Quantum Computing in Omics Medicine

May 10 (Fri) at 16:00 - 17:15, 2024

Tatsuhiko Tsunoda (Professor, Department of Biological Sciences, Graduate School of Science, The University of Tokyo)

(The speaker is also the team leader of Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences. This is a joint seminar with the iTHEMS Biology Group.) In medical science, the recent explosive development of omics technologies has enabled the measurement not only of bulk data from entire tissues, but also data for individual cells and their spatial location information, and even allowed collection of such information in real-time. Meaningful interpretation of these rich data requires an ability to understand high-order and complex relationships that underpin biological phenomena such as drug response, simulating their dynamics, and selecting the optimal treatment for each patient based on these results. While these data are large-scale and of ultra-high dimensionality, they are also often sparse, with many missing values in the measurements and frequent higher-order interactions among variables, making them hard to handle with conventional statistics. To make further progress, machine learning – especially deep learning – is emerging as one of the promising ways forward. We have developed a method to transform omics data into an image-like representation for analysis with deep learning (DeepInsight) and have successfully used it to predict drug response and to identify original cell types from single-cell RNA-seq data. However, anticipation of the vast amount of medical data being accumulated gives particular urgency to addressing the problems of the time it actually takes to train deep learning models and the complexity of the necessary computational solutions. One possible way to resolve many of these problems is “quantum transcendence”, which is made possible by quantum superposition computation. Among all the different ways to apply quantum computation to medical science, we are particularly interested in quantum deep learning based on optimization and search problems, quantum modeling of single nucleotide detection by observational systems and statistical techniques such as regression analysis by inverse matrix computation and eigenvalue computation. In this seminar, I will first present an overview of how quantum machine learning and quantum deep learning can be used to formulate treatment strategies in medicine. We will discuss how to implement the quantum DeepInsight method, the challenges of noise in quantum computation when training QCNNs, feature mapping issues, problems of pretraining in quantum deep learning, and concerns relating to handling sensitive data such as genomic sequences. I hope this seminar will enhance our understanding of how to effectively facilitate medical research with quantum computing.

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

Event Official Language: English

Surrogate Modeling for Supernova Feedback toward Star-by-Star Simulations of Milky-Way-sized Galaxies

May 10 (Fri) at 14:00 - 15:15, 2024

Keiya Hirashima (Ph.D. Student, Department of Astronomy, Graduate School of Science, The University of Tokyo)

Galaxy simulations have found the interdependence of multiscale gas physics, such as star formation, stellar feedback, inflow/outflow, and so on, by improving the physical models and resolution. The mass resolution remains capped at around 1,000 solar masses (e.g., Applebaum et al. 2021). To overcome the limitations, we are developing a new N-body/SPH code, ASURA-FDPS, to leverage exascale computing (e.g., Fugaku), handle approximately one billion particles, and simulate individual stars and stellar feedback within the galaxy. However, the emergence of communication costs hinders scalability beyond one thousand CPU cores. One of the causes is short timescale events localized in tiny regions, such as supernova explosions. In response, we have developed a surrogate model using machine learning to duplicate supernova feedback quickly (Hirashima et al., 2023a,b). In the presentation, I report the fidelity and progress of the simulations with our new machine-learning technique.

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

Event Official Language: English

Deep Learning for Estimating Two-Body Interactions in Mixed-Species Collective Motion

May 9 (Thu) at 16:00 - 17:00, 2024

Masahito Uwamichi (Project Researcher, Graduate School of Arts and Sciences, The University of Tokyo)

(This is a joint seminar with the Information Theory Study Group.) Collective motion is a fundamental phenomenon observed in various biological systems, characterized by the coordinated movement of individual entities. Such dynamics are especially crucial in understanding cellular behaviors, which can now be observed at an individual level in complex tissue formations involving multiple types of cells, thanks to recent advancements in imaging technology. To harness this rich data and uncover the hidden mechanisms of such dynamics, we developed a deep learning framework that estimates equations of motion from observed trajectories. By integrating graph neural networks with neural differential equations, our framework effectively predicts the two-body interactions as a function of the states of the interacting entities. In this seminar, I will first introduce the structure and hyperparameters of our framework. Subsequently, I will detail two numerical experiments. The first is a simple toy model that was employed to generate data for testing our framework to refine the hyperparameters. The second explores a more complex scenario mimicking the collective motion of cellular slime molds, highlighting our model's ability to adapt to mixed-species interactions.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

Role of self-gravity on the central halo structure of fuzzy dark matter

April 30 (Tue) at 13:30 - 15:00, 2024

Yusuke Manita (Affiliated Scientist, Yukawa Institute for Theoretical Physics, Kyoto University)

Fuzzy dark matter (FDM) is a dark matter model that is characterized by the ultralight masses around 10−22 eV. As FDM has the wave-like nature, the self-gravitating structure is described by the Schrödinger-Poisson equation. Previous simulations based on the Schrödinger-Poisson equation have demonstrated that soliton-like structure having a high-density flat core is formed at the central region of the FDM halos, and the size of such a core is typically determined by the de Broglie wavelength. Away from the central core, the density profile of the FDM halos resembles that of the cold dark matter halos on average, and is shown to be described by the Navarro-Frenk-White (NFW) profile. In this paper, we study the role of the self-gravity of the soliton core, and its relation to the bulk halo properties by solving the Schrödinger-Poisson equation in a simplified setup. The findings indicate that the contribution from the soliton self-gravity must dominate over the NFW potential in order to sustain the soliton.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

How Stars End Their Lives

April 26 (Fri) at 14:00 - 15:15, 2024

Philipp Podsiadlowski (Professor, University of Oxford, UK)

While the basic evolution of stars has been understood for many decades, there are still major uncertainties in our overall understanding of how stars end their lives, both in the context of low- and intermediate-mass stars (including the Sun) and massive stars. I will first review some of key principles that govern the structure and evolution of stars and then present recent progress that has been made for both groups of stars. I will argue and present numerical simulations that show that all stars become dynamically unstable when they become large giant stars, which leads to sporadic, dynamical mass ejections. Low- and intermediate-mass stars may lose all of their envelopes as a consequence, leaving white-dwarf remnants. More massive stars experience core collapse, leaving a neutron-star or black-hole remnant, possibly associated with a supernova explosion. I will show how the dramatic recent progress on understanding the core-collapse process, for the first time, allows us to connect the late evolution of massive stars with the resulting supernova explosions and the final remnants and discuss how observations with current gravitational-wave detectors (such as LIGO) will allow us to test this theoretical connection.

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

Event Official Language: English

Tracing link of cell ageing and disease progression: Joining factors and facilitators

April 25 (Thu) at 16:00 - 17:00, 2024

Rajkumar Singh Kalra (Staff Scientist, Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University (OIST))

Cell ageing is an inevitable biological process. It marks declined homeostatic processes in a cell, the impact of which is reflected in the organism’s function/physiology. Ageing, thus, raises risks of disease progression in elderly people and compromises their immunity. Progression of cancer and neurodegenerative diseases and weak immune response against a pathogen(s) represent cases of ageing-related diseases. What molecular factors/signaling could be associated with disease progression or take part in governing such decisions in aging? – remained a key focus of my research so far. In my talk, I shall shed light on the part characterizing key proteins and their signalling in ageing-related diseases with an emphasis on cancer, neurodegenerative disease, and immunity. Taking advantage of wet lab and system biology studying gene networks, and genomic, proteomic, and metabolomic readouts, I investigated the molecular expression and processes impacted and compromised by ageing. I shall be discussing new knowledge from my work on the linkage of cell ageing and disease progression and therein role of key factors and facilitators I studied.

Venue: via Zoom

Event Official Language: English

A night out with ghosts

April 24 (Wed) at 16:00 - 17:30, 2024

Veronica Errasti Diez (Research Fellow, Faculty of Physics, Ludwig-Maximilians-Universität München, Germany)

Field theories are the chief theoretical framework for physics. For instance, the Standard Model and General Relativity are widely accepted as accounting for subatomic particle and gravitational behavior, respectively. Nonetheless, even such acclaimed field theories have their limitations, such as the mysterious neutrino masses and dark sector. A natural and popular way around the hurdles consists in generalizations of field theories, via the inclusion of non-linear and/or higher-order corrections. Unless painstakingly avoided, these corrections lead to the propagation of negative kinetic energy modes, or ghosts for short. Ghosts have earned an appalling fame: kill, exorcise, avoid… No efforts are spared to guarantee their absence. In this talk, we will delve into the root causes for the ill name of ghosts. As a result, we will take up the cudgels for ghosts. While they do have a strong tendency to yield ill-behaved theories, ghosts are not intrinsically pathological. As we will see, good-natured ghosts open the door to multi-disciplinary tantalizing opportunities…! And ghosts make excellent party-goers, so make sure not to miss this appointment!

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

iTHEMS x academist Online Event "World of Mathematical Sciences 2024"

April 21 (Sun) at 10:00 - 15:30, 2024

Shingo Gibo (Postdoctoral Researcher, iTHEMS)
Taketo Sano (Special Postdoctoral Researcher, iTHEMS)
Misako Tatsuuma (Research Scientist, iTHEMS)
Tomoya Naito (Special Postdoctoral Researcher, iTHEMS)

Venue: via Zoom

Event Official Language: Japanese

RIKEN DAY: Let's Talk with Researchers! Let's get to know each other through "Mathematics: One S&T poster for Every Household”!

April 19 (Fri) at 18:00 - 18:50, 2024

In this RIKEN DAY, we will introduce various phenomena in the world (all things in the universe) that are understood using "mathematics” and the use of "mathematics", including the latest research, while looking at the annual S&T poster for everyone titlled “Mathematics: One S&T poster for Every Household”. For details, please see the related links.

Venue: via Zoom

Event Official Language: Japanese

The 25th MACS Colloquium

April 19 (Fri) at 14:45 - 18:30, 2024

Wataru Morita (Researcher, Department of Anthropology, National Museum of Nature and Science / Associate Professor, Department of Biological Sciences, Graduate School of Science, The University of Tokyo)

14:45-15:00 Teatime discussion 15:00-16:00 Talk by Dr. Wataru Morita (Researcher, Department of Anthropology, National Museum of Nature and Science / Associate Professor, Department of Biological Sciences, Graduate School of Science, The University of Tokyo) 16:15-17:20 2024 Study Group introduction session 17:30-18:30 Discussion

Venue: Maskawa Hall, 1F, Maskawa Building for Education and Research

Event Official Language: Japanese

Zooming into the ancient world by reconstructing the joint genealogies of modern and ancient humans

April 18 (Thu) at 16:00 - 18:00, 2024

Leo Speidel (Senior Research Fellow, Genetics Institute, University College London, UK)

In recent years, we have gone from databases that store the genetic differences observed between hundreds of thousands of sequenced people to using this information to build the actual genetic trees that relate individuals through their shared ancestors back in time. These genetic trees describe how our genomes have evolved up to millions of years into the past. Additionally, sequencing of DNA from ancient human bone has enabled the direct observation of genomic change over past millennia and has unlocked numerous previously hidden genetic histories. In this talk, I will illustrate how we can unearth the human past from these data, ranging from ancient migrations out of Africa and subsequent mixtures with now extinct Neanderthals to waves of ancestry transformations in a nation’s recent past.

Venue: via Zoom

Event Official Language: English

Quantum Fine-Grained Complexity

April 18 (Thu) at 10:30 - 12:00, 2024

Harry Buhrman (Chief Scientist for Algorithms and Innovation, Quantinuum, UK)

(The speaker is also a professor at University of Amsterdam & QuSoft. This is a joint seminar with the iTHEMS Quantum Computation Study Group.) One of the major challenges in computer science is to establish lower bounds on the resources, typically time, that are needed to solve computational problems, especially those encountered in practice. A promising approach to this challenge is the study of fine-grained complexity, which employs special reductions to prove time lower bounds for many diverse problems based on the conjectured hardness of key problems. For instance, the problem of computing the edit distance between two strings, which is of practical interest for determining the genetic distance between species based on their DNA, has an algorithm that takes O(n^2) time. Through a fine-grained reduction, it can be demonstrated that a faster algorithm for edit distance would imply a faster algorithm for the Boolean Satisfiability (SAT) problem. Since faster algorithms for SAT are generally considered unlikely to exist, this implies that faster algorithms for the edit distance problem are also unlikely to exist. Other problems used for such reductions include the 3SUM problem and the All Pairs Shortest Path (APSP) problem. The quantum regime presents similar challenges; almost all known lower bounds for quantum algorithms are defined in terms of query complexity, which offers limited insight for problems where the best-known algorithms take super-linear time. Employing fine-grained reductions in the quantum setting, therefore, represents a natural progression. However, directly translating classical fine-grained reductions to the quantum regime poses various challenges. In this talk, I will present recent results in which we overcome these challenges and prove quantum time lower bounds for certain problems in BQP, conditioned on the conjectured quantum hardness of, for example, SAT (and its variants), the 3SUM problem, and the APSP problem. This presentation is based on joint works with Andris Ambainis, Bruno Loff, Florian Speelman, and Subhasree Patro.

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

Event Official Language: English

Sustainable Organic Synthesis with Abundant Resources

April 15 (Mon) at 13:00 - 14:00, 2024

Sobi Asako (Senior Scientist, Advanced Organic Synthesis Research Team, RIKEN Center for Sustainable Resource Science (CSRS))

The sustainable development of modern society necessitates technologies that harness earth-abundant metals and organic resources, minimizing reliance on scarce materials. This presentation will introduce our recent efforts towards this goal. We have developed sustainable organic synthesis using sodium dispersion, a molybdenum-quinone species for the diazo-free generation of carbene species from stable and readily available compounds, and a SpiroBpy ligand that enables the site-selective functionalization of arenes under remote steric control. I will also share some of the challenges we face in developing these reactions in order to ensure reproducibility.

Venue: 3rd floor public space, Main Research Building

Event Official Language: English

Short-Lived Hawking Radiation Under Stringy Effects

April 11 (Thu) at 13:30 - 15:00, 2024

Wei-Hsiang Shao (Ph.D. Student, Department of Physics, National Taiwan University, Taiwan)

A UV theory is required in order to describe the origin of late-time Hawking radiation. In this talk, I will explore Hawking radiation in a non-local model of the radiation field inspired by Witten's open string field theory. An attempt at extracting the correlators of this theory will be discussed, which leads to a space-time uncertainty relation. As a result, the characteristics of trans-Planckian field modes differ significantly from that in the standard low-energy effective theory, and I will argue that this ultimately results in the termination of Hawking radiation around the scrambling time of the black hole.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

A socio-ecological and genomic approach to mixed-species formation of African forest guenons

April 4 (Thu) at 16:00 - 17:00, 2024

Haruka Kitayama (Ph.D. Student, Graduate School of Environmental Science, Hokkaido University)

While many animal groups consist of a single species, some species have been observed forming mixed-species groups (MSGs). It is thought that by forming groups with different species, animals may reduce predation risk, improve foraging efficiency, and even gain social and reproductive benefits. Red-tailed monkeys and blue monkeys, African forest guenons (Tribe Cercopithecini), are known to form MSGs in several regions in Africa, despite the large niche overlap. The underlying mechanisms driving the formation of MSGs in red-tailed monkeys and blue monkeys are still unclear. One reason is that previous studies have been limited to behavioral ecological approaches. By combining field observations with genomic analyses in the laboratory, we seek to shed light on the role of genetic factors in mediating interspecies interactions within MSGs. In this talk, I will introduce our studies on genomic introgression and gut microbiome sharing within the mixed-species population of red-tailed monkeys and blue monkeys in the Kalinzu Forest Reserve, Uganda.

Venue: via Zoom

Event Official Language: English

Quantum simulation of QCD matter: from hadronic scattering to gauge field qubit encoding

April 3 (Wed) at 10:00 - 11:00, 2024

Tianyin Li (Ph.D. Student, Institute of Quantum Matter, South China Normal University, China)

Recently, quantum computing (QC) has become a new method for solving non-perturbative problems in high-energy physics. Compared to traditional Monte Carlo simulations, the QC method does not encounter the sign problem, making it an effective approach for solving dynamical and finite density problems. The first part of this talk focuses on the quantum simulation of the hadronic scattering process, including the initial state parton distribution functions, intermediate state partonic scattering amplitudes, and final state hadronization. The second part of this talk concentrates on the qubit encoding of Hamiltonian formalism in lattice gauge field theory with a Coulomb gauge. As a preliminary attempt, the qubit encoding of (3+1)-dimensional Coulomb gauge QED will be discussed.

Venue: via Zoom

Event Official Language: English

TadaFest 2024: Toward understanding of the Origin of Spacetime

April 2 (Tue) at 14:00 - 18:00, 2024

Tsukasa Tada (Deputy Program Director, iTHEMS)

Program 14:00-14:05 Welcome address T. Hatsuda (RIKEN iTHEMS) 14:05-15:35 T. Tada (RIKEN iTHEMS) "Toward understanding of the origin of spacetime" (This talk is in English) 15:35-16:00 coffee break 16:00-16:30 Shin Nakamura (Chuo Univ.) "Application of gauge/gravity duality: application to non-equilibrium physics" (This talk is in Japanese) 16:30-17:00 Kinya Oda (Tokyo Woman's Chiristian Univ.) "Gaussian formalism: From Hesenberg's Uncertainty Principle to Time-Boundary Effect and Lorentz-Covariant Complete Basis for Spinors" (This talk is in Japanese) 17:00-17:30 Gen Tatara (RIKEN, CEMS) "Some topics of spintronics" (This talk is in Japanese) 17:30-18:00 Asato Tsuchiya (Shizuoka Univ.) "Recent progress in the studies of the emergence of space-time in the type IIB matrix model" (This talk is in Japanese) 18:15- informal discussion @ Common space on 3F of the main research building

Venue: Okochi Hall (Main Venue) / via Zoom

Event Official Language: English