arXiv subjects

Ryo Yoshida

Publications and source records attributed to Ryo Yoshida.

At least 19 recordsLinked to original sources

arXiv2026

Simulation-Supervised Foundation Models for Retention Time Prediction in High-Performance Liquid Chromatography beyond Experimental Data Coverage

Accurate prediction of high-performance liquid chromatography (HPLC) retention times (RTs) across diverse molecules and chromatographic methods remains challenging because experimental training data cover only a limited region of chemical and method spaces. Here, we develop FUSE-RT (Foundation model Unifying Simulation and Experimental supervision for Retention Time), a multitask foundation model that integrates RT data from 179 chromatographic methods and adapts to unseen molecules and methods using limited target-domain data. To extend transferability beyond experimental coverage, we introduce simulation-to-real (Sim2Real) transfer learning, in which molecular representations learned from large-scale computational data are transferred to experimental RT prediction. Specifically, we use PolyOmics, comprising 39 properties for approximately 21,400 molecules generated by molecular dynamics and density-functional theory calculations, as auxiliary supervision. We evaluate generalization under molecular, method, and joint molecular--method distribution shifts. Simulation-derived supervision substantially improves transfer beyond the experimental molecular domain, particularly under pronounced coverage gaps and few-shot adaptation. Moreover, RT-prediction error decreases systematically with increasing simulation-data size, following a significant power-law relationship. These results establish Sim2Real transfer as a scalable strategy for extending RT prediction beyond the finite coverage of experimental chromatographic data.

physics.chem-ph↗

arXiv2026

Language Acquisition Device in Large Language Models

Large Language Models (LLMs) remain substantially less data-efficient than humans. Pre-pretraining (PPT) on synthetic languages has been proposed to close this gap, with prior work emphasizing highly expressive formal languages such as $k$-Shuffle Dyck. Inspired by the Language Acquisition Device (LAD) hypothesis, which posits that innate constraints preemptively restrict the learner's hypothesis space to natural-language-like structure, we propose LAD-inspired PPT: pre-pretraining on MP-STRUCT, a formal language whose strings encode hierarchical composition, feature-based dependencies, and long-distance displacement via MERGE, AGREE, and MOVE. A brief 500-step PPT with MP-STRUCT matches strong formal-language baselines in token efficiency while additionally imparting a human-like resistance to structurally implausible languages (e.g., REVERSE). Analyzing simplified variants, we find that MP-STRUCT CORE outperforms $k$-Shuffle Dyck despite not being definable in C-RASP (a formal bound on transformer expressivity), challenging the prior hypothesis that effective PPT languages must be both hierarchically expressive and circuit-theoretically learnable. We show that functional landmarks, which reduce dependency resolution ambiguity, are a key driver, suggesting that effective PPT design depends not only on expressivity but also on the accessibility of dependency resolution.

cs.CL↗

arXiv2026

An Existence Proof for Neural Language Models That Can Explain Garden-Path Effects via Surprisal

Surprisal theory hypothesizes that the difficulty of human sentence processing increases linearly with surprisal, the negative log-probability of a word given its context. Computational psycholinguistics has tested this hypothesis using language models (LMs) as proxies for human prediction. While surprisal derived from recent neural LMs generally captures human processing difficulty on naturalistic corpora that predominantly consist of simple sentences, it severely underestimates processing difficulty on sentences that require syntactic disambiguation (garden-path effects). This leads to the claim that the processing difficulty of such sentences cannot be reduced to surprisal, although it remains possible that neural LMs simply differ from humans in next-word prediction. In this paper, we investigate whether it is truly impossible to construct a neural LM that can explain garden-path effects via surprisal. Specifically, instead of evaluating off-the-shelf neural LMs, we fine-tune these LMs on garden-path sentences so as to better align surprisal-based reading-time estimates with actual human reading times. Our results show that fine-tuned LMs do not overfit and successfully capture human reading slowdowns on held-out garden-path items; they even improve predictive power for human reading times on naturalistic corpora and preserve their general LM capabilities. These results provide an existence proof for a neural LM that can explain both garden-path effects and naturalistic reading times via surprisal, but also raise a theoretical question: what kind of evidence can truly falsify surprisal theory?

cs.CL↗

arXiv2026

Neural Reconstruction of LiDAR Point Clouds under Jamming Attacks via Full-Waveform Representation and Simultaneous Laser Sensing

LiDAR sensors are critical for autonomous driving perception, yet remain vulnerable to spoofing attacks. Jamming attacks inject high-frequency laser pulses that completely blind LiDAR sensors by overwhelming authentic returns with malicious signals. We discover that while point clouds become randomized, the underlying full-waveform data retains distinguishable signatures between attack and legitimate signals. In this work, we propose PULSAR-Net, capable of reconstructing authentic point clouds under jamming attacks by leveraging previously underutilized intermediate full-waveform representations and simultaneous laser sensing in modern LiDAR systems. PULSAR-Net adopts a novel U-Net architecture with axial spatial attention mechanisms specifically designed to identify attack-induced signals from authentic object returns in the full-waveform representation. To address the lack of full-waveform representations in existing LiDAR datasets under jamming attacks, we introduce a physics-aware dataset generation pipeline that synthesizes realistic full-waveform representations under jamming attacks. Despite being trained exclusively on synthetic data, PULSAR-Net achieves reconstruction rates of 92% and 73% for vehicles obscured by jamming attacks in real-world static and driving scenarios, respectively.

cs.CV↗

arXiv2025

AI4X Roadmap: Artificial Intelligence for the advancement of scientific pursuit and its future directions

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.

physics.soc-ph↗

arXiv2025

Omics-scale polymer computational database transferable to real-world artificial intelligence applications

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.

physics.chem-ph↗

arXiv2025

Machine Learning for Polymer Chemical Resistance to Organic Solvents

Predicting the chemical resistance of polymers to organic solvents is a longstanding challenge in materials science, with significant implications for sustainable materials design and industrial applications. Here, we address the need for interpretable and generalizable frameworks to understand and predict polymer chemical resistance beyond conventional solubility models. We systematically analyze a large dataset of polymer solvent combinations using a data-driven approach. Our study reveals that polymer crystallinity and density, as well as solvent polarity, are key factors governing chemical resistance, and that these trends are consistent with established theoretical models. These findings provide a foundation for rational screening and design of polymer materials with tailored chemical resistance, advancing both fundamental understanding and practical applications.

cond-mat.soft↗

arXiv2025

Derivational Probing: Unveiling the Layer-wise Derivation of Syntactic Structures in Neural Language Models

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.

cs.CL↗

arXiv2025

Rethinking the Relationship between the Power Law and Hierarchical Structures

Statistical analysis of corpora provides an approach to quantitatively investigate natural languages. This approach has revealed that several power laws consistently emerge across different corpora and languages, suggesting universal mechanisms underlying languages. In particular, the power-law decay of correlations has been interpreted as evidence of underlying hierarchical structures in syntax, semantics, and discourse. This perspective has also been extended beyond corpora produced by human adults, including child speech, birdsong, and chimpanzee action sequences. However, the argument supporting this interpretation has not been empirically tested in natural languages. To address this gap, the present study examines the validity of the argument for syntactic structures. Specifically, we test whether the statistical properties of parse trees align with the assumptions in the argument. Using English and Japanese corpora, we analyze the mutual information, deviations from probabilistic context-free grammars (PCFGs), and other properties in natural language parse trees, as well as in the PCFG that approximates these parse trees. Our results indicate that the assumptions do not hold for syntactic structures and that it is difficult to apply the proposed argument not only to sentences by human adults but also to other domains, highlighting the need to reconsider the relationship between the power law and hierarchical structures.

cs.CL↗

arXiv2025

Database and deep-learning scalability of anharmonic phonon properties by automated brute-force first-principles calculations

Understanding the anharmonic phonon properties of crystal compounds -- such as phonon lifetimes and thermal conductivities -- is essential for investigating and optimizing their thermal transport behaviors. These properties also impact optical, electronic, and magnetic characteristics through interactions between phonons and other quasiparticles and fields. In this study, we develop an automated first-principles workflow to calculate anharmonic phonon properties and build a comprehensive database encompassing more than 6,000 inorganic compounds. Utilizing this dataset, we train a graph neural network model to predict thermal conductivity values and spectra from structural parameters, demonstrating a scaling law in which prediction accuracy improves with increasing training data size. High-throughput screening with the model enables the identification of materials exhibiting extreme thermal conductivities -- both high and low. The resulting database offers valuable insights into the anharmonic behavior of phonons, thereby accelerating the design and development of advanced functional materials.

cond-mat.mtrl-sci↗

arXiv2025

Bayesian Kernel Regression for Functional Data

In supervised learning, the output variable to be predicted is often represented as a function, such as a spectrum or probability distribution. Despite its importance, functional output regression remains relatively unexplored. In this study, we propose a novel functional output regression model based on kernel methods. Unlike conventional approaches that independently train regressors with scalar outputs for each measurement point of the output function, our method leverages the covariance structure within the function values, akin to multitask learning, leading to enhanced learning efficiency and improved prediction accuracy. Compared with existing nonlinear function-on-scalar models in statistical functional data analysis, our model effectively handles high-dimensional nonlinearity while maintaining a simple model structure. Furthermore, the fully kernel-based formulation allows the model to be expressed within the framework of reproducing kernel Hilbert space (RKHS), providing an analytic form for parameter estimation and a solid foundation for further theoretical analysis. The proposed model delivers a functional output predictive distribution derived analytically from a Bayesian perspective, enabling the quantification of uncertainty in the predicted function. We demonstrate the model's enhanced prediction performance through experiments on artificial datasets and density of states prediction tasks in materials science.

stat.ML↗

arXiv2025

If Attention Serves as a Cognitive Model of Human Memory Retrieval, What is the Plausible Memory Representation?

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.

cs.CL↗

arXiv2025

Developmentally-plausible Working Memory Shapes a Critical Period for Language Acquisition

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.

cs.CL↗

arXiv2024

SPACIER: On-Demand Polymer Design with Fully Automated All-Atom Classical Molecular Dynamics Integrated into Machine Learning Pipelines

Machine learning has rapidly advanced the design and discovery of new materials with targeted applications in various systems. First-principles calculations and other computer experiments have been integrated into material design pipelines to address the lack of experimental data and the limitations of interpolative machine learning predictors. However, the enormous computational costs and technical challenges of automating computer experiments for polymeric materials have limited the availability of open-source automated polymer design systems that integrate molecular simulations and machine learning. We developed SPACIER, an open-source software program that integrates RadonPy, a Python library for fully automated polymer property calculations based on all-atom classical molecular dynamics into a Bayesian optimization-based polymer design system to overcome these challenges. As a proof-of-concept study, we successfully synthesized optical polymers that surpass the Pareto boundary formed by the tradeoff between the refractive index and Abbe number.

cond-mat.mtrl-sci↗

arXiv2024

Scaling Law of Sim2Real Transfer Learning in Expanding Computational Materials Databases for Real-World Predictions

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.

cond-mat.mtrl-sci↗

arXiv2024

Advancing Extrapolative Predictions of Material Properties through Learning to Learn

Recent advancements in machine learning have showcased its potential to significantly accelerate the discovery of new materials. Central to this progress is the development of rapidly computable property predictors, enabling the identification of novel materials with desired properties from vast material spaces. However, the limited availability of data resources poses a significant challenge in data-driven materials research, particularly hindering the exploration of innovative materials beyond the boundaries of existing data. While machine learning predictors are inherently interpolative, establishing a general methodology to create an extrapolative predictor remains a fundamental challenge, limiting the search for innovative materials beyond existing data boundaries. In this study, we leverage an attention-based architecture of neural networks and meta-learning algorithms to acquire extrapolative generalization capability. The meta-learners, experienced repeatedly with arbitrarily generated extrapolative tasks, can acquire outstanding generalization capability in unexplored material spaces. Through the tasks of predicting the physical properties of polymeric materials and hybrid organic--inorganic perovskites, we highlight the potential of such extrapolatively trained models, particularly with their ability to rapidly adapt to unseen material domains in transfer learning scenarios.

cond-mat.mtrl-sci↗

arXiv2024

Tree-Planted Transformers: Unidirectional Transformer Language Models with Implicit Syntactic Supervision

Syntactic Language Models (SLMs) can be trained efficiently to reach relatively high performance; however, they have trouble with inference efficiency due to the explicit generation of syntactic structures. In this paper, we propose a new method dubbed tree-planting: instead of explicitly generating syntactic structures, we "plant" trees into attention weights of unidirectional Transformer LMs to implicitly reflect syntactic structures of natural language. Specifically, unidirectional Transformer LMs trained with tree-planting will be called Tree-Planted Transformers (TPT), which inherit the training efficiency from SLMs without changing the inference efficiency of their underlying Transformer LMs. Targeted syntactic evaluations on the SyntaxGym benchmark demonstrated that TPTs, despite the lack of explicit generation of syntactic structures, significantly outperformed not only vanilla Transformer LMs but also various SLMs that generate hundreds of syntactic structures in parallel. This result suggests that TPTs can learn human-like syntactic knowledge as data-efficiently as SLMs while maintaining the modeling space of Transformer LMs unchanged.

cs.CL↗

arXiv2024

Emergent Word Order Universals from Cognitively-Motivated Language Models

The world's languages exhibit certain so-called typological or implicational universals; for example, Subject-Object-Verb (SOV) languages typically use postpositions. Explaining the source of such biases is a key goal of linguistics. We study word-order universals through a computational simulation with language models (LMs). Our experiments show that typologically-typical word orders tend to have lower perplexity estimated by LMs with cognitively plausible biases: syntactic biases, specific parsing strategies, and memory limitations. This suggests that the interplay of cognitive biases and predictability (perplexity) can explain many aspects of word-order universals. It also showcases the advantage of cognitively-motivated LMs, typically employed in cognitive modeling, in the simulation of language universals.

cs.CL↗