Reasoning over TKGs has two challenges: 1.

The focus on'food as medicine' is gaining traction in the field of health and several studies conducted in the past few years discussed this aspect of food in the literature. However, very little research has been done on representing the relationship between food and health in a standardized, machine - readable fo rmat using a semantic web that can help us leverage this knowledge effectively. To address this gap, this study aims to create a knowledge graph to link food and health through the knowledge graphs' ability to combine information from various platforms foc using on flavonoid contents of food found in the USDA's databases and cancer connections found in the literature. We looked closely at these relationships using KNARM methodology and represented them in machine - operable format. The proposed knowledge graph serves as an example for researchers, enabling them to explore the complex interplay between dietary choices and disease management. Future work for this study involves expanding the scope of the knowledge graph by capturing nuances, adding more related d ata, and performing inferences on the acquired knowledge to uncover hidden relationships.

Finding an optimal word representation algorithm is particularly important in terms of domain specific data, as the same word can have different meanings and hence, different representations depending on the domain and context. While Generative AI and transformer architecture does a great job at generating contextualized embeddings for any given work, they are quite time and compute extensive, especially if we were to pre-train such a model from scratch. In this work, we focus on the scientific domain and finding the optimal word representation algorithm along with the tokenization method that could be used to represent words in the scientific domain. The goal of this research is two fold: 1) finding the optimal word representation and tokenization methods that can be used in downstream scientific domain NLP tasks, and 2) building a comprehensive evaluation suite that could be used to evaluate various word representation and tokenization algorithms (even as new ones are introduced) in the scientific domain. To this end, we build an evaluation suite consisting of several downstream tasks and relevant datasets for each task. Furthermore, we use the constructed evaluation suite to test various word representation and tokenization algorithms.

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.

Sec. 2 provides more experimental details on Few-shot Learning for our GraphAdapter. Sec. 3 describes more details about datasets and implementation. Sec. 4 visualizes the textual graph nodes used for classification before and after utilizing our Sec. Notably, the TaskRes* exploits the enhanced base classifier. We present the numerical results of "Figure 3 in the main text" as Table 2.

Machine learning in healthcare requires effective representation of structured medical codes, but current methods face a trade-off: knowledge graph-based approaches capture formal relationships but miss real-world patterns, while data-driven methods learn empirical associations but often overlook structured knowledge in medical terminologies. We present KEEP (Knowledge-preserving and Empirically refined Embedding Process), an efficient framework that bridges this gap by combining knowledge graph embeddings with adaptive learning from clinical data. KEEP first generates embeddings from knowledge graphs, then employs regularized training on patient records to adaptively integrate empirical patterns while preserving ontological relationships. Importantly, KEEP produces final embeddings without task-specific axillary or end-to-end training enabling KEEP to support multiple downstream applications and model architectures. Evaluations on structured EHR from UK Biobank and MIMIC-IV demonstrate that KEEP outperforms both traditional and Language Model-based approaches in capturing semantic relationships and predicting clinical outcomes. Moreover, KEEP's minimal computational requirements make it particularly suitable for resource-constrained environments. Data and Code Availability This research has been conducted using data from UK Biobank (Sud-low et al., 2015) and MIMIC-IV Johnson et al. (2021). Researchers can request access via https:// www.ukbiobank.ac.uk/ and https://physionet.

Multi-hop reasoning over financial disclosures is often a retrieval problem before it becomes a reasoning or generation problem: relevant facts are dispersed across sections, filings, companies, and years, and LLMs often expend excessive tokens navigating noisy context. Without precise Knowledge Graph (KG)-guided selection of relevant context, even strong reasoning models either fail to answer or consume excessive tokens, whereas KG-linked evidence enables models to focus their reasoning on composing already retrieved facts. We present FinReflectKG - MultiHop, a benchmark built on FinReflectKG, a temporally indexed financial KG that links audited triples to source chunks from S&P 100 filings (2022-2024). Mining frequent 2-3 hop subgraph patterns across sectors (via GICS taxonomy), we generate financial analyst style questions with exact supporting evidence from the KG. A two-phase pipeline first creates QA pairs via pattern-specific prompts, followed by a multi-criteria quality control evaluation to ensure QA validity. We then evaluate three controlled retrieval scenarios: (S1) precise KG-linked paths; (S2) text-only page windows centered on relevant text spans; and (S3) relevant page windows with randomizations and distractors. Across both reasoning and non-reasoning models, KG-guided precise retrieval yields substantial gains on the FinReflectKG - MultiHop QA benchmark dataset, boosting correctness scores by approximately 24 percent while reducing token utilization by approximately 84.5 percent compared to the page window setting, which reflects the traditional vector retrieval paradigm. Spanning intra-document, inter-year, and cross-company scopes, our work underscores the pivotal role of knowledge graphs in efficiently connecting evidence for multi-hop financial QA. We also release a curated subset of the benchmark (555 QA Pairs) to catalyze further research.

Mass spectrometry metabolomics generates vast amounts of data requiring advanced methods for interpretation. Knowledge graphs address these challenges by structuring mass spectrometry data, metabolite information, and their relationships into a connected network (Gaudry et al. 2024). However, effective use of a knowledge graph demands an in-depth understanding of its ontology and its query language syntax. To overcome this, we designed MetaboT, an AI system utilizing large language models (LLMs) to translate user questions into SPARQL semantic query language for operating on knowledge graphs (Steve Harris 2013). We demonstrate its effectiveness using the Experimental Natural Products Knowledge Graph (ENPKG), a large-scale public knowledge graph for plant natural products (Gaudry et al. 2024).MetaboT employs specialized AI agents for handling user queries and interacting with the knowledge graph by breaking down complex tasks into discrete components, each managed by a specialised agent (Fig. 1a). The multi-agent system is constructed using the LangChain and LangGraph libraries, which facilitate the integration of LLMs with external tools and information sources (LangChain, n.d.). The query generation process follows a structured workflow. First, the Entry Agent determines if the question is new or a follow-up to previous interactions. New questions are forwarded to the Validator Agent, which verifies if the question is related to the knowledge graph. Then, the valid question is sent to the Supervisor Agent, which identifies if the question requires chemical conversions or standardized identifiers. In this case it delegates the question to the Knowledge Graph Agent, which can use tools to extract necessary details, such as URIs or taxonomies of chemical names, from the user query. Finally, an agent responsible for crafting the SPARQL queries equipped with the ontology of the knowledge graph uses the provided identifiers to generate the query. Then, the system executes the generated query against the metabolomics knowledge graph and returns structured results to the user (Fig. 1b). To assess the performance of MetaboT we have curated 50 metabolomics-related questions and their expected answers. In addition to submitting these questions to MetaboT, we evaluated a baseline by submitting them to a standard LLM (GPT-4o) with a prompt that incorporated the knowledge graph ontology but did not provide specific entity IDs. This baseline achieved only 8.16% accuracy, compared to MetaboT's 83.67%, underscoring the necessity of our multi-agent system for accurately retrieving entities and generating correct SPARQL queries. MetaboT demonstrates promising performance as a conversational question-answering assistant, enabling researchers to retrieve structured metabolomics data through natural language queries. By automating the generation and execution of SPARQL queries, it removes technical barriers that have traditionally hindered access to knowledge graphs. Importantly, MetaboT leverages the capabilities of LLMs while maintaining experimentally grounded query generation, ensuring that outputs remain aligned with domain-specific standards and data structures. This approach facilitates data-driven discoveries by bridging the gap between complex semantic technologies and user-friendly interaction. MetaboT is accessible at [https://metabot.holobiomicslab.eu/], and its source code is available at [https://github.com/HolobiomicsLab/MetaboT].

Building upon a formal, event-centric model for the diachronic evolution of legal norms grounded in the IFLA Library Reference Model (LRMoo), this paper addresses the essential first step of publishing this model's foundational entity-the abstract legal Work (F1)-on the Semantic Web. We propose a detailed, property-by-property mapping of the LRMoo F1 Work to the widely adopted schema.org/Legislation vocabulary. Using Brazilian federal legislation from the Normas.leg.br portal as a practical case study, we demonstrate how to create interoperable, machine-readable descriptions via JSON-LD, focusing on stable URN identifiers, core metadata, and norm relationships. This structured mapping establishes a stable, URI-addressable anchor for each legal norm, creating a verifiable "ground truth". It provides the essential, interoperable foundation upon which subsequent layers of the model, such as temporal versions (Expressions) and internal components, can be built. By bridging formal ontology with web-native standards, this work paves the way for building deterministic and reliable Legal Knowledge Graphs (LKGs), overcoming the limitations of purely probabilistic models.

Analysis of multi-modal content can be tricky, computationally expensive, and require a significant amount of engineering efforts. Lots of work with pre-trained models on static data is out there, yet fusing these opensource models and methods with complex data such as videos is relatively challenging. In this paper, we present a framework that enables efficiently prototyping pipelines for multi-modal content analysis. W e craft a candidate recipe for a pipeline, marrying a set of pre-trained models, to convert videos into a temporal semi-structured data format. W e translate this structure further to a frame-level indexed knowledge graph representation that is query-able and supports continual learning, enabling the dynamic incorporation of new domain-specific knowledge through an interactive medium.