Ryoji Kubo

Portrait of Ryoji Kubo

Computer Science · National University of Singapore Contact: ryoji[last_name][at]u.nus.edu

About

I’m a second-year PhD student at the School of Computing, National University of Singapore, advised by Xavier Bresson.

Previously, I worked as a research fellow at New York University Abu Dhabi, advised by Djellel Difallah. I received my Bachelor of Science from NYU Abu Dhabi, majoring in Computer Science and Mathematics.

Research

My research interests are AI for science, graph machine learning, and deep learning. I’m especially interested in applying machine learning to materials science. Can we build models that respect physical constraints and generate materials that can be synthesized?

News

  • DBRAG was accepted to the AACL-IJCNLP main conference. See you in Hengqin!

  • RAW-Explainer was accepted to Learning on Graphs. See you in Boston!

  • Selected for the NUS School of Computing Teaching Fellowship Scheme.

  • Started my PhD in Computer Science at the National University of Singapore.

Publications

  • DBRAG: Multi-Table Retrieval-Augmented Generation for Complex Database Queries

    Prince Larbi Ampofo, Ryoji Kubo, Djellel Difallah

    AACL-IJCNLP 2026 · Accepted, main conference

    DBRAG answers questions whose evidence is spread across multiple database tables. It retrieves and reranks relevant tables, then uses program-aided reasoning over their full contents while keeping the language model’s initial context compact.

  • Composable Crystals: Controllable Materials Discovery via Concept Learning

    Nian Liu, Yuwei Zeng, Ryoji Kubo, Nikita Kazeev, Stephen Gregory Dale, Artem Maevskiy, Pengru Huang, Thomas Laurent, Kostya S. Novoselov, Xavier Bresson

    Preprint · 2026

    We learn reusable crystal concepts that capture local atomic environments and global symmetry, then recombine them to guide the generation of new materials. This gives more control over exploration beyond known structures and improves the discovery of novel crystals.

  • Crys-JEPA: Accelerating Crystal Discovery via Embedding Screening and Generative Refinement

    Nian Liu, Nikita Kazeev, Stephen Gregory Dale, Artem Maevskiy, Yuwei Zeng, Ryoji Kubo, Pengru Huang, Thomas Laurent, Yann LeCun, Kostya S. Novoselov, Xavier Bresson

    Preprint · 2026

    Crys-JEPA learns crystal representations that preserve differences in formation energy, allowing candidate stability to be assessed through embedding comparisons. Promising candidates are then used to refine the generator, improving the search for crystals that are both stable and novel.

  • XGExplainer: Robust Evaluation-based Explanation for Graph Neural Networks

    Ryoji Kubo, Djellel Difallah

    SIAM International Conference on Data Mining (SDM) · 2024

    XGExplainer improves graph-neural-network explanations by training a separate evaluator on randomized subgraphs. This helps existing explanation methods recognize informative subgraphs even when they differ from the data used to train the original prediction model.

Selected Awards

  • NUS School of Computing Teaching Fellowship

    Selected as one of two Computer Science PhD students recognized for exceptional teaching.

  • NYU Abu Dhabi Post-graduation Research Fellowship

    A highly selective research fellowship for graduating NYU Abu Dhabi students.

Teaching

  • Semester I, AY 2026/2027

    Graph Machine Learning (CS5284)

    Teaching Assistant · National University of Singapore

  • Semester II, AY 2025/2026

    Neural Networks and Deep Learning (CS5242)

    Teaching Assistant · National University of Singapore

  • Semester I, AY 2025/2026

    Graph Machine Learning (CS5284)

    Teaching Assistant · National University of Singapore

  • Spring Semester, AY 2024/2025

    Directed Study: Graph Machine Learning (CS-UH 3250)

    Teaching Assistant · NYU Abu Dhabi

Professional service

  • 2025/26

    Student Chair, AI Area Search Committee for Faculty Hiring

    National University of Singapore

  • Post-graduation Research Fellow Selection Committee

    Committee member · NYU Abu Dhabi