arXiv subjects

Koji Tsuda

Publications and source records attributed to Koji Tsuda.

At least 19 recordsLinked to original sources

arXiv2026

WetRobo: A Reproducible Robot Kit for Coding Agents in Biological Laboratories

Automating biological research requires general-purpose, reproducible robot systems that allow individual wet-lab researchers to delegate robot tasks without performing teleoperation or neural-network training. Vision-language-action policies have been proposed for general-purpose arms, but can lose performance when their operating environment changes. We therefore built WetRobo, a robot kit that can readily transfer between laboratories. It consists of one robot arm, laboratory equipment (an incubator, a reagent bottle with a cap, and a Petri dish), the existing code that moves the arm, teleoperation demonstrations of each task that we recorded, and a general AGENTS.md skill file. A biological experimentalist provides natural-language tasks without collecting local teleoperation training data or training a neural network. The coding agent observes the local laboratory and writes and executes programs, using external tools as needed for adaptation. We demonstrate use of WetRobo with OpenAI Codex (gpt-5.6-sol) on three successful tasks: lifting a Petri dish lid, removing a bottle cap, and opening the incubator door, all in real-world laboratories. The coding agent achieved the cap task in both laboratories, Lab X and Lab Y, whereas a VLA fine-tuned on Lab X demonstrations succeeded there but failed to transfer to Lab Y. These results point to a practical route for laboratory robotics: instead of training a policy for each laboratory, distribute a kit and let a coding agent adapt it in each laboratory. Code, demonstrations, and the evolved programs are available at https://github.com/tsudalab/WetRobo.

cs.AI↗

arXiv2026

AutoSchema: Live Schema Grounding for Agentic Text-to-Sparql over Heterogeneous Knowledge Graphs

Life science knowledge graphs make large collections of structured data available through SPARQL, but each resource uses its own schema, identifiers, and links. TogoMCP helps language model agents query these resources by providing curated Metadata Interoperability Exchange files. Creating and maintaining these files still requires language model assisted drafting, validation, and manual review. We study \emph{live schema grounding}, where an agent obtains the schema evidence needed for a question directly from the current endpoints. We present \textsc{autoschema}, a general framework for live schema grounding that requires no training. It inspects live schemas, maps entity names in a question to graph identifiers, explores relation paths, and finds possible connections between resources during iterative query construction. We use TogoMCP as our main comparison framework. We evaluate \textsc{autoschema} on Resource Focused Biomedical KGQA, Multi Resource Biomedical KGQA, Longitudinal Biomedical Semantic QA over BioASQ Task B, and Chemistry Knowledge Graph Transfer to a previously undocumented RDF graph. \textsc{autoschema} improves mean factoid accuracy over TogoMCP in the biomedical KGQA tasks and gives consistent gains in the longitudinal BioASQ evaluation. It also reduces iteration budget exhaustion and uses fewer tool calls on average in the core evaluation. The transfer study gives preliminary evidence that live schema grounding can support irregular and previously unseen graphs without first creating a curated schema file.

cs.LG↗

arXiv2026

On a linear fused Gromov-Wasserstein distance for graph structured data

We present a framework for embedding graph structured data into a vector space, taking into account node features and topology of a graph into the optimal transport (OT) problem. Then we propose a novel distance between two graphs, named linearFGW, defined as the Euclidean distance between their embeddings. The advantages of the proposed distance are twofold: 1) it can take into account node feature and structure of graphs for measuring the similarity between graphs in a kernel-based framework, 2) it can be much faster for computing kernel matrix than pairwise OT-based distances, particularly fused Gromov-Wasserstein, making it possible to deal with large-scale data sets. After discussing theoretical properties of linearFGW, we demonstrate experimental results on classification and clustering tasks, showing the effectiveness of the proposed linearFGW.

cs.LG↗

arXiv2026

SAGA: Schema-Aware Grounding for Agentic Text-to-SPARQL Generation

Complex knowledge base question answering (KBQA) is commonly approached through either information retrieval over a question-specific subgraph or semantic parsing into an executable logical form. We study the latter paradigm. Recent large language model agents make semantic parsing interactive: they alternate between reasoning, querying the knowledge base, and extending a partial SPARQL query. This interleaving reduces reliance on one-shot generation, but makes the quality of \emph{KB grounding} depend on what the interaction tools expose. Existing agents retrieve or prune candidate properties mainly through lexical relevance and instance-level observations, without systematically conditioning on entity types, property domains and ranges, or the expected answer type. We call this failure mode \emph{type-blind grounding}. It enlarges the grounding search space and often produces plausible-looking but semantically incompatible triple patterns that execute to empty results. We propose SAGA (\underline{S}chema-\underline{A}ware \underline{G}rounding for \underline{A}gentic Text-to-SPARQL Generation), a training-free framework that turns property exploration into a schema-constrained grounding operation. SAGA maintains a persistent bidirectional type state, filters known-incompatible property candidates at construction time, presents the remaining graph patterns in a compact schema-annotated format, and handles missing schema information permissively through empirical and trace-local evidence. Across nine benchmark settings over Wikidata and Freebase, SAGA achieves the highest F1 on all nine settings and the highest exact-match accuracy on eight, while reducing empty-result queries across all reported Wikidata settings.

cs.AI↗

arXiv2026

NIMO: A Software Platform for Closed-Loop Materials Exploration with Diverse AI Algorithms

Self-driving laboratories (SDLs), where artificial intelligence proposes subsequent experiments and robotic systems execute them, are rapidly becoming the vanguard of materials discovery. A critical bottleneck, however, lies in seamlessly bridging diverse AI algorithms tailored for specific exploration goals with the heterogeneous robotic hardware found across different laboratories. Here, we present NIMO, an open-source software platform designed to dissolve this barrier through three core paradigms: a modular AI-robot decoupling mediated via simple CSV file exchange, a discrete candidate-pool architecture that seamlessly absorbs domain knowledge, and a unified Python interface pre-loaded with twelve distinct AI algorithms. In this Perspective, we review the operational principles of each algorithm alongside six diverse SDL implementations driven by NIMO, covering electrolyte discovery, organic synthesis, thin-film exploration, fuel-cell process informatics, coffee-ring phase exploration, and legacy liquid-handling automation. One of these also demonstrates NIMO's seamless interoperability with the IvoryOS orchestration framework. To democratize autonomous science, we also introduce a no-code desktop application that enables intuitive, human-in-the-loop exploration for non-programmers. NIMO is freely available at https://github.com/NIMS-DA/nimo, offering a versatile, plug-and-play foundation to accelerate autonomous materials exploration across diverse experimental landscapes.

cond-mat.mtrl-sci↗

arXiv2026

ProvMind: Provenance-grounded reasoning for materials synthesis

Materials process optimization requires reasoning over routes, conditions, tools and causal dependencies, yet most computational formulations flatten synthesis procedures into text or ordered steps. We introduce MatProcBench, a provenance-grounded benchmark constructed from literature-mined MatPROV graphs, to evaluate seven process-reasoning tasks spanning route continuity, step-level variable inference and global causal consistency under both same-split and shift-aware evaluation, including a strict dual-OOD split that combines temporal and material-class shift. We further introduce ProvMind, a process-memory reasoning framework that retrieves analogous training processes, converts them into provenance-aware option-level compatibility scores, and uses a language model for constrained final decision making. ProvMind achieves 52.84\% accuracy on the dual-OOD split, outperforming prompting, retrieval-augmented and supervised fine-tuning baselines.

cs.AI↗

arXiv2026

LLM-guided phase diagram construction through high-throughput experimentation

Constructing phase diagrams for multicomponent alloys requires extensive experimental measurements and is a time-consuming task. Here we investigate whether large language models (LLMs) can guide experimental planning for phase diagram construction. In our framework, a general-purpose LLM serves as the experimental planner, suggesting compositions for measurement at each cycle in a closed loop with high-throughput synthesis and X-ray diffraction phase identification. Using this framework, we experimentally constructed the ternary phase diagram of the Co-Al-Ge system at 900 degree C through iterative synthesis and characterization. We compared two strategies that differ in how the initial compositions are selected: one uses predictions from a domain-specific LLM trained on phase diagram data (aLLoyM), while the other relies solely on the general-purpose LLM. The two strategies exhibited complementary strengths. aLLoyM directed the initial measurements toward compositionally complex regions in the interior of the ternary diagram, enabling the earliest discovery of all three novel phases that form only in the ternary system. In contrast, the general-purpose LLM adopted a textbook-like approach which efficiently identified a larger number of phases in fewer cycles. In addition, a simulated benchmark comparing the LLM against conventional machine learning confirmed that the LLM achieves more efficient exploration. The results demonstrate that LLMs have high potential as experimental planners for phase diagram construction.

cond-mat.mtrl-sci↗

arXiv2026

Update of PHYSBO: Improving Usability and Portability of Bayesian Optimization for Physics and Materials Research

Bayesian optimization (BO) is widely used to accelerate physics and materials research, where objective function evaluations are computationally or experimentally expensive. While many BO frameworks focus on algorithmic efficiency, practical usability and portability are equally critical for sustained use in real research environments. PHYSBO is a Bayesian optimization library designed to address these needs by enabling optimization over user-defined candidate pools and by supporting domain-specific problem settings. This paper presents the major updates introduced in PHYSBO versions 2 and 3, with a focus on improvements in usability, portability, and practical deployment rather than on new optimization algorithms. In PHYSBO version 2, the software license was changed from GPL to MPL to improve compatibility with a wider range of research and software ecosystems. Building on this revision, PHYSBO version 3 introduces a set of implementation-oriented updates aimed at improving usability and portability, without modifying the core optimization algorithms. These updates include improvements in computational performance and scalability, extended support for multi-objective optimization, the introduction of range-based policies for continuous-variable optimization, the removal of environment-dependent components such as tightly coupled Cython modules, and compatibility with NumPy 2. These improvements reduce the technical and organizational burden on users, enabling PHYSBO to be deployed across diverse computing environments and research workflows. By emphasizing portability and ease of integration while maintaining sufficient performance, PHYSBO version 3 is positioned as a sustainable research infrastructure for Bayesian optimization in physics and materials science.

physics.comp-ph↗

arXiv2026

Scalable Dielectric Tensor Predictions for Inorganic Materials using Equivariant Graph Neural Networks

Accurate prediction of dielectric tensors is essential for accelerating the discovery of next-generation inorganic dielectric materials. Existing machine learning approaches, such as equivariant graph neural networks, typically rely on specially-designed network architectures to enforce O(3) equivariance. However, to preserve equivariance, these specially-designed models restrict the update of equivariant features during message passing to linear transformations or gated equivariant nonlinearities. The inability to implicitly characterize more complex nonlinear structures may reduce the predictive accuracy of the model. In this study, we introduce a frame-averaging-based approach to achieve equivariant dielectric tensor prediction. We propose GoeCTP, an O(3)-equivariant framework that predicts dielectric tensors without imposing any structural restrictions on the backbone network. We benchmark its performance against several state-of-the-art models and further employ it for large-scale virtual screening of thermodynamically stable materials from the Materials Project database. GoeCTP successfully identifies various promising candidates, such as Zr(InBr$_3$)$_2$ (band gap $E_g = 2.41$ eV, dielectric constant $\overline{\varepsilon} = 194.72$) and SeI$_2$ (anisotropy ratio $α_r = 96.763$), demonstrating its accuracy and efficiency in accelerating the discovery of advanced inorganic dielectric materials.

cond-mat.mtrl-sci↗

arXiv2025

aLLoyM: A large language model for alloy phase diagram prediction

Large Language Models (LLMs) are general-purpose tools with wide-ranging applications, including in materials science. In this work, we introduce aLLoyM, a fine-tuned LLM specifically trained on alloy compositions, temperatures, and their corresponding phase information. To develop aLLoyM, we curated question-and-answer (Q&A) pairs for binary and ternary phase diagrams using the open-source Computational Phase Diagram Database (CPDDB) and assessments based on CALPHAD (CALculation of PHAse Diagrams). We fine-tuned Mistral, an open-source pre-trained LLM, for two distinct Q&A formats: multiple-choice and short-answer. Benchmark evaluations demonstrate that fine-tuning substantially enhances performance on multiple-choice phase diagram questions. Moreover, the short-answer model of aLLoyM exhibits the ability to generate novel phase diagrams from its components alone, underscoring its potential to accelerate the discovery of previously unexplored materials systems. To promote further research and adoption, we have publicly released the short-answer fine-tuned version of aLLoyM, along with the complete benchmarking Q&A dataset, on Hugging Face.

cond-mat.mtrl-sci↗

arXiv2025

Molecule Graph Networks with Many-body Equivariant Interactions

Message passing neural networks have demonstrated significant efficacy in predicting molecular interactions. Introducing equivariant vectorial representations augments expressivity by capturing geometric data symmetries, thereby improving model accuracy. However, two-body bond vectors in opposition may cancel each other out during message passing, leading to the loss of directional information on their shared node. In this study, we develop Equivariant N-body Interaction Networks (ENINet) that explicitly integrates l = 1 equivariant many-body interactions to enhance directional symmetric information in the message passing scheme. We provided a mathematical analysis demonstrating the necessity of incorporating many-body equivariant interactions and generalized the formulation to $N$-body interactions. Experiments indicate that integrating many-body equivariant representations enhances prediction accuracy across diverse scalar and tensorial quantum chemical properties.

cs.LG↗

arXiv2025

NbBench: Benchmarking Language Models for Comprehensive Nanobody Tasks

Nanobodies -- single-domain antibody fragments derived from camelid heavy-chain-only antibodies -- exhibit unique advantages such as compact size, high stability, and strong binding affinity, making them valuable tools in therapeutics and diagnostics. While recent advances in pretrained protein and antibody language models (PPLMs and PALMs) have greatly enhanced biomolecular understanding, nanobody-specific modeling remains underexplored and lacks a unified benchmark. To address this gap, we introduce NbBench, the first comprehensive benchmark suite for nanobody representation learning. Spanning eight biologically meaningful tasks across nine curated datasets, NbBench encompasses structure annotation, binding prediction, and developability assessment. We systematically evaluate eleven representative models -- including general-purpose protein LMs, antibody-specific LMs, and nanobody-specific LMs -- in a frozen setting. Our analysis reveals that antibody language models excel in antigen-related tasks, while performance on regression tasks such as thermostability and affinity remains challenging across all models. Notably, no single model consistently outperforms others across all tasks. By standardizing datasets, task definitions, and evaluation protocols, NbBench offers a reproducible foundation for assessing and advancing nanobody modeling.

cs.LG↗

arXiv2025

Black-box optimization using factorization and Ising machines

Black-box optimization (BBO) is used in materials design, drug discovery, and hyperparameter tuning in machine learning. The world is experiencing several of these problems. In this review, a factorization machine with quantum annealing or with quadratic-optimization annealing (FMQA) algorithm to realize fast computations of BBO using Ising machines (IMs) is discussed. The FMQA algorithm uses a factorization machine (FM) as a surrogate model for BBO. The FM model can be directly transformed into a quadratic unconstrained binary optimization model that can be solved using IMs. This makes it possible to optimize the acquisition function in BBO, which is a difficult task using conventional methods without IMs. Consequently, it has the advantage of handling large BBO problems. To be able to perform BBO with the FMQA algorithm immediately, we introduce the FMQA algorithm along with Python packages to run it. In addition, we review examples of applications of the FMQA algorithm in various fields, including physics, chemistry, materials science, and social sciences. These successful examples include binary and integer optimization problems, as well as more general optimization problems involving graphs, networks, and strings, using a binary variational autoencoder. We believe that BBO using the FMQA algorithm will become a key technology in IMs including quantum annealers.

cond-mat.stat-mech↗

arXiv2025

Inverse Design of Metamaterials with Manufacturing-Guiding Spectrum-to-Structure Conditional Diffusion Model

Metamaterials are artificially engineered structures that manipulate electromagnetic waves, having optical properties absent in natural materials. Recently, machine learning for the inverse design of metamaterials has drawn attention. However, the highly nonlinear relationship between the metamaterial structures and optical behaviour, coupled with fabrication difficulties, poses challenges for using machine learning to design and manufacture complex metamaterials. Herein, we propose a general framework that implements customised spectrum-to-shape and size parameters to address one-to-many metamaterial inverse design problems using conditional diffusion models. Our method exhibits superior spectral prediction accuracy, generates a diverse range of patterns compared to other typical generative models, and offers valuable prior knowledge for manufacturing through the subsequent analysis of the diverse generated results, thereby facilitating the experimental fabrication of metamaterial designs. We demonstrate the efficacy of the proposed method by successfully designing and fabricating a free-form metamaterial with a tailored selective emission spectrum for thermal camouflage applications.

physics.optics↗

arXiv2025

CRYSIM: Prediction of Symmetric Structures of Large Crystals with GPU-based Ising Machines

Solving black-box optimization problems with Ising machines is increasingly common in materials science. However, their application to crystal structure prediction (CSP) is still ineffective due to symmetry agnostic encoding of atomic coordinates. We introduce CRYSIM, an algorithm that encodes the space group, the Wyckoff positions combination, and coordinates of independent atomic sites as separate variables. This encoding reduces the search space substantially by exploiting the symmetry in space groups. When CRYSIM is interfaced to Fixstars Amplify, a GPU-based Ising machine, its prediction performance was competitive with CALYPSO and Bayesian optimization for crystals containing more than 150 atoms in a unit cell. Although it is not realistic to interface CRYSIM to current small-scale quantum devices, it has the potential to become the standard CSP algorithm in the coming quantum age.

cond-mat.mtrl-sci↗

arXiv2025

Human-AI collaboration for modeling heat conduction in nanostructures

In recent years, materials informatics, which combines data science and artificial intelligence (AI), has garnered significant attention owing to its ability to accelerate material development, reduce costs, and enhance product design. However, despite the widespread use of AI, human involvement is often limited to the initiation and oversight of machine learning processes and rarely includes more substantial roles that capitalize on human intuition or domain expertise. Consequently, true human-AI collaborations, where integrated insights can be maximized, are scarce. This study considers the problem of heat conduction in a two-dimensional nanostructure as a case study. An integrated human-AI collaboration framework is designed and used to construct a model to predict the thermal conductivity. This approach is used to determine the parameters that govern phonon transmission over the full range of frequencies and incidence angles. During operation, the self-learning entropic population annealing technique, which combines entropic sampling with a surrogate machine learning model, generates a small dataset that can be interpreted by a human. Therefore, data-efficient and global modeling is achieved, and parameters with physical interpretations are developed, which can guide nanostructural design to produce materials with specific properties. The proposed framework can leverage the complementary strengths of humans and AI, thereby enhancing the understanding and control of materials.

physics.comp-ph↗

arXiv2024

Preference-Optimized Pareto Set Learning for Blackbox Optimization

Multi-Objective Optimization (MOO) is an important problem in real-world applications. However, for a non-trivial problem, no single solution exists that can optimize all the objectives simultaneously. In a typical MOO problem, the goal is to find a set of optimum solutions (Pareto set) that trades off the preferences among objectives. Scalarization in MOO is a well-established method for finding a finite set approximation of the whole Pareto set (PS). However, in real-world experimental design scenarios, it's beneficial to obtain the whole PS for flexible exploration of the design space. Recently Pareto set learning (PSL) has been introduced to approximate the whole PS. PSL involves creating a manifold representing the Pareto front of a multi-objective optimization problem. A naive approach includes finding discrete points on the Pareto front through randomly generated preference vectors and connecting them by regression. However, this approach is computationally expensive and leads to a poor PS approximation. We propose to optimize the preference points to be distributed evenly on the Pareto front. Our formulation leads to a bilevel optimization problem that can be solved by e.g. differentiable cross-entropy methods. We demonstrated the efficacy of our method for complex and difficult black-box MOO problems using both synthetic and real-world benchmark data.

cs.LG↗

arXiv2023

Boltzmann sampling with quantum annealers via fast Stein correction

Despite the attempts to apply a quantum annealer to Boltzmann sampling, it is still impossible to perform accurate sampling at arbitrary temperatures. Conventional distribution correction methods such as importance sampling and resampling cannot be applied, because the analytical expression of sampling distribution is unknown for a quantum annealer. Stein correction (Liu and Lee, 2017) can correct the samples by weighting without the knowledge of the sampling distribution, but the naive implementation requires the solution of a large-scale quadratic program, hampering usage in practical problems. In this letter, a fast and approximate method based on random feature map and exponentiated gradient updates is developed to compute the sample weights, and used to correct the samples generated by D-Wave quantum annealers. In benchmarking problems, it is observed that the residual error of thermal average calculations is reduced significantly. If combined with our method, quantum annealers may emerge as a viable alternative to long-established Markov chain Monte Carlo methods.

cond-mat.stat-mech↗