Search Results for author: Vinh Nguyen

Found 12 papers, 4 papers with code

Evaluating Biomedical Word Embeddings for Vocabulary Alignment at Scale in the UMLS Metathesaurus Using Siamese Networks

no code implementations insights (ACL) 2022 Goonmeet Bajaj, Vinh Nguyen, Thilini Wijesiriwardene, Hong Yung Yip, Vishesh Javangula, Amit Sheth, Srinivasan Parthasarathy, Olivier Bodenreider

Recent work uses a Siamese Network, initialized with BioWordVec embeddings (distributed word embeddings), for predicting synonymy among biomedical terms to automate a part of the UMLS (Unified Medical Language System) Metathesaurus construction process.

Word Embeddings

Solving the Right Problem is Key for Translational NLP: A Case Study in UMLS Vocabulary Insertion

1 code implementation25 Nov 2023 Bernal Jimenez Gutierrez, Yuqing Mao, Vinh Nguyen, Kin Wah Fung, Yu Su, Olivier Bodenreider

In this work, we study the case of UMLS vocabulary insertion, an important real-world task in which hundreds of thousands of new terms, referred to as atoms, are added to the UMLS, one of the most comprehensive open-source biomedical knowledge bases.

Language Modelling

p-Laplacian Transformer

no code implementations6 Nov 2023 Tuan Nguyen, Tam Nguyen, Vinh Nguyen, Tan M. Nguyen

$p$-Laplacian regularization, rooted in graph and image signal processing, introduces a parameter $p$ to control the regularization effect on these data.

From Coupled Oscillators to Graph Neural Networks: Reducing Over-smoothing via a Kuramoto Model-based Approach

no code implementations6 Nov 2023 Tuan Nguyen, Hirotada Honda, Takashi Sano, Vinh Nguyen, Shugo Nakamura, Tan M. Nguyen

We propose the Kuramoto Graph Neural Network (KuramotoGNN), a novel class of continuous-depth graph neural networks (GNNs) that employs the Kuramoto model to mitigate the over-smoothing phenomenon, in which node features in GNNs become indistinguishable as the number of layers increases.

Revisiting Over-smoothing and Over-squashing Using Ollivier-Ricci Curvature

1 code implementation28 Nov 2022 Khang Nguyen, Hieu Nong, Vinh Nguyen, Nhat Ho, Stanley Osher, Tan Nguyen

Graph Neural Networks (GNNs) had been demonstrated to be inherently susceptible to the problems of over-smoothing and over-squashing.

VidConv: A modernized 2D ConvNet for Efficient Video Recognition

1 code implementation8 Jul 2022 Chuong H. Nguyen, Su Huynh, Vinh Nguyen, Ngoc Nguyen

Since being introduced in 2020, Vision Transformers (ViT) has been steadily breaking the record for many vision tasks and are often described as ``all-you-need" to replace ConvNet.

Action Recognition Video Recognition

UVA Resources for the Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus

no code implementations21 May 2022 Vinh Nguyen, Olivier Bodenreider

In this paper, we present a set of reusable and reproducible resources including (1) a dataset generator, (2) three datasets generated by using the generator, and (3) three baseline approaches.

Evaluating Biomedical BERT Models for Vocabulary Alignment at Scale in the UMLS Metathesaurus

no code implementations14 Sep 2021 Goonmeet Bajaj, Vinh Nguyen, Thilini Wijesiriwardene, Hong Yung Yip, Vishesh Javangula, Srinivasan Parthasarathy, Amit Sheth, Olivier Bodenreider

Given the SOTA performance of these BERT models for other downstream tasks, our experiments yield surprisingly interesting results: (1) in both model architectures, the approaches employing these biomedical BERT-based models do not outperform the existing approaches using Siamese Network with BioWordVec embeddings for the UMLS synonymy prediction task, (2) the original BioBERT large model that has not been pre-trained with the UMLS outperforms the SapBERT models that have been pre-trained with the UMLS, and (3) using the Siamese Networks yields better performance for synonymy prediction when compared to using the biomedical BERT models.

Task 2 Word Embeddings

Alternative Blockmodelling

no code implementations27 Jul 2019 Oscar Correa, Jeffrey Chan, Vinh Nguyen

Secondly, blockmodelling is a summary representation of a network which regards not only membership of nodes but also relations between clusters.


Logical Inferences with Contexts of RDF Triples

no code implementations20 Jan 2017 Vinh Nguyen, Amit Sheth

This formal semantics also allows us to derive a new set of entailment rules that could entail new contextual triples about triples.

World Knowledge

On Reasoning with RDF Statements about Statements using Singleton Property Triples

no code implementations15 Sep 2015 Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan, Gang Fu, Evan Bolton, Núria Queralt Rosinach, Laura I. Furlong, Michel Dumontier, Amit Sheth

If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples?

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