Medical deep learning models depend heavily on domain-specific knowledge to perform well on knowledge-intensive clinical tasks. Prior work has primarily leveraged unimodal knowledge graphs, such as the Unified Medical Language System (UMLS), to enhance model performance. However, integrating multimodal medical knowledge graphs remains largely underexplored, mainly due to the lack of resources linking imaging data with clinical concepts. To address this gap, we propose MEDMKG, a Medical Multimodal Knowledge Graph that unifies visual and textual medical information through a multi-stage construction pipeline. MEDMKG fuses the rich multimodal data from MIMIC-CXR with the structured clinical knowledge from UMLS, utilizing both rule-based tools and large language models for accurate concept extraction and relationship modeling. To ensure graph quality and compactness, we introduce Neighbor-aware Filtering (NaF), a novel filtering algorithm tailored for multimodal knowledge graphs. We evaluate MEDMKG across three tasks under two experimental settings, benchmarking twenty-four baseline methods and four state-of-the-art vision-language backbones on six datasets. Results show that MEDMKG not only improves performance in downstream medical tasks but also offers a strong foundation for developing adaptive and robust strategies for multimodal knowledge integration in medical artificial intelligence.

Vision-Language Models (VLMs) have demonstrated remarkable success in natural language generation, excelling at instruction following and structured output generation. Knowledge graphs play a crucial role in radiology, serving as valuable sources of factual information and enhancing various downstream tasks. However, generating radiology-specific knowledge graphs presents significant challenges due to the specialized language of radiology reports and the limited availability of domain-specific data. Existing solutions are predominantly unimodal, meaning they generate knowledge graphs only from radiology reports while excluding radiographic images. Additionally, they struggle with long-form radiology data due to limited context length. To address these limitations, we propose a novel multimodal VLM-based framework for knowledge graph generation in radiology. Our approach outperforms previous methods and introduces the first multimodal solution for radiology knowledge graph generation.

Uncertainty quantification in Knowledge Graph Embedding (KGE) methods is crucial for ensuring the reliability of downstream applications. A recent work applies conformal prediction to KGE methods, providing uncertainty estimates by generating a set of answers that is guaranteed to include the true answer with a predefined confidence level. However, existing methods provide probabilistic guarantees averaged over a reference set of queries and answers (marginal coverage guarantee). In high-stakes applications such as medical diagnosis, a stronger guarantee is often required: the predicted sets must provide consistent coverage per query (conditional coverage guarantee). We propose CondKGCP, a novel method that approximates predicate-conditional coverage guarantees while maintaining compact prediction sets. CondKGCP merges predicates with similar vector representations and augments calibration with rank information. We prove the theoretical guarantees and demonstrate empirical effectiveness of CondKGCP by comprehensive evaluations.

Complex Query Answering (CQA) aims to retrieve answer sets for complex logical formulas from incomplete knowledge graphs, which is a crucial yet challenging task in knowledge graph reasoning. While neuro-symbolic search utilized neural link predictions achieve superior accuracy, they encounter significant complexity bottlenecks: (i) Data complexity typically scales quadratically with the number of entities in the knowledge graph, and (ii) Query complexity becomes NP-hard for cyclic queries. Consequently, these approaches struggle to effectively scale to larger knowledge graphs and more complex queries. To address these challenges, we propose an efficient and scalable symbolic search framework. First, we propose two constraint strategies to compute neural logical indices to reduce the domain of variables, thereby decreasing the data complexity of symbolic search. Additionally, we introduce an approximate algorithm based on local search to tackle the NP query complexity of cyclic queries. Experiments on various CQA benchmarks demonstrate that our framework reduces the computational load of symbolic methods by 90\% while maintaining nearly the same performance, thus alleviating both efficiency and scalability issues.

Temporal Knowledge Graphs (TKGs), which utilize quadruples in the form of (subject, predicate, object, timestamp) to describe temporal facts, have attracted extensive attention. N-tuple TKGs (N-TKGs) further extend traditional TKGs by utilizing n-tuples to incorporate auxiliary elements alongside core elements (i.e., subject, predicate, and object) of facts, so as to represent them in a more fine-grained manner. Reasoning over N-TKGs aims to predict potential future facts based on historical ones. However, existing N-TKG reasoning methods often lack explainability due to their black-box nature. Therefore, we introduce a new Reinforcement Learning-based method, named MT-Path, which leverages the temporal information to traverse historical n-tuples and construct a temporal reasoning path. Specifically, in order to integrate the information encapsulated within n-tuples, i.e., the entity-irrelevant information within the predicate, the information about core elements, and the complete information about the entire n-tuples, MT-Path utilizes a mixture policy-driven action selector, which bases on three low-level policies, namely, the predicate-focused policy, the core-element-focused policy and the whole-fact-focused policy. Further, MT-Path utilizes an auxiliary element-aware GCN to capture the rich semantic dependencies among facts, thereby enabling the agent to gain a deep understanding of each n-tuple. Experimental results demonstrate the effectiveness and the explainability of MT-Path.

Geometric embedding methods have shown to be useful for multi-hop reasoning on knowledge graphs by mapping entities and logical operations to geometric regions and geometric transformations, respectively. Geometric embeddings provide direct interpretability framework for queries. However, current methods have only leveraged the geometric construction of entities, failing to map logical operations to geometric transformations and, instead, using neural components to learn these operations. We introduce GeometrE, a geometric embedding method for multi-hop reasoning, which does not require learning the logical operations and enables full geometric interpretability. Additionally, unlike previous methods, we introduce a transitive loss function and show that it can preserve the logical rule $\forall a,b,c: r(a,b) \land r(b,c) \to r(a,c)$. Our experiments show that GeometrE outperforms current state-of-the-art methods on standard benchmark datasets.

Knowledge graphs (KGs) serve as fundamental structures for organizing interconnected data across diverse domains. However, most KGs remain incomplete, limiting their effectiveness in downstream applications. Knowledge graph completion (KGC) aims to address this issue by inferring missing links, but existing methods face critical challenges: deep graph neural networks (GNNs) suffer from over-smoothing, while embedding-based models fail to capture abstract relational features. This study aims to overcome these limitations by proposing a unified framework that integrates GNN distillation and abstract probabilistic interaction modeling (APIM). GNN distillation approach introduces an iterative message-feature filtering process to mitigate over-smoothing, preserving the discriminative power of node representations. APIM module complements this by learning structured, abstract interaction patterns through probabilistic signatures and transition matrices, allowing for a richer, more flexible representation of entity and relation interactions. We apply these methods to GNN-based models and the APIM to embedding-based KGC models, conducting extensive evaluations on the widely used WN18RR and FB15K-237 datasets. Our results demonstrate significant performance gains over baseline models, showcasing the effectiveness of the proposed techniques. The findings highlight the importance of both controlling information propagation and leveraging structured probabilistic modeling, offering new avenues for advancing knowledge graph completion. And our codes are available at https://anonymous.4open.science/r/APIM_and_GNN-Distillation-461C.

Knowledge graphs (KGs) have become an effective paradigm for managing real-world facts, which are not only complex but also dynamically evolve over time. The temporal validity of facts often serves as a strong clue in downstream link prediction tasks, which predicts a missing element in a fact. Traditional link prediction techniques on temporal KGs either consider a sequence of temporal snapshots of KGs with an ad-hoc defined time interval or expand a temporal fact over its validity period under a predefined time granularity; these approaches not only suffer from the sensitivity of the selection of time interval/granularity, but also face the computational challenges when handling facts with long (even infinite) validity. Although the recent hyper-relational KGs represent the temporal validity of a fact as qualifiers describing the fact, it is still suboptimal due to its ignorance of the infinite validity of some facts and the insufficient information encoded from the qualifiers about the temporal validity. Against this background, we propose VITA, a $\underline{V}$ersatile t$\underline{I}$me represen$\underline{TA}$tion learning method for temporal hyper-relational knowledge graphs. We first propose a versatile time representation that can flexibly accommodate all four types of temporal validity of facts (i.e., since, until, period, time-invariant), and then design VITA to effectively learn the time information in both aspects of time value and timespan to boost the link prediction performance. We conduct a thorough evaluation of VITA compared to a sizable collection of baselines on real-world KG datasets. Results show that VITA outperforms the best-performing baselines in various link prediction tasks (predicting missing entities, relations, time, and other numeric literals) by up to 75.3%. Ablation studies and a case study also support our key design choices.

The intrinsic complexity of human biology presents ongoing challenges to scientific understanding. Researchers collaborate across disciplines to expand our knowledge of the biological interactions that define human life. AI methodologies have emerged as powerful tools across scientific domains, particularly in computational biology, where graph data structures effectively model biological entities such as protein-protein interaction (PPI) networks and gene functional networks. Those networks are used as datasets for paramount network medicine tasks, such as gene-disease association prediction, drug repurposing, and polypharmacy side effect studies. Reliable predictions from machine learning models require high-quality foundational data. In this work, we present a comprehensive multi-purpose biological knowledge graph constructed by integrating and refining multiple publicly available datasets. Building upon the Drug Repurposing Knowledge Graph (DRKG), we define a pipeline tasked with a) cleaning inconsistencies and redundancies present in DRKG, b) coalescing information from the main available public data sources, and c) enriching the graph nodes with expressive feature vectors such as molecular fingerprints and gene ontologies. Biologically and chemically relevant features improve the capacity of machine learning models to generate accurate and well-structured embedding spaces. The resulting resource represents a coherent and reliable biological knowledge graph that serves as a state-of-the-art platform to advance research in computational biology and precision medicine. Moreover, it offers the opportunity to benchmark graph-based machine learning and network medicine models on relevant tasks. We demonstrate the effectiveness of the proposed dataset by benchmarking it against the task of drug repurposing, PPI prediction, and side-effect prediction, modeled as link prediction problems.

Outdated facts in temporal knowledge graphs (TKGs) result from exceeding the expiration date of facts, which negatively impact reasoning performance on TKGs. However, existing reasoning methods primarily focus on positive importance of historical facts, neglecting adverse effects of outdated facts. Besides, training on these outdated facts yields extra computational cost. To address these challenges, we propose an outdated fact filtering framework named HALO, which quantifies the temporal validity of historical facts by exploring the half-life theory to filter outdated facts in TKGs. HALO consists of three modules: the temporal fact attention module, the dynamic relation-aware encoder module, and the outdated fact filtering module. Firstly, the temporal fact attention module captures the evolution of historical facts over time to identify relevant facts. Secondly, the dynamic relation-aware encoder module is designed for efficiently predicting the half life of each fact. Finally, we construct a time decay function based on the half-life theory to quantify the temporal validity of facts and filter outdated facts. Experimental results show that HALO outperforms the state-of-the-art TKG reasoning methods on three public datasets, demonstrating its effectiveness in detecting and filtering outdated facts (Codes are available at https://github.com/yushuowiki/K-Half/tree/main ).