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Vanessa King - One of the best experts on this subject based on the ideXlab platform.
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LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Introduction.
2014Co-Authors: Vanessa KingAbstract:LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Introduction.
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LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Secondary Sources.
2014Co-Authors: Vanessa KingAbstract:LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Secondary Sources.
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LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Starting Points.
2014Co-Authors: Vanessa KingAbstract:LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Starting Points.
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LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Finding a Topic.
2014Co-Authors: Vanessa KingAbstract:LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Finding a Topic.
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libguides law 841a feminist legal theory prof fineman prof Mols fall 2014 introduction
2014Co-Authors: Vanessa KingAbstract:LibGuides. LAW 841A - Feminist Legal Theory (Prof. Fineman / Prof. Mols, Fall 2014). Introduction.
N. Gautham - One of the best experts on this subject based on the ideXlab platform.
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iMolsdock induced fit docking using mutually orthogonal latin squares Mols
Journal of Molecular Graphics & Modelling, 2017Co-Authors: Sam D Paul, N. GauthamAbstract:Abstract We have earlier reported the MolsDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the Mols method, developed in our laboratory. In this paper we report iMolsDOCK, the ‘flexible receptor’ extension we have carried out to the algorithm MolsDOCK. iMolsDOCK uses mutually orthogonal Latin squares (Mols) to sample the conformation and the docking pose of the ligand and also the flexible residues of the receptor protein. The method then uses a variant of the mean field technique to analyze the sample to arrive at the optimum. We have benchmarked and validated iMolsDOCK with a dataset of 44 peptide-protein complexes with peptides. We have also compared iMolsDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time.
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Mols 2.0: software package for peptide modeling and protein–ligand docking
Journal of Molecular Modeling, 2016Co-Authors: D. Sam Paul, N. GauthamAbstract:We previously developed an algorithm to perform conformational searches of proteins and peptides, and to perform the docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (Mols) to rationally sample the vast conformational (or docking) space, and then analyzes this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was denoted Mols 1.0. The docking portion of the algorithm, which allows only “flexible ligand/rigid receptor” docking, was denoted MolsDOCK. Both are FORTRAN-based command-line-only molecular docking computer programs, though a GUI was developed later for Mols 1.0. Both the conformational search and the rigid receptor docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating “induced fit” side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the flexible receptor portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both flexible ligand/rigid receptor and flexible ligand/flexible receptor techniques) more accessible to the research community, we have developed Mols 2.0, which incorporates a new Java-based graphical user interface (GUI). Here, we give a detailed description of Mols 2.0. The source code and binary for Mols 2.0 are distributed free (under a GNU Lesser General Public License) to the scientific community. They are freely available for download at https://sourceforge.net/projects/Mols2-0/files/ .
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Mols 2 0 software package for peptide modeling and protein ligand docking
Journal of Molecular Modeling, 2016Co-Authors: Sam D Paul, N. GauthamAbstract:We previously developed an algorithm to perform conformational searches of proteins and peptides, and to perform the docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (Mols) to rationally sample the vast conformational (or docking) space, and then analyzes this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was denoted Mols 1.0. The docking portion of the algorithm, which allows only “flexible ligand/rigid receptor” docking, was denoted MolsDOCK. Both are FORTRAN-based command-line-only molecular docking computer programs, though a GUI was developed later for Mols 1.0. Both the conformational search and the rigid receptor docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating “induced fit” side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the flexible receptor portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both flexible ligand/rigid receptor and flexible ligand/flexible receptor techniques) more accessible to the research community, we have developed Mols 2.0, which incorporates a new Java-based graphical user interface (GUI). Here, we give a detailed description of Mols 2.0. The source code and binary for Mols 2.0 are distributed free (under a GNU Lesser General Public License) to the scientific community. They are freely available for download at https://sourceforge.net/projects/Mols2-0/files/.
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conformational space exploration of met and leu enkephalin using the Mols method molecular dynamics and monte carlo simulation a comparative study
Biopolymers, 2012Co-Authors: L Ramya, N. GauthamAbstract:We report here a comparative study of the molecular conformational energy landscape generated using the mutually orthogonal Latin squares (Mols) method, molecular dynamics (MD), and Monte Carlo (MC) simulation. The Mols method, as described earlier from our laboratory, uses an experimental design technique to rapidly and exhaustively sample the low energy conformations of a molecule. MD and MC simulations have been used to perform similar tasks. In the comparison reported here, the three methods were applied to a pair of neuropeptides, namely Met- and Leu-enkephalin. A set of 1500 conformations of these enkephalins were generated using these methods with CHARMM22 force field, and the resulting samples were analyzed to determine the extent and nature of coverage of the conformational space. The results indicate that the Mols method samples a larger number of possible conformations and identifies conformations closer to the experimental structures than the MD and MC simulations.
Aymeric Blot - One of the best experts on this subject based on the ideXlab platform.
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Configuration of a Dynamic Mols Algorithm for Bi-objective Flowshop Scheduling
2019Co-Authors: Camille Pageau, Aymeric Blot, Marie-Éléonore Kessaci, Holger Hoos, Laetitia JourdanAbstract:In this work, we propose a dynamic multi-objective local search (Mols) algorithm whose parameters are modified while it is running and a protocol for automatically configuring this algorithm. Our approach applies automated configuration to a static pipeline that sequentially runs multiple configurations of the Mols algorithm. In a series of experiments for well-known benchmark instances of the bi-objective permutation flowshop scheduling problem, we show that our dynamic approach produces substantially better results than static Mols, and that longer pipeline (with a higher number of parameters) outperform shorter ones.
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Reacting and Adapting to the Environment
2018Co-Authors: Aymeric BlotAbstract:Large-scale optimisation problems are usually hard to solve optimally. Approximation algorithms such as metaheuristics, able to quickly find sub-optimal solutions, are often preferred. This thesis focuses on multi-objective local search (Mols) algorithms, metaheuristics able to deal with the simultaneous optimisation of multiple criteria. As many algorithms, metaheuristics expose many parameters that significantly impact their performance. These parameters can be either predicted and set before the execution of the algorithm, or dynamically modified during the execution itself. While in the last decade many advances have been made on the automatic design of algorithms, the great majority of them only deal with single-objective algorithms and the optimisation of a single performance indicator such as the algorithm running time or the final solution quality. In this thesis, we investigate the relations between automatic algorithm design and multi-objective optimisation, with an application on Mols algorithms. We first review possible Mols strategies ans parameters and present a general, highly configurable, Mols framework. We also propose MO-ParamILS, an automatic configurator specifically designed to deal with multiple performance indicators. Then, we conduct several studies on the automatic offline design of Mols algorithms on multiple combinatorial bi-objective problems. Finally, we discuss two online extensions of classical algorithm configuration: first the integration of parameter control mechanisms, to benefit from having multiple configuration predictions; then the use of configuration schedules, to sequentially use multiple configurations.
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Adaptive Multi-Objective Local Search Algorithms for the Permutation Flowshop Scheduling Problem
2018Co-Authors: Aymeric Blot, Laetitia Jourdan, Marie-Éléonore Kessaci, Patrick De CausmaeckerAbstract:Automatic algorithm configuration (AAC) is an increasingly critical factor in the design of efficient metaheuristics. AAC was previously successfully applied to multi-objective local search (Mols) algorithms using offline tools. However, offline approaches are usually very expensive, draw general recommendations regarding algorithm design for a given set of instances, and does generally not allow per-instance adaptation. Online techniques for automatic algorithm control are usually applied to single-objective evolutionary algorithms. In this work we investigate the impact of including control mechanisms to Mols algorithms on a classical bi-objective permutation flowshop scheduling problem (PFSP), and demonstrate how even simple control mechanisms can complement traditional offline configuration techniques.
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Automatic Design of Multi-Objective Local Search Algorithms
2017Co-Authors: Aymeric Blot, Laetitia Jourdan, Marie-Éléonore KessaciAbstract:Multi-objective local search (Mols) algorithms are efficient metaheuristics, which improve a set of solutions by using their neighbourhood to iteratively find better and better solutions. Mols algorithms are versatile algorithms with many available strategies, first to select the solutions to explore, then to explore them, and finally to update the archive using some of the visited neighbours. In this paper, we propose a new generalisation of Mols algorithms incorporating new recent ideas and algorithms. To be able to instantiate the many Mols algorithms of the literature, our generalisation exposes numerous numerical and categorical parameters, raising the possibility of being automatically designed by an automatic algorithm configuration (AAC) mechanism. We investigate the worth of such an automatic design of Mols algorithms using MO-ParamILS, a multi-objective AAC configurator, on the permutation flowshop scheduling problem, and demonstrate its worth against a traditional manual design.
Yazıcı, Emine Şule - One of the best experts on this subject based on the ideXlab platform.
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Embedding partial Latin squares in Latin squares with many mutually orthogonal mates
'Elsevier BV', 2020Co-Authors: Donovan Diane, Grannell Mike, Yazıcı, Emine ŞuleAbstract:In this paper it is shown that any partial Latin square of order n can be embedded in a Latin square of order at most 16n which has at least 2n mutually orthogonal mates. Further, for any t⩾2, it is shown that a pair of orthogonal partial Latin squares of order n can be embedded in a set of t mutually orthogonal Latin squares (Mols) of order a polynomial with respect to n. A consequence of the constructions is that, if N(n) denotes the size of the largest set of Mols of order n, then N(n)⩾N(n)+2. In particular, it follows that N(576)⩾9, improving the previously known lower bound N(576)⩾8
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Embedding partial Latin squares in Latin squares with many mutually orthogonal mates
'Elsevier BV', 2020Co-Authors: Donovan Diane, Grannell Mike, Yazıcı, Emine ŞuleAbstract:In this paper it is shown that any partial Latin square of order $n$ can be embedded in a Latin square of order at most $16n^2$ which has at least $2n$ mutually orthogonal mates. Further, for any $t\geq 2$, it is shown that a pair of orthogonal partial Latin squares of order $n$ can be embedded in a set of $t$ mutually orthogonal Latin squares (Mols) of order a polynomial with respect to $n$. A consequence of the constructions is that, if $N(n)$ denotes the size of the largest set of Mols of order $n$, then $N(n^2)\geq N(n)+2$. In particular, it follows that $N(576)\ge 9$, improving the previously known lower bound $N(576)\ge 8$
Marie-Éléonore Kessaci - One of the best experts on this subject based on the ideXlab platform.
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Configuration of a Dynamic Mols Algorithm for Bi-objective Flowshop Scheduling
2019Co-Authors: Camille Pageau, Aymeric Blot, Marie-Éléonore Kessaci, Holger Hoos, Laetitia JourdanAbstract:In this work, we propose a dynamic multi-objective local search (Mols) algorithm whose parameters are modified while it is running and a protocol for automatically configuring this algorithm. Our approach applies automated configuration to a static pipeline that sequentially runs multiple configurations of the Mols algorithm. In a series of experiments for well-known benchmark instances of the bi-objective permutation flowshop scheduling problem, we show that our dynamic approach produces substantially better results than static Mols, and that longer pipeline (with a higher number of parameters) outperform shorter ones.
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Adaptive Multi-Objective Local Search Algorithms for the Permutation Flowshop Scheduling Problem
2018Co-Authors: Aymeric Blot, Laetitia Jourdan, Marie-Éléonore Kessaci, Patrick De CausmaeckerAbstract:Automatic algorithm configuration (AAC) is an increasingly critical factor in the design of efficient metaheuristics. AAC was previously successfully applied to multi-objective local search (Mols) algorithms using offline tools. However, offline approaches are usually very expensive, draw general recommendations regarding algorithm design for a given set of instances, and does generally not allow per-instance adaptation. Online techniques for automatic algorithm control are usually applied to single-objective evolutionary algorithms. In this work we investigate the impact of including control mechanisms to Mols algorithms on a classical bi-objective permutation flowshop scheduling problem (PFSP), and demonstrate how even simple control mechanisms can complement traditional offline configuration techniques.
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Automatic Design of Multi-Objective Local Search Algorithms
2017Co-Authors: Aymeric Blot, Laetitia Jourdan, Marie-Éléonore KessaciAbstract:Multi-objective local search (Mols) algorithms are efficient metaheuristics, which improve a set of solutions by using their neighbourhood to iteratively find better and better solutions. Mols algorithms are versatile algorithms with many available strategies, first to select the solutions to explore, then to explore them, and finally to update the archive using some of the visited neighbours. In this paper, we propose a new generalisation of Mols algorithms incorporating new recent ideas and algorithms. To be able to instantiate the many Mols algorithms of the literature, our generalisation exposes numerous numerical and categorical parameters, raising the possibility of being automatically designed by an automatic algorithm configuration (AAC) mechanism. We investigate the worth of such an automatic design of Mols algorithms using MO-ParamILS, a multi-objective AAC configurator, on the permutation flowshop scheduling problem, and demonstrate its worth against a traditional manual design.