arXiv subjects

Vetle I. Torvik

Publications and source records attributed to Vetle I. Torvik.

7 recordsLinked to original sources

arXiv2025

AutoDCWorkflow: LLM-based Data Cleaning Workflow Auto-Generation and Benchmark

Data cleaning is a time-consuming and error-prone manual process, even with modern workflow tools such as OpenRefine. We present AutoDCWorkflow, an LLM-based pipeline for automatically generating data-cleaning workflows. The pipeline takes a raw table and a data analysis purpose, and generates a sequence of OpenRefine operations designed to produce a minimal, clean table sufficient to address the purpose. Six operations correspond to common data quality issues, including format inconsistencies, type errors, and duplicates. To evaluate AutoDCWorkflow, we create a benchmark with metrics assessing answers, data, and workflow quality for 142 purposes using 96 tables across six topics. The evaluation covers three key dimensions: (1) Purpose Answer: can the cleaned table produce a correct answer? (2) Column (Value): how closely does it match the ground truth table? (3) Workflow (Operations): to what extent does the generated workflow resemble the human-curated ground truth? Experiments show that Llama 3.1, Mistral, and Gemma 2 significantly enhance data quality, outperforming the baseline across all metrics. Gemma 2-27B consistently generates high-quality tables and answers, while Gemma 2-9B excels in producing workflows that closely resemble human-annotated versions.

cs.DB↗

arXiv2025

PubMed knowledge graph 2.0: Connecting papers, patents, and clinical trials in biomedical science

Papers, patents, and clinical trials are essential scientific resources in biomedicine, crucial for knowledge sharing and dissemination. However, these documents are often stored in disparate databases with varying management standards and data formats, making it challenging to form systematic and fine-grained connections among them. To address this issue, we construct PKG 2.0, a comprehensive knowledge graph dataset encompassing over 36 million papers, 1.3 million patents, and 0.48 million clinical trials in the biomedical field. PKG 2.0 integrates these dispersed resources through 482 million biomedical entity linkages, 19 million citation linkages, and 7 million project linkages. The construction of PKG 2.0 wove together fine-grained biomedical entity extraction, high-performance author name disambiguation, multi-source citation integration, and high-quality project data from the NIH Exporter. Data validation demonstrates that PKG 2.0 excels in key tasks such as author disambiguation and biomedical entity recognition. This dataset provides valuable resources for biomedical researchers, bibliometric scholars, and those engaged in literature mining.

cs.DL↗

arXiv2025

What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs

Graphs, as a relational data structure, have been widely used for various application scenarios, like molecule design and recommender systems. Recently, large language models (LLMs) are reorganizing in the AI community for their expected reasoning and inference abilities. Making LLMs understand graph-based relational data has great potential, including but not limited to (1) distillate external knowledge base for eliminating hallucination and breaking the context window limit for LLMs' inference during the retrieval augmentation generation process; (2) taking graph data as the input and directly solve the graph-based research tasks like protein design and drug discovery. However, inputting the entire graph data to LLMs is not practical due to its complex topological structure, data size, and the lack of effective and efficient semantic graph representations. A natural question arises: Is there a kind of graph representation that can be described by natural language for LLM's understanding and is also easy to require to serve as the raw input for LLMs? Based on statistical computation, graph laws pre-define a set of parameters (e.g., degree, time, diameter) and identifie their relationships and values by observing the topological distribution of plenty of real-world graph data. We believe this kind of parametric representation of graphs, graph laws, can be a solution for making LLMs understand graph data as the input. In this survey, we first review the previous study of graph laws from multiple perspectives, i.e., macroscope and microscope of graphs, low-order and high-order graphs, static and dynamic graphs, different observation spaces, and newly proposed graph parameters. After we review various real-world applications benefiting from the guidance of graph laws, we conclude the paper with current challenges and future research directions.

cs.AI↗

arXiv2024

T-KAER: Transparency-enhanced Knowledge-Augmented Entity Resolution Framework

Entity resolution (ER) is the process of determining whether two representations refer to the same real-world entity and plays a crucial role in data curation and data cleaning. Recent studies have introduced the KAER framework, aiming to improve pre-trained language models by augmenting external knowledge. However, identifying and documenting the external knowledge that is being augmented and understanding its contribution to the model's predictions have received little to no attention in the research community. This paper addresses this gap by introducing T-KAER, the Transparency-enhanced Knowledge-Augmented Entity Resolution framework. To enhance transparency, three Transparency-related Questions (T-Qs) have been proposed: T-Q(1): What is the experimental process for matching results based on data inputs? T-Q(2): Which semantic information does KAER augment in the raw data inputs? T-Q(3): Which semantic information of the augmented data inputs influences the predictions? To address the T-Qs, T-KAER is designed to improve transparency by documenting the entity resolution processes in log files. In experiments, a citation dataset is used to demonstrate the transparency components of T-KAER. This demonstration showcases how T-KAER facilitates error analysis from both quantitative and qualitative perspectives, providing evidence on "what" semantic information is augmented and "why" the augmented knowledge influences predictions differently.

cs.CL↗

arXiv2023

KAER: A Knowledge Augmented Pre-Trained Language Model for Entity Resolution

Entity resolution has been an essential and well-studied task in data cleaning research for decades. Existing work has discussed the feasibility of utilizing pre-trained language models to perform entity resolution and achieved promising results. However, few works have discussed injecting domain knowledge to improve the performance of pre-trained language models on entity resolution tasks. In this study, we propose Knowledge Augmented Entity Resolution (KAER), a novel framework named for augmenting pre-trained language models with external knowledge for entity resolution. We discuss the results of utilizing different knowledge augmentation and prompting methods to improve entity resolution performance. Our model improves on Ditto, the existing state-of-the-art entity resolution method. In particular, 1) KAER performs more robustly and achieves better results on "dirty data", and 2) with more general knowledge injection, KAER outperforms the existing baseline models on the textual dataset and dataset from the online product domain. 3) KAER achieves competitive results on highly domain-specific datasets, such as citation datasets, requiring the injection of expert knowledge in future work.

cs.CL↗

arXiv2020

Building a PubMed knowledge graph

PubMed is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguated, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National Institutes of Health (NIH) ExPORTER, collecting affiliation history and educational background of authors from ORCID, and identifying fine-grained affiliation data from MapAffil. Through the integration of the credible multi-source data, we could create connections among the bio-entities, authors, articles, affiliations, and funding. Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation (AND) achieving a F1 score of 98.09%. PKG can trigger broader innovations, not only enabling us to measure scholarly impact, knowledge usage, and knowledge transfer, but also assisting us in profiling authors and organizations based on their connections with bio-entities. The PKG is freely available on Figshare (https://figshare.com/s/6327a55355fc2c99f3a2, simplified version that exclude PubMed raw data) and TACC website (http://er.tacc.utexas.edu/datasets/ped, full version).

cs.DL↗

arXiv2019

Geographical Distribution of Biomedical Research in the USA and China

We analyze nearly 20 million geocoded PubMed articles with author affiliations. Using K-means clustering for the lower 48 US states and mainland China, we find that the average published paper is within a relatively short distance of a few centroids. These centroids have shifted very little over the past 30 years, and the distribution of distances to these centroids has not changed much either. The overall country centroids have gradually shifted south (about 0.2° for the USA and 1.7° for China), while the longitude has not moved significantly. These findings indicate that there are few large scientific hubs in the USA and China and the typical investigator is within geographical reach of one such hub. This sets the stage to study centralization of biomedical research at national and regional levels across the globe, and over time.

cs.DL↗