Robin Gras

Robin Gras
University of Windsor · School of Computer Science

PhD

About

135
Publications
26,366
Reads
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1,230
Citations
Introduction
I am Professor in the School of Computer Science at the university of Windsor and CSO and partner at Movyl Technology and MVYL Associates (San Francisco). I am also cross-appointed by the Biology Department and the Great Lakes Institute for Environmental Research. I was post doctorate and then senior scientist in the Swiss Institute of Bioinformatics, Geneva. My domains of research are: machine learning, Deep Learning, artificial life, theoretical biology, ecosystem simulation, bioinformatics, combinatorial optimization.
Additional affiliations
July 2017 - present
Movyl Technologies
Position
  • Acting CSO
July 2006 - present
University of Windsor
Position
  • Professor (Full)
Description
  • We study evolutionary process and emergence of species. We have conceived EcoSim, an individual-based evolving predator-prey ecosystem simulation. This is the only simulation modeling the fact that individual behaviors affect evolution and speciation.
August 1998 - December 2004
Swiss Institute of Bioinformatics
Position
  • Senior Researcher
Description
  • Bioinformatics, combinatorial optimization, machine learning
Education
September 1994 - December 1997
Université de Rennes 1
Field of study
  • Computer Science

Publications

Publications (135)
Article
One possible explanation for the prevalence of sexual reproduction in animal species is that in the context of predator-prey dynamics, sexually reproducing prey are better able to evade predators than their asexual counterparts. This is known as the Red Tooth hypothesis, a term coined by French (2010). It is a special case of the more generic Red Q...
Article
The prevalence of sexual reproduction of animal species is a paradox for evolutionary theory since it remains unclear whether the evolutionary benefits of sexual reproduction outweigh the costs. One attempt at explaining the maintenance of sex is the Tangled Bank hypothesis: Sexual reproduction shuffles around alleles through crossing over and reco...
Article
The prevalence of sexual reproduction in most animal species despite its considerable costs such as useless males, energy spent on mating, the cost of meiosis and genome dilution remains a puzzle in evolutionary theory. One prominent single-factor attempt to solve this persistent puzzle is the claim that sexual reproduction is instrumental in elimi...
Article
We investigated the establishment success of introduced populations from multiple introductions using an individual-based predator-prey ecosystem simulation called EcoSim. The experiment was a simulated reciprocal transplant over two environments (one with homogeneous and abundant resources, one with heterogeneous and fewer resources) with five lev...
Article
Animal communication impacts many kinds of behavior including mating and courtship, escaping from predators and foraging activity. In this article, our investigation focuses primarily on how alarm communication impacts foraging activity, using individual based computer simulations. We used this approach to help resolve a debate in the literature be...
Chapter
This chapter discusses individual-based models (IBMs) and uses the Overview, Design concepts, and Details (ODD) protocol to describe a predator-prey evolutionary ecosystem IBM called EcoSim. EcoSim is one of the most complex and large-scale IBMs of its kind, allowing hundreds of thousands of intricate individuals to interact and evolve over thousan...
Article
There are three non-mutually-exclusive key strategies evolved by gene pools to cope with fluctuating food resource availability, including evolutionary adaptation, phenotypic plasticity, and migration. We focus primarily on evolutionary adaptation and behavioral plasticity, which is a type of phenotypic plasticity, resulting in life-history changes...
Article
It is not clear from empirical and simulation studies that populations with females who employ sexual selection have any evolutionary advantages over populations where mates are randomly selected. There is an ongoing debate regarding whether speciation rates and extinction rates differ significantly between sexual selection and random selection. Al...
Article
Full-text available
Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic, or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors since optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic...
Article
The connection between reproductive fitness and animal personality is not fully understood. Using computer simulations and machine learning, we found high accuracy rules that predict which personalities are associated with fitness for two correlated measures of components of fitness applied a posteriori for classificatory purposes: fitness componen...
Article
Full-text available
An individual-based model, EcoSim, was employed to investigate if specialized resource use could promote sympatric speciation. Prey individuals in the original version of EcoSim were supplied with a single primary food resource. A dual resource version with different food resources (Food 1 and Food 2) was also developed to create favorable conditio...
Article
Full-text available
Decision trees are examples of easily interpretable models whose predictive accuracy is normally low. In comparison, decision tree ensembles (DTEs) such as random forest (RF) exhibit high predictive accuracy while being regarded as black-box models. We propose three new rule extraction algorithms from DTEs. The RF+DHC method, a hill climbing method...
Article
Full-text available
The complexity of behavioural interactions in predator-prey systems has recently begun to capture trait effects, or non-lethal effects, of predators on prey via induced behavioural changes. Non-lethal predation effects play crucial roles in shaping population and community dynamics, particularly by inducing changes to foraging, movement and reprodu...
Conference Paper
Full-text available
Population modelling spans many domains and techniques, and new technologies offer cutting-edge opportunities to a growing field. The population modelling working group has been recently active in coordination amongst different population modellers of different fields. One activity is mapping the population modelling domain by examples of work. This...
Conference Paper
Full-text available
In nature, the resources available to organisms in an ecosystem fluctuate regularly due to abiotic factors like weather patterns and seasonality, and are also impacted by humans. The effects of resource fluctuation or stability have been studied in real ecosystems at small physical and temporal scale because of physical and temporal constraints on...
Conference Paper
Next-generation sequencing and clustering pipelines have several applications, including obtaining biodiversity estimates and the early detection of non-native species. One can obtain an eDNA sample from an aquatic source and monitor for invaders by performing sequencing, clustering, and BLAST. Such an approach allows improved detection of cryptic...
Conference Paper
Full-text available
Polychlorinated biphenyls (PCBs) are classified as one the most extremely regulated anthropogenic contaminants and they have been deeply probed in aquatic ecosystems. However, there is very limited understanding of the population level effects of exposure to PCBs on terrestrial animal species and this has been unanimously indicated as a critical ga...
Article
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The forces promoting and constraining speciation are often studied in theoretical models because the process is hard to observe, replicate, and manipulate in real organisms. Most models analyzed to date include pre-defined functions influencing fitness, leaving open the question of how speciation might proceed without these built-in determinants. T...
Conference Paper
Full-text available
Random forest (RF) is a tree-based learning method, which exhibits a high ability to generalize on real data sets. Nevertheless, a possible limitation of RF is that it generates a forest consisting of many trees and rules, thus it is viewed as a black box model. In this paper, the RF+HC methods for rule extraction from RF are proposed. Once the RF...
Article
Full-text available
Time series forecasting is of fundamental importance for a variety of domains including the prediction of earthquakes, financial market prediction, and the prediction of epileptic seizures. Only a handful of research programs have been undertaken with respect to long-term time series forecasting, and no satisfactory results have been achieved becau...
Patent
The invention relates to a method (method 2) and system for performing predictive modeling on complex data, and more particularly a system for achieving the predictive chaos analysis of non-linear data or events, and more preferably EEG readings used to indicate the likely onset of epileptic seizures. Method 2 is a further refinement of method 1 (M...
Conference Paper
Full-text available
http://mitpress.mit.edu/sites/default/files/titles/content/alife14/ch111.html
Patent
Full-text available
The invention relates to a method and system for performing predictive data modeling, and more particularly a system for achieving the predictive chaos analysis of non-linear data or events, such as stock and financial market performance. The system and method however, may further be applied to the prediction and/or analysis of other non-linear eve...
Article
Full-text available
Abstract Species abundance distribution (SAD) is one of the important measures of biodiversity and one of the most significant concepts in ecology communities. Using this concept, the biologists can infer a lot of information from their collected data. In this article, we proposed a new method for predicting SAD. This method is based on the combina...
Conference Paper
Full-text available
The emergence of complex adaptive traits and behaviors in artificial life systems requires long term evolution with continuous emergence governed by natural selection. We model organism’s genomes in an individual-based evolutionary ecosystem simulation (EcoSim) coding for their behavioral model and represented by fuzzy cognitive maps (FCM). Our sys...
Conference Paper
Full-text available
Artificial life evolutionary systems facilitate addressing lots of fundamental questions in evolutionary genetics. Behavioral adaptation requires long term evolution with continuous emergence of new traits, governed by natural selection. We model organism’s genomes coding for their behavioral model and represented by fuzzy cognitive maps (FCM), in...
Conference Paper
Full-text available
Phylogenetic trees are constructed frequently in biological research to provide an understanding of the evolutionary history of the organisms being studied. Often, the actual phylogenetic tree is unknown and the phylogenetic tree constructed is an estimate. There are many methods of phylogenetic tree construction which fall into two main categories...
Article
Full-text available
The origin of species remains one of the most controversial and least understood topics in evolution. While it is being widely accepted that complete cessation of gene-flow between populations owing to long-lasting geographical barriers results in a steady, irreversible increase of divergence and eventually speciation, the extent to which various d...
Conference Paper
Full-text available
The process of evolution involves the emergence and disappearance of species. Many factors affect on the survival of species. Real study of factors' influence is particularly difficult due to the complex interaction between them. An individual-based model (IBM) can assist in the analysis of effective factors. In this study, using an IBM called EcoS...
Chapter
Full-text available
Estimation of Distribution Algorithm (EDA) is a relatively new optimization method in the field of evolutionary algorithm. EDAs use probabilistic models to learn properties of the problem to solve from promising solutions and use them to guide the search process. These models can also reveal some unknown regularity patterns in search space. These a...
Conference Paper
Full-text available
Biologists are interested in studying the relation between the genetic diversity of a population and its fitness. We adopt the notion of entropy as a measure of genetic diversity and correlate it with fitness of an evolutionary ecosystem simulation. EcoSim is a predator-prey individual based simulation which models co-evolving sexual individuals ev...
Data
Supplementary Table S1. List of 43 gene names and their lengths (Number of amino acid positions encoded by the gene).
Article
Full-text available
Since the discovery of the "living fossil" in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has not been resolved for decades. Three principal hypotheses (...
Conference Paper
Full-text available
Introducing efficient Bayesian learning algorithms in Bayesian network based EDAs seems necessary in order to use them for large problems. In this paper we propose an algorithm, called CMSS-BOA, which uses a recently introduced heuristic called max-min parent children (MMPC) [3] in order to constraint the models search space. This algorithm does no...
Conference Paper
Full-text available
— This paper presents a multifractal analysis of EcoSim, a large evolving ecosystem simulation. Multifractal analysis of ecosystem time series using the Rényi fractal dimension spectrum demonstrates a self-similarity characteristic for a complex ecosystem. Results suggest the applicability of Rényi dimensions spectra to individuals ' spatial d...
Conference Paper
Full-text available
The goal of this research is to find how dependencies affect the capability of several feature selection approaches to extract of the relevant features for a classification purpose. The hypothesis is that more dependencies and higher level dependencies mean more complexity for the task. Some experiments are used to intend to discover some limitatio...
Article
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We analyze the results of a large simulation of an evolving ecosystem to evaluate its complexity. In particular, we are interested to know how close to a stochastic or a deterministic behavior our simulation is. Four methods have been used for this analysis: Higuchi fractal dimension, correlation dimension, largest Lyapunov exponent, and P&H method...
Conference Paper
Full-text available
We present a new method for modeling speciation within a previously created individual-based evolving predator-prey ecosystem simulation. As an alternative to the classical speciation mechanism originally implemented, k-means clustering provides a more realistic method for modeling speciation that, among other things, allows for the recreation of t...
Article
Discovering the dependencies among the variables of a domain from examples is an important problem in optimization. Many methods have been proposed for this purpose, but few large-scale evaluations were conducted. Most of these methods are based on measurements of conditional probability. The statistical implicative analysis offers another perspect...
Article
One of the applications of DNA microarrays is recognizing the presence or absence of different biological components (targets) in a sample. Hence, the quality of the microarrays design which includes selecting short Oligonucleotide sequences (probes) to be affixed on the surface of the microarray becomes a major issue. A good design is the one that...
Conference Paper
Full-text available
Dependencies among the features can decrease the performance and efficiency in many algorithms. Traditional methods can only find the linear dependencies or the dependencies among few features. In our research, we try to use feature selection approaches for finding dependencies. We use and compare Relief, CFS, NB-GA and NB-BOA as feature selection...
Article
Full-text available
We have developed an individual-based evolving predator-prey ecosystem simulation that integrates, for the first time, a complex individual behaviour model, an evolutionary mechanism and a speciation process, at an acceptable computational cost. In this article, we analyse the species abundance patterns observed in the communities generated by our...
Article
Thirty-six single genes of 6 plants inferred 18 unique trees using maximum parsimony. Such incongruence is an important challenge. How to reconstruct the congruent tree is still one of the most challenges in molecular phylogenetics. For resolving this problem, a genome-wide EST data mining approach was systematically investigated by retrieving a la...
Article
Full-text available
The origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the Bayesian method under the coalescence model with the latest program (BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear genes...
Article
Full-text available
Since its discovery of the living fossil in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has been the subject of intense debate for decades. The three pri...
Article
This paper has been withdrawn by the author(s), due t a modification in Eqn. 1. Comment: 1 Pages, 0 Figures and 0 tables