Topic 1

Location: seminar room L5D23 (map)

9:30-10:30: 1st lecture  by Gašper Tkačik

10:30-11:00: Break

11:00-12:00: 2nd lecture  by Corentin Briat

12:00-14:00: Lunch

14:00-15:00: 3rd lecture by Naoki Honda

15:00-15:30: Break

15:30-16:30: 4th lecture by Sanjay Jain

18:00-21:00: Dinner (taxi leave at 18:00 from Lab5 Parking Lot)

Statistical analysis and optimality in biological systems

Lecturer: Gašper Tkačik

Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data.

In contrast, statistical inference focuses on the efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function. I’ll give a basic review of these two approaches, which were developed independently and applied separately. I will then outline how the two approaches can be unified in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy ‘‘optimization priors.’’ This family defines a smooth interpolation between a data-rich inference regime and a data-limited prediction regime. This framework allows one to address fundamental challenges relating to inference in high-dimensional, biological problems.

Cybergenetics: A Control Theory for Living Cells

Lecturer: Corentin Briat (FHNW)

The objective of this talk is to give an idea of the problems encountered in the control of biological systems, and how they can be solved. In particular, we will discuss the concept of reaction networks as models for a wide class of dynamical systems including biological, ecological, and epidemiological systems. The concept of noise or randomness an its role in those systems will be also discussed. When starting the discussion on the control of biological processes, a parallel between the concept of regulation, integral action, homeostasis and perfect adaptation will be drawn and will serve as a bridge between control theory and biology. Various control paradigms will be briefly introduced, with a specific emphasis on the in-vivo control of cellular networks, that is the design of controllers that can be implemented inside living organisms, such as bacteria. A solution to the robust regulation problem based on the so-called Antithetic Integral Controller will also be discussed and shown to theoretically work both in the deterministic and the stochastic settings. Finally, the approach discussed in the talk will be illustrated via simulations and experimental results.

Data-driven biology with generative model

Lecturer: Naoki Honda

In recent years, advances in next-generation sequencing and live imaging technologies have dramatically increased the availability of biological data. This explosion of data necessitates a data-driven approach to uncover the hidden patterns and mechanisms that govern biological systems. In this talk, we introduce generative models, which are essential for solving inverse problems—problems in which latent states are estimated from observed data. We discuss the concept of inverse problems and explore their applications in key topics such as spatial transcriptomics, mental conflict, and disease progression.

Autocatalytic sets and the origin of life

Lecturer: Sanjay Jain

The talk will review certain aspects of the origin of life problem. It will focus on the contrast between the structures and processes in the simplest living cells and those that plausibly existed on the prebiotic Earth. The former are far more complex than the latter. The idea of autocatalytic sets will be introduced. We will discuss how autocatalytic sets can represent primitive chemical organization, metabolism, and self-reproduction, and thus contribute to our understanding of the origin of life. Some models of the structure, dynamics and evolution of autocatalytic sets will be described. Certain open questions will be mentioned.