CECAM Workshop “Active Matter and Artificial Intelligence Location”, Lausanne, Switzerland 30 September – 2 October 2019

Active Matter and Artificial Intelligence
Location : CECAM-HQ-EPFL, Lausanne, Switzerland
September 30, 2019 – October 2, 2019

Organizers:
Frank Cichos (Universität Leipzig, Germany)
Klaus Kroy (Universität Leipzig, Germany)
Fernando Peruani (Université Nice Sophia Antipolis, France)
Giovanni Volpe (University of Gothenburg, Sweden)

Website:
https://www.cecam.org/workshp1750/

Description:
Biological active matter is composed of self-propelling agents, such as molecular motors, cells, bacteria and animals [1,2], which can perform tasks and feature emergent collective behaviors thanks to their capability of sensing their environment, processing this information and exploiting it through feedback cycles [3]. These processes are intrinsically noisy [4] both at the microscale (e.g. thermal noise [5]) and at the macroscale (e.g. turbulence [6]). Therefore, through millions of years, biological systems have evolved powerful strategies to accomplish specific tasks and thrive in their environment – strategies that are encoded in their shape, biophysical properties, and signal processing networks [13].

Artificial active matter is now being explored as a powerful means to address the big challenges that our society is facing [7]: from new strategies for targeted drug delivery, to the decontamination of polluted soils, to the extraction of energy from naturally occurring out-of-equilibrium conditions. In this context, biological active matter provides an ideal source of tested ideas and approaches [8,9], which we are now trying to exploit to develop artificial systems [10,11].

However, in biological systems, there is only a limited possibility to reduce complexity and introduce controllable perturbations. Therefore, the development of computational models and of proof-of-principle experiments provides an ideal test bench to explore the origin of complexity in biological systems and to harness it for the development of new applications. For example, tuning of sensorial delays yield different behaviors in gradient fields relevant for cellular systems [12], and, inspired by neuronal networks, relevant past experience is harnessed to predict the evolution of complex systems.

In this process, we have been led to the application of machine learning to active matter. Machine learning is an abstraction of the adaption processes found in biological active matter and researchers have recently started to explore these algorithms in active matter in some pioneering works. For example, reinforcement learning [14], which reflects a type of learning based on rewards, has been used to steer the motion of microscopic particles [15,16], to understand how birds can exploit turbulent thermal air flows to soar [6], to control the motion of artificial microswimmers in complex flow patterns [17] as well as in collective field taxis [18].

We are now at a critical crossroad in the development of active matter research where biological and artificial active matter are meeting with machine learning. The specific aim of this workshop is to bring together researchers from the fields of physics, biology, mathematics and machine learning to lay the groundwork of a scientific network to address the pressing questions:

1. What can machine learning do for biological active matter? Can we gain new insight into how powerful strategies have evolved? Can we understand the role of information processing, feedback cycles and sensorial delay in these strategies?

2. What can machine learning do for artificial active matter? Can we learn new approaches towards high-impact applications? For example, how can signaling and feedback be introduced into artificial active matter?

3. What insights can active matter provide for machine learning? Can we get some insight from the natural strategies optimized by evolution?

References

[1] Ramaswamy, S., The mechanics and statistics of active matter. Annu. Rev. Condens. Matter Phys. 1, 323–345 (2010).

[2] Marchetti, M. C. et al., Hydrodynamics of soft active matter. Rev. Mod. Phys. 85, 1143–1189 (2013).

[3] Katz, Y., Tunstrøm, K., Ioannou, C. C., Huepe, C., Couzin, I. D., Inferring the structure and dynamics of interactions in schooling fish. Proc. Natl. Acad. Sci. USA 108, 18720–18725 (2011).

[4] Yates, C. A. et al., Inherent noise can facilitate coherence in collective swarm motion. Proc. Natl. Acad. Sci. USA 106, 5464–5469 (2009).

[5] Kromer, J. A., Märcker, S., Lange, S., Baier, C., Friedrich, B. M., Decision making improves sperm chemotaxis in the presence of noise. PLoS Comput. Biol. 14, e1006109–15 (2018).

[6] Reddy, G., Celani, A., Sejnowski, T. J., Vergassola, M., Learning to soar in turbulent environments. Proc. Natl. Acad. Sci. USA 113, E4877–84 (2016).

[7] Bechinger, C. et al., Active particles in complex and crowded environments. Rev. Mod. Phys. 88, 045006 (2016).

[8] Pearce, D. J. G., Miller, A. M., Rowlands, G., Turner, M. S., Role of projection in the control of bird flocks. Proc. Natl. Acad. Sci. USA 111, 10422–10426 (2014).

[9] Bierbach, D. et al., Insights into the social behavior of surface and cave-dwelling fish (Poecilia mexicana) in light and darkness through the use of a biomimetic robot. Front. Robot. AI 5, 15 (2018).

[10] Buttinoni, I. et al., Dynamical clustering and phase separation in suspensions of self-propelled colloidal particles (2017).

[11] Qian, B., Montiel, D., Bregulla, A., Cichos, F., Yang, H., Harnessing thermal fluctuations for purposeful activities: the manipulation of single micro-swimmers by adaptive photon nudging. Chem. Sci. 4, 1420–1429 (2013).

[12] Mijalkov, M., McDaniel, A., Wehr, J., Volpe, G., Engineering sensorial delay to control phototaxis and emergent collective behaviors. Phys. Rev. X 6, 011008 (2016).

[13] Palmer, S. E., Marre, O., Berry, M. J., Bialek, W., Predictive information in a sensory population. Proc. Natl. Acad. Sci. USA 112, 6908–6913 (2015).

[14] Sutton, R. S., Barto, A. G., Reinforcement learning: an introduction. MIT Press, Cambridge (1998).

[15] Colabrese, S., Gustavsson, K., Celani, A., Biferale, L., Flow navigation by smart microswimmers via reinforcement learning. Phys. Rev. Lett. 118, 158004 (2017).

[16] Muiños-Landin, S., Ghazi-Zahedi, K., Cichos, F., Reinforcement learning of artificial microswimmers. arXiv 1803.06425v2 (2018).

[17] Gustavsson, K., Biferale, L., Celani, A., Colabrese, S., Finding efficient swimming strategies in a three-dimensional chaotic flow by reinforcement learning. Eur. Phys. J. E Soft Matter 40, 313–7 (2017).

[18] Palmer, G., Yaida, S., Optimizing collective fieldtaxis of swarming agents through reinforcement learning. arXiv 1709.02379 (2017).

Seminar by G. Volpe at MTL BrainHack School 2019, Montreal, Canada, 22 August 2019

Be friendly to your users:
Add comments and tutorials to your code
Giovanni Volpe
MTL BrainHack School 2019, Montreal, 22 August 2019
https://brainhackmtl.github.io/school2019/

When releasing a software package, it is critical to provide potential users with all the information they need to help them using it.
Using the example of Braph — a software we recently developed to study brain connectivity http://braph.org/ —, I’ll illustrate how we have commented the code, created a website and off-line documentation, and recoded video tutorials.
I’ll conclude with some practical advice and some best practices.

Talk by G. Volpe at SPIE OTOM XVI, San Diego, 14 Aug 2019

FORMA: a high-performance algorithm for the calibration of optical tweezers
Laura Pérez-García, Alejandro V. Arzola, Jaime Donlucas Pérez, Giorgio Volpe  & Giovanni Volpe
SPIE Nanoscience + Engineering, Optical trapping and Optical Manipulation XV, San Diego (CA), USA
11-15 August 2019

We introduce a powerful algorithm (FORMA) for the calibration of optical tweezers. FORMA estimates accurately the conservative and non-conservative components of the force field with important advantages over established techniques, being parameter-free, requiring ten-fold less data and executing orders-of-magnitude faster. We demonstrate FORMA performance using optical tweezers, showing how, outperforming other available techniques, it can identify and characterise stable and unstable equilibrium points in generic force fields.

Reference: Pérez-García et al., Nature Communications 9, 5166 (2018)
doi: 10.1038/s41467-018-07437-x

Plenary Presentation by G. Volpe at SPIE Nanoscience + Engineering, San Diego, 12 Aug 2019

Optical forces go smart
Giovanni Volpe
Plenary Presentation
SPIE Nanoscience + Engineering, San Diego (CA), USA
11-15 August 2019

Optical forces have revolutionized nanotechnology. In particular, optical forces have been used to measure and exert femtonewton forces on nanoscopic objects. This has provided the essential tools to develop nanothermodynamics, to explore nanoscopic interactions such as critical Casimir forces, and to realize microscopic devices capable of autonomous operation. The future of optical forces now lies in the development of smarter experimental setups and data-analysis algorithms, partially empowered by the machine-learning revolution. This will open unprecedented possibilities, such as the study of the energy and information flows in nanothermodynamics systems, the design of novel forms of interactions between nanoparticles, and the realization of smart microscopic devices.

Clustering of Janus Particles published in Soft Matter

Clustering of Janus particles in optical potential driven by hydrodynamic fluxes

Clustering of Janus Particles in Optical Potential Driven by Hydrodynamic Fluxes
S. Masoumeh Mousavi, Iryna Kasianiuk, Denis Kasyanyuk, Sabareesh K. P. Velu, Agnese Callegari, Luca Biancofiore & Giovanni Volpe
Soft Matter 15(28), 5748—5759 (2019)
doi: 10.1039/C8SM02282H
arXiv: 1811.01989

Self-organisation is driven by the interactions between the individual components of a system mediated by the environment, and is one of the most important strategies used by many biological systems to develop complex and functional structures. Furthermore, biologically-inspired self-organisation offers opportunities to develop the next generation of materials and devices for electronics, photonics and nanotechnology. In this work, we demonstrate experimentally that a system of Janus particles (silica microspheres half-coated with gold) aggregates into clusters in the presence of a Gaussian optical potential and disaggregates when the optical potential is switched off. We show that the underlying mechanism is the existence of a hydrodynamic flow induced by a temperature gradient generated by the light absorption at the metallic patches on the Janus particles. We also perform simulations, which agree well with the experiments and whose results permit us to clarify the underlying mechanism. The possibility of hydrodynamic-flux-induced reversible clustering may have applications in the fields of drug delivery, cargo transport, bioremediation and biopatterning.

Invited talk by G. Volpe at MPI-PKS Workshop, Dresden, Germany, 23 July 2019

Deep Learning Applications in Photonics and Active Matter
Giovanni Volpe
Invited talk at the “
Microscale Motion and Light” MPI-PKS Workshop, Dresden, Germany, 22-26 July 2019
https://www.pks.mpg.de/mml19/

After a brief overview of artificial intelligence, machine learning and deep learning, I will present a series of recent works in which we have employed deep learning for applications in photonics and active matter. In particular, I will explain how we employed deep learning to enhance digital video microscopy [1], to estimate the properties of anomalous diffusion [2], and to improve the calculation of optical forces. Finally, I will provide an outlook for the application of deep learning in photonics and active matter.

References

[1] S. Helgadottir, A. Argun and G. Volpe, Digital video microscopy enhanced by deep learning. Optica 6(4), 506—513 (2019)
doi: 10.1364/OPTICA.6.000506

[2] S. Bo, F Schmidt, R. Eichborn and G. Volpe, Measurement of Anomalous Diffusion Using Recurrent Neural Networks. arXiv: 1905.02038

Anomalous Diffusion Measurement with Neural Networks published in Phys Rev E

Measurement of Anomalous Diffusion Using Recurrent Neural Networks

Measurement of Anomalous Diffusion Using Recurrent Neural Networks
Stefano Bo, Falko Schmidt, Ralf Eichborn & Giovanni Volpe
Physical Review E 100(1), 010102(R) (2019)
doi: 10.1103/PhysRevE.100.010102
arXiv: 1905.02038

Anomalous diffusion occurs in many physical and biological phenomena, when the growth of the mean squared displacement (MSD) with time has an exponent different from one. We show that recurrent neural networks (RNN) can efficiently characterize anomalous diffusion by determining the exponent from a single short trajectory, outperforming the standard estimation based on the MSD when the available data points are limited, as is often the case in experiments. Furthermore, the RNN can handle more complex tasks where there are no standard approaches, such as determining the anomalous diffusion exponent from a trajectory sampled at irregular times, and estimating the switching time and anomalous diffusion exponents of an intermittent system that switches between different kinds of anomalous diffusion. We validate our method on experimental data obtained from sub-diffusive colloids trapped in speckle light fields and super-diffusive microswimmers.

Influence of Sensorial Delay on Clustering and Swarming published in Phys. Rev. E

Influence of Sensorial Delay on Clustering and Swarming

Influence of Sensorial Delay on Clustering and Swarming
Rafal Piwowarczyk, Martin Selin, Thomas Ihle & Giovanni Volpe
Physical Review E 100(1), 012607 (2019)
doi: 10.1103/PhysRevE.100.012607
arXiv:  1803.06026

We show that sensorial delay alters the collective motion of self-propelling agents with aligning interactions: In a two-dimensional Vicsek model, short delays enhance the emergence of clusters and swarms, while long or negative delays prevent their formation. In order to quantify this phenomenon, we introduce a global clustering parameter based on the Voronoi tessellation, which permits us to efficiently measure the formation of clusters. Thanks to its simplicity, sensorial delay might already play a role in the organization of living organisms and can provide a powerful tool to engineer and dynamically tune the behavior of large ensembles of autonomous robots.

Intracavity Optical Trapping published in Nature Commun.

Intracavity Optical Trapping

Intracavity optical trapping of microscopic particles in a ring-cavity fiber laser
Fatemeh Kalantarifard, Parviz Elahi, Ghaith Makey, Onofrio M. Maragò, F. Ömer Ilday & Giovanni Volpe
Nature Communications 10, 2683 (2019)
doi: 10.1038/s41467-019-10662-7
arXiv: 1808.07831

Standard optical tweezers rely on optical forces arising when a focused laser beam interacts with a microscopic particle: scattering forces, pushing the particle along the beam direction, and gradient forces, attracting it towards the high-intensity focal spot. Importantly, the incoming laser beam is not affected by the particle position because the particle is outside the laser cavity. Here, we demonstrate that intracavity nonlinear feedback forces emerge when the particle is placed inside the optical cavity, resulting in orders-of-magnitude higher confinement along the three axes per unit laser intensity on the sample. This scheme allows trapping at very low numerical apertures and reduces the laser intensity to which the particle is exposed by two orders of magnitude compared to a standard 3D optical tweezers. These results are highly relevant for many applications requiring manipulation of samples that are subject to photodamage, such as in biophysics and nanosciences.