a synthetic multihop reasoning environment designed to closely replicate the structure and distribution of real-world large-scale knowledge graphs. Our reasoning task involves completing missing edges in the graph, which requires advanced multi-hop reasoning and mimics real-world reasoning scenarios. To evaluate this, we pretrain language models (LMs) from scratch solely on triples from the incomplete graph and assess their ability to infer the missing edges. Interestingly, we observe that overparameterization can impair reasoning performance due to excessive memorization. We investigate different factors that affect this U-shaped loss curve, including graph structure, model size, and training steps. To predict the optimal model size for a specific knowledge graph, we find an empirical scaling that linearly maps the knowledge graph search entropy to the optimal model size. This work provides new insights into the relationship between scaling and reasoning in LLMs, shedding light on possible ways to optimize their performance for reasoning tasks.
Large Language Models (LLMs) have impressive capabilities in text understanding and zero-shot reasoning. However, delays in knowledge updates may cause them to reason incorrectly or produce harmful results. Knowledge Graphs (KGs) provide rich and reliable contextual information for the reasoning process of LLMs by structurally organizing and connecting a wide range of entities and relations. Existing KG-based LLM reasoning methods only inject KGs' knowledge into prompts in a textual form, ignoring its structural information. Moreover, they mostly rely on close-source models or open-source models with large parameters, which poses challenges to high resource consumption. To address this, we propose a novel Lightweight and efficient Prompt learning-ReasOning Framework for KGQA (LightPROF), which leverages the full potential of LLMs to tackle complex reasoning tasks in a parameter-efficient manner. Specifically, LightPROF follows a "Retrieve-Embed-Reason process", first accurately, and stably retrieving the corresponding reasoning graph from the KG through retrieval module. Next, through a Transformer-based Knowledge Adapter, it finely extracts and integrates factual and structural information from the KG, then maps this information to the LLM's token embedding space, creating an LLM-friendly prompt to be used by the LLM for the final reasoning. Additionally, LightPROF only requires training Knowledge Adapter and can be compatible with any open-source LLM. Extensive experiments on two public KGQA benchmarks demonstrate that LightPROF achieves superior performance with small-scale LLMs. Furthermore, LightPROF shows significant advantages in terms of input token count and reasoning time.
Knowledge graph embedding (KGE) models encode the structural information of knowledge graphs to predicting new links. Effective training of these models requires distinguishing between positive and negative samples with high precision. Although prior research has shown that improving the quality of negative samples can significantly enhance model accuracy, identifying high-quality negative samples remains a challenging problem. This paper theoretically investigates the condition under which negative samples lead to optimal KG embedding and identifies a sufficient condition for an effective negative sample distribution. Based on this theoretical foundation, we propose \textbf{E}mbedding \textbf{MU}tation (\textsc{EMU}), a novel framework that \emph{generates} negative samples satisfying this condition, in contrast to conventional methods that focus on \emph{identifying} challenging negative samples within the training data. Importantly, the simplicity of \textsc{EMU} ensures seamless integration with existing KGE models and negative sampling methods. To evaluate its efficacy, we conducted comprehensive experiments across multiple datasets. The results consistently demonstrate significant improvements in link prediction performance across various KGE models and negative sampling methods. Notably, \textsc{EMU} enables performance improvements comparable to those achieved by models with embedding dimension five times larger. An implementation of the method and experiments are available at https://github.com/nec-research/EMU-KG.
Knowledge graph embedding (KGE) is a technique that enhances knowledge graphs by addressing incompleteness and improving knowledge retrieval. A limitation of the existing KGE models is their underutilization of ontologies, specifically the relationships between properties. This study proposes a KGE model, TransU, designed for knowledge graphs with well-defined ontologies that incorporate relationships between properties. The model treats properties as a subset of entities, enabling a unified representation. We present experimental results using a standard dataset and a practical dataset.
Large Language Models (LLMs) are revolutionizing the development of AI assistants capable of performing diverse tasks across domains. However, current state-of-the-art LLM-driven agents face significant challenges, including high operational costs and limited success rates on complex benchmarks like GAIA. To address these issues, we propose the Knowledge Graph of Thoughts (KGoT), an innovative AI assistant architecture that integrates LLM reasoning with dynamically constructed knowledge graphs (KGs). KGoT extracts and structures task-relevant knowledge into a dynamic KG representation, iteratively enhanced through external tools such as math solvers, web crawlers, and Python scripts. Such structured representation of task-relevant knowledge enables low-cost models to solve complex tasks effectively. For example, KGoT achieves a 29% improvement in task success rates on the GAIA benchmark compared to Hugging Face Agents with GPT-4o mini, while reducing costs by over 36x compared to GPT-4o. Improvements for recent reasoning models are similar, e.g., 36% and 37.5% for Qwen2.5-32B and Deepseek-R1-70B, respectively. KGoT offers a scalable, affordable, and high-performing solution for AI assistants.
Harmful text detection has become a crucial task in the development and deployment of large language models, especially as AI-generated content continues to expand across digital platforms. This study proposes a joint retrieval framework that integrates pre-trained language models with knowledge graphs to improve the accuracy and robustness of harmful text detection. Experimental results demonstrate that the joint retrieval approach significantly outperforms single-model baselines, particularly in low-resource training scenarios and multilingual environments. The proposed method effectively captures nuanced harmful content by leveraging external contextual information, addressing the limitations of traditional detection models. Future research should focus on optimizing computational efficiency, enhancing model interpretability, and expanding multimodal detection capabilities to better tackle evolving harmful content patterns. This work contributes to the advancement of AI safety, ensuring more trustworthy and reliable content moderation systems.
In this paper, we propose a new geometric approach for knowledge graph completion via low rank tensor approximation. We augment a pretrained and well-established Euclidean model based on a Tucker tensor decomposition with a novel hyperbolic interaction term. This correction enables more nuanced capturing of distributional properties in data better aligned with real-world knowledge graphs. By combining two geometries together, our approach improves expressivity of the resulting model achieving new state-of-the-art link prediction accuracy with a significantly lower number of parameters compared to the previous Euclidean and hyperbolic models.
GraphRAG enhances large language models (LLMs) to generate quality answers for user questions by retrieving related facts from external knowledge graphs. Existing GraphRAG methods adopt a fixed graph traversal strategy for fact retrieval but we observe that user questions come in different types and require different graph traversal strategies. As such, existing GraphRAG methods are limited in effectiveness (i.e., quality of the generated answers) and/or efficiency (i.e., response time or the number of used tokens). In this paper, we propose to classify the questions according to a complete four-class taxonomy and adaptively select the appropriate graph traversal strategy for each type of questions. Our system PolyG is essentially a query planner for GraphRAG and can handle diverse questions with an unified interface and execution engine. Compared with SOTA GraphRAG methods, PolyG achieves an overall win rate of 75% on generation quality and a speedup up to 4x on response time.
The recent advancements in Deep Learning models and techniques have led to significant strides in performance across diverse tasks and modalities. However, while the overall capabilities of models show promising growth, our understanding of their internal reasoning processes remains limited, particularly concerning systematic inconsistencies or errors patterns of logical or inferential flaws. These inconsistencies may manifest as contradictory outputs, failure to generalize across similar tasks, or erroneous conclusions in specific contexts. Even detecting and measuring such reasoning discrepancies is challenging, as they may arise from opaque internal procedures, biases and imbalances in training data, or the inherent complexity of the task. Without effective methods to detect, measure, and mitigate these errors, there is a risk of deploying models that are biased, exploitable, or logically unreliable. This thesis aims to address these issues by producing novel methods for deep learning models that reason over knowledge graphs, natural language, and images. The thesis contributes two techniques for detecting and quantifying predictive inconsistencies originating from opaque internal procedures in natural language and image processing models. To mitigate inconsistencies from biases in training data, this thesis presents a data efficient sampling method to improve fairness and performance and a synthetic dataset generation approach in low resource scenarios. Finally, the thesis offers two techniques to optimize the models for complex reasoning tasks. These methods enhance model performance while allowing for more faithful and interpretable exploration and exploitation during inference. Critically, this thesis provides a comprehensive framework to improve the robustness, fairness, and interpretability of deep learning models across diverse tasks and modalities.
Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code will be publicly available.