Ryo Yoshida

Stephen G. Dale, Nikita Kazeev, Alastair J. A. Price et al.

Artificial intelligence and machine learning are reshaping how we approach scientific discovery, not by replacing established methods but by extending what researchers can probe, predict, and design. In this roadmap we provide a forward-looking view of AI-enabled science across biology, chemistry, climate science, mathematics, materials science, physics, self-driving laboratories and unconventional computing. Several shared themes emerge: the need for diverse and trustworthy data, transferable electronic-structure and interatomic models, AI systems integrated into end-to-end scientific workflows that connect simulations to experiments and generative systems grounded in synthesisability rather than purely idealised phases. Across domains, we highlight how large foundation models, active learning and self-driving laboratories can close loops between prediction and validation while maintaining reproducibility and physical interpretability. Taken together, these perspectives outline where AI-enabled science stands today, identify bottlenecks in data, methods and infrastructure, and chart concrete directions for building AI systems that are not only more powerful but also more transparent and capable of accelerating discovery in complex real-world environments.

Shunya Minami, Kenji Fukumizu, Yoshihiro Hayashi et al.

Supervised transfer learning has received considerable attention due to its potential to boost the predictive power of machine learning in scenarios where data are scarce. Generally, a given set of source models and a dataset from a target domain are used to adapt the pre-trained models to a target domain by statistically learning domain shift and domain-specific factors. While such procedurally and intuitively plausible methods have achieved great success in a wide range of real-world applications, the lack of a theoretical basis hinders further methodological development. This paper presents a general class of transfer learning regression called affine model transfer, following the principle of expected-square loss minimization. It is shown that the affine model transfer broadly encompasses various existing methods, including the most common procedure based on neural feature extractors. Furthermore, the current paper clarifies theoretical properties of the affine model transfer such as generalization error and excess risk. Through several case studies, we demonstrate the practical benefits of modeling and estimating inter-domain commonality and domain-specific factors separately with the affine-type transfer models.

Ryo Yoshida, Yoshihiro Hayashi, Hidemine Furuya et al.

Developing large-scale foundational datasets is a critical milestone in advancing artificial intelligence (AI)-driven scientific innovation. However, unlike AI-mature fields such as natural language processing, materials science, particularly polymer research, has significantly lagged in developing extensive open datasets. This lag is primarily due to the high costs of polymer synthesis and property measurements, along with the vastness and complexity of the chemical space. This study presents PolyOmics, an omics-scale computational database generated through fully automated molecular dynamics simulation pipelines that provide diverse physical properties for over $10^5$ polymeric materials. The PolyOmics database is collaboratively developed by approximately 260 researchers from 48 institutions to bridge the gap between academia and industry. Machine learning models pretrained on PolyOmics can be efficiently fine-tuned for a wide range of real-world downstream tasks, even when only limited experimental data are available. Notably, the generalisation capability of these simulation-to-real transfer models improve significantly as the size of the PolyOmics database increases, exhibiting power-law scaling. The emergence of scaling laws supports the "more is better" principle, highlighting the significance of ultralarge-scale computational materials data for improving real-world prediction performance. This unprecedented omics-scale database reveals vast unexplored regions of polymer materials, providing a foundation for AI-driven polymer science.

Qi Zhang, Chang Liu, Stephen Wu et al.

In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods for synthetic route design using deep neural networks have been studied intensively in recent years. However, little progress has been made in designing molecules and their synthetic routes simultaneously. Here, we formulate the problem of simultaneously designing molecules with the desired set of properties and their synthetic routes within the framework of Bayesian inference. The design variables consist of a set of reactants in a reaction network and its network topology. The design space is extremely large because it consists of all combinations of purchasable reactants, often in the order of millions or more. In addition, the designed reaction networks can adopt any topology beyond simple multistep linear reaction routes. To solve this hard combinatorial problem, we present a powerful sequential Monte Carlo algorithm that recursively designs a synthetic reaction network by sequentially building up single-step reactions. In a case study of designing drug-like molecules based on commercially available compounds, compared with heuristic combinatorial search methods, the proposed method shows overwhelming performance in terms of computational efficiency and coverage and novelty with respect to existing compounds.

Shunya Minami, Yoshihiro Hayashi, Stephen Wu et al.

To address the challenge of limited experimental materials data, extensive physical property databases are being developed based on high-throughput computational experiments, such as molecular dynamics simulations. Previous studies have shown that fine-tuning a predictor pretrained on a computational database to a real system can result in models with outstanding generalization capabilities compared to learning from scratch. This study demonstrates the scaling law of simulation-to-real (Sim2Real) transfer learning for several machine learning tasks in materials science. Case studies of three prediction tasks for polymers and inorganic materials reveal that the prediction error on real systems decreases according to a power-law as the size of the computational data increases. Observing the scaling behavior offers various insights for database development, such as determining the sample size necessary to achieve a desired performance, identifying equivalent sample sizes for physical and computational experiments, and guiding the design of data production protocols for downstream real-world tasks.

Ryo Yoshida, Yohei Oseki

In this paper, we propose a novel architecture called Composition Attention Grammars (CAGs) that recursively compose subtrees into a single vector representation with a composition function, and selectively attend to previous structural information with a self-attention mechanism. We investigate whether these components -- the composition function and the self-attention mechanism -- can both induce human-like syntactic generalization. Specifically, we train language models (LMs) with and without these two components with the model sizes carefully controlled, and evaluate their syntactic generalization performance against six test circuits on the SyntaxGym benchmark. The results demonstrated that the composition function and the self-attention mechanism both play an important role to make LMs more human-like, and closer inspection of linguistic phenomenon implied that the composition function allowed syntactic features, but not semantic features, to percolate into subtree representations.

Masato Mita, Ryo Yoshida, Yohei Oseki

Large language models possess general linguistic abilities but acquire language less efficiently than humans. This study proposes a method for integrating the developmental characteristics of working memory during the critical period, a stage when human language acquisition is particularly efficient, into the training process of language models. The proposed method introduces a mechanism that initially constrains working memory during the early stages of training and gradually relaxes this constraint in an exponential manner as learning progresses. Targeted syntactic evaluation shows that the proposed method outperforms conventional methods without memory constraints or with static memory constraints. These findings not only provide new directions for designing data-efficient language models but also offer indirect evidence supporting the role of the developmental characteristics of working memory as the underlying mechanism of the critical period in language acquisition.

Taiga Someya, Ryo Yoshida, Hitomi Yanaka et al.

Recent work has demonstrated that neural language models encode syntactic structures in their internal representations, yet the derivations by which these structures are constructed across layers remain poorly understood. In this paper, we propose Derivational Probing to investigate how micro-syntactic structures (e.g., subject noun phrases) and macro-syntactic structures (e.g., the relationship between the root verbs and their direct dependents) are constructed as word embeddings propagate upward across layers. Our experiments on BERT reveal a clear bottom-up derivation: micro-syntactic structures emerge in lower layers and are gradually integrated into a coherent macro-syntactic structure in higher layers. Furthermore, a targeted evaluation on subject-verb number agreement shows that the timing of constructing macro-syntactic structures is critical for downstream performance, suggesting an optimal timing for integrating global syntactic information.

Ryo Yoshida, Shinnosuke Isono, Kohei Kajikawa et al.

Recent work in computational psycholinguistics has revealed intriguing parallels between attention mechanisms and human memory retrieval, focusing primarily on vanilla Transformers that operate on token-level representations. However, computational psycholinguistic research has also established that syntactic structures provide compelling explanations for human sentence processing that token-level factors cannot fully account for. In this paper, we investigate whether the attention mechanism of Transformer Grammar (TG), which uniquely operates on syntactic structures as representational units, can serve as a cognitive model of human memory retrieval, using Normalized Attention Entropy (NAE) as a linking hypothesis between models and humans. Our experiments demonstrate that TG's attention achieves superior predictive power for self-paced reading times compared to vanilla Transformer's, with further analyses revealing independent contributions from both models. These findings suggest that human sentence processing involves dual memory representations -- one based on syntactic structures and another on token sequences -- with attention serving as the general memory retrieval algorithm, while highlighting the importance of incorporating syntactic structures as representational units.

Ryo Yoshida, Hiroshi Noji, Yohei Oseki

In computational linguistics, it has been shown that hierarchical structures make language models (LMs) more human-like. However, the previous literature has been agnostic about a parsing strategy of the hierarchical models. In this paper, we investigated whether hierarchical structures make LMs more human-like, and if so, which parsing strategy is most cognitively plausible. In order to address this question, we evaluated three LMs against human reading times in Japanese with head-final left-branching structures: Long Short-Term Memory (LSTM) as a sequential model and Recurrent Neural Network Grammars (RNNGs) with top-down and left-corner parsing strategies as hierarchical models. Our computational modeling demonstrated that left-corner RNNGs outperformed top-down RNNGs and LSTM, suggesting that hierarchical and left-corner architectures are more cognitively plausible than top-down or sequential architectures. In addition, the relationships between the cognitive plausibility and (i) perplexity, (ii) parsing, and (iii) beam size will also be discussed.