PREPRINT 2026
ConforFlux: Particle-Guided Trunk Repulsion for Diverse Protein Conformations
S. Suzuki, T. Amagasa
bioRxiv
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Ph.D. Student
Graduate School of Systems and Information Engineering
University of Tsukuba
I am a Ph.D. student in Computer Science at the University of Tsukuba, supervised by Toshiyuki Amagasa at the Knowledge and Data Engineering Laboratory, where I work on conformational sampling in deep learning models of protein structure. As an undergraduate I studied under Tohru Ariizumi in the Ariizumi Laboratory, developing non-destructive, high-throughput metabolite measurement for Micro-Tom tomato mutant populations, and under Naoya Fukuda for my master's, working on genomic language models for plant genomes. I continue that work on genomic language models as a research assistant at the ROIS AI-Empowered Life Science Initiative (ALIS).
Education
Ph.D. in Computer Science
University of Tsukuba · 2025.04 - 2028.03 (expected)
M.S. in Agro-Bioresources Science
University of Tsukuba · 2023.04 - 2025.03
B.S. in Agro-Biological Resource Sciences
University of Tsukuba · 2019.04 - 2023.03
Funding & Computing
JSPS DC2
日本学術振興会 特別研究員 DC2
JSPS Research Fellowship for Young Scientists (DC2)
2026.04 - 2028.03
JST SPRING
次世代研究者挑戦的研究プログラム
Support for Pioneering Research Initiated by the Next Generation
2025.04 - 2026.03
Osaka Univ. D3 Center SQUID
世界と伍する学生育成特設枠
Special Quota for Fostering Globally Competitive Students
2026.04 - 2027.03
Research Assistant
Research Organization of Information and Systems (ROIS)
AI-Empowered Life Science Initiative (ALIS)
2026.06 - Present
National Institute of Advanced Industrial Science and Technology (AIST)
Human Informatics and Interaction Research Institute
2024.09 - 2026.03
National Agriculture and Food Research Organization (NARO)
Agro-Environmental Informatics Group
2022.04 - 2024.08
Research
My work sits on the internal representations of biological foundation models: what they encode, and how they can be steered.
Generative Models for Biomolecules
Deep generative models of protein structure and sequence, and the problem of controlling what they produce: recovering the alternative conformations a confident single prediction hides, then carrying that control into design.
Protein Structure Prediction Conformational Ensembles Inference-time Control Protein Design
Mechanistic Interpretability
The same models read from the inside: which features their representations encode, and how far those features correspond to biology we can already name. Reading them is what makes steering them deliberate.
Genomic Language Models Sparse Autoencoders Feature Decomposition Representation Analysis
Publications
PAPER 2026
Biasing Conformational Sampling in AlphaFold 3 and Boltz-2 via Pair Representation Scaling
S. Suzuki, T. Amagasa
Journal of Chemical Information and Modeling, Articles ASAP
PAPER 2025
Genomic language models with k-mer tokenization strategies for plant genome annotation and regulatory element strength prediction
S. Suzuki, K. Horie, T. Amagasa, N. Fukuda
Plant Molecular Biology, 115(4), 100
Conferences
BMB2026 - MBSJ / JBS Joint Meeting
Dec 2026Yokohama, Japan
1 presentation
- Generating diverse protein conformations by repulsion in the conditioning representation
ICBBS 2026 - 64th Annual Meeting of the BSJ
Nov 2026Poster · Busan, Korea
1 presentation
- Surfacing the alternative conformations latent in deep-learning protein structure predictors
CBI Society Annual Meeting 2026
Oct 2026Tokyo, Japan
IIBMP 2026 - JSBi Annual Meeting
Aug 2026Poster / Workshop · Sagamihara, Japan
2 presentations
- Expanding conformational sampling in diffusion-based protein structure prediction models at inference time
- ゲノム基盤モデルは雄性不稔を学んでいるか：Sparse Autoencoder による解釈 Open-call workshop: 生命の理解と設計・制御を目指すバイオ生成AI Workshop ↗
The 66th Biophysics Summer School
Aug 2026Hands-on / Poster · Nagano, Japan
2 presentations
- タンパク質構造予測のペア表現への推論時介入によるアンサンブル拡張
- ゲノム配列生成AIの仕組みと実践 Teaching assistant for the hands-on lecture by Koichi Higashi (ROIS ALIS) Lecture ↗Materials ↗
Pacific Symposium on Biocomputing (PSB) 2026
Jan 2026Poster · Hawaii, USA
1 presentation
- Predicting alternative protein conformations by perturbing pair representations
The 48th Annual Meeting of the Molecular Biology Society of Japan
Dec 2025Poster / Forum · Yokohama, Japan
1 presentation
- Steering dynamic protein structures by latent space manipulation of deep generative models
The 143rd Meeting of the Japanese Society of Breeding
Mar 2023Oral · Shizuoka, Japan
1 presentation
- Development of non-destructive, high-throughput metabolite measurement for a Micro-Tom mutant population
Awards
MBSJ-EMBO Poster Award
The 48th Annual Meeting of the Molecular Biology Society of Japan
Top 3% (51 selected from 1,599 entries)
8th Place, Protein Design Competition (EGFR)
Adaptyv Bio
Top 10 out of 130+ participants worldwide
Japan Biology Olympiad - Excellence Award
158th place out of 4,189 competitors
Top 3%