René Doursat, Ph.D. Habil.

Research Scientist,
   Research Group in Biomimetics (GEB),
   Universidad de Málaga (UMA)

Fmr. Director, Complex Systems Institute
   Paris Ile-de-France (ISC-PIF)

Elected Full Member, CREA Laboratory,
   Ecole Polytechnique & CNRS (UMR 7656)


phone: +34 952 137 036







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Research
   • Artificial Life
       Artificial Development
       Programmed Nets
       Spatial Evolution
   • Neural Dynamics
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Full CV (March 12, 2012)

Artificial Development
Modeling and simulation of the fundamental principles of self-patterning and self-assembly during embryonic development, with exportation to artificial systems
The spontaneous making of an entire organism from a single cell is the epitome of a self-organizing and programmable complex system. Through a precise spatiotemporal interplay of genetic switches and chemical gradients, an elaborate form is created without explicit architectural plan or engineering intervention. This original study, which I designed and developed, proposes a multi-agent simulation and exploitation of these fundamental morphogenetic mechanisms.
Overview
On the one hand, natural phenomena of spontaneous pattern formation are generally random and repetitive, whereas, on the other hand, complicated heterogeneous architectures are the product of human design. The only examples of self-organized and structured systems are biological organisms produced by development. Can we export their precise self-formation capabilities to computing systems?

This work proposes an "embryomorphic engineering" approach inspired by evo-devo to solve the paradoxical challenge of planning autonomous systems. Its goal is to artificially reconstruct complex morphogenesis by integrating three fundamental ingredients: self-assembly (SA) and pattern formation (PF) under genetic regulation (GR).

It presents a spatial computational agent-based model that can be equivalently construed as (a) moving cellular automata, in which cell rearrangement is influenced by the pattern they form, or (b) heterogeneous swarm motion, in which agents differentiate into patterns according to their location. It offers a new abstract framework to explore the causal and programmable link from genotype to phenotype that is needed in many emerging computational domains, such as "amorphous computing" or "artificial embryogeny".

Bio-inspiration
One of biology's modern challenges is to elucidate the genetics and evolution of biological development, or "evo-devo", i.e., unify organisms in a generative way beyond their seemingly endless diversity of form. How do nonspatial gene interactions extend in 3-D space? My work schematizes and simulates some principles of biological development using an expanding lattice of cells (Fig. c). Each cell contains a genetic regulatory network (GRN), modeled as a feed-forward hierarchy of switches that can settle in various on/off expression states (Fig. a-b).

Local morphogen gradients (X, Y) provide positional information in input, which is integrated by each GRN to produce differential expression of identity genes (I, J, ...) in output. Similarly to striping in the Drosophila embryo, the lattice becomes segmented into spatial domains of homogeneous genetic expression (one for each identity gene; Carroll et al. 2001) that resemble stained glass motifs (Fig. d).

Meanwhile, it also expands by cell proliferation, creating new local gradients of positional information within former single-identity domains (Fig. d, right). Analogous to a growing canvas that paints itself (Coen 2000), the alternation of growth and patterning results in the creation of a form.

   
Ultimately, more realistic details can be added by linking this artificial model with biological studies that provide a close observation and measure of multicellular behavior during development. I recently collaborated in two large European projects, Embryomics and Bioemergences, focused on automating the morphodynamical reconstruction of the cell lineage tree underlying the processes of animal embryogenesis. An organism's "embryome" is defined as a description of the multiscale dynamics of the early stages of development. Its reconstruction necessitates a paradigm of systematic investigation of cell behaviors and lineage as a branching process in space and time. Biologists produce and annotate time-lapse series of organism development, while mathematicians and computer scientists process these images to reconstruct and model cell dynamics.
Toward artificial development
This study attempts to reproduce morphogenesis through a multiscale and modular distributed process. Abstracting from biological development, an important goal is to contribute to a novel engineering paradigm of system assembly that would replace omniscient architects with large-scale decentralized collectivities of agents.

Various research works have investigated the possibility of obtaining self-formation capabilities from a variety of complex computing systems. Since functionality is distributed over a great number of components, it would be an insurmountable task to assemble and instruct each of them individually. Rather, in a way similar to biological cells, these components should be easily mass-produced, initially as identical copies of each other, and only acquire their specialized positions and functions by themselves within the system, once mixed together.

For example, MIT's "amorphous computing" has set the stage for a myriad of micro-processors containing the same instructions to self-organize without exact blueprint map or functional reliability, unlike traditional VLSI (e.g., Abelson et al. 1999, Nagpal 2002). Such self-assembling components can also represent mobile sensors and actuators in complex self-managing networks (Beal & Bachrach 2006). In software applications (servers, security, etc.), a swarm of small-footprint software agents can diversify and self-deploy to achieve a desired level of service (Hofmeyr & Forrest 2000). In robotics, too, whether articulated parts of reconfigurable devices (Lipson & Pollack 2000), or mobile formations of mini-robots (Christensen et al. 2007), there is also great demand for controllable complex morphologies.

Selected publications

Doursat, R. (2006b) The growing canvas of biological development: Multiscale pattern generation on an expanding lattice of gene regulatory networks. InterJournal: Complex Systems 1809. PAPER

Doursat, R. (2008b) Organically grown architectures: Creating decentralized, autonomous systems by embryomorphic engineering. In Organic Computing, R. P. Würtz, ed., pp. 167-200, Springer-Verlag. PREPRINT

Doursat, R. (2009b) Facilitating evolutionary innovation by developmental modularity and variability. Generative & Developmental Systems Workshop (GDS 2009), at 18th Genetic and Evolutionary Computation Conference (GECCO 2009), July 8-12, 2009, Montreal, Canada. PAPER

Doursat, R., Sayama, H. & Michel, O., eds. (2010) Morphogenetic Engineering: Toward Programmable Complex Systems, NECSI "Studies on Complexity" Series, Springer-Verlag. In Preparation. PROPOSAL

References

Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., Knight, Jr., T., Nagpal, R., Rauch, E., Sussman, G. & Weiss, R. (1999) Amorphous Computing. MIT Artificial Intelligence Laboratory memo no. 1665, Aug. 1999.

Beal, J. & Bachrach, J. (2006) Infrastructure for engineered emergence on sensor/actuator networks. IEEE Intelligent Systems, 21(2): 10-19.

Carroll, S. B., Grenier, J. K. & Weatherbee, S. D. (2001) From DNA to Diversity. Blackwell Scientific, Malden, MA.

Christensen A., O'Grady, R. & Dorigo, M. (2007) Morphology control in a self-assembling multi-robot system. IEEE Robotics & Automation Magazine, 14(4): 18-25.

Coen, E. (2000) The Art of Genes. Oxford University Press.

Hofmeyr, S. A. & Forrest, S. (2000) Architecture for an artificial immune system. Evolutionary Computation, 8(4): 443-473.

Lipson, H. & Pollack, J. B. (2000) Automatic design and manufacture of robotic lifeforms. Nature, 406: 974-978.

Nagpal, R. (2002) Programmable self-assembly using biologically-inspired multi-agent control. 1st International Conference on Autonomous Agents, July 15-19, Bologna, Italy.