Text-Guided Object Removal for Drone-Based 3D Reconstruction with Gaussian Splatting International-journal Peer-reviewed

Kikuchi Y, Yamada KD, Koike A

IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops　2026

NexusFlow: Unifying Disparate Tasks under Partial Supervision via Invertible Flow Networks International-journal International-coauthorship Peer-reviewed

Lin F, Wang Y, Guo Y, Huang Z, Huang X, Zhang H, Yamada KD, Tu Z, Ren L, Zhang Z

IEEE/CVF Conference on Computer Vision and Pattern Recognition　2026

Physics-Aware Video Instance Removal Benchmark International-journal International-coauthorship Peer-reviewed

Li Z, Chen X, Jiang L, Hou D, Yamada KD, Lin F, Gao X, Tu Z

IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops　2026

Procedural Content Generation via Generative Artificial Intelligence International-journal International-coauthorship Peer-reviewed

Mao X., Yu W., Okawara Y., Zhan X., Yamada KD, Zielewski MR

Interdisciplinary Information Sciences　2026

Simulating Metabolic Pathways to Enhance Interpretations of Metabolome Genome-wide Association Studies International-journal Peer-reviewed

Kodate S, Sato M, Hishinuma E, Kojima K, Motoike IN, ToMMo Study Group, Koshiba S, Yamamoto M, Yamada KD, Kinoshita K

Scientific Reports　2025

Effect of Cumulative Exposure on the Efficacy of Paroxetine: a Population Pharmacokinetic-pharmacodynamic and Machine Learning Analyses International-journal Peer-reviewed

Shigetome K, Egarashi T, Tomita T, Higa N, Iwashita K, Morita K, Nishimura M, Kankeko T, Maeda H, Yamada KD, Kajiwara-Morita A, Oniki K, Yasui-Furukori N, Saruwatari J

Pharmacometrics and Systems Pharmacology　2025

GPS: A Probabilistic Distributional Similarity with Gumbel Priors for Set-to-Set Matching International-journal International-coauthorship Peer-reviewed

Lin F, Liu H, Zhang Z, Morales J, Zhang HK, Yamada KD, Kolachalama V, Saligrama V

International Conference on Learning Representations　2025

Learning Random Numbers to Realize Appendable Memory System for Artificial Intelligence to Acquire New Knowledge after Deployment International-journal International-coauthorship Peer-reviewed

Kubota A, Kodate S, Li Y, Lin F, Fukuda H, Baladram MS, Yamada KD

Interdisciplinary Information Sciences　2025

Loss Distillation via Gradient Matching for Point Cloud Completion with Weighted Chamfer Distance International-journal International-coauthorship Peer-reviewed

Lin F, Liu H, Zhou H, Hou S, Yamada KD, Fischer GS, Li Y, Zhang H, Zhang Z

IEEE/RSJ International Conference on Intelligent Robots and Systems　2024

Question generation for English reading comprehension exercises using Transformers International-journal Peer-reviewed

Maas A, Yamada KD, Nagahama T, Kawada T, Horita T

Letters on Informatics and Interdisciplinary Research　2024

InfoCD: A contrastive chamfer distance loss for point cloud completion International-journal International-coauthorship Peer-reviewed

Lin F, Yue Y, Zhang Z, Hou S, Yamada KD, Kolachalama VB, Saligrama V

Advances in Neural Information Processing Systems　2023

Hyperbolic chamfer distance for point cloud completion International-journal International-coauthorship Peer-reviewed

Lin F, Yue Y, Hou S, Yu X, Xu Y, Yamada KD, Zhang Z

International Conference on Computer Vision　2023

Serum fatty acid composition balance by fuzzy c-means method in individuals with or without metabolic dysfunction-associated fatty liver disease International-journal Peer-reviewed

Nagase Y, Satoh T, Shigetome K, Tokumaru N, Matsumoto E, Yamada KD, Imafuku T, Watanabe H, Maruyama T, Ogata Y, Yoshida M, Saruwatari J, Oniki K

Nutrients　15　(4)　809-809　2023

DOI： 10.3390/nu15040809 　

eISSN： 2072-6643

Identifying latent traits of questions for controllable machine generation International-journal Peer-reviewed

Maas A, Kawada T, Yamada K, Nagahama T, Horita T

EdMedia + Innovate Learning　2022

Redox imaging of dextran sodium sulfate-induced colitis mice treated with nitric oxide synthase inhibitors International-journal Peer-reviewed

Yasukawa K, Yamada K, Tokuda H, Koyama S, Utsumi H

Advances in Redox Research　6　100047-100047　2022

DOI： 10.1016/j.arres.2022.100047 　

ISSN： 2667-1379

Relation is an option for processing context information International-journal Peer-reviewed

Yamada KD, Baladram MS, Lin F

Frontiers in Artificial Intelligence　5　2022

DOI： 10.3389/frai.2022.924688 　

eISSN： 2624-8212

Cosmos Propagation Network: Deep learning model for point cloud completion International-journal Peer-reviewed

Lin F, Xu Y, Zhang Z, Gao C, Yamada KD

Neurocomputing　507　221-234　2022

DOI： 10.1016/j.neucom.2022.08.007 　

ISSN： 0925-2312

Progress in research on implementing machine consciousness International-journal Peer-reviewed

Yamada KD, Baladram MS, Lin F

Interdisciplinary Information Sciences　28　(1)　95-105　2022

DOI： 10.4036/iis.2022.r.02 　

ISSN： 1340-9050

eISSN： 1347-6157

An effective convolutional neural network for visualized understanding transboundary air pollution based on Himawari-8 satellite images International-journal Peer-reviewed

Lin F, Gao C, Yamada KD

IEEE Geoscience and Remote Sensing Letters　19　1-5　2022

DOI： 10.1109/LGRS.2021.3102939 　

Developing a novel recurrent neural network architecture with fewer parameters and good learning performance International-journal Peer-reviewed

Yamada KD, Lin F, Nakamura T

Interdisciplinary Information Sciences　27　(1)　25-40　2021

DOI： 10.4036/iis.2020.r.01 　

ISSN： 1340-9050

eISSN： 1347-6157

Introduction to supervised machine learning for data science International-journal Peer-reviewed

Baladram MS, Koike A, Yamada KD

Interdisciplinary Information Sciences　26　(1)　87-121　2020

DOI： 10.4036/iis.2020.a.03 　

ISSN： 1340-9050

eISSN： 1347-6157

In vivo redox imaging of dextran sodium sulfate-induced colitis in mice using Overhauser-enhanced magnetic resonance imaging International-journal Peer-reviewed

Yasukawa K, Hirago A, Yamada K, Tun X, Ohkuma K, Utsumi H

Free Radical Biology and Medicine　136　1-11　2019

DOI： 10.1016/j.freeradbiomed.2019.03.025 　

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization International-journal Peer-reviewed

Katoh K, Rozewicki J, Yamada KD

Briefings in Bioinformatics　20　(4)　1160-1166　2019

DOI： 10.1093/bib/bbx108 　

ISSN： 1467-5463

eISSN： 1477-4054

De novo profile generation based on sequence context specificity with the long short-term memory network International-journal Peer-reviewed

Yamada KD, Kinoshita K

BMC Bioinformatics　2018

DOI： 10.1186/s12859-018-2284-1 　

Parallelization of MAFFT for large-scale multiple sequence alignments International-journal Peer-reviewed

Nakamura T, Yamada KD, Tomii K, Katoh K

Bioinformatics　34　(14)　2490-2492　2018

DOI： 10.1093/bioinformatics/bty121 　

ISSN： 1367-4803

eISSN： 1460-2059

Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment International-journal Peer-reviewed

Yamada KD

Algorithms for molecular biology　2018

DOI： 10.1186/s13015-018-0123-6 　

Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on crystal-packing propensity of amino acids International-journal Peer-reviewed

Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K

Acta Crystallographica Section D　73　(Pt 9)　757-766　2017

DOI： 10.1107/S2059798317010932 　

Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach International-journal International-coauthorship Peer-reviewed

Yamada KD, Omori S, Nish H, Miyagi M

BMC Bioinformatics　18　(1)　289-289　2017

DOI： 10.1186/s12859-017-1699-4 　

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix International-journal Peer-reviewed

Lim K, Yamada KD, Frith MC, Tomii K

Journal of Structural and Functional Genomics　17　(4)　147-154　2016

DOI： 10.1007/s10969-016-9210-4 　

Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees International-journal Peer-reviewed

Yamada KD, Tomii K, Katoh K

Bioinformatics　32　(21)　3246-3251　2016

DOI： 10.1093/bioinformatics/btw412 　

ISSN： 1367-4803

eISSN： 1460-2059

Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins International-journal Peer-reviewed

Yamada KD, Nishi H, Nakata J, Kinoshita K

Biophysics and Physicobiology　13　157-163　2016

DOI： 10.2142/biophysico.13.0_157 　

Identification of hepta-histidine as a candidate drug for Huntington’s disease by in silico-in vitro-in vivo-integrated screens of chemical libraries International-journal International-coauthorship Peer-reviewed

Imamura T, Fujita K, Tagawa K, Ikura T, Chen X, Homma H, Tamura T, Mao Y, Taniguchi JB, Motoki K, Nakabayashi M, Ito N, Yamada K, Tomii K, Okano H, Kaye J, Finkbeiner S, Okazawa H

Scientific Reports　6　33861-33861　2016

DOI： 10.1038/srep33861 　

Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2 International-journal Peer-reviewed

Kakisaka M, Yamada K, Yamaji-Hasegawa A, Kobayashi T, Aida Y

Virology　496　116-126　2016

DOI： 10.1016/j.virol.2016.05.018 　

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment International-journal International-coauthorship Peer-reviewed

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ

Proteins　84　(S1)　323-348　2016

DOI： 10.1002/prot.25007 　

ISSN： 0887-3585

eISSN： 1097-0134

Systematic exploration of an efficient amino acid substitution matrix: MIQS International-journal Peer-reviewed

Tomii K, Yamada K

Methods in Molecular Biology　2016

DOI： 10.1007/978-1-4939-3572-7_11 　

A new genotype of bovine leukemia virus in South America identified by NGS-based whole genome sequencing and molecular evolutionary genetic analysis International-journal International-coauthorship Peer-reviewed

Polat M, Takeshima SN, Hosomichi K, Kim J, Miyasaka T, Yamada K, Arainga M, Murakami T, Matsumoto Y, de la Barra Diaz V, Panei CJ, González ET, Kanemaki M, Onuma M, Giovambattista G, Aida Y

Retrovirology　13　2016

DOI： 10.1186/s12977-016-0239-z 　

eISSN： 1742-4690

Refinement of Amino Acid Substitution Matrix for Detecting Distant Relationships of Proteins Peer-reviewed

Yamada K, Tomii K

Seibutsu Butsuri　55　(3)　133-136　2015

DOI： 10.2142/biophys.55.133 　

ISSN： 0582-4052

eISSN： 1347-4219

A novel antiviral target structure involved in the RNA binding, dimerization, and nuclear export functions of the influenza A virus nucleoprotein International-journal Peer-reviewed

Kakisaka M, Sasaki Y, Yamada K, Kondoh Y, Hikono H, Osada H, Tomii K, Saito T, Aida Y

PLOS Pathogens　11　(7)　e1005062　2015

DOI： 10.1371/journal.ppat.1005062 　

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs International-journal Peer-reviewed

Ito JI, Ikeda K, Yamada K, Mizuguchi K, Tomii K

Nucleic Acids Research (NAR)　2015

DOI： 10.1093/nar/gku1144 　

Comparative analysis of seven viral nuclear export signals (NESs) reveals the crucial role of nuclear export mediated by the third NES consensus sequence of nucleoprotein (NP) in influenza A virus replication International-journal Peer-reviewed

Chutiwitoonchai N, Kakisaka M, Yamada K, Aida Y

PLOS ONE　9　(8)　e105081　2014

DOI： 10.1371/journal.pone.0105081 　

Revisiting amino acid substitution matrices for identifying distantly related proteins International-journal Peer-reviewed

Yamada K, Tomii K

Bioinformatics　2014

DOI： 10.1093/bioinformatics/btt694 　

Importin α3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function International-journal Peer-reviewed

Sasaki Y, Hagiwara K, Kakisaka M, Yamada K, Murakami T, Aida Y

PLOS ONE　8　(1)　e55765　2013

DOI： 10.1371/journal.pone.0055765 　

Identification of a novel compound with antiviral activity against influenza A virus depending on PA subunit of viral RNA polymerase International-journal Peer-reviewed

Yamada K, Koyama H, Hagiwara K, Ueda A, Sasaki Y, Kanesashi SN, Ueno R, Nakamura HK, Kuwata K, Shimizu K, Suzuki M, Aida Y

Microbes and Infection　14　(9)　740-7　2012

DOI： 10.1016/j.micinf.2012.02.012 　

Discovery of novel antiviral agents directed against the influenza A virus nucleoprotein using photo-cross-linked chemical arrays International-journal Peer-reviewed

Hagiwara K, Kondoh Y, Ueda A, Yamada K, Goto H, Watanabe T, Nakata T, Osada H, Aida Y

Biochemical and Biophysical Research Communications　394　(3)　721-7　2010

DOI： 10.1016/j.bbrc.2010.03.058