Koji Tsuda

Tokyo Medical University — Japan

Materials Science · Physical Sciences

55h-index13.8kcitations404works1.52yr avg
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Research Topics

Machine Learning in Materials Science(89), Computational Drug Discovery Methods(75), Gene expression and cancer classification(33), Bioinformatics and Genomic Networks(29), Data Mining Algorithms and Applications(23)

Publications404 total

Predicting symmetric structures of large crystals with GPU-based Ising machines
Communications Physics·2025· 1 citedOpen Access
NbBench: benchmarking language models for comprehensive nanobody tasks
Machine Learning Science and Technology·2025· 1 citedOpen Access
Deep Learning-Assisted De Novo Molecule Identification through Vibrational Spectra
2025
DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies
Bioinformatics·2025Open Access
Seamless integration of legacy robotic systems into a self-driving laboratory via NIMO: a case study on liquid handler automation
Science and Technology of Advanced Materials Methods·2025Open Access
Harnessing Explainable AI to Explore Structure–Activity Relationships in Artificial Olfaction
ACS Applied Materials & Interfaces·2025· 3 citedOpen Access
MolAtlas: a visualization framework for molecular property distributions to guide functional molecule development
2025Open Access
Optimizing progeny allocation strategies in breeding schemes while updating genomic prediction models
2025Open Access
Molecule Graph Networks with Many-Body Equivariant Interactions
Journal of Chemical Theory and Computation·2025· 3 citedOpen Access
Ab-VS: Evaluating Large Language Models for Virtual Antibody Screening via Antibody-Antigen Interaction Prediction
2025Open Access
Black-box optimization using factorization and Ising machines
arXiv (Cornell University)·2025Open Access
GPepT: A Foundation Language Model for Peptidomimetics Incorporating Noncanonical Amino Acids
ACS Medicinal Chemistry Letters·2025Open Access
Trajectory analysis reveals an uncommitted neuroblastic state in MYCN-driven neuroblastoma development
Neuro-Oncology·2025Open Access
Inverse Design of Metamaterials with Manufacturing-Guiding Spectrum-to-Structure Conditional Diffusion Model
ArXiv.org·2025Open Access
Discovery and affinity maturation of antibody fragments from an unfavorably enriched phage display selection by deep sequencing and machine learning
Journal of Bioscience and Bioengineering·2025· 2 cited
Human–AI collaboration for modeling heat conduction in nanostructures
npj Computational Materials·2025· 1 citedOpen Access
Starrydata: from published plots to shared materials data
Science and Technology of Advanced Materials Methods·2025· 4 citedOpen Access
HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen–Deuterium Exchange Data
Journal of Chemical Theory and Computation·2025Open Access
NbBench: Benchmarking Language Models for Comprehensive Nanobody Tasks
ArXiv.org·2025· 2 citedOpen Access
CRYSIM: Prediction of Symmetric Structures of Large Crystals with GPU-based Ising Machines
arXiv (Cornell University)·2025Open Access
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Frequent Co-authors

Ryo Tamura(5), Bernhard Schölkopf(4), Zhufeng Hou(4), Kei Terayama(4), Gunnar Rätsch(3), Hisashi Kashima(3), Sebastian Nowozin(3), Shenghong Ju(3), Junichiro Shiomi(3), Kiyoshi Asai(3), Tadashi Kadowaki(3), Taku Kudo(3), Tsuyoshi Kato(3), Akihiro Inokuchi(2), Atsuto Seko(2), Isao Tanaka(2), Tsuyoshi Ueno(2), Teruyasu Mizoguchi(2), Xiufeng Yang(2), Kazuki Yoshizoe(2)