Using natural language processing to find research topics in Living Machines conferences and their intersections with Bioinspiration & Biomimetics publications.

The number of published scientific articles is increasing dramatically and makes it difficult to keep track of research topics. This is particularly difficult in interdisciplinary research areas where different communities from different disciplines are working together. It would be useful to develop methods to automate the detection of research topics in a research domain. Here we propose a natural language processing (NLP) based method to automatically detect topics in defined corpora. We start by automatically generating a global state of the art of Living Machines conferences. Our NLP-based method classifies all published papers into different clusters corresponding to the research topic published in these conferences. We perform the same study on all papers published in the journals Bioinspiration & Biomimetics and Soft Robotics. In total this analysis concerns 2099 articles. Next, we analyze the intersection between the research themes published in the conferences and the corpora of these two journals. We also examine the evolution of the number of papers per research theme which determines the research trends. Together, these analyses provide a snapshot of the current state of the field, help to highlight open questions, and provide insights into the future.

Random forest algorithms to classify frailty and falling history in seniors using plantar pressure measurement insoles: a large-scale feasibility study.

BACKGROUND: Frailty and falls are two adverse characteristics of aging that impair the quality of life of senior people and increase the burden on the healthcare system. Various methods exist to evaluate frailty, but none of them are considered the gold standard. Technological methods have also been proposed to assess the risk of falling in seniors. This study aims to propose an objective method for complementing existing methods used to identify the frail state and risk of falling in older adults. METHOD: A total of 712 subjects (age: 71.3 ± 8.2 years, including 505 women and 207 men) were recruited from two Japanese cities. Two hundred and three people were classified as frail according to the Kihon Checklist. One hundred and forty-two people presented with a history of falling during the previous 12 months. The subjects performed a 45 s standing balance test and a 20 m round walking trial. The plantar pressure data were collected using a 7-sensor insole. One hundred and eighty-four data features were extracted. Automatic learning random forest algorithms were used to build the frailty and faller classifiers. The discrimination capabilities of the features in the classification models were explored. RESULTS: The overall balanced accuracy for the recognition of frail subjects was 0.75 ± 0.04 (F1-score: 0.77 ± 0.03). One sub-analysis using data collected for men aged > 65 years only revealed accuracies as high as 0.78 ± 0.07 (F1-score: 0.79 ± 0.05). The overall balanced accuracy for classifying subjects with a recent history of falling was 0.57 ± 0.05 (F1-score: 0.62 ± 0.04). The classification of subjects relative to their frailty state primarily relied on features extracted from the plantar pressure series collected during the walking test. CONCLUSION: In the future, plantar pressures measured with smart insoles inserted in the shoes of senior people may be used to evaluate aspects of frailty related to the physical dimension (e.g., gait and balance alterations), thus allowing assisting clinicians in the early identification of frail individuals.

Automated optimization of multilevel models of collective behaviour: application to mixed society of animals and robots.

Animal societies exhibit complex dynamics that require multi-level descriptions. They are difficult to model, as they encompass information at different levels of description, such as individual physiology, individual behaviour, group behaviour and features of the environment. The collective behaviour of a group of animals can be modelled as a dynamical system. Typically, models of behaviour are either macroscopic (differential equations of population dynamics) or microscopic (such as Markov chains, explicitly specifying the spatio-temporal state of each individual). These two kind of models offer distinct and complementary descriptions of the observed behaviour. Macroscopic models offer mean field description of the collective dynamics, where collective choices are considered as the stable steady states of a nonlinear system governed by control parameters leading to bifurcation diagrams. Microscopic models can be used to perform computer simulations or as building blocks for robot controllers, at the individual level, of the observed spatial behaviour of animals. Here, we present a methodology to translate a macroscopic model into different microscopic models. We automatically calibrate the microscopic models so that the resulting simulated collective dynamics fit the solutions of the reference macroscopic model for a set of parameter values corresponding to a bifurcation diagram leading to multiple steady states. We apply evolutionary algorithms to simultaneously optimize the parameters of the models at different levels of description. This methodology is applied, in simulation, to an experimentally validated shelter-selection problem solved by gregarious insects and robots. Our framework can be used for multi-level modelling of collective behaviour in animals and robots.

Accelerating the Finite-Element Method for Reaction-Diffusion Simulations on GPUs with CUDA.

DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling waves. The Finite Element Method (FEM) is a standard tool to simulate the physics of such systems where boundary conditions play a crucial role. However, a fine discretization in time and space is required for complex geometries (like sharp corners) and highly nonlinear chemistry. Graphical Processing Units (GPUs) are increasingly used to speed up scientific computing, but their application to accelerate simulations of reaction-diffusion in DNA nanotechnology has been little investigated. Here we study reaction-diffusion equations (a DNA-based predator-prey system) in a tortuous geometry (a maze), which was shown experimentally to generate subtle geometric effects. We solve the partial differential equations on a GPU, demonstrating a speedup of ∼100 over the same resolution on a 20 cores CPU.

Strategies to modulate zebrafish collective dynamics with a closed-loop biomimetic robotic system.

The objective of this study is to integrate biomimetic robots into small groups of zebrafish and to modulate their collective behaviours. A possible approach is to have the robots behave like sheepdogs. In this case, the robots would behave like a different species than the fish and would present different relevant behaviours. In this study, we explore different strategies that use biomimetic zebrafish behaviours. In past work, we have shown that robots biomimicking zebrafish can be socially integrated into zebrafish groups. We have also shown that a fish-like robot can modulate the rotation choice of zebrafish groups in a circular set-up. Here, we further study the modulation capabilities of such robots in a more complex set-up. To do this, we exploit zebrafish social behaviours we identified in previous studies. We first modulate collective departure by replicating the leadership mechanisms with the robot in a set-up composed of two rooms connected by a corridor. Then, we test different behavioural strategies to drive the fish groups towards a predefined target room. To drive the biohybrid groups towards a predefined choice, they have to adopt some specific fish-like behaviours. The first strategy is based on a single robot using the initiation behaviour. In this case, the robot keeps trying to initiate a group transition towards the target room. The second strategy is based on two robots, one initiating and one staying in the target room as a social attractant. The third strategy is based on a single robot behaving like a zebrafish but staying in the target room as a social attractant. The fourth strategy uses two robots behaving like zebrafish but staying in the target room. We conclude that robots can modulate zebrafish group behaviour by adopting strategies based on existing fish behaviours. Under these conditions, robots enable the testing of hypotheses about the behaviours of fish.

Collective departures and leadership in zebrafish.

In social animals, morphological and behavioural traits may give to some individuals a stronger influence on the collective decisions, even in groups assumed to be leaderless such as fish shoals. Here, we studied and characterized the leadership in collective movements of shoals of zebrafish Danio rerio by observing groups of 2, 3, 5, 7 and 10 zebrafish swimming in a two resting sites arena during one hour. We quantified the number of collective departures initiated by each fish and the number of attempts that they made. To do so, we developed an automated pipeline that analysed the individual trajectories generated by the tracking software. For all shoal sizes, the leadership was distributed among several individuals. However, it was equally shared among all the fish in some shoals while other groups showed a more asymmetrical sharing of the initiation of collective departures. To quantify this distribution, we computed the entropy associated with the time series of the identity of all initiators for each experiment and confirmed the presence of a continuum between a homogeneous and a heterogeneous distribution of the leadership. While some fish led more departures than others, an individual analysis showed that all fish had actually the same success rate to lead the shoal out of a resting site after an attempt. Thus, some individuals monopolized the leadership by attempting more often than others to exit a resting site. Finally, we highlight that the intra-group ranking of a fish for the initiative is correlated to its intra-group ranking for the average speed with mobile individuals more prone to lead the shoal. These results demonstrate that the collective behaviour of a shoal can be mainly driven by a subset of individuals even in the absence of higher influence of a fish on its congeneers.

Loose social organisation of AB strain zebrafish groups in a two-patch environment.

We study the collective behaviour of zebrafish shoals of different numbers of individuals (1, 2, 3, 5, 7, 10 and 20 AB zebrafish Danio rerio) in a constraint environment composed of two identical square rooms connected by a corridor. This simple set-up is similar to a natural patchy environment. We track the positions and the identities of the fish and compute the metrics at the group and at the individual levels. First, we show that the number of fish affects the behaviour of each individual in a group, the cohesion of the groups, the preferential interactions and the transition dynamics between the two rooms. Second, during collective departures, we show that the rankings of exit correspond to the topological organisations of the fish prior to their collective departure. This spatial organisation appears in the group a few seconds before a collective departure. These results provide new evidences on the spatial organisation of the groups and the effect of the number of fish on individual and collective behaviours in a patchy environment.

How mimetic should a robotic fish be to socially integrate into zebrafish groups?

Biomimetic robots are promising tools in animal behavioural studies. If they are socially integrated in a group of animals, they can produce calibrated social stimuli to test the animal responses. However, the design of such social robots is challenging as it involves both a luring capability including appropriate robot behaviours, and the acceptation of the robots by the animals as social companions. Here, we investigate the integration of a biomimetic robot driven by biomimetic behavioural models into a group of zebrafish (Danio rerio). The robot behaviours are based on a stochastic model linking zebrafish visual perception to individual behaviour and calibrated experimentally to correspond to the behaviour of zebrafish. We show that our robot can be integrated into a group of zebrafish, mimic their behaviour and exhibit similar collective dynamics compared to fish-only groups. This study shows that an autonomous biomimetic robot was enhanced by a biomimetic behavioural model so that it can socially integrate into groups of fish.