Analyzing heterogeneous spreading dynamics

People involved:
Liubov Tupikina
Marc Santolini
Aurelie de Faure
Gael Simon

Keywords: spreading, diffusion, heterogeneity, attributes, networks, epidemics, information

Project description

The theoretical part of the project is analysis of spreading dynamics on heterogeneous networks. Why heterogeneous? Because most of the real world networks are intrinsically heterogeneous: transportation networks with different width, biological fractal network of human lungs etc. The main question is how to characterize the influence of the heterogeneity on the transportation phenomena. This includes designing the network indicators for characterizing complex dynamics, developing the fundamental framework applicable for disease spreading processes. In this project we are working on designing and testing heterogeneous epidemics spreading models inspired by the real data.
The practical aspect of this project is then to dissect the influence of the heterogeneity from the other factors and to incorporate physical, epidemiological and socio-economic mechanisms into the heterogeneous spreading models. The most existing part of the project is actually implementation of the indicators to such complex models in order to detect the localisation of epidemics spreading and to identify influential spreaders even in the heterogeneous setup. For more information about the networks please visit  here.


Innovative educational methods for research integrity

People involved:
Aida Bafeta
Ariel Lindner

Keywords: ethics, research, misconduct, serious games

Project description

Research misconduct and misbehaviors are perceived as a risk of weakening the institutions and the scientific community. Why would the public fund research and trust its researchers if they are not honest?  In the media sphere, fraud, data fabrication and falsification, and plagiarism receive a particular public attention, but according to a meta-analysis of survey data only 2% of researchers admit to having used these practices at least once. While  a third of scientists admitted to having used questionable research practices, such as modifying the design, methodology, or results of a study in response to pressure from a funding source. Today, it is important to rethink the concept of integrity research beyond of misconduct (fraud, data fabrication and falsification,  and plagiarism). One of the proposed solutions is to educate scientists on research integrity. Improved research integrity training is now variously supported and mandatored. However most of studies evaluating research integrity training have mostly been inconclusive, long-term impacts on behavior have not been demonstrated, and focused on the  plagiarism. It is crucial to identify questionable research practices and to propose training for researchers. We believe that developing simple, playful and adequate educational resources on questionable research practices in the form of serious games, could help to solve this problem. In this project we will want to create several tools dedicated to early researchers and students to raise awareness of the integrity of research.

Exploring sexual sensory-system evolution using synthetic and systems biology approaches

People involved:
Alvaro Banderas
Ariel Lindner

Keywords: bacterial sex, sensory system evolution, systems biology, synthetic biology

Project description

The existence of populations with exactly two sexes is an open problem in evolutionary biology. Why not three sexes? Or even better, why not one? Although exceptions exist, two-sex systems are the overwhelming majority. The diversity of sex determination systems only makes their tendency to produce binary sexual populations more mysterious, but at the same time suggests that general principles govern this naturally converging pattern. The study of binary sexual populations has been traditionally reserved for animal systems. However, it has been acknowledged that in order to understand its origins and general principles, asymmetries in simple unicellular systems must be understood. In this project we study the evolution of asymmetrical sexual populations by using a synthetic biology approach that allows the analysis to be independent from the details of specific organisms. By studying natural conjugation and engineering synthetic sexual systems in bacteria, we hope to build experimental models for the evolution of the sexes.

This project is part of the LabEx – Who am I? Initiative 


Intervention Platform for Citizen Science

People involved: Avi Segal

KeywordsCitizen Science, Artificial Intelligence, Machine Learning, Reinforcement Learning

Project Description

As users in volunteer‐based crowdsourcing platforms are not motivated by monetary incentives, it can be challenging to keep them engaged and productive on tasks. In this project we will build on past research in this area and develop an intervention platform for CRI’s citizen science projects. This platform will focus on exploring and extending engagement in CRI’s citizen science projects by combining machine learning with intervention design. It will use real‐time predictions about forthcoming dis‐ engagement and deep reinforcement learning methods to guide online interventions messages based on signals available from CRI’s platforms. The intervention messages will be developed through interaction with CRI’s citizen science community and according the ethical guidelines. Past research has shown that combining traditional AI planning with incentive design can significantly increase the contributions of users in similar systems.

Beyond networks: the evolution of dynamic regulatory systems

People involved: Johannes Jaeger

Keywords: process thinking, evolutionary systems biology, organicism,
complex adaptive system, dynamical systems theory

Project Description

I am writing a book on evolutionary systems biology from an organismal,
dynamical systems perspective. It is based on the fundamental notion that
evolutionary dynamics arise from the struggle for survival of goal-oriented
organismal agents. In this radical view, organisms and their perceived
environments co-generate each other. The notion of organismal agency is
based on the organizationally closed but thermodynamically open structure
of living systems. Organismal agents are paradigm examples of complex
adaptive systems. I combine empirical, mathematical, and conceptual
approaches to approach this broad and complicated topic. I start from a
processual ontological perspective, examining the fundamental nature of
change and the patterned dynamics that constitute a system. The book then
develops a graphical and intuitive introduction to dynamical systems, based
on the notion that flow (a generalized mapping through time) is
fundamental, while abstract notions such as instantaneous states or
integral paths through time are derived. It presents a number of examples,
where dynamical systems theory in general, and the geometrical analysis of
configuration space in particular, have been successfully applied to
problems in organismic development, ecology, and evolution. It then goes on
to examine the limits of dynamical systems theory, the validity of
steady-state assumptions, the need for non-autonomous systems, and the
difficulties in integrating organizational closure into the formalism. It
discusses radical notions of organism-environment co-evolution, based on
the idea that living beings are not passive sufferers of evolutionary
processes, but actively engage in autonomous exploratory and adaptive
activities. Such an agent-based view leads to a tight interdependence of a
system and its configuration space. I am developing conceptual foundations
for new mathematical formalisms able to deal with this commingling, while
still remaining amenable to (numerical) analysis that enables novel
causal-mechanistic insights into organisms as autonomous agents and their

The book is aimed at an interdisciplinary audience with a wide variety of
intellectual backgrounds. My aim is to make the reader familiar with the
conceptual problems of agent-based evolution without presupposing an
advanced level of technical mathematical skills. The book is based on a
masterclass at the University of Vienna with 14 lectures, each one
providing one of the chapters. The aim of my six-month stay at the CRI is
to work on the book, while turning its content into a massive open online
course (MOOC) with the help of the infrastructure and the multi-media teams
at the CRI.