Yuki Yamagata

29 papers B 1C 2Journal 8Unranked 17
YearRankTypeTitle / Venue / Authors
2026 — conf
Better Generalizing to Unseen Concepts: An Evaluation Framework and An LLM-Based Auto-Labeled Pipeline for Biomedical Concept Recognition.
EACL (Volume 1: Long Papers)
Shanshan Liu, Noriki Nishida, Fei Cheng, Narumi Tokunaga, Rumana Ferdous Munne, Yuki Yamagata, Kouji Kozaki, Takehito Utsuro, Yuji Matsumoto
2026 J jnl
Better Generalizing to Unseen Concepts: An Evaluation Framework and An LLM-Based Auto-Labeled Pipeline for Biomedical Concept Recognition.
CoRR
Shanshan Liu, Noriki Nishida, Fei Cheng, Narumi Tokunaga, Rumana Ferdous Munne, Yuki Yamagata, Kouji Kozaki, Takehito Utsuro, Yuji Matsumoto
2026 — ed.
Proceedings of the 16th International Conference on Biological and Biomedical Ontology (ICBO 2025), Virtual Event, Bethesda, USA, November 9-11, 2025.
ICBO
Yuki Yamagata, Muhammad Tuan Amith, Giorgio A. Ubbiali, Ludger Jansen, William D. Duncan, Asiyah Yu Lin
2025 — conf
A Semantic Web-Based Infrastructure for Purpose-Driven Retrieval of Life Science Bioresources.
ISWC (Industry/Doctoral Consortium/Posters/Demos)
Tatsuya Kushida, Daiki Usuda, Masanobu Yamagata, Norio Kobayashi, Shoichiro Shindo, Tatsuya Yamada, Yuki Yamagata, Hiroshi Masuya
2025 — conf
MA-COIR: Leveraging Semantic Search Index and Generative Models for Ontology-Driven Biomedical Concept Recognition.
ACL (4)
Shanshan Liu, Noriki Nishida, Rumana Ferdous Munne, Narumi Tokunaga, Yuki Yamagata, Kouji Kozaki, Yuji Matsumoto
2025 J jnl
MA-COIR: Leveraging Semantic Search Index and Generative Models for Ontology-Driven Biomedical Concept Recognition.
CoRR
Shanshan Liu, Noriki Nishida, Rumana Ferdous Munne, Narumi Tokunaga, Yuki Yamagata, Kouji Kozaki, Yuji Matsumoto
2025 — conf
SSBD Ontology: A Two-Tier Approach for Interoperable Bioimaging Metadata.
ISWC (2)
Yuki Yamagata, Koji Kyoda, Hiroya Itoga, Emi Fujisawa, Shuichi Onami
2025 J jnl
SSBD Ontology: A Two-Tier Approach for Interoperable Bioimaging Metadata.
CoRR
Yuki Yamagata, Koji Kyoda, Hiroya Itoga, Emi Fujisawa, Shuichi Onami
2025 B conf
Zero-Shot Entailment Learning for Ontology-Based Biomedical Annotation Without Explicit Mentions.
COLING
Rumana Ferdous Munne, Noriki Nishida, Shanshan Liu, Narumi Tokunaga, Yuki Yamagata, Kouji Kozaki, Yuji Matsumoto
2024 J jnl
Homeostasis imbalance process ontology: a study on COVID-19 infectious processes.
BMC Medical Informatics Decis. Mak.
Yuki Yamagata, Tatsuya Kushida, Shuichi Onami, Hiroshi Masuya
2024 — conf
Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles.
BioNLP@ACL
Oumaima El Khettari, Noriki Nishida, Shanshan Liu, Rumana Ferdous Munne, Yuki Yamagata, Solen Quiniou, Samuel Chaffron, Yuji Matsumoto
2022 — conf
Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology.
ICBO
Yuki Yamagata, Shuichi Onami, Hiroshi Masuya
2022 — conf
Ontology Integration for Discovering Bioresources Contributing to Medical Science Research.
ICBO
Tatsuya Kushida, Daiki Usuda, Toyoyuki Takada, Yuki Yamagata, Hiroshi Masuya
2021 — conf
A Community Effort for COVID-19 Ontology Harmonization.
ICBO
Asiyah Yu Lin, Yuki Yamagata, William D. Duncan, Leigh C. Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He
2020 J jnl
A performance evaluation of read/write burst transfer by high-level synthesizable software for the alpha blending processing.
Artif. Life Robotics
Yuki Yamagata, Akira Yamawaki
2019 C conf
Development of Filled Circle Drawing in High-Level Synthesis Oriented Game Programming Library.
PDCAT
Yuki Yamagata, Akira Yamawaki
2019 — conf
TXPO: A Toxic Process Ontology for Better Understanding of Drug-Induced Liver Injury.
ICBO
Yuki Yamagata, Yoshinobu Igarashi, Noriyuki Nakatsu, Hiroshi Yamada
2018 C conf
An Evaluation of Burst Transfer Inferred by a High-level Synthesis Tool.
TENCON
Yuki Yamagata, Akira Yamawaki
2017 J jnl
Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques.
J. Biomed. Semant.
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
2015 — conf
Disease Compass - a navigation system for disease knowledge based on ontology and linked data techniques.
ICBO
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
2014 J jnl
An ontological modeling approach for abnormal states and its application in the medical domain.
J. Biomed. Semant.
Yuki Yamagata, Kouji Kozaki, Takeshi Imai, Kazuhiko Ohe, Riichiro Mizoguchi
2014 — conf
Towards the Integration of Abnormality in Diseases.
ICBO
Yuki Yamagata, Kouji Kozaki, Takeshi Imai, Kazuhiko Ohe, Riichiro Mizoguchi
2013 — conf
Ontological Model of Abnormal States and its Application in the Medical Domain.
ICBO
Yuki Yamagata, Hiroko Kou, Kouji Kozaki, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
2013 — conf
Publishing a Disease Ontologies as Linked Data.
JIST
Kouji Kozaki, Yuki Yamagata, Takeshi Imai, Kazuhiko Ohe, Riichiro Mizoguchi
2012 — conf
Browsing Causal Chains in a Disease Ontology.
ISWC (Posters & Demos)
Kouji Kozaki, Hiroko Kou, Yuki Yamagata, Takeshi Imai, Kazuhiko Ohe, Riichiro Mizoguchi
2012 — conf
Ontological Modeling of Interoperable Abnormal States.
JIST
Yuki Yamagata, Hiroko Kou, Kouji Kozaki, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
2011 — conf
River Flow Model of Diseases.
ICBO
Riichiro Mizoguchi, Kouji Kozaki, Hiroko Kou, Yuki Yamagata, Takeshi Imai, Kayo Waki, Kazuhiko Ohe
2003 J jnl
FREX: A query interface for biological processes with hierarchical and recursive structures.
Silico Biol.
Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi
2003 — conf
Implementation of Memory Tester Consisting of SRAM-Based Reconfigurable Cells.
Asian Test Symposium
Yuki Yamagata, Kenichi Ichino, Masayuki Arai, Satoshi Fukumoto, Kazuhiko Iwasaki, Masayuki Satoh, Hiroyuki Itabashi, Takashi Murai, Nobuyuki Otsuka