Hirofumi Tsuruta

Hirofumi Tsuruta, Hiroyuki Yamazaki, Ryota Maeda et al.

Antibodies have become an important class of therapeutic agents to treat human diseases. To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria. However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences. To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens. By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences. All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method. Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein. This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations. We report experimental benchmark results on AVIDa-hIL6 by using machine learning models. The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants. The dataset is available at https://avida-hil6.cognanous.com.

Hirofumi Tsuruta, Yukari Katsura, Masaya Kumagai

Machine learning (ML) is becoming increasingly popular for predicting material properties to accelerate materials discovery. Because material properties are strongly affected by its crystal structure, a key issue is converting the crystal structure into the features for input to the ML model. Currently, the most common method is to convert the crystal structure into a graph and predicting its properties using a graph neural network (GNN). Some GNN models, such as crystal graph convolutional neural network (CGCNN) and atomistic line graph neural network (ALIGNN), have achieved highly accurate predictions of material properties. Despite these successes, using a graph to represent a crystal structure has the notable limitation of losing the crystal structure's three-dimensional (3D) information. In this work, we propose DeepCrysTet, a novel deep learning approach for predicting material properties, which uses crystal structures represented as a 3D tetrahedral mesh generated by Delaunay tetrahedralization. DeepCrysTet provides a useful framework that includes a 3D mesh generation method, mesh-based feature design, and neural network design. The experimental results using the Materials Project dataset show that DeepCrysTet significantly outperforms existing GNN models in classifying crystal structures and achieves state-of-the-art performance in predicting elastic properties.

Fumikazu Konishi, Yuuki Tsubouchi, Hirofumi Tsuruta

SAKURAONE is a managed high performance computing (HPC) cluster developed and operated by the SAKURA Internet Research Center. It builds on the KOKARYOKU PHY bare metal GPU platform and is optimized for advanced workloads, including large language model (LLM) training. In ISC 2025 TOP500, SAKURAONE is ranked 49th by HPL and is the only top 100 system that uses a fully open networking stack - 800 GbE with SONiC - demonstrating the scalability of vendor-neutral technology. Measured performance is 33.95 PFLOP/s (HPL Rmax), 396.295 TFLOP/s (HPCG), and 339.86 PFLOP/s on HPL-MxP with FP8. The system consists of 100 nodes, each with eight NVIDIA H100 GPUs and a 2 PB all-flash Lustre file system, interconnected via a rail-optimized 800 GbE leaf-spine fabric with RoCEv2. Through exclusive use by a single research project, we observed the characteristics of development-related jobs. Consistent with previous HPC studies, small-scale jobs dominated in number, while a few large-scale jobs accounted for most GPU resource time. As the project progressed, resource use shifted from large-scale to mid-scale jobs, reflecting a transition from initial large-scale training to iterative refinement. These observations illustrate the real-world utilization dynamics of GPU clusters under unified project workloads.

Yifan Sun, Hirofumi Tsuruta, Masaya Kumagai et al.

Thirteen years after the Fukushima Daiichi nuclear power plant accident, Japan's nuclear energy accounts for only approximately 6% of electricity production, as most nuclear plants remain shut down. To revitalize the nuclear industry and achieve sustainable development goals, effective communication with Japanese citizens, grounded in an accurate understanding of public sentiment, is of paramount importance. While nationwide surveys have traditionally been used to gauge public views, the rise of social media in recent years has provided a promising new avenue for understanding public sentiment. To explore domestic sentiment on nuclear energy-related issues expressed online, we analyzed the content and comments of over 3,000 YouTube videos covering topics related to nuclear energy. Topic modeling was used to extract the main topics from the videos, and sentiment analysis with large language models classified user sentiments towards each topic. Additionally, word co-occurrence network analysis was performed to examine the shift in online discussions during August and September 2023 regarding the release of treated water. Overall, our results provide valuable insights into the online discourse on nuclear energy and contribute to a more comprehensive understanding of public sentiment in Japan.

Hirofumi Tsuruta, Masaya Kumagai

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis procedures from scientific literature as structured data. However, existing studies often rely on rigid, domain-specific schemas with predefined fields for structuring synthesis procedures or assume that synthesis procedures are linear sequences of operations, which limits their ability to capture the structural complexity of real-world procedures. To address these limitations, we adopt PROV-DM, an international standard for provenance information, which supports flexible, graph-based modeling of procedures. We present MatPROV, a dataset of PROV-DM-compliant synthesis procedures extracted from scientific literature using large language models. MatPROV captures structural complexities and causal relationships among materials, operations, and conditions through visually intuitive directed graphs. This representation enables machine-interpretable synthesis knowledge, opening opportunities for future research such as automated synthesis planning and optimization.