Quantitative phylogenomics

February 24 (Tue) 13:00 - 14:00, 2026

Hector Banõs (Assistant Professor, Department of Mathematics, California State University, USA)
Benjamin Teo (Postdoc, Mathematical Analysis of Cellular Systems, University of Melbourne, Australia)

This session features two speakers: Hector Banos, Assistant Professor of Mathematics at California State University, whose research focuses on phylogenetic inference and network models, and Benjamin Teo, a Postdoctoral Researcher at the University of Melbourne, working on probabilistic and computational methods for continuous trait evolution on phylogenetic networks. See below for details. 【Talk 1】 Speaker: Hector Banos Title: Bringing a Knife to a Gunfight: Pitfalls of Phylogenetic Inference under Model Misspecification Abstract: Phylogenetic networks provide a flexible framework for representing evolutionary histories that include hybridization, introgression, and other reticulate processes. However, inferring such networks remains computationally and statistically difficult. Many current methods often scale only to restricted classes of networks. Consequently, researchers frequently analyze their data using simpler models (most commonly phylogenetic trees) even when there is strong evidence that the underlying evolutionary history is more complex. In this talk, we examine the impact of model misspecification on phylogenetic inference, focusing on situations in which data are generated by a complex network but are analyzed using simpler tree or network models. I then show how this mismatch can influence the topology of inferred trees, as well as the structure of inferred networks. These results highlight the limitations and the practical consequences of using simplified models for phylogenetic inference. 【Talk2】 Speaker: Benjamin Teo Title: Adapting cluster graphs for inference of continuous trait evolution on phylogenetic networks Abstract: I consider a new approach ("loopy belief propagation") for fitting Gaussian models on a phylogenetic network to explain the data observed across present-day species for a continuous univariate or multivariate trait. We previously showed [1] that a trait evolution model coupled to a network can be readily cast as a probabilistic graphical model, so that the likelihood can be efficiently computed using a dynamic programming framework ("belief propagation") defined on an auxiliary graph ("cluster graph") that is tree-structured. Even so, maximum likelihood estimation can grow computationally prohibitive for large complex networks. Belief propagation can be applied more generally to non-tree ("loopy") cluster graphs to compute a factored energy approximation to the log-likelihood. "Loopy" belief propagation may provide a more practical trade-off between estimation accuracy and runtime. However, the influence of cluster graph structure on this trade-off is not precisely understood. We conduct a simulation study using our Julia package PhyloGaussianBeliefProp [2] to investigate how varying the maximum cluster size of a cluster graph affects this trade-off. We discuss recommended choices for maximum cluster size, and prove the equivalence of likelihood-based and factored-energy based estimates for the homogeneous Brownian motion trait model. The talk is based on our preprint [3]. I will introduce the key concepts from the ground up.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Basic Conceptual and Mathematical Problems of QFT

February 20 (Fri) 14:00 - 15:30, 2026

Christy Koji Kelly

In this talk we discuss some of the most basic conceptual and mathematical difficulties that arise in the standard physics analysis of QFT. In particular we shall discuss the origin of UV divergences in QFT—pointing out that there is both a kinematic and a dynamic aspect to this problem, and that the standard physics explanation (’new physics’) only considers the latter—and suggest that despite the notoriety of the problem, UV divergences are essentially under control. Secondly we discuss Haag’s theorem—which ensures the nonexistence of the interaction picture and the triviality of the perturbative S-Matrix—and indicate how this is the most elementary manifestation of a series of infrared problems in QFT. Finally we will outline why the rigorous construction of path-integral measures is difficult. If we have time, we may discuss some difficulties associated with gauge theories such as the infraparticle problem of QED and the mass-gap problem of Yang-Mills theory.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Tunneling with physics-informed renormalisation group flows in the anharmonic oscillator

February 20 (Fri) 10:00 - 11:00, 2026

Friederike Ihssen (Postdoctoral Fellow, Physics, Ruhr University Bochum, Germany)

The resolution of strongly correlated physical systems is computationally hard, but can be simplified enormously by a formulation in terms of suitable dynamical degrees of freedom. Within the functional renormalisation group framework, physics-informed renormalisation group flows (PIRG flows) [1] implement scale-dependent coordinate transformations that can be used to devise optimal expansion schemes around such degrees of freedom. Recently, we have applied PIRG flows to the anharmonic oscillator, with an emphasis on the weak coupling regime with its instanton-dominated tunnelling processes [2]. We show that the instanton physics behind the exponential decay of the energy gap is already covered in the first order of the derivative expansion of the PIRG. The crucial new ingredients in the present analysis are the use of the ground state expansion within PIRG flows, as well as precision numerics based on Galerkin methods. Our result a_inst = 1.910(2) for the decay constant is in quantitative agreement with the analytic one, a_inst = 1.886 with a deviation of 1%. This illustrates very impressively the capacity of the PIRG for fully capturing non-perturbative physics already in relatively simple approximations.

Venue: via Zoom / #359, Main Research Building

Event Official Language: English

Spectral Codes : A Geometric Formalism for QEC

February 19 (Thu) 15:00 - 16:30, 2026

Satoshi Kanno (Researcher, Research Institute of Advanced Technology, SoftBank Corp.)

In this talk, I will introduce a novel geometric framework for quantum error correction based on spectral triples in noncommutative geometry. In this formulation, quantum error-correcting codes are described as spectral projections onto the low-energy eigenspaces of Dirac-type operators, where the separation between logical information and local errors is captured geometrically. This approach provides a unified spectral and geometric understanding of key properties such as code distance and error thresholds. Moreover, it accommodates various existing codes, including classical linear codes, stabilizer codes, GKP codes, and topological codes. This geometric perspective also suggests intriguing connections to deformation quantization and holographic quantum error correction, offering promising directions for future research.

Venue: #359, Seminar Room #359

Event Official Language: English

Binary neutron Star Merger as a Probe of Hadron-Quark Transition

February 19 (Thu) 14:00 - 15:00, 2026

Yongjia Huang (Research Associate, Purple Mountain Observatory, Chinese Academy of Sciences, China)

This seminar is a joint seminar between GWX-EOS and the iTHEMS-ABBL Joint Astro SG. The recent rise of multi-messenger astronomy—including radius measurements from NICER, tidal deformability constraints from gravitational-wave events GW170817, and first-principles calculations from chiral effective field theory (χEFT) and perturbative QCD—has significantly tightened constraints on the neutron star equation of state. These advances consistently point to a non-monotonic sound speed in dense matter, suggesting that the cores of massive neutron stars may host exotic phases such as quark matter. However, the masquerade effect in static neutron stars makes it difficult to directly probe the nature of the transition (e.g., a smooth crossover or a sharp phase transition) near the core through observation alone.

Venue: #345, 3F, Main Research Building, RIKEN Wako Campus (Main Venue) / via Zoom

Event Official Language: English

The sample complexity of species tree estimation: How many genes does it take to infer a species tree?

February 19 (Thu) 13:00 - 14:00, 2026

Max Hill (Assistant Professor, University of Hawaiʻi, USA)

In this talk, I will discuss the problem of inferring an evolutionary tree from DNA sequence data. The main focus will be on the sample complexity of this problem---i.e., the question of how much data is required to achieve high probability of correct inference. After introducing a standard stochastic model of gene and DNA evolution, I will highlight some surprising features of DNA sequence data that complicate inference. Finally, I will present an impossibility result which takes the form of an information-theoretic lower bound on the minimum amount of data needed for accurate inference when genes exhibit variation in mutation rates. No prior knowledge of phylogenetics or information theory is assumed. Based on joint work with Sebastien Roch.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

The 31th MACS Colloquium & 2025 MACS Achievement Report Meeting

February 18 (Wed) 14:45 - 18:00, 2026

Yujiro Eto (Associate Professor, Center for Science Adventure and Collaborative Research Advancement (SACRA), Graduate School of Science, Kyoto University)

14:45-15:00 Teatime discussion [15:00-16:00 The 31th MACS Colloquium] Talk by Dr. Yujiro Eto (Associate Professor, Center for Science Adventure and Collaborative Research Advancement (SACRA), Graduate School of Science, Kyoto University) [16:10-18:30 2025 MACS Achievement Report Meeting] 16:10-17:10 Flash Talks to report results 17:10-18:00 Poster Session by SG participating students

Venue: ＃401, Graduate School of Science Bldg. No.6 , Kyoto University

Event Official Language: Japanese

Brainstorming session on data assimilation with quantum computing

February 18 (Wed) 14:00 - 16:00, 2026

Takemasa Miyoshi (Team Principal, Data Assimilation Research Team, RIKEN Center for Computational Science (R-CCS))

We will discuss the potential of quantum computing for applications in data assimilation.

Venue: #359, Seminar Room #359

Event Official Language: English

Taming the Butterfly: A New "Duality Principle" Turns Chaos into Control

February 18 (Wed) 13:00 - 14:00, 2026

Takemasa Miyoshi (Team Principal, Data Assimilation Research Team, RIKEN Center for Computational Science (R-CCS))

Data Assimilation (DA) is the backbone of modern weather forecasting. It integrates observational data into computer simulations to synchronize the model with nature. The Duality Principle posits that chaos control is mathematically the "twin" (dual) of DA. Data Assimilation: Uses observations to synchronize the Model to Nature. Chaos Control: Uses interventions to synchronize Nature to a desired Model ("target trajectory"). "The butterfly effect has long been a symbol of unpredictability," says Dr. Miyoshi. "But I asked a simple question: If a butterfly's wings can change the future, does that not imply that with the right, tiny push, we could choose a better future?" Instead of suppressing the chaotic system with massive force, this method acts like mathematical judo—leveraging the system's inherent instability. By applying minute, calculated "interventions" (analogous to the butterfly's flap), the system can be guided toward a "target trajectory"—for instance, shifting real-world conditions just enough to align with a model-simulated scenario where a typhoon causes no damage. Once synchronized, control becomes much easier to maintain. This study establishes the theoretical foundation for "Control Simulation Experiments" (CSE), a framework previously proposed by Miyoshi’s team. It provides a roadmap for future disaster prevention research, moving beyond passive prediction to active mitigation. Beyond meteorology, this general framework is expected to serve as a universal tool for studying interventions in various chaotic systems, from ecosystems to economics. Following the seminar, we will hold an informal discussion (brainstorming) on data assimilation with quantum computing in the same room from 2-4 pm.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

The Rectangular Peg Problem and microlocal sheaf theory

February 17 (Tue) 14:00 - 15:00, 2026

Yuichi Ike (Associate Professor, Graduate School of Mathematical Sciences, The University of Tokyo)

The Square Peg Problem asks whether every Jordan curve in the plane contains four distinct points that form the vertices of a square. This problem was proposed by Toeplitz in 1911 and remains unsolved in full generality. It can be generalized to the Rectangular Peg Problem, which concerns the existence of inscribed rectangles with a prescribed aspect ratio. Recently, Greene and Lobb successfully applied techniques in symplectic geometry to the problem and obtained new results. In this talk, I will explain how microlocal sheaf theory allows us to further extend their approach and affirmatively solve the Rectangular Peg Problem for a large class of Jordan curves, including all curves of finite length. This is joint work with Tomohiro Asano.

Venue: Seminar Room #359

Event Official Language: English

Persistent homology and its applications

February 17 (Tue) 11:00 - 12:00, 2026

Yuichi Ike (Associate Professor, Graduate School of Mathematical Sciences, The University of Tokyo)

Persistent homology is one of the main tools in topological data analysis (TDA), which encodes the topological features of given data into persistence diagrams. It has been successfully applied to various fields such as material science and computer graphics. In this talk, I will provide an overview of persistent homology and its applications. Furthermore, I will also discuss its integration with machine learning, specifically how persistent-homology-based loss functions can be used to regularize the topological structure of parameters.

Venue: Seminar Room #359

Event Official Language: English

Monitoring the complexity and dynamics of mitochondrial translation

February 12 (Thu) 16:00 - 17:00, 2026

Taisei Wakigawa (Research Associate, RNA Systems Biochemistry Laboratory, RIKEN Pioneering Research Institute (PRI))

Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Recent progress in the resource theory of asymmetry and its applications

February 12 (Thu) 13:30 - 15:00, 2026

Hiroyasu Tajima (Associate Professor, Department of Informatics, Faculty of Information Science and Electrical Engineering, Kyushu University)

If you are not affiliated with RIKEN, please register using the registration form. Registration deadline: 12nd Feb. (Thu), 2026 Symmetry and symmetry breaking are among the central themes in physics and have attracted the interest of many physicists. Recently, the resource theory of asymmetry (RTA) [1-4], which approaches these issues from the perspective of resource theories, has been actively studied. In the past few years, several foundational advances have been made in this framework. In particular, the iid-complete monotone that plays a role analogous to entanglement entropy has been identified for arbitrary compact Lie groups [2] as well as for arbitrary finite groups [3]. The resolution for compact Lie groups includes, as a corollary, a solution to the Marvian–Spekkens conjecture [4]. Building on this theoretical foundation, several developments related to the Wigner–Araki–Yanase (WAY) theorem [5-7] have also been obtained. These include extensions of the WAY theorem to the implementation of arbitrary unitary gates [8], and a unification of the WAY-type theorems, i.e. the WAY theorem, the Eastin–Knill theorem (a fundamental limitation on error correction under symmetry) [9], and the above unitary-gate results. The unification is formulated a universal trade-off inequality relating symmetry, irreversibility, and quantumness for arbitrary quantum dynamics [10]. Using this tradeoff relation, the WAY-type limitations can now be applied, for example, to quantum thermodynamics[11] and black hole evaporation [10] etc. If time permits, I will also briefly touch upon some other recent developments, such as extensions of the above tradeoff and the WAY theorem to general resource theory beyond symmetry [12].

Venue: #359, Seminar Room #359

Event Official Language: English

Quantum Electrodynamics of Strong Laser-Matter Interaction: The Ongoing Journey and Beyond

February 10 (Tue) 10:00 - 12:00, 2026

Ciappina Marcelo (Professor, Guangdong Technion, China)

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Finite-size effects on the QCD critical point

February 9 (Mon) 15:30 - 17:30, 2026

Gyozo Kovacs (Research Fellow, Institute of Theoretical Physics, University of Wroclaw, Poland)

[Joint seminar hosted by QMS Team (iTHEMS) and FTR Team (R-CCS)] While effective approaches are important tools in the search for the QCD critical point, the physical systems they describe differ in several aspects from those in heavy-ion collisions and from unextrapolated lattice QCD. A primary discrepancy is the system size, which is infinite only in effective model calculations. Various implementations exist to account for the resulting finite-size effects. Beyond the frequently used methods, we present a comprehensive mean-field approach that allows for both infinite- and finite-size calculations, even within a complex parameter space. We discuss the general impact of finite-size effects on key observables, such as conserved charge fluctuations, and on the analytic structure of the thermodynamic potential. 15:30-16:30 Lecture 16:30-17:30 Discussion with coffee

Venue: #359, Main Research Building (Main Venue) / via Zoom

Event Official Language: English

What can we learn from kilonovae about nucleosynthesis and high-density matter?

February 9 (Mon) 14:00 - 15:15, 2026

Oliver Just (Postdoctoral Researcher, GSI Helmholtzzentrum für Schwerionenforschung, Germany)

The electromagnetic transients accompanying neutron-star mergers (NSMs), called kilonovae, are powered by the radioactive decay of freshly synthesized heavy elements. As such they should contain rich information about the ejected matter and the properties of the extremely dense meta-stable neutron-star remnant formed right after the collision. However, extracting such information from observed kilonova light curves and spectra remains a challenging endeavor, which requires sophisticated models of various hydrodynamic processes and neutrino transport effects, detailed knowledge of nuclear and atomic physics, as well as complex radiative transfer calculations. In this talk I will report recent efforts from our "HeavyMetal" collaboration aimed at deciphering kilonovae.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Mathematical Application Research Team Meeting #12

February 6 (Fri) 14:00 - 15:30, 2026

Riccardo Muolo (Special Postdoctoral Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Mathematical Application Research Team invites Riccardo Muolo fom Division of Fundamental Mathematical Science to this meeting. You are welcome to join the meeting. Title: Dynamics beyond nodes: a topological framework for oscillatory dynamics on higher-order networks Abstract: In recent years, increasing attention has been given to dynamical processes taking place on higher-order networks, where interactions are not limited to links, but may involve also higher-dimensional simplices [1]. While classical network models assume that state variables live on nodes and interact through links, many real systems — including brain, climate, and transportation systems — cannot be fully described within this node-centric perspective [2]. In this seminar, I will introduce the framework of higher-order networks and the concept of topological signals, namely, dynamical variables defined on simplices of higher dimensions. I will briefly present the basic tools required for this setting, including elementary notions of discrete calculus, discrete topology and geometric algebra, which serve as the mathematical foundation for modeling dynamical processes beyond the node-based paradigm. Next, I will discuss models of oscillatory dynamics extended to this framework. First, I will present the topological Kuramoto model [3], in which phases are not restricted to nodes but may also be associated with links, and where the coupling arises from the combinatorial structure of the simplicial complex. Then, I will introduce the discrete Hodge Laplacian and the Dirac-Bianconi operator [4], the former generalizing diffusive interactions to the higher-order setting, while the latter provides cross-talk between signals defined on simplices of different dimensions. Finally, I will introduce the notion of Dirac-Bianconi driven oscillators, where the dynamics of node- and link-signals coexist, interact and may give rise to collective oscillatory behaviors [5].

Venue: #359, 3F, Main Research Building (Main Venue) / via Zoom

Event Official Language: English

Quantitative characterization of microbial diversity and environmental adaptation

February 5 (Thu) 13:00 - 14:30, 2026

Mio Matsumoto (Junior Research Associate, Geobiology and Astrobiology Laboratory, RIKEN Pioneering Research Institute (PRI))
Shino Suzuki (Chief Scientist, Geobiology and Astrobiology Laboratory, RIKEN Pioneering Research Institute (PRI))

Event Official Language: English

Scalable Simulation of Quantum Many-Body Dynamics with Or-Represented Quantum Algebra

February 4 (Wed) 14:30 - 16:00, 2026

Lukas Broers (Postdoctoral Researcher, Computational Materials Science Research Team, RIKEN Center for Computational Science (R-CCS))

High-performance numerical methods are essential for advancing quantum many-body physics, as well as for enabling the integration of supercomputers with emerging quantum computing platforms. We have developed a scalable and general-purpose numerical framework for quantum simulations based on or-represented quantum algebra (ORQA). This framework applies to arbitrary spin-systems and naturally integrates with quantum circuit simulation in the Heisenberg picture, particularly relevant to recent large-scale experiments on superconducting qubit processors [Kim et al., Nature 618, 500 (2023)]. As a benchmark, we simulate the kicked Ising model on a 127-qubit heavy-hexagon lattice, successfully tracking the time-evolution of local magnetization using up to one trillion Pauli strings. Our simulations exhibit strong scaling up to 2^17 parallel processes with near-linear communication overhead. Further, we show that our framework is naturally extended to a broader range of quantum systems, superseding the capabilities of recently established Pauli propagation methods. We present possible future directions on how to utilize our algorithm.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

JST-Sakura Science Exchange Program: AI for Atmospheric Science

February 4 (Wed) - 10 (Tue) 2026

This JST-Sakura Science Exchange Program leverages the complementary strengths and research foundations of Fudan University and RIKEN in atmospheric science, focusing on the important scientific challenge of applying artificial intelligence to cloud remote sensing and data assimilation. The exchange program also includes one-day workshop in R-CCS with Data Assimilation Research Team.

Venue: S704-S705, Integrated Innovation Building (IIB) (Main Venue) / via Zoom / RIKEN Center for Computational Science, 1F Seminar room

Event Official Language: English