List of use cases of HomCloud

By our research group and collabolators

• Materials science

  • Emi Minamitani, Takenobu Nakamura, Ippei Obayashi & Hideyuki Mizuno. Persistent homology elucidates hierarchical structures responsible for mechanical properties in covalent amorphous solids. Nature Communications 16, Article number: 8226 (2025). https://doi.org/10.1038/s41467-025-63424-z

  • Michiki Taniwaki, Ryunosuke Nagaoka, Ken Masuzawa, Shunsuke Sato, Alexandre Lira Foggiatto, Chiharu Mitsumata, Takahiro Yamazaki, Ippei Obayashi, Yasuaki Hiraoka, Yasuhiko Igarashi, Yuta Mizutori, Sepehri Amin Hossein, Tadakatsu Ohkubo, Hisashi Mogi and Masato Kotsugi. Automated identification of the origin of energy loss in nonoriented electrical steel by feature extended Ginzburg–Landau free energy framework. Scientific Reports. 15, Article number: 23758 (2025). https://doi.org/10.1038/s41598-025-00357-z

  • Misato Tone, Shunsuke Sato, Sotaro Kunii, Ippei Obayashi, Yasuaki Hiraoka, Yui Ogawa, Hirokazu Fukidome, Alexandre Lira Foggiatto, Chiharu Mitsumata, Ryunsuke Nagaoka, Arpita Varadwaj, Iwao Matsuda, and Masato Kotsugi. Linking structure and process in dendritic growth using persistent homology with energy analysis. Science and Technology of Advanced Materials: Methods. 5(1), (2025) https://doi.org/10.1080/27660400.2025.2475735

  • Naoto Kitamura, Hikari Matsubara, Koji Kimura, Ippei Obayashi, Yohei Onodera, Ken Nakashima, Hidetoshi Morita, Motoki Shiga, Yasuhiro Harada, Chiaki Ishibashi, Yasushi Idemoto and Koichi Hayashi. Relationship between network topology and negative electrode properties in Wadsley–Roth phase TiNb2O7. NPG Asia Materials, 16, Article number: 62 (2024). https://doi.org/10.1038/s41427-024-00581-5

  • R. Nagaoka, K. Masuzawa, M. Taniwaki, A. L. Foggiatto, T. Yamazaki, I. Obayashi, Y. Hiraoka, C. Mitsumata, M. Kotsugi. Quantification of the coercivity factor in soft magnetic materials at different frequencies using topological data analysis. IEEE Transactions on Magnetics, 60 (9), Art no. 4000305, 1–5, (2024). https://doi.org/10.1109/TMAG.2024.3408002

  • A. L. Foggiatto, R. Nagaoka, M. Taniwaki, T. Yamazaki, T. Ogasawara, I. Obayashi, Y. Hiraoka, C. Mitsumata, M. Kotsugi. Analysis of the excess loss in high-frequency magnetization process through machine learning and topological data analysis. vol. 60, no. 9, pp. 1-5, Sept. 2024, Art IEEE Transactions on Magnetics, 60 (9), Art no. 7001305, 1–5 (2024). https://doi.org/10.1109/TMAG.2024.3406717

  • Yuta Shuseki, Shinji Kohara, Tomoaki Kaneko, Keitaro Sodeyama, Yohei Onodera, Chihiro Koyama, Atsunobu Masuno, Shunta Sasaki, Shohei Hatano, Motoki Shiga, Ippei Obayashi, Yasuaki Hiraoka, Junpei T. Okada, Akitoshi Mizuno, Yuki Watanabe, Yui Nakata, Koji Ohara, Motohiko Murakami, Matthew G. Tucker, Marshall T. McDonnell, Hirohisa Oda, and Takehiko Ishikawa. Atomic and Electronic Structure in MgO–SiO2. J. Phys. Chem. A 128 (4), 716–726 (2024). https://doi.org/10.1021/acs.jpca.3c05561

  • Emi Minamitani, Ippei Obayashi, Koji Shimizu, and Satoshi Watanabe. Persistent homology-based descriptor for machine-learning potential of amorphous structures. The Journal of Chemical Physics 159, 084101 (2023). https://doi.org/10.1063/5.0159349

  • Ippei Obayashi, and Masao Kimura. Persistent homology analysis with nonnegative matrix factorization for 3D voxel data of iron ore sinters. JSIAM Letters 14, 151–154 (2022) https://doi.org/10.14495/jsiaml.14.151

  • Emi Minamitani, Takuma Shiga, Makoto Kashiwagi, and Ippei Obayashi. Topological descriptor of thermal conductivity in amorphous Si. J. Chem. Phys. 156, 244502 (2022) https://doi.org/10.1063/5.0093441

  • Emi Minamitani, Takuma Shiga, Makoto Kashiwagi, and Ippei Obayashi. Relationship between local coordinates and thermal conductivity in amorphous carbon. Journal of Vacuum Science & Technology A 40, 033408 (2022). https://doi.org/10.1116/6.0001744

  • Yohei Onodera, Shinji Kohara, Philip S. Salmon, Akihiko Hirata, Norimasa Nishiyama, Suguru Kitani, Anita Zeidler, Motoki Shiga, Atsunobu Masuno, Hiroyuki Inoue, Shuta Tahara, Annalisa Polidori, Henry E. Fischer, Tatsuya Mori, Seiji Kojima, Hitoshi Kawaji, Alexander I. Kolesnikov, Matthew B. Stone, Matthew G. Tucker, Marshall T. McDonnell, Alex C. Hannon, Yasuaki Hiraoka, Ippei Obayashi, Takenobu Nakamura, Jaakko Akola, Yasuhiro Fujii, Koji Ohara, Takashi Taniguchi and Osami Sakata. Structure and properties of densified silica glass: characterizing the order within disorder. NPG Asia Materials volume 12, 85 (2020). https://doi.org/10.1038/s41427-020-00262-z

  • Akihiko Hirata, Tomohide Wada, Ippei Obayashi and Yasuaki Hiraoka. Structural changes during glass formation extracted by computational homology with machine learning. Communications Materials 1, 98 (2020). https://doi.org/10.1038/s43246-020-00100-3

  • Chihiro Koyama, Shuta Tahara, Shinji Kohara, Yohei Onodera, Didrik R. Småbråten, Sverre M. Selbach, Jaakko Akola, Takehiko Ishikawa, Atsunobu Masuno, Akitoshi Mizuno, Junpei. T. Okada, Yuki Watanabe, Yui Nakata, Koji Ohara, Haruka Tamaru, Hirohisa Oda, Ippei Obayashi, Yasuyuki Hiraoka, and Osami Sakata. Very sharp diffraction peak in non-glass forming liquid with the formation of distorted tetraclusters. NPG Asia Materials 12, 43, (2020). https://doi.org/10.1038/s41427-020-0220-0

  • Emi Minamitani, Takuma Shiga, Makoto Kashiwagi, and Ippei Obayashi. Relationship between local coordinates and thermal conductivity in amorphous carbon. Journal of Vacuum Science & Technology A 40, 033408 (2022). https://doi.org/10.1116/6.0001744

  • Yohei Onodera, Yasuyuki Takimoto, Hiroyuki Hijiya, Taketoshi Taniguchi, Shingo Urata, Seiji Inaba, Sanae Fujita, Ippei Obayashi, Yasuaki Hiraoka and Shinji Kohara. Origin of the mixed alkali effect in silicate glass. NPG Asia Materials 11 75 (2019). https://doi.org/10.1038/s41427-019-0180-4

  • Yohei ONODERA, Shinji KOHARA, Shuta TAHARA, Atsunobu MASUNO, Hiroyuki INOUE, Motoki SHIGA, Akihiko HIRATA, Koichi TSUCHIYA, Yasuaki HIRAOKA, Ippei OBAYASHI, Koji OHARA, Akitoshi MIZUNO, and Osami SAKATA. Understanding diffraction patterns of glassy, liquid and amorphous materials via persistent homology analyses. Journal of the Ceramic Society of Japan 2019 127(12) 853–863, (2019). (article (open access))

  • M. Murakami, S. Kohara, N. Kitamura, J. Akola, H. Inoue, A. Hirata, Y. Hiraoka, Y. Onodera, I. Obayashi, J. Kalikka, N. Hirao, T. Musso, A. S. Foster, Y. Idemoto, O. Sakata, and Y. Ohishi. Ultrahigh-pressure form of SiO2 glass with dense pyrite-type crystalline homology. Phys. Rev. B 99, 045153 (2019). (article)

  • M. Kimura, I. Obayashi, Y. Takeichi, R. Murao, and Y. Hiraoka. Non-empirical identification of trigger sites in heterogeneous processes using persistent homology. Scientific Reports 8, 3553, (2018). (article (open access))

  • Takashi Ichinomiya, Ippei Obayashi, and Yasuaki Hiraoka. Persistent homology analysis of craze formation. Phys. Rev. E 95, 012504, (2017) . (article)

• Geology
  • Anna Suzuki, Miyuki Miyazawa, James M. Minto, Takeshi Tsuji, Ippei Obayashi, Yasuaki Hiraoka, an Takatoshi Ito. Flow estimation solely from image data through persistent homology analysis. Scientific Reports 11, 17948 (2021). https://doi.org/10.1038/s41598-021-97222-6
  • A.Suzuki, M.Miyazawa, A.Okamoto, H.Shimizu, I.Obayashi, Y.Hiraoka, T.Tsuji, P.K.Kang, and T.Ito. Inferring fracture forming processes by characterizing fracture network patterns with persistent homology. Computers & Geosciences 143, 104550 (2020). https://doi.org/10.1016/j.cageo.2020.104550

• Life science

  • Structural biology
    • Takashi Ichinomiya, Ippei Obayashi, and Yasuaki Hiraoka. Protein folding analysis using features obtained by persistent homology. Biophysical Journal 118, 2926–2937, (2020). https://doi.org/10.1016/j.bpj.2020.04.032
  • Medical science
    • Asuka Oyama, Yasuaki Hiraoka, Ippei Obayashi, Yusuke Saikawa, Shigeru Furui, Kenshiro Shiraishi, Shinobu Kumagai, Tatsuya Hayashi and Jun’ichi Kotoku. Hepatic tumor classification using texture and topology analysis of non-contrast-enhanced three-dimensional T1-weighted MR images with a radiomics approach. Scientific Reports 9, 8764 (2019). (article (open access))

Other use cases

• Materials science
  • Takayuki Shiraiwa, Shoya Kato, Fabien Briffod, Manabu Enoki. Exploration of outliers in strength-ductility relationship of dual-phase steels

  • Yohei Shimizu, Takanori Kurokawa, Hirokazu Arai, Hitoshi Washizu. Higher-order structure of polymer melt described by persistent homology: Applications to the atomic data of polymer copmuted by MD simulations

  • Fumihiko Uesugi, Masashi Ishii. Classification for transmission electron microscope images from different amorphous states using persistent homology: TEM image analysis with ML

  • Isshin Ando, Yasutaka Mugita, Kyosuke Hirayama, Shinji Munetoh, Masatoshi Aramaki, Fei Jiang, Takeshi Tsuji, Akihisa Takeuchi, Masayuki Uesugi, Yukiko Ozaki. Elucidation of pore connection mechanism during ductile fracture of sintered pure iron by applying persistent homology to 4D images of pores: Role of open pore

  • Sungyeon Hong, Donghun Kim. Medium-range order in amorphous ices revealed by persistent homology

  • Ryosuke Yano, Minkyu Kim. Topological analysis of pattern formation in cooling granular gases confined by elastic wall

  • 松原典恵, 藤元伸悦, 谷口裕一, 林敬一. 分子動力学シミュレーションを用いた熱硬化性高分子材料の解析

  • 長島大, 畑尾卓也. 分子動力学計算と機械学習による熱硬化性樹脂に関する階層的構造-物性相関解析

  • Martin Cramer Pedersen, Vanessa Robins, Kell Mortensen, Jacob J. K. Kirkensgaard. Evolution of local motifs and topological proximity in self-assembled quasi-crystalline phases: 3D quasi-crystal

  • Ryuhei Sato, Shinya Kawakami, Hirotaka Ejima, Takahiro Ujii, Koichi Sato, Takanori Ichiki, and Yasushi Shibuta. Dynamic Correlation Analysis between Stress–Strain Curve and Polymer Film Structure Using Persistent Homology. Journal of Chemical Theory and Computation. 20 (24) 10751–11104 (2024)
• Life science
  • Medical science
    • Y. Kawata, N. Niki, M. Kusumoto, H. Ohamatsu, K. Aokage, G. Ishii, Y. Matsumoto, T. Tsuchida, K. Eguchif, M. Kaneko. Representation of texture structures with topological data analysis for stage IA lung adenocarcinoma in three-dimensional thoracic CT images: Analysis of tumor images obtained by 3D thoracic CT

    • Keita Koseki, Hiroshi Kawasaki, Toru Atsugi, Miki Nakanishi, Makoto Mizuno, Eiji Naru, Tamotsu Ebihara, Masayuki Amagai, Eiryo Kawakami. Assessment of skin barrier function using skin images with topological data analysis

    • Ysanne Pritchard, Aikta Sharma, Claire Clarkin, Helen Ogden, Sumeet Mahajan, Rubén J. Sánchez-García. Persistent homology analysis distinguishes pathological bone microstructure in non-linear microscopy images

    • Kohei Watarai, Hajime Omura, Teruya Minamoto, Esophageal Abnormality Detection from Endoscopic Images Using DT-CDWT and Persistent Homology

    • Hunter Dlugas. Electrocardiogram feature extraction and interval measurements using optimal representative cycles from persistent homology

    • Kei Takahashi, Ko Abe, Shimpei I. Kubota, Noriaki Fukatsu, Yasuyuki Morishita, Yasuhiro Yoshimatsu, Satoshi Hirakawa, Yoshiaki Kubota, Tetsuro Watabe, Shogo Ehata, Hiroki R. Ueda, Teppei Shimamura, Kohei Miyazono. An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis

  • Developmental biology

    • Yukiko Nakaya, Mitsusuke Tarama, Sohei Tasaki, Ayako Isomura, Tatsuo Shibata. Migrating mesoderm cells self-organize into a dynamic meshwork structure during chick gastrulation
• Geology

  • 鈴木和将, Huynh Quang Huy Viet, 宇田智紀, 水藤寛. デジタル廃棄物モデルを利用した間隙幾何情報の抽出及び評価法の検討

  • Majid Bizhani, Omid Haeri Ardakani. Pore Characterization of Organic-Rich Shales through Application of Topological Data Analysis and Persistent Homology: Analysis of voxel data of organic-rich shales

• QCD (quantum chromodynamics)

  • Hiroaki Kouno, Kouji Kashiwa, Takehiro Hirakida. Z3-QCD and persistent homology

  • Takehiro Hirakida, Kouji Kashiwa, Junpei Sugano, Junichi Takahashi, Hiroaki Kouno, Masanobu Yahiro. Persistent homology analysis of deconfinement transition in effective Polyakov-line model

  • Kouji Kashiwa, Takehiro Hirakida, Hiroaki Kouno. Persistent homology analysis for dense QCD effective model with heavy quarks

• CFD (computational fluid dynamics)
  • 伊藤雅仁, 奥脇弘次, 望月祐志, 小杉範仁. 題名：2次元翼モデルの可視化CFD結果に関する深層学習と位相的データ解析（Deep learning and Topological Data Analysis for Visualized CFD Results of 2-dimensional Wing Model）
• Astrophysics P. Santamarina Guerrero, Yukio Katsukawa, Shin Toriumi, and D. Orozco Suárez. Persistent Homology Analysis for Solar Magnetograms. The Astrophysical Journal 964 (1) Article number:32 (2024)