Didier Devaurs

Bio: Didier Devaurs is an academic researcher from Rice University. The author has contributed to research in topics: Motion planning & Ontology (information science). The author has an hindex of 16, co-authored 47 publications receiving 890 citations. Previous affiliations of Didier Devaurs include University of Edinburgh & Graz University of Technology.

Optimal Path Planning in Complex Cost Spaces With Sampling-Based Algorithms

Abstract: Sampling-based algorithms for path planning, such as the Rapidly-exploring Random Tree (RRT), have achieved great success, thanks to their ability to efficiently solve complex high-dimensional problems. However, standard versions of these algorithms cannot guarantee optimality or even high-quality for the produced paths. In recent years, variants of these methods, such as T-RRT, have been proposed to deal with cost spaces: by taking configuration-cost functions into account during the exploration process, they can produce high-quality (i.e., low-cost) paths. Other novel variants, such as RRT*, can deal with optimal path planning: they ensure convergence toward the optimal path, with respect to a given path-quality criterion. In this paper, we propose to solve a complex problem encompassing this two paradigms: optimal path planning in a cost space. For that, we develop two efficient sampling-based approaches that combine the underlying principles of RRT* and T-RRT. These algorithms, called T-RRT* and AT-RRT, offer the same asymptotic optimality guarantees as RRT*. Results presented on several classes of problems show that they converge faster than RRT* toward the optimal path, especially when the topology of the search space is complex and/or when its dimensionality is high.

An individual-based evolving predator-prey ecosystem simulation using a fuzzy cognitive map as the behavior model

Abstract: We present an individual-based predator-prey model with, for the first time, each agent behavior being modeled by a fuzzy cognitive map (FCM), allowing the evolution of the agent behavior through the epochs of the simulation. The FCM enables the agent to evaluate its environment (e.g., distance to predator or prey, distance to potential breeding partner, distance to food, energy level) and its internal states (e.g., fear, hunger, curiosity), and to choose several possible actions such as evasion, eating, or breeding. The FCM of each individual is unique and is the result of the evolutionary process. The notion of species is also implemented in such a way that species emerge from the evolving population of agents. To our knowledge, our system is the only one that allows the modeling of links between behavior patterns and speciation. The simulation produces a lot of data, including number of individuals, level of energy by individual, choice of action, age of the individuals, and average FCM associated with each species. This study investigates patterns of macroevolutionary processes, such as the emergence of species in a simulated ecosystem, and proposes a general framework for the study of specific ecological problems such as invasive species and species diversity patterns. We present promising results showing coherent behaviors of the whole simulation with the emergence of strong correlation patterns also observed in existing ecosystems.

Understanding the challenges of protein flexibility in drug design

Abstract: Introduction: Protein–ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug discovery. Molecular docking is widely used to predict the structure of protein–ligand complexes, and protein flexibility stands out as one of the most important and challenging issues for binding mode prediction. Various docking methods accounting for protein flexibility have been proposed, tackling problems of ever-increasing dimensionality.Areas covered: This paper presents an overview of conformational sampling methods treating target flexibility during molecular docking. Special attention is given to approaches considering full protein flexibility. Contrary to what is frequently done, this review does not rely on classical biomolecular recognition models to classify existing docking methods. Instead, it applies algorithmic considerations, focusing on the level of flexibility accounted for. This review also discusses the diversity of d...

DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach

Abstract: Molecular docking is a standard computational approach to predict binding modes of protein–ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research. To overcome this limitation, our group has previously proposed a meta-docking strategy, called DINC, to predict binding modes of large ligands. By incrementally docking overlapping fragments of a ligand, DINC allowed predicting binding modes of peptide-based inhibitors of transcription factors involved in cancer. Here, we describe DINC 2.0, a revamped version of the DINC webserver with enhanced capabilities and a more user-friendly interface. DINC 2.0 allows docking ligands that were previously too challenging for DINC, such as peptides with more than 25 flexible bonds. The webserver is freely accessible at http://dinc.kavrakilab.org, together with additional documentation and video tutorials. Our team will provide continuous support for this tool and is working on extending its applicability to other challenging fields, such as personalized immunotherapy against cancer. Cancer Res; 77(21); e55–57. ©2017 AACR .

Motion planning for 6-D manipulation with aerial towed-cable systems

Abstract: Performing aerial 6-dimensional manipulation using flying robots is a challenging problem, to which only little work has been devoted. This paper proposes a motion planning approach for the reliable 6-dimensional quasi-static manipulation with an aerial towed-cable system. The novelty of this approach lies in the use of a cost-based motion-planning algorithm together with some results deriving from the static analysis of cable-driven manipulators. Based on the so-called wrench-feasibility constraints applied to the cable tensions, as well as thrust constraints applied to the flying robots, we formally characterize the set of feasible configurations of the system. Besides, the expression of these constraints leads to a criterion to evaluate the quality of a configuration. This allows us to define a cost function over the configuration space, which we exploit to compute good-quality paths using the T-RRT algorithm. As part of our approach, we also propose an aerial towed-cable system that we name the FlyCrane. It consists of a platform attached to three flying robots using six fixed-length cables. We validate the proposed approach on two simulated 6-D quasi-static manipulation problems involving such a system, and show the benefit of taking the cost function into account for such motion planning tasks.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

Coarse-Grained Protein Models and Their Applications

Abstract: The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies.

Context-Aware Recommender Systems for Learning: A Survey and Future Challenges

Abstract: Recommender systems have been researched extensively by the Technology Enhanced Learning (TEL) community during the last decade. By identifying suitable resources from a potentially overwhelming variety of choices, such systems offer a promising approach to facilitate both learning and teaching tasks. As learning is taking place in extremely diverse and rich environments, the incorporation of contextual information about the user in the recommendation process has attracted major interest. Such contextualization is researched as a paradigm for building intelligent systems that can better predict and anticipate the needs of users, and act more efficiently in response to their behavior. In this paper, we try to assess the degree to which current work in TEL recommender systems has achieved this, as well as outline areas in which further work is needed. First, we present a context framework that identifies relevant context dimensions for TEL applications. Then, we present an analysis of existing TEL recommender systems along these dimensions. Finally, based on our survey results, we outline topics on which further research is needed.