• April 24, 2024. 15:30-17:00 Fugaku monthly seminar on Zoom

  • Invited speaker

  • Dr. Tsuyoshi Ishizone (Meiji University)
    石曽根 毅 博士 (明治大学)

  • Language
    English

  • Title
    Representation Learning for Biomolecule Dynamics

  • Abstract
    Protein strucure / conformational space are often high-dimensional and diffucult to interpret. To provide interpretability and improve downstream tasks such as Markov state model construction, representation learning are useful. In this talk, we first explain basis of neural network and representation learning followed by representation learning for protein dynamics. The methodologies include the existing continuous embedding methods and methods we previously developed. We will explain our in silico experiment and compare the representation learning methods for chignolin folding dynamics.

• April 19-22, 2024. Participated in International Conference on Theoretical and High Performance Computational Chemistry 2024 (ICT-HPCC24) held in Wuhan, Chia. Dr. Matsunaga served as the chair of the conference. Dr. Matsunaga, Dr. Brandani, and Dr. Miyashita gave invited talks from this project.  

• February 28, 2024. 15:30-17:00 Fugaku monthly seminar on Zoom

  • Invited speaker
    Dr. Atsushi Tokuhisa (Senior Scientist, RIKEN Center for Computational Science, HPC- and AI-driven Drug Development Platform Division, Biomedical Computational Intelligence Unit)
    徳久 淳師 博士 (上級研究員 理化学研究所 計算科学研究センター HPC/AI駆動型医薬プラットフォーム部門 バイオメディカル計算知能ユニット)

  • Language
    Japanese

  • Title
    Accelerating AI Inference of Protein 3D Structures utilizing the Supercomputer “Fugaku” for Genome-Scale Simulations
    ゲノム規模のシミュレーションを目指した、スーパーコンピューター「富岳」を活用したタンパク質構造推論AIの高速化

  • Abstract
    We report that the developed “OpenFold-for-Fugaku" dramatically improves the throughput of protein 3D structure inference by using multiple nodes in the supercomputer “Fugaku”.  We believe that the achievements enable for realizing genome-scale simulations. https://github.com/RIKEN-RCCS/OpenFold-for-Fugaku
    開発した「OpenFold-for-Fugaku」は、スーパーコンピュータ「富岳」の複数ノードを利用することで、タンパク質の立体構造推論のスループット性を飛躍的に向上することを報告する。この成果により、ゲノムスケールシミュレーションの実現が期待できる。 https://github.com/RIKEN-RCCS/OpenFold-for-Fugaku

• January 31, 2024. 15:30-17:40 Fugaku monthly seminar on Zoom

  • Invited speaker
    Dr. Koya Sakuma (Nagoya University)
    佐久間 航也 博士 (名古屋大学)

  • Language
    Japanese

  • Title
    AlphaFold2について：とくに構造モジュールの仕組み

  • Abstract
    AlphaFold2は構造生物学や構造バイオインフォマティイクス界隈に多大な影響を与えた。その予測性能に注目が集まりがちであるが、深層学習をEnd-to-endな形で立体構造予測問題に適用したという点でもAlphaFold2は革新的であった。AlphaFold2はEncoderとしてEvoformerを、DecoderとしてStructure moduleを備えた、広い意味でのTransformerモデルと解釈することができる。本セミナーでは、特に「デコーディングとしての立体構造モデリング」を担当するStructure moduleについて、AF2原著論文の情報などに基づき議論した上で、その利用可能性などにも触れる。

• January 9-10, 2024. 富岳成果創出プログラム標準課題ワークショップ Workshop on "Program for Promoting Researches on the Supercomputer Fugaku"

Venue:

6F IIB salon @ RIKEN Integrated Innovation Building (IIB)

Address 住所 兵庫県神戸市中央区港島南町６丁目７−１

https://koberc.jp/iib-salon/

https://ithems.riken.jp/en/access/integrated-innovation-building

Connected by a pedestrian bridge from the port liner Iryo Center station, 

and the entrance is on the 2nd floor. 

Please receive a guest ID card from the security guard and go to the 6F floor.

ポートライナー医療センター駅から歩道橋でつながっており

2Fが入口です。守衛さんにゲストIDカードをもらって6Fへ上がってください。

Program:

Jan. 9th

13:00-13:30 Matsunaga group (including discussion)

13:30-14:00 Takada group (including discussion)

15 minutes break

14:15-14:45 Tama group (including discussion)

14:45-15:15 Mori group (including discussion)

15 minutes break

15:30-16:00 Kobayashi group (including discussion)

16:00-16:30 Nakamura group (including discussion)

10 minutes break

16:40-17:30 Invited talk by Dr. Yuji Sugita (RIKEN)

Jan. 10th

10:00 - 10:45 Discussion on GENESIS and ML/AI (discussion leader: Matsunaga)

15 minutes break

11:00 - 12:30 Talks by post-docs and students (10 minuites slot including discussion. some talks are given in Japanese)

Tsuyoshi Ishizone (Meiji Univ) Onsight
Yu Han (Meiji Univ) Onsight

   Riku Sugiura (Meiji Univ) Onsight
Soichiro Oda (Saitama Univ) Onsight

    Ryuhei Oshima (Saitama Univ) via Zoom
    Hironori Matsubara (Saitama Univ) via Zoom

• August 9-10, 2023. International workshop on “Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems” was held at RIKEN Wako Campus, co-hosted by this project. The organizers are Dr. Sugita (RIKEN), Dr. Yagi (RIKEN), Prof. Okamoto (Nagoya Univ.) and Dr. Matsunaga. Dr. Matsunaga, Dr. Brandani, and Dr. Miyashita gave invited talks form this project. 

• April 28, 2023. The kick-off meeting for this project was held.