Genome Language Models: From DNA Sequences to Biological Foundation Models

2026年8月13日(木) 15:00 - 16:00

Minrui Chen (九州大学 博士課程)

Recent advances in protein language models have greatly transformed protein structure prediction, functional annotation, and biomolecular design. In contrast, genome language models aim to learn directly from DNA sequences, which represent a more upstream layer of biological information encoding genes, regulatory logic, variant effects, and evolutionary signals. In this talk, I will introduce the basic motivation and recent progress of DNA and genome language models, including DNABERT, DNABERT-2, HyenaDNA, Evo, Evo 2, and AlphaGenome. I will discuss how different model architectures and tokenization strategies address the challenges of genomic sequence modeling, such as long-range dependencies, multi-scale biological structure, and genome-scale context.

会場: 研究本館 3階 359号室 (メイン会場) / via Zoom

イベント公式言語: 英語

In Search of The Building Blocks of the Universe

2026年8月7日(金) 15:00 - 16:30

Anamaria Hell (カブリ数物連携宇宙研究機構 (Kavli IPMU) 特任研究員)

We live in an exceptional era of precision cosmology, marked by rapidly advancing observational probes that explore the Universe across many length scales. While these experiments offer clues about the geometry, dynamics, and large-scale structure of the cosmos, they still leave the origin and much of the evolution and structure of the Universe unknown. One of the key steps to answer these questions is to uncover the building blocks of theoretical models in both linear and non-linear regimes. In this talk, I will present methods for uncovering physical degrees of freedom, outlining the standard approaches and presenting an alternative, simple and straightforward way. I will then show how one can naturally connect this approach to machine learning. Finally, I will introduce the framework of constrained gravity, and discuss how such approaches can help address long-standing challenges in fundamental physics and open new directions across disciplines.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

How Reputation Sustains Cooperation: Mathematical Theories of Indirect Reciprocity

2026年8月6日(木) 15:00 - 16:00

村瀬 洋介 (理化学研究所 数理創造研究センター (iTHEMS) 数理展開部門 数理社会科学チーム チームディレクター)

Cooperation among unrelated individuals is a central puzzle in the evolution of social behavior. Indirect reciprocity offers one influential explanation: people help others not only because they expect direct returns, but also because their actions affect their reputation. In this seminar, I will review mathematical theories of indirect reciprocity, focusing on how reputation and social norms can sustain cooperation. I will begin with the classical framework of public assessment, where everyone shares the same view of each individual’s reputation, including the seminal work of Ohtsuki and Iwasa on the “leading eight” social norms. I will then turn to private assessment, where individuals may disagree about others’ reputations, and discuss why synchronization of opinions becomes essential for cooperation. Overall, the seminar aims to provide an accessible overview of how mathematical models allow us to formalize moral judgments—what counts as good or bad behavior—and to understand the evolution of cooperation through reputation.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Theoretical Approaches for Cell Deaths

2026年8月6日(木) 13:00 - 14:00

姫岡 優介 (東京大学 生物普遍性研究機構 助教)

Understanding the boundary between cell life and death is a fundamental challenge and a highly important theme in biology. In this talk, focusing on microbial cell death, I would like to discuss how "cell death" can be understood from the perspective of mathematical sciences. Research on microbial cell death has progressed by identifying the molecular mechanisms that drive relevant biochemical processes, which are identified based on empirically known cell death markers. However, there has been little discussion on what death actually is in the first place, or how it can be "defined." Furthermore, recent reports have shown that commonly used live/dead assays—such as dead-cell staining and metabolic activity measurements—can yield conflicting results regarding cell viability, highlighting the growing need to discuss what criteria we should use to define "death." In this study, we propose a definition: a cell is "dead" if it cannot return to a predetermined "representative point of the living state," no matter how gene expression levels or external nutrient concentrations are controlled. Plant seeds may appear "dead" at first glance due to their lack of apparent biochemical activity, yet they germinate when watered. Our proposal in this study is to determine the life or death of a cell based on whether an operation equivalent to "watering" exists [1]. Of course, it is experimentally impossible to prove that a cell cannot regain activity under any operation; however, it is theoretically possible using mathematical models. We developed a method called "Stoichiometric Rays" to calculate the controllability of metabolic reaction systems. Using this, we calculated states that cannot be controlled back to the "representative point of the living state" regardless of how enzyme levels and external nutrient concentrations are manipulated. Consequently, we succeeded in quantifying the separating hyperplane between the "living state" and the "dead state" in a mathematical model of metabolism [2], which we call the Separating Alive and Non-life Zone (SANZ) Hypersurface. In this talk, I will outline the theory, the quantification of the SANZ hypersurface, and its biological interpretation. In addition, through our research [3], we have partially identified a class of models that do not exhibit "death" in the sense described above. I would also like to discuss the relationship between the absence of "death" in these models and the autonomy of life.

会場: セミナー室 (359号室) 3階 359号室 (メイン会場) / via Zoom

イベント公式言語: 英語

Four Fermi Theory in Four Dimensions is Renormalisable

2026年8月3日(月) 15:00 - 16:30

Charlie Cresswell-Hogg (Post-Doctoral fellow, Department of Physics, Sussex University, UK / Post-Doctoral fellow, Dortmund University, Germany)

We demonstrate the renormalisability of quantum field theories in four dimensions with elementary self-interacting Dirac fermions and to leading order in the limit of many fermion flavours Nf. Starting from the underlying divergence structure and using Gross-Neveu-type interactions as a template, we explain why extended four-fermion theories including higher-derivative interactions are well-defined, renormalisable, and predictive with only a few free parameters. We also provide the exact large-Nf leading beta functions of couplings and discuss quantum scaling dimensions, universality, 1/Nf corrections, and extensions to other types of four fermion interactions. Implications for effective theory and model building are indicated.

会場: via Zoom

イベント公式言語: 英語

Quantum Gravity and Emergent Cosmology: A Group Field Theory Perspective

2026年7月31日(金) 14:00 - 16:00

Luca Marchetti (カブリ数物連携宇宙研究機構 (Kavli IPMU) 特任研究員)

This seminar is the second part of a two-part mini-seminar series organized by the Quantum Gravity Gatherings study group. It is intended to have a more lecture-style format, with an extended duration of up to two hours. This will allow the speaker sufficient time to introduce the framework in a clear and pedagogical manner, while also leaving ample room for questions and discussion with the audience. Title: Quantum Gravity and Emergent Cosmology: A Group Field Theory Perspective Abstract: I will introduce the Group Field Theory (GFT) approach to quantum gravity, emphasizing its connections with matrix and tensor models, discrete gravity path integrals, and loop quantum gravity. Through these connections, GFTs emerge naturally as quantum field theories of "spacetime atoms". I will then discuss how semiclassical, macroscopic physics can emerge from GFT, touching upon the challenges of defining locality and coarse-graining in quantum gravity, and on how these can be naturally addressed within relational frameworks. I will present a concrete implementation of this relational strategy in GFT and show how a simple relational coarse-graining scheme can be used to extract cosmological physics. Within the resulting cosmological models, the initial singularity is resolved into a quantum bounce, while cosmological perturbations emerge from the quantum entanglement of the underlying quantum-gravity degrees of freedom, with effective dynamics modified on trans-Planckian scales. Finally, I will show that quantum-gravitational interactions alone can generate cosmic acceleration, leading both to dynamical dark energy and to a slow-roll inflationary phase. I will conclude by showing recent observational constraints on such emergent dynamical dark energy models, and by providing an outlook on future research directions.

会場: 研究本館 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Loop expansion in polymer field theory: application to phase separation

2026年7月30日(木) 16:00 - 17:00

川名 清晴 (Research Fellow, Korea Institute for Advanced Study (KIAS), Republic of Korea)

Liquid-liquid phase separation underlies phenomena ranging from protein condensate formation to the phase coexistence of synthetic polymers. In this talk, we develop a field theoretic loop expansion in homopolymer systems by identifying the inverse polymer density ρ^{-1} as the Planck constant ℏ in quantum field theory. The 1-loop approximation is known as the random phase approximation (RPA) and has been extensively applied to many (hetero)polymer systems. We calculate the leading-order (2-loop) and next-to-leading-order (3-loop) corrections to the RPA free energy, denoted as RPA+ and RPA++, respectively. Testing the binodal predicted by the RPA+ against molecular dynamics simulations of bead-spring chains with Gaussian pair interactions, we find that the RPA+ qualitatively improves the dilute-phase coexistence density over the RPA, while the critical point error remains comparable to that of the RPA. Our results establish the loop expansion as a systematic route for refining the RPA-based binodal predictions for polymer phase separation. This talk is based on arXiv: 2605.01261.

会場: via Zoom

イベント公式言語: 英語

Quantum Reference Frames for Quantum Gravity

2026年7月30日(木) 14:00 - 16:00

Luca Marchetti (カブリ数物連携宇宙研究機構 (Kavli IPMU) 特任研究員)

This seminar is the first part of a two-part mini-seminar series organized by the Quantum Gravity Gatherings study group. It is intended to have a more lecture-style format, with an extended duration of up to two hours. This will allow the speaker sufficient time to introduce the framework in a clear and pedagogical manner, while also leaving ample room for questions and discussion with the audience. Title: Quantum Reference Frames for Quantum Gravity Abstract: Internal quantum reference frames provide a general framework for handling symmetries in quantum theory, with applications ranging from quantum gravity and gauge theories to quantum information and foundational physics. I will first introduce the formalism in simple mechanical systems, before turning to classical gravity. There, I will motivate the need for internal, dynamical frames in background-independent theories to define relationally local gauge-invariant observables, and show how this framework leads to a relational update of general covariance: frame covariance. I will then move to non-perturbative quantum gravity, showing how quantum reference frames can be used to define a manifestly gauge-invariant relational path integral, which is also invariant under transformations between quantum reference frames. It therefore provides a perspective-neutral description of quantum gravitational physics. I will also discuss the associated relational effective actions. Although effective actions are, in general, not frame-covariant off shell, the on-shell physics they encode is. Finally, I will present several physical consequences of this framework, including the fuzziness of frame-changed local correlators, the non-trivial interplay between quantum-reference-frame transformations and time evolution, and the frame-dependence properties of ground sectors and Hartle-Hawking prescriptions. I will conclude by outlining future directions, with particular emphasis on a relational notion of the renormalization group flow.

会場: 研究本館 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Current challenges teaching undergraduate first year physics in Canada

2026年7月30日(木) 13:00 - 14:00

カトゥリン・ボシゥメン (理化学研究所 数理創造研究センター (iTHEMS) 副センター長)

I will talk about the challenges of teaching first year physics in 2026 to undergraduate students in computer science and engineering in Canada. Topics will include issues with textbook publishers (online vs physical books), open access textbook/homework systems, teaching, learning and setting evaluations, labs and homework in the era of AI, student attitudes towards learning, academic accommodation for disabilities, etc. This seminar could be interesting to those of you who will face teaching in your future, especially abroad. Although my perspective is based on physics and Canada, a number of issues raised are broadly relevant to other fields and countries.

会場: 研究本館 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

An optimal transport and information geometric framework for infinite-dimensional Gaussian measures and Gaussian processes (II)

2026年7月28日(火) 15:00 - 16:15

Minh Ha Quang (理化学研究所 革新知能統合研究センター (AIP) 不完全情報学習チーム 上級研究員)

Divergences between probability distributions play a crucial role in many areas of probability theory, statistics, machine learning, and their applications. While a large part of the literature is focused on divergences between finite-dimensional distributions, there is a growing body of work on infinite-dimensional distances/divergences, which are motivated by applications in functional data analysis, Bayesian inverse problems, and functional Bayesian neural networks, among others. In this lecture, we present an overview of recent results on some of the most important divergences being studied, including the Kullback-Leibler, Renyi, and Geometric Jensen-Shannon divergences. We discuss the many challenges that arise in the infinite-dimensional setting, e.g. the lack of a natural reference measure such as the Lebesgue measure and the fact that many functions such as determinants and logarithm are only well-defined in specific settings. In particular, in the setting of Gaussian measures on infinite-dimensional Hilbert spaces, the closed form expressions for the above divergences are only generalizable to equivalent Gaussian measures. We present the resolution to the above challenges via the geometrical framework of positive definite unitized (or regularized) trace class and Hilbert-Schmidt operators, including the Alpha and Alpha-Beta Log-Determinant divergences. Using this framework and the methodology of reproducing kernel Hilbert spaces (RKHS), we furthermore obtain consistent finite-dimensional  approximations of the above divergences in the Gaussian process setting, with dimensional-independent sample complexities. The resulting numerical algorithms can be readily employed in practical applications. We shall also discuss the generalization of the above classical divergences above to the quantum setting, namely the Quantum Jensen-Shannon divergence between quantum states, defined in terms of the von Neumann and Tsallis entropies, from finite to infinite-dimensional settings.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

An optimal transport and information geometric framework for infinite-dimensional Gaussian measures and Gaussian processes (I)

2026年7月28日(火) 13:30 - 14:45

Minh Ha Quang (理化学研究所 革新知能統合研究センター (AIP) 不完全情報学習チーム 上級研究員)

Optimal transport (OT) and information geometry (IG) have been attracting much research attention in various fields, in particular machine learning and statistics. In this lecture, we present results on the generalization of IG and OT distances for finite-dimensional Gaussian measures to the setting of infinite-dimensional Gaussian measures and Gaussian processes. Our focus is on the Entropic Regularization of the 2-Wasserstein distance and the generalization of the Fisher-Rao Riemannian metric and related quantities. In both settings, regularization leads to many desirable theoretical properties, including in particular dimension-independent convergence and sample complexity. The mathematical formulation involves the interplay of IG and OT with Gaussian processes and the methodology of reproducing kernel Hilbert spaces (RKHS). All of the presented formulations admit closed form expressions that can be efficiently computed and applied practically. The mathematical formulations will be illustrated with numerical experiments on Gaussian processes.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Center-vortex condensation and monopole condensation in 4d gapped phases

2026年7月27日(月) 14:00 - 15:30

林 優依 (京都大学 基礎物理学研究所 学振特別研究員PD)

Two well-known scenarios for quark confinement are center-vortex proliferation and monopole condensation. We consider gauge-invariant criteria for center-vortex condensation and monopole condensation in terms of Z(N) 1-form symmetry. The condensation of a soliton can be characterized by the non-suppression of the partition function with a proper twisted boundary condition, and we utilize this idea for these criteria. With these definitions, we show that gapped phases with the center-vortex condensation necessarily exhibit the monopole condensation.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Some instances where topological illustration induced new mathematics

2026年7月24日(金) 16:30 - 18:00

Sofia Lambropoulou (Professor, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Greece)

We shall present instances from generalized knot theory, braid theory and their interactions, where illustration promoted understanding and inspired new mathematics. The first instance addresses a question of V.F.R. Jones whether one can make analogous constructions to the (2-variable) Jones polynomial using other braid groups and other types of Hecke algebras. The second instance addresses the question of formulating braid equivalences, analogous to the Markov theorem for classical braids, in settings where we may not even have available algebraic structures for the related braids. The third instance is about the theory of bonded knots and bonded knotoids used for modelling proteins.

会場: via Zoom / セミナー室 (359号室)

イベント公式言語: 英語

Unraveling the very early universe with black holes, boson stars, and cannibal stars

2026年7月24日(金) 14:00 - 16:00

小林 洸 (Associate Professor, International School for Advanced Studies (SISSA), Italy)

According to the standard picture of cosmology, the rich structure of our universe began to form roughly 50,000 years after the big bang. In this talk I will explore the possibility that cosmic structures could also have formed in the extremely early universe, within a fraction of a second after inflation. I will show how this early structure formation can give rise to compact objects, including exotic stars and primordial black holes. These relics provide powerful probes of the first instants of cosmic history, especially the reheating epoch, and may even act as seeds for cosmological phase transitions. Note: This seminar is jointly organized by the iTHEMS-phys Study Group and the iTHEMS-ABBL Joint Astro Study Group.

会場: セミナー室 (359号室) / via Zoom

イベント公式言語: 英語

The decision intelligence of humans and machines

2026年7月24日(金) 10:30 - 11:30

Petter Holme (Professor, Department of Computer Science, Aalto University, Finland)

The event has been rescheduled from July 22 to July 24. To understand our near-future of artificial intelligence firmly integrated into many levels of social life, a challenge is to understand the differences and similarities between human and AI decision-making. In controlled laboratory settings assessing risk and uncertainty, LLMs demonstrate superhuman efficiency but fundamentally diverge from human behavior through a rigid hyper-rationality and an inability to disengage from obsolete strategies. However, when applied to messy, real-world dilemmas "in the wild," these models pivot to function as highly effective "satisficers". Human subjects consistently prefer this artificial counsel over human peer advice, noting its ability to carefully balance emotional context with logical constraints while actively reducing anxiety and regret. Ultimately, this synthesis shows that while AI can offer near-optimal laboratory performance and therapeutic impact in daily life, they also have a distinct lack of behavioral plasticity that we need to account for in models of the future.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

When Is Collective Intelligence a Lottery? Toward a Physics of Bounded Agent Societies

2026年7月22日(水) 16:00 - 17:30

田中 秀宣 (Group Leader, CBS-NTT Physics of Intelligence Program, Center for Brain Science, Harvard University, USA)

Multi-agent LLM systems can reach agreement quickly, but agreement alone does not reveal whether a group has integrated evidence, amplified a bias, or merely locked in the luck of early samples. In this talk, I will develop a physics-style approach to this problem through two synthetic games. In reward-free naming games, populations form conventions through mutual in-context learning: agents treat one another's sampled outputs as evidence, so early fluctuations compound into consensus. A minimal model, Quantized Simplex Gossip (QSG), identifies this regime as memetic drift and predicts scaling laws and a crossover from lottery-like drift to bias-driven selection. I will then introduce the Flag Game, in which a hidden country flag provides verifiable ground truth but each agent sees only a private crop of it. Here, bounded agents must balance private evidence against social input. We find rich phenomenologies, where adding agents can help or hurt, large groups can polarize, and social-awareness prompting, model diversity, and organizational structure all reshape collective performance. Extending QSG with grounded evidence and model-specific update rules explains these effects. More broadly, these studies frame an LLM society as a network of networks, neural networks coupled through social interaction, and outline a route toward a multiscale physics of interacting AI agents, linking model-internal representations, agent-level decision mechanisms, and population-level social dynamics.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Workshop on Discrete & Continuous Aspects of Reaction-Diffusion in Pattern Formation (DiCoRD2026)

2026年7月22日(水) - 24日(金)

富安 亮子 (九州大学 マス・フォア・インダストリ研究所 教授)
佐藤 純 (金沢大学 教授)
末松 信彦 (明治大学 総合数理学部 専任教授)
西浦 廉政 (北海道大学 名誉教授)
リッカルド・ムオロ (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 基礎科学特別研究員)
Jonathan Dawes (Professor, University of Bath, UK)
Henrik Weyer (Postdoctoral Scholar, University of California, Santa Barbara, USA)
加藤 譲 (公立はこだて未来大学 システム情報科学部 複雑系知能学科 准教授)
小澤 歩 (海洋研究開発機構 (JAMSTEC) Young Research Fellow)
杉本 貴則 (関西大学 システム理工学部 准教授)
義永 那津人 (公立はこだて未来大学 システム情報科学部 教授)
Jens Rademacher (Professor, University of Hamburg, Germany)
深尾 武史 (龍谷大学 先端理工学部 教授)
田中 吉太郎 (公立はこだて未来大学 システム情報科学部 准教授)
石原 秀至 (東京大学 特任准教授)
石井 宙志 (北海道大学 電子科学研究所 助教授)
渡辺 毅 (長野大学 准教授)
アントワーヌ・ディエズ (理化学研究所 数理創造研究センター (iTHEMS) 数理展開部門 数学応用研究チーム 研究員)

会場: via Zoom / 明治大学 中野キャンパス 高層棟6F 研究セミナー室3

イベント公式言語: 英語

Entanglement suppression for ΩΩ scattering

2026年7月17日(金) 15:00 - 16:30

曽根 克佳 (東京都立大学 大学院理学研究科 博士課程)

The S-matrix describing the scattering process can be expressed in terms of projection operators onto the allowed spin–flavor channels and the corresponding phase shifts. Using the entanglement entropy in the spin space of the two-particle state, one can define the entanglement power, which quantifies the ability of the S-matrix to generate entanglement in the system. By investigating the conditions under which the entanglement power of the S-matrix is minimized, namely, the conditions for entanglement suppression, one can derive relations among the phase shifts in different spin–flavor channels. Furthermore, by comparing these relations with the interaction Lagrangian, one can identify the underlying symmetries [1,2]. In this work, we apply the entanglement suppression framework to two-baryon scattering involving spin-3/2 baryons in the flavor decuplet [3]. Lattice QCD calculations have shown that the spin-0 ΩΩ system exhibits scattering close to the unitary limit. Combining this result with the relation between the phase shifts obtained from entanglement suppression, we discuss the scattering behavior of the spin-2 ΩΩchannel.

会場: 研究本館 4階 445-447号室 (メイン会場) / via Zoom

イベント公式言語: 英語

第33回 MACSコロキウム

2026年7月17日(金) 14:45 - 18:00

成瀬 元 (京都大学 大学院理学研究科 地球惑星科学専攻 教授)
村瀬 洋介 (理化学研究所 数理創造研究センター (iTHEMS) 数理展開部門 数理社会科学チーム チームディレクター)

14:45-15:00 ティータイムディスカッション 15:00-16:00 成瀬 元（京都大学大学院理学研究科 地球惑星科学専攻 教授）「地層は何を覚えているのか？―機械学習で探る過去の地球環境―」 16:15-17:15 村瀬 洋介（理化学研究所 数理創造研究センター チームディレクター）「社会における協力行動の数理：直接互恵と間接互恵から見る協力の進化」 17:15-18:00 継続討論会

会場: 京都大学 理学研究科セミナーハウス（建物配置図（北部構内）【10】の建物）

イベント公式言語: 日本語

A first step towards Non-Archimedean Geometric Quantization

2026年7月17日(金) 14:00 - 15:30

後藤 慶太 (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 基礎科学特別研究員)

Calabi--Yau manifolds have long attracted interest from both mathematics and physics, particularly in the context of mirror symmetry, and form an important class of compact Kähler manifolds. A compact Kähler manifold is Calabi--Yau if and only if it admits a Ricci-flat Kähler metric, which we shall call a CY metric. Such a metric is highly analytic in nature, as it is given as the solution to a second-order PDE on the manifold, namely the complex Monge--Ampère equation. When the Calabi--Yau manifold is a complex projective variety, one algebraic approach to understanding this analytically defined CY metric is to approximate it by algebraically defined metrics called balanced metrics. This framework was initiated by Donaldson and is now known as geometric quantization. In this talk, following the spirit of this theory, we consider a non-Archimedean analogue of this approximation theory. More precisely, for a non-Archimedean analytic space associated with a maximally degenerating family of Calabi--Yau manifolds, we study the approximation of the NACY metric, a non-Archimedean analogue of the CY metric, by algebraically defined metrics. In particular, we introduce NA balanced metrics, which are expected to provide such an approximation, and explain that, for totally degenerating families of abelian varieties, NA balanced metrics indeed approximate the NACY metric.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語