セミナー

Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs

2022年7月21日(木) 16:00 - 17:00

濱崎 甲資 (東京大学 大学院農学生命科学研究科 博士課程)

In recent years, the genomic prediction that predicts phenotypic values from marker genotype data has attracted much more attention in the area of breeding. Especially, genomic selection using prediction values based on genomic prediction models has been contributing to more efficient and rapid breeding. In genomic prediction, it is important to construct the prediction model so that its accuracy becomes higher. Thus, multivariate genomic prediction models with secondary traits, such as data from various omics technologies including high-throughput phenotyping (e.g., unmanned aerial vehicle-based remote sensing), have started to be applied to many datasets because it offers improved accuracy gains compared with genomic prediction based only on marker genotypes. Although there is a trade-off between accuracy gains and phenotyping costs of secondary traits, no attempt has been made to optimize these trade-offs. In this study, we propose a novel approach to optimize multivariate genomic prediction models with secondary traits measurable at early growth stages for improved accuracy gains and phenotyping costs. The proposed approach employs Bayesian optimization for efficient Pareto frontier estimation, representing the maximum accuracy at a given cost. The proposed approach successfully estimated the optimal secondary trait combinations across a range of costs while providing genomic predictions for only about 20% of all possible combinations. The simulation results reflecting the characteristics of each scenario of the simulated target traits showed that the obtained optimal combinations were reasonable. Analysis of real-time target trait data showed that the proposed multivariate genomic prediction model had significantly superior accuracy compared to the univariate genomic prediction model.

会場: via Zoom

イベント公式言語: 英語

Seiberg-Witten Floer homotopy

2022年7月15日(金) 14:00 - 16:30

今野 北斗 (東京大学 大学院数理科学研究科 助教)

I will survey a mathematical object called the Seiberg-Witten Floer homotopy type introduced by Manolescu. This is a machinery that extracts interesting aspects of 3- and 4-dimensional manifolds through the Seiberg-Witten equations. This framework assigns a 3-manifold to a "space" (more precisely, the stable homotopy type of a space), and this space contains rich information that is strong enough to recover the monopole Floer homology of the 3-manifold, which is known already as a strong invariant. I shall sketch how this theory is constructed along Manolescu's original work, and introduce major applications. If time permits, I will also explain recent developments of Seiberg-Witten Floer homotopy theory. If you are not familiar with the mathematical formulation of TQFT and categorification, I recommended you to watch Dr. Sano's recent talk in advance (see related links).

会場: コモンルーム 246-248号室 とZoomのハイブリッド開催

イベント公式言語: 英語

Dual stochasticity of neurons and synapses for sampling-based learning in the brain

2022年7月14日(木) 16:00 - 17:00

寺前 順之介 (京都大学 大学院情報学研究科 先端数理科学専攻 非線形物理学講座 准教授)

Neurons and synapses behave highly stochastically in the brain. However, how this stochasticity is beneficial for computation and learning in the brain remains largely unknown. In this presentation, we will see that the stochastic processes in neurons and synapses can be integrated into a unified framework to optimally sample events from the environments, resulting in an efficient learning algorithm consistent with various experimental results. In particular, the learning algorithm enables us to reproduce the recently discovered efficient power-law coding in the cortex. These results suggest that synapses and neurons work cooperatively to implement a fundamental method for stochastic computing in the brain.

会場: via Zoom

イベント公式言語: 英語

Speed limits for macroscopic transitions

2022年7月13日(水) 13:30 - 15:00

濱崎 立資 (理化学研究所 開拓研究本部 (CPR) 濱崎非平衡量子統計力学理研白眉研究チーム 理研白眉研究チームリーダー)

Speed of state transitions in macroscopic systems is a crucial concept for foundations of nonequilibrium statistical mechanics as well as various applications in quantum technology represented by optimal quantum control. While extensive studies have made efforts to obtain rigorous constraints on dynamical processes since Mandelstam and Tamm, speed limits that provide tight bounds for macroscopic transitions have remained elusive. Here, by employing the local conservation law of probability, the fundamental principle in physics, we develop a general framework for deriving qualitatively tighter speed limits for macroscopic systems than many conventional ones. We show for the first time that the speed of the expectation value of an observable defined on an arbitrary graph, which can describe general many-body systems, is bounded by the “gradient” of the observable, in contrast with conventional speed limits depending on the entire range of the observable. This framework enables us to derive novel quantum speed limits for macroscopic unitary dynamics. Unlike previous bounds, the speed limit decreases when the expectation value of the transition Hamiltonian increases; this intuitively describes a new trade-off relation between time and the quantum phase difference. Our bound is dependent on instantaneous quantum states and thus can achieve the equality condition, which is conceptually distinct from the Lieb-Robinson bound. We also find that, beyond expectation values of macroscopic observables, the speed of macroscopic quantum coherence can be bounded from above by our general approach. The newly obtained bounds are verified in transport phenomena in particle systems and nonequilibrium dynamics in many-body spin systems. We also demonstrate that our strategy can be applied for finding new speed limits for macroscopic transitions in stochastic systems, including quantum ones, where the bounds are expressed by the entropy production rate. Our work elucidates novel speed limits on the basis of local conservation law, providing fundamental limits to various types of nonequilibrium quantum macroscopic phenomena.

会場: コモンルーム 246-248号室 とZoomのハイブリッド開催

イベント公式言語: 英語

Adiabatic pumps in quantum spin systems

2022年7月12日(火) 16:00 - 17:15

塩崎 謙 (京都大学 基礎物理学研究所 助教)

The Thouless pump is a one-parameter cycle of 1-dimensional gapped quantum systems with U(1) symmetry, which is classified by integers. In this talk, I introduce a generalization of the Thouless pump to quantum spin systems in any dimension with any finite group onsite symmetry. I show a simple model with Z_2 onsite symmetry, and how it is nontrivial via boundary degrees of freedom. Using the framework of the injective matrix product state, one can construct the topological invariant in a way similar to the Berry phase. If time allows, I will briefly introduce a group cohomology model by Roy and Harper for generic space dimensions and discuss its properties.

会場: via Zoom

イベント公式言語: 英語

Stem cells determine complexity of hematopoiesis and immunity: A key in maintenance of homeostasis and fighting disease

2022年7月11日(月) 10:00 - 11:30

石川 文彦 (理化学研究所 生命医科学研究センター (IMS) ヒト疾患モデル研究チーム チームリーダー)

The hematopoietic system, is a complex organ in which all cells, including white blood cells (also known as leukocytes), red blood cells and platelets originate from the hematopoietic stem cells. White blood cells/leukocytes are critical effectors of immunity. At baseline, we have about 5000-10000/microL circulating white blood cells/leukocytes, composed of more than ten distinct subsets. Among them, the most abundant (50-60%) is the neutrophil, which are capable of preventing bacterial and fungal infection. Others include T lymphocytes which attack tumors and virus-infected cells and B lymphocytes that produce immunoglobulins. Each of the leukocyte subsets have different roles in protecting us from diseases. Defects in white blood cell number or function expose us to risks of infections and tumors. Maintenance of normal homeostasis of these white blood cells is governed by expression levels of approximately 20,000 genes in hematopoietic stem cells. In this presentation, first, I will discuss current understanding of a hierarchical system of stem cells generating many different kinds of leukocytes. Second, I will talk about leukemia, a cancer of white blood cells, in which critical genes are hit by mutations, resulting in a loss or gain of function of those genes in stem cells. Third, I would like to discuss with the iTHEMS scientists potential approaches by which we can collaborate to understand the normal and diseased human blood/immune systems.

会場: コモンルーム 246-248号室 とZoomのハイブリッド開催

イベント公式言語: 英語

Virus vs. Bacteria: Art of the war in the microbial world

2022年7月7日(木) 16:00 - 17:00

御手洗 菜美子 (Associate Professor, Niels Bohr Institute, University of Copenhagen, Denmark)

A virulent phage (virus that infects bacteria) infection to a host bacterial cell results in lysis of the cell, where possibly hundreds of phage particles are released after a latency time. The phage pressure is believed to be an important factor to shape the microbial communities and a driving force of their evolution, and yet we are far from having a full picture of their warfare. In this talk, I highlight a few factors that play significant roles in phage-bacteria interactions and their coexistence, such as the effect of herd immunity and the importance of the spatial structure in a few cells scale to the colony scale. *Her talk will be accessible to physicists, mathematicians, and also biologists.

会場: via Zoom

イベント公式言語: 英語

Gradient flow exact renormalization group 2

2022年7月6日(水) 13:30 - 17:00

鈴木 博 (九州大学 大学院理学研究院 教授)

Wilson’s exact renormalization group (ERG), which tells how a system changes under the scale transformation, provides a fundamental framework to define quantum field theory even beyond the perturbation theory. It has however been known that it is difficult to preserve a manifest gauge symmetry in ERG because of the usage of the momentum cutoff in ERG. Here, we propose a possible modification of ERG, the gradient flow exact renormalization (GFERG), which preserves a manifest gauge symmetry being based on a gauge-covariant diffusion equation. I explain the basic idea and properties of GFERG. If time permits, I want to present a possible application of GFERG to the consideration of the axial anomaly.

会場: via Zoom

イベント公式言語: 英語

Gradient flow exact renormalization group 1

2022年7月5日(火) 13:30 - 17:00

鈴木 博 (九州大学 大学院理学研究院 教授)

Wilson’s exact renormalization group (ERG), which tells how a system changes under the scale transformation, provides a fundamental framework to define quantum field theory even beyond the perturbation theory. It has however been known that it is difficult to preserve a manifest gauge symmetry in ERG because of the usage of the momentum cutoff in ERG. Here, we propose a possible modification of ERG, the gradient flow exact renormalization (GFERG), which preserves a manifest gauge symmetry being based on a gauge-covariant diffusion equation. I explain the basic idea and properties of GFERG. If time permits, I want to present a possible application of GFERG to the consideration of the axial anomaly.

会場: via Zoom

イベント公式言語: 英語

Long-term evolution of a supernova remnant hosting a double neutron star binary

2022年7月1日(金) 14:00 - 15:00

松岡 知紀 (京都大学 大学院理学研究科 博士課程)

Stellar mass loss is one of the crucial elements which determine the fate of progenitors of core-collapse supernovae (SNe). Since the material released from the progenitor will be distributed as circumstellar medium (CSM), it can also have an influence on the subsequent evolution of the SN or supernova remnant (SNR). Despite its importance, mass loss histories predicted by stellar evolution models have not been incorporated with modeling for SNRs. As a first step, we investigate the dynamical evolution of an ultra-stripped supernova remnant (USSNR), originated from a type of core-collapse SN explosion proposed to be a candidate formation site of a double neutron star binary. By accounting for the mass-loss history of the progenitor binary using a model developed by a previous study, we construct the large-scale structure of the CSM up to a radius ∼100 pc, and simulate the explosion and subsequent evolution of a USSN surrounded by such a CSM environment. We find that the CSM encompasses an extended region characterized by a hot plasma with a temperature ∼10^8 K located around the termination shock of the wind from the progenitor binary (∼10 pc), and the USSNR blast wave is drastically weakened while penetrating through this hot plasma. Radio continuum emission from a young USSNR is sufficiently bright to be detectable if it inhabits our galaxy but faint compared to the observed Galactic SNRs. In this seminar I will talk about the background of the connection between the models for stellar evolution and SNRs, the details of our methods, and future prospects.

会場: via Zoom

イベント公式言語: 英語

Topological quantum effects in low-dimensional spin systems - The power of the boundary

2022年6月30日(木) 17:00 - 18:15

Thore Posske (Group Leader, I. Institute for Theoretical Physics, University of Hamburg, Germany)

Manipulating the boundary of low-dimensional magnetic structures could grant control about topological magnetic quantum sates. I will discuss the creation of one- and two-dimensional topological quantum magnets by manipulating the boundary magnetization, address their stability against external perturbations, and discuss their possible application to quantum information processing.

会場: via Zoom

イベント公式言語: 英語

Predicting local patterns of diversity: coexistence models, networks and wildflowers

2022年6月30日(木) 10:00 - 11:30

Margie Mayfield (Professor, University of Melbourne, Australia)

The question of how species coexist in diverse natural communities has challenged ecologists for generations. Theoretical models of species coexistence have been developed, but primarily as proof of concept for specific coexistence theories. These theories and associated models focus on coexistence between species pairs and ignore the great complexity of interactions found in most natural systems. Though useful for advancing ecological theory, these models are often of limited use for understanding and predicting diversity in real natural communities. In this talk, I explore the three main assumptions made by coexistence models developed under the framework of Modern Coexistence Theory (MCT): that only direct competition is important, that demographic variation is noise, not valuable biological information, and that only the average environment matters. Using Bayesian statistical approaches with population growth models applied to field data from the annual plant communities of the York gum woodlands of SW Western Australia, I illustrate the issues with these assumptions in predicting coexistence in diverse systems. I show how these Bayesian approaches to MCT can improve on frequentist approaches and discuss the potential value of interaction networks for studying coexistence dynamics in diverse natural systems.

会場: 大河内記念ホール (メイン会場) / via Zoom

イベント公式言語: 英語

Mathematical modeling of understanding how adaptive evolution of sexual traits can affect coexistence

2022年6月23日(木) 16:00 - 17:00

森田 慶一 (総合研究大学院大学 先導科学研究科 生命共生体進化学専攻 博士課程)

One of the challenges in ecology is understanding the processes of species coexistence. Recent studies have underlined the importance of the interaction between rapid adaptation and population dynamics (i.e., eco-evolutionary feedbacks) in coexistence. Reproductive interference may reduce population growth rate due to costs of hybridization by incomplete recognition of sexual traits such as ornaments and songs in birds. Recent theoretical studies have suggested that eco-evolutionary feedbacks in sexual traits can affect coexistence. I will present mathematical modeling for investigating how reproductive interference can affect coexistence. Furthermore, I will present an analytical method, adaptive dynamics for understanding how evolution of sexual traits can affect coexistence.

会場: via Zoom

イベント公式言語: 英語

Dress code for infrared safe S-matrix in QED

2022年6月22日(水) 13:30 - 15:00

杉下 宗太郎 (名古屋大学 高等研究院 (IAR) 特任助教)

We consider the infrared (IR) aspects of the gauge invariant S-matrix in QED. I will review the problem of IR divergences in QED, and introduce the dressed state formalism to obtain IR-safe S-matrix elements. I will show a condition for dressed states to obtain IR-safe S-matrix elements, and explain that this condition can be interpreted as the memory effect and is related to asymptotic symmetry. I also explain that IR divergences are necessary to prohibit the violation of asymptotic symmetry. We also argue that the difference between dressed and undressed states can be observed, even if we are able to observe an inclusive cross-section summing over soft photons.

会場: コモンルーム 246-248号室 とZoomのハイブリッド開催

イベント公式言語: 英語

Topological aspects of non-Hermitian physics

2022年6月21日(火) 16:00 - 17:15

大熊 信之 (京都大学 基礎物理学研究所 助教)

The past decades have witnessed an explosion of interest in topological materials, and a lot of mathematical concepts have been introduced in condensed matter physics. Among them, the bulk-boundary correspondence is the central topic in topological physics, which has inspired researchers to focus on boundary physics. Recently, the concepts of topological phases have been extended to non-Hermitian Hamiltonians, whose eigenvalues can be complex. Besides the topology, non-Hermiticity can also cause a boundary phenomenon called the non-Hermitian skin effect, which is an extreme sensitivity of the spectrum to the boundary condition. In this talk, I will explain recent developments in non-Hermitian topological physics by focusing mainly on the boundary problem. As well as the competition between non-Hermitian and topological boundary phenomena, I will discuss the topological nature inherent in non-Hermiticity itself. Field: condensed matter physics Keywords: topological materials, non-Hermitian systems, skin effect, bulk-boundary correspondence

会場: via Zoom

イベント公式言語: 英語

Self-organisation of a dynamic meshwork structure in the mesoderm during the development of a chick embryo and its characterisation using persistent homology

2022年6月16日(木) 16:00 - 17:00

多羅間 充輔 (理化学研究所 生命機能科学研究センター (BDR) フィジカルバイオロジー研究チーム 研究員)

Morphogenesis is a fundamental process of development. Appropriate morphogenesis of tissues is achieved by coordinated motion of individual cells. To elucidate the mechanism behind this self-organisation of cells, one needs to develop a theoretical model based on experimental observations. In our recent study, our experimental colleague found that the mesoderm cells in early chick embryo organise into a meshwork structure, which changes dynamically. To understand the mechanism behind this dynamic meshwork structure formation, we developed an agent-based mechanical model of cells that interact through a short-range attractive interaction. To compare the simulation results with the experiment, we utilized persistent homology, a method of topological data analysis that allows to systematically characterise irregular structures. In this seminar, we will talk about the mechanical mechanism behind the mesoderm structure formation during the development of the early chick embryo, and how the persistent homology analysis is applied to our biological system.

会場: via Zoom

イベント公式言語: 英語

Implications of singularity theorem for non-singular universe

2022年6月16日(木) 13:30 - 15:00

吉田 大介 (名古屋大学 大学院多元数理科学研究科 特任助教)

The singularity theorem by Penrose shows that a spacetime singularity arises in certain universal situations. The existence of a spacetime singularity is thought to represent a breakdown in the validity of theories such as general relativity and the phenomenological models of the universe. Thus, if we could build a correct model that describes the beginning of the universe, the universe predicted by that model should be non-singular. In this talk, we will discuss general properties that a non-singular universe must satisfy in order to avoid the singularity theorem. In particular, we will see that the universe must be, in some sense, smaller than the corresponding closed de Sitter spacetime.

会場: コモンルーム 246-248号室 とZoomのハイブリッド開催

イベント公式言語: 英語

Non-Abelian vortices in two-flavor dense QCD

2022年6月15日(水) 13:30 - 15:00

藤本 悠輝 (Postdoctoral Scholars, Department of Physics, University of Washington, USA)

Recently, the phase of the two-flavor quark matter with the new pattern of color superconductivity was proposed so that the continuous crossover from the hadronic to the quark phase is realized [1]; it is in consonance with the recent observation of neutron stars. In this talk, I will show the classification of the topological vortices in this phase. We found that the stable vortices are what we call the "non-Abelian Alice strings" [2]. They are superfluid vortices carrying 1/3 quantized circulation and color magnetic fluxes. I will discuss their properties in comparison to the well-established CFL vortices in three-flavor symmetric setup, by putting some emphasis on their peculiarity: the non-Abelian generalization of the Alice property. I will then discuss in detail the possibility that these vortices are confined as well as how the vortices in the quark phase can be connected to those in the hadronic phase [3]. [1] Y. Fujimoto, K. Fukushima, W. Weise, PRD 101, 094009 (2020) [1908.09360]. [2] Y. Fujimoto, M. Nitta, PRD 103, 054002 (2021) [2011.09947]; JHEP 09 (2021) 192 [2103.15185]. [3] Y. Fujimoto, M. Nitta, PRD 103, 114003 (2021) [2102.12928].

会場: via Zoom

イベント公式言語: 英語

Introduction to Topological Insulators: The Ten-fold Classification of Topological Insulators and Superconductors Part.2

2022年6月13日(月) 14:00 - 15:30

邱 靖凱 (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)

会場: via Zoom

イベント公式言語: 英語

Algebraic geometry in mixed characteristic

2022年6月10日(金) 14:00 - 16:30

吉川 翔 (理化学研究所 数理創造プログラム (iTHEMS) 基礎科学特別研究員)

In algebraic geometry, we study the geometry of algebraic varieties, which are sets defined by algebraic equations. There are two types of algebraic varieties, they are varieties over characteristic zero and varieties over positive characteristic. Algebraic geometry in characteristic zero is similar to analytic geometry, so it is related to many other subjects. In this talk, I will introduce the notion of algebraic geometry in positive characteristic and relationships between positive characteristic and characteristic zero. In order to study it, we consider families consisting of varieties over characteristic zero and varieties over positive characteristic, called mixed characteristic.

会場: コモンルーム 246-248号室 とZoomのハイブリッド開催

イベント公式言語: 英語