Vincent Rodin

An immune oriented multi-agent system for biological image processing

Abstract In this article, we present a parallel image processing system based on the concept of reactive agents. Our system lies in the oRis language, which allows to describe finely and simply the agents’ behaviors to detect image features. We also present a method of segmentation using a multi-agent system, and two biological applications made with oRis. The stopping of this multi-agent system is implemented through a technique issued from immunology: the apoptosis.

Use of deformable template for two-dimensional growth ring detection of otoliths by digital image processing:: Application to plaice (Pleuronectes platessa) otoliths

Abstract Today, most computer-assisted age reading software is limited to one-dimensional processing. Automated two-dimensional growth ring detection is closely linked to the ability of image processing algorithms to perceive structure continuity. By using deformable models, based on closed B-splines, it is possible to fit a shape to the image features using maximum or minimum criteria according to the nature of translucent or opaque zones. Otolith edge contours were used as templates that were inflated from the core toward the edge in order to detect the growth zones. Template step sizes were modulated by an a priori growth pattern in order to take into account the decrease in ring size. A reference test image set ( n =102) of plaice otoliths, previously aged by one reader, was processed. For the first age groups, there was a total agreement with reader estimates. Mean agreement with reader estimates for age groups 1–5 averaged 80% but decreased for age groups 6–8. Overall, age was significantly underestimated by an average of −0.89 year.

Autonomous agents for edge detection and continuity perception on otolith images

Abstract An automatic method for edge detection on biological images (otolith images) using a multi-agent system is presented. One of the major problems encountered during an automatic contour detection is the lack of structure continuity perception. In this paper we present a new approach to perceive continuity based on a 2D reconstruction of closed contours using a multi-agent system. Each agent is provided with sensors on the image, which allow it to follow local intensity extremes. The purpose is to detect alternative light and dark concentric structures in an image. To improve the detection of these reactive agents, we have added high-level information about the shape of the contour. An application to fish otolith growth ring detection is presented in this paper.

Multi-Agents System to Model Cell Signalling by Using Fuzzy Cognitive Maps. Application to Computer Simulation of Multiple Myeloma

In order to simulate biological processes, we use multi-agents system. However, modelling cell behavior in systems biology is complex and may be based on intracellular biochemical pathway. So, we have developed in this study a Fuzzy Influence Graph to model MAPK pathway. A Fuzzy Influence Graph is also called Fuzzy Cognitive Map.This model can be integrated in agents representing cells. Results indicate that despite individual variations, the average behavior of MAPK pathway in a cells group is close to results obtained by ordinary differential equations. So, we have also modelled multiple myeloma cells signalling by using this approach.

Growth ring detection on fish otoliths by a graph construction

We present an algorithm for the detection of fish otolith growth rings based on a graph construction method. The identification of growth rings, for age estimation, is routinely achieved in fishery laboratories by human readers. One of the major problem encountered during an automatic image processing is the lack of ring continuity perception. We present an approach to this continuity perception based on the 2D reconstruction of rings from the restoration of the connectivity of nodes detected in polar coordinates. The node connection is based on an a priori knowledge of ring geometry.

Formal Validation of Asynchronous Interaction-Agents Algorithms for Reaction-Diffusion Problems

In the context of biological complex systems multi-agent simulation, we present an interaction-agent model for reaction-diffusion problems that enables interaction with the simulation during the execution, and we establish a mathematical validation for our model. We use two types of interaction-agents: on one hand, in a chemical reactor with no spatial dimension -e.g. a cell-, a reaction-agent represents an autonomous chemical reaction between several reactants, and modifies the concentration of reaction products. On the other hand, we use interface-agents in order to take into account the spatial dimension that appears with diffusion : interface-agents achieve the matching transfer of reactants between cells. This approach, where the simulation engine makes agents intervene in a chaotic and asynchronous way, is an alternative to the classical model - which is not relevant when the limits conditions are frequently modified- based on partial derivative equations. We enounciate convergence results for our interaction-agent methods, and illustrate our model with an example about coagulation inside a blood vessel.

Reaction-agents: first mathematical validation of a multi-agent system for dynamical biochemical kinetics

In the context of multi-agent simulation of biological complex systems, we present a reaction-agent model for biological chemical kinetics that enables interaction with the simulation during the execution. In a chemical reactor with no spatial dimension -e.g. a cell-, a reaction-agent represents an autonomous chemical reaction between several reactants : it reads the concentration of reactants, adapts its reaction speed, and modifies consequently the concentration of reaction products. This approach, where the simulation engine makes agents intervene in a chaotic and asynchronous way, is an alternative to the classical model -which is not relevant when the limits conditions change- based on differential systems. We establish formal proofs of convergence for our reaction-agent methods, generally quadratic. We illustrate our model with an example about the extrinsic pathway of blood coagulation.

A multiagent system for edge detection and continuity perception on fish otolith images

We present an algorithm for fish otolith growth ring detection using a multiagent system. Up to now, the identification of growth rings, for age estimation, is routinely achieved by human readers, but this task is tedious and depends on the reader subjectivity. One of the major problems encountered during an automatic contour detection is the lack of ring continuity perception. We present an approach to improve this continuity perception based on a 2D reconstruction of rings using a multiagent system. The originality of the approach is to use local edge detection achieved by agents and combine it with continuity perception that active contours allow.

Simulation of thrombin generation during plasmatic coagulation and primary hemostasis

Describes a simulation of the platelet agglutination in a damaged vein. This agglutination, called plasmatic coagulation, appears in the human body and its malfunction involves dramatic diseases like thrombosis or hemophilia. We designed an in-machina experimentation that is very difficult to do in-vitro. The first aim of this simulation is to verify one of the biological models of plasmatic coagulation and primary hemostasis. The second aim is to test different ways to regulate the thrombin production. Then, we simulate a haemophilia-like disease and one of its possible treatments.

A multiagent architecture for distributed virtual environments

This paper introduces a distributed virtual reality platform based on oRis, our dynamic and interpreted multiagent language. This platform, called AReViDis, has been designed for collaborative interactive prototyping. Thanks to the dynamic properties of oRis, we propose to let the designers of a system enter inside the system and dynamically build and modify the model. During an AReViDis session, this language allows the addition or the modification of virtual agents in a distributed virtual environment. These modifications may either be introduced by the agents themselves or by the users through various human computer interfaces. These modifications may also be received by the network allowing communications in shared virtual worlds.