Author

Shoichi Ishida

Yokohama City UniversityORCID 0000-0002-5638-3579Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Assay:electronic health records· 1 Approach:large language model· 1 Approach:machine learning (classical)· 1 Assay:metagenomics· 1 Assay:protein sequence· 1 Research Focus:protein structure prediction· 1

Frequent Co-Authors

Kei TerayamaiD· 3 shared Chin Ka Yin· 1 shared Ka Yin Chin· 1 shared Mitsugu ArakiiD· 1 shared Satoru FujiiiD· 1 shared Shigeyuki MatsumotoiD· 1 shared Takayuki KatoiD· 1 shared Yasushi OkunoiD· 1 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

8 top collaborators · 14 mutual co-author links

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3 shared papersBioinformatics

Kei TerayamaORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

Assessing the Performance of LLMs in Multimodal Information Extraction for Biological Research: A Case Study on LLPS

Ka Yin Chin, Satoru Fujii, Shoichi Ishida, Kei Terayama

This study evaluates a multimodal LLM workflow for extracting biological information from text and figures, achieving an F1-score of 0.847 using Gemini 2.5 Pro.

bioRxiv · Oct 29, 2025 · PreprintBioinformatics

Predicting condensate formation of protein and RNA under various environmental conditions

Chin Ka Yin, Shoichi Ishida, Kei Terayama

The paper builds a dataset and two models to predict protein-RNA condensate formation under various environmental conditions.

bioRxiv · Jun 1, 2023 · PreprintBioinformatics

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning

Shigeyuki Matsumoto, Shoichi Ishida, Mitsugu Araki, Takayuki Kato, Kei Terayama, Yasushi Okuno

This paper introduces DEFMap, a deep learning method that extracts dynamics information from cryo-EM maps, achieving results comparable to molecular dynamics simulations and experimental approaches.

Nature Machine Intelligence · Feb 4, 2021Peer-reviewedMolecular Biology