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Causal knowledge graph analysis identifies adverse drug effects

Toonsi, Sumyyah, Schofield, Paul, Hoehndorf, Robert

arXiv.org Artificial Intelligence

Knowledge graphs and structural causal models have each proven valuable for organizing biomedical knowledge and estimating causal effects, but remain largely disconnected: knowledge graphs encode qualitative relationships focusing on facts and deductive reasoning without formal probabilistic semantics, while causal models lack integration with background knowledge in knowledge graphs and have no access to the deductive reasoning capabilities that knowledge graphs provide. To bridge this gap, we introduce a novel formulation of Causal Knowledge Graphs (CKGs) which extend knowledge graphs with formal causal semantics, preserving their deductive capabilities while enabling principled causal inference. CKGs support deconfounding via explicitly marked causal edges and facilitate hypothesis formulation aligned with both encoded and entailed background knowledge. We constructed a Drug-Disease CKG (DD-CKG) integrating disease progression pathways, drug indications, side-effects, and hierarchical disease classification to enable automated large-scale mediation analysis. Applied to UK Biobank and MIMIC-IV cohorts, we tested whether drugs mediate effects between indications and downstream disease progression, adjusting for confounders inferred from the DD-CKG. Our approach successfully reproduced known adverse drug reactions with high precision while identifying previously undocumented significant candidate adverse effects. Further validation through side effect similarity analysis demonstrated that combining our predicted drug effects with established databases significantly improves the prediction of shared drug indications, supporting the clinical relevance of our novel findings. These results demonstrate that our methodology provides a generalizable, knowledge-driven framework for scalable causal inference.


Deconstructing Depression Stigma: Integrating AI-driven Data Collection and Analysis with Causal Knowledge Graphs

Meng, Han, Zhang, Renwen, Wang, Ganyi, Yang, Yitian, Qin, Peinuan, Lee, Jungup, Lee, Yi-Chieh

arXiv.org Artificial Intelligence

Mental-illness stigma is a persistent social problem, hampering both treatment-seeking and recovery. Accordingly, there is a pressing need to understand it more clearly, but analyzing the relevant data is highly labor-intensive. Therefore, we designed a chatbot to engage participants in conversations; coded those conversations qualitatively with AI assistance; and, based on those coding results, built causal knowledge graphs to decode stigma. The results we obtained from 1,002 participants demonstrate that conversation with our chatbot can elicit rich information about people's attitudes toward depression, while our AI-assisted coding was strongly consistent with human-expert coding. Our novel approach combining large language models (LLMs) and causal knowledge graphs uncovered patterns in individual responses and illustrated the interrelationships of psychological constructs in the dataset as a whole. The paper also discusses these findings' implications for HCI researchers in developing digital interventions, decomposing human psychological constructs, and fostering inclusive attitudes.


Agent-as-Judge for Factual Summarization of Long Narratives

Jeong, Yeonseok, Kim, Minsoo, Hwang, Seung-won, Kim, Byung-Hak

arXiv.org Artificial Intelligence

Large Language Models (LLMs) have demonstrated near-human performance in summarization tasks based on traditional metrics such as ROUGE and BERTScore. However, these metrics do not adequately capture critical aspects of summarization quality, such as factual accuracy, particularly for long narratives (>100K tokens). Recent advances, such as LLM-as-a-Judge, address the limitations of metrics based on lexical similarity but still exhibit factual inconsistencies, especially in understanding character relationships and states. In this work, we introduce NarrativeFactScore, a novel "Agent-as-a-Judge" framework for evaluating and refining summaries. By leveraging a Character Knowledge Graph (CKG) extracted from input and generated summaries, NarrativeFactScore assesses the factual consistency and provides actionable guidance for refinement, such as identifying missing or erroneous facts. We demonstrate the effectiveness of NarrativeFactScore through a detailed workflow illustration and extensive validation on widely adopted benchmarks, achieving superior performance compared to competitive methods. Our results highlight the potential of agent-driven evaluation systems to improve the factual reliability of LLM-generated summaries.


KGIF: Optimizing Relation-Aware Recommendations with Knowledge Graph Information Fusion

Jeon, Dong Hyun, Sun, Wenbo, Song, Houbing Herbert, Liu, Dongfang, Alvaro, Velasquez, Xie, Yixin Chloe, Niu, Shuteng

arXiv.org Artificial Intelligence

While deep-learning-enabled recommender systems demonstrate strong performance benchmarks, many struggle to adapt effectively in real-world environments due to limited use of user-item relationship data and insufficient transparency in recommendation generation. Traditional collaborative filtering approaches fail to integrate multifaceted item attributes, and although Factorization Machines account for item-specific details, they overlook broader relational patterns. Collaborative knowledge graph-based models have progressed by embedding user-item interactions with item-attribute relationships, offering a holistic perspective on interconnected entities. However, these models frequently aggregate attribute and interaction data in an implicit manner, leaving valuable relational nuances underutilized. This study introduces the Knowledge Graph Attention Network with Information Fusion (KGIF), a specialized framework designed to merge entity and relation embeddings explicitly through a tailored self-attention mechanism. The KGIF framework integrates reparameterization via dynamic projection vectors, enabling embeddings to adaptively represent intricate relationships within knowledge graphs. This explicit fusion enhances the interplay between user-item interactions and item-attribute relationships, providing a nuanced balance between user-centric and item-centric representations. An attentive propagation mechanism further optimizes knowledge graph embeddings, capturing multi-layered interaction patterns. The contributions of this work include an innovative method for explicit information fusion, improved robustness for sparse knowledge graphs, and the ability to generate explainable recommendations through interpretable path visualization.


Fine-tuning and Prompt Engineering with Cognitive Knowledge Graphs for Scholarly Knowledge Organization

Rabby, Gollam, Auer, Sören, D'Souza, Jennifer, Oelen, Allard

arXiv.org Artificial Intelligence

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.


A knowledge representation approach for construction contract knowledge modeling

Zheng, Chunmo, Wong, Saika, Su, Xing, Tang, Yinqiu

arXiv.org Artificial Intelligence

The emergence of large language models (LLMs) presents an unprecedented opportunity to automate construction contract management, reducing human errors and saving significant time and costs. However, LLMs may produce convincing yet inaccurate and misleading content due to a lack of domain expertise. To address this issue, expert-driven contract knowledge can be represented in a structured manner to constrain the automatic contract management process. This paper introduces the Nested Contract Knowledge Graph (NCKG), a knowledge representation approach that captures the complexity of contract knowledge using a nested structure. It includes a nested knowledge representation framework, a NCKG ontology built on the framework, and an implementation method. Furthermore, we present the LLM-assisted contract review pipeline enhanced with external knowledge in NCKG. Our pipeline achieves a promising performance in contract risk reviewing, shedding light on the combination of LLM and KG towards more reliable and interpretable contract management.


Snowman: A Million-scale Chinese Commonsense Knowledge Graph Distilled from Foundation Model

Wang, Jiaan, Qu, Jianfeng, Liang, Yunlong, Li, Zhixu, Liu, An, Liu, Guanfeng, Zheng, Xin

arXiv.org Artificial Intelligence

Constructing commonsense knowledge graphs (CKGs) has attracted wide research attention due to its significant importance in cognitive intelligence. Nevertheless, existing CKGs are typically oriented to English, limiting the research in non-English languages. Meanwhile, the emergence of foundation models like ChatGPT and GPT-4 has shown promising intelligence with the help of reinforcement learning from human feedback. Under the background, in this paper, we utilize foundation models to construct a Chinese CKG, named Snowman. Specifically, we distill different types of commonsense head items from ChatGPT, and continue to use it to collect tail items with respect to the head items and pre-defined relations. Based on the preliminary analysis, we find the negative commonsense knowledge distilled by ChatGPT achieves lower human acceptance compared to other knowledge. Therefore, we design a simple yet effective self-instruct filtering strategy to filter out invalid negative commonsense. Overall, the constructed Snowman covers more than ten million Chinese commonsense triples, making it the largest Chinese CKG. Moreover, human studies show the acceptance of Snowman achieves 90.6\%, indicating the high-quality triples distilled by the cutting-edge foundation model. We also conduct experiments on commonsense knowledge models to show the usability and effectiveness of our Snowman.


CKG: Dynamic Representation Based on Context and Knowledge Graph

Tang, Xunzhu, Sun, Tiezhu, Zhu, Rujie, Wang, Shi

arXiv.org Artificial Intelligence

Recently, neural language representation models pre-trained on large corpus can capture rich co-occurrence information and be fine-tuned in downstream tasks to improve the performance. As a result, they have achieved state-of-the-art results in a large range of language tasks. However, there exists other valuable semantic information such as similar, opposite, or other possible meanings in external knowledge graphs (KGs). We argue that entities in KGs could be used to enhance the correct semantic meaning of language sentences. In this paper, we propose a new method CKG: Dynamic Representation Based on \textbf{C}ontext and \textbf{K}nowledge \textbf{G}raph. On the one side, CKG can extract rich semantic information of large corpus. On the other side, it can make full use of inside information such as co-occurrence in large corpus and outside information such as similar entities in KGs. We conduct extensive experiments on a wide range of tasks, including QQP, MRPC, SST-5, SQuAD, CoNLL 2003, and SNLI. The experiment results show that CKG achieves SOTA 89.2 on SQuAD compared with SAN (84.4), ELMo (85.8), and BERT$_{Base}$ (88.5).


MICO: A Multi-alternative Contrastive Learning Framework for Commonsense Knowledge Representation

Su, Ying, Wang, Zihao, Fang, Tianqing, Zhang, Hongming, Song, Yangqiu, Zhang, Tong

arXiv.org Artificial Intelligence

Commonsense reasoning tasks such as commonsense knowledge graph completion and commonsense question answering require powerful representation learning. In this paper, we propose to learn commonsense knowledge representation by MICO, a Multi-alternative contrastve learning framework on COmmonsense knowledge graphs (MICO). MICO generates the commonsense knowledge representation by contextual interaction between entity nodes and relations with multi-alternative contrastive learning. In MICO, the head and tail entities in an $(h,r,t)$ knowledge triple are converted to two relation-aware sequence pairs (a premise and an alternative) in the form of natural language. Semantic representations generated by MICO can benefit the following two tasks by simply comparing the distance score between the representations: 1) zero-shot commonsense question answering task; 2) inductive commonsense knowledge graph completion task. Extensive experiments show the effectiveness of our method.


Do Language Models Perform Generalizable Commonsense Inference?

Wang, Peifeng, Ilievski, Filip, Chen, Muhao, Ren, Xiang

arXiv.org Artificial Intelligence

Inspired by evidence that pretrained language models (LMs) encode commonsense knowledge, recent work has applied LMs to automatically populate commonsense knowledge graphs (CKGs). However, there is a lack of understanding on their generalization to multiple CKGs, unseen relations, and novel entities. This paper analyzes the ability of LMs to perform generalizable commonsense inference, in terms of knowledge capacity, transferability, and induction. Our experiments with these three aspects show that: (1) LMs can adapt to different schemas defined by multiple CKGs but fail to reuse the knowledge to generalize to new relations. (2) Adapted LMs generalize well to unseen subjects, but less so on novel objects. Future work should investigate how to improve the transferability and induction of commonsense mining from LMs.