Abdul Sattar - Academia.edu (original) (raw)

Papers by Abdul Sattar

Research paper thumbnail of Evolving algorithms for constraint satisfaction

Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753)

This paper proposes a framework for automatically evolving constraint satisfaction algorithms usi... more This paper proposes a framework for automatically evolving constraint satisfaction algorithms using genetic programming. The aim is to overcome the difficulties associated with matching algorithms to specific constraint satisfaction problems. A representation is introduced that is suitable for genetic programming and that can handle both complete and local search heuristics. In addition, the representation is shown to have considerably more flexibility than existing alternatives, being able to discover entirely new heuristics and to exploit synergies between heuristics. In a preliminary empirical study, it is shown that the new framework is capable of evolving algorithms for solving the well-studied problem of boolean satisfiability testing.

Research paper thumbnail of On the efficiency of logic-based diagnosis

Proceedings of the third international conference on Industrial and engineering applications of artificial intelligence and expert systems - IEA/AIE '90, 1990

Diagnosis is a problem in which one must ex-plain the discrepancy between the observed and correc... more Diagnosis is a problem in which one must ex-plain the discrepancy between the observed and correct system behavior by assuming some component (possibly multiple components) of the system is functioning abnormally. A diag-nostic reasoning system must deal with two is- ...

Research paper thumbnail of Dual Encoding Using Constraint Coverings

Pacific Rim International Conference on Artificial Intelligence, 2000

Constraint satisfaction problems (CSPs) involve finding an assignment of values to variables that... more Constraint satisfaction problems (CSPs) involve finding an assignment of values to variables that satisfy a set of constraints between variables. Non-binary constraints have recently begun to attract more attention, since many real-life problems are naturally expressed as non-binary formulations. In order to solve a non-binary CSP, one either uses an algorithm that has been generalised for non-binary constraint satisfaction or

Research paper thumbnail of An apparent Effect of Immunopotentiation During Late Gestation on the Postpartum Reproductive Performance of Nili-Ravi Buffaloes ( Bubalus Bubalis )

Veterinary Research Communications, 1997

Thirty-two Nili-Ravi buffaloes were used to determine the effect of prepartum immunopotentiation ... more Thirty-two Nili-Ravi buffaloes were used to determine the effect of prepartum immunopotentiation in late gestation with levamisole hydrochloride (0.5 mg/kg), vitamin E+selenium (vitE-Se) (Etosol-SE, 10 ml intramuscularly) or Bacille Calmette Guerin (BCG) (0.5 ml/animal, subcutaneously) on postpartum reproductive performance. The immunopotentiating treatment was given twice, with treatments one week apart, approximately 80 days prior to the expected date of parturition.

Research paper thumbnail of Advances in Local Search for Satisfiability

AI 2007: Advances in Artificial Intelligence

In this paper we describe a stochastic local search (SLS) procedure for finding satisfying models... more In this paper we describe a stochastic local search (SLS) procedure for finding satisfying models of satisfiable propositional formulae. This new algorithm, gNovelty + , draws on the features of two other WalkSAT family algorithms: R+AdaptNovelty + and G 2 WSAT, while also successfully employing a dynamic local search (DLS) clause weighting heuristic to further improve performance. gNovelty + was a Gold Medal winner in the random category of the 2007 SAT competition. In this paper we present a detailed description of the algorithm and extend the SAT competition results via an empirical study of the effects of problem structure and parameter tuning on the performance of gNovelty +. The study also compares gNovelty + with two of the most representative WalkSAT-based solvers: G 2 WSAT, AdaptNovelty + , and two of the most representative DLS solvers: RSAPS and PAWS. Our new results augment the SAT competition results and show that gNovelty + is also highly competitive in the domain of solving structured satisfiability problems in comparison with other SLS techniques.

Research paper thumbnail of An integer programming-based nurse rostering system

Lecture Notes in Computer Science, 1996

Research paper thumbnail of GAGM-AAM: A genetic optimization with Gaussian mixtures for Active Appearance Models

2008 15th IEEE International Conference on Image Processing, 2008

Abstract This paper proposes an optimization technique of genetic algorithm (GA) combined with Ga... more Abstract This paper proposes an optimization technique of genetic algorithm (GA) combined with Gaussian mixtures (GAGM) to make a robust, efficient and real time face alignment application for embedded systems. It uses 2.5 D Active Appearance Model (AAM) for the ...

Research paper thumbnail of Solving Overconstrained Temporal Reasoning Problems

Lecture Notes in Computer Science, 2001

Representing and reasoning with temporal information is an essential part of many t a s k s i n A... more Representing and reasoning with temporal information is an essential part of many t a s k s i n A I s u c h a s s c heduling, planning and natural language processing. Two i n u e n tial frameworks for representing temporal information are: interval algebra and point algebra 1, 8]. Given a k n o wledge-base consisting of temporal relations, the main reasoning problem is to determine whether this knowledge-base is satis able, i.e., there is a scenario which is consistent with the information provided. However, when a given set of temporal relations is unsatis able, no further reasoning is performed. We argue that many real world problems are inherently overconstrained, and we can not just ignore them, we m ust address them. This paper investigates approaches for handling overconstrainedness in temporal reasoning. We a d a p t a w ell studied notion of partial satisfaction to de ne partial scenarios: an optimal partial solution. We propose two reasoning procedures for computing an optimal partial solution to a problem or a complete solution if it exists.

Research paper thumbnail of On the Behavior and Application of Constraint Weighting

Lecture Notes in Computer Science, 1999

In this paper we compare the performance of three constraint weighting schemes with one of the la... more In this paper we compare the performance of three constraint weighting schemes with one of the latest and fastest WSAT heuristics: rnovelty. We extend previous results from satisfiability testing by looking at the broader domain of constraint satisfaction and test for differences in performance using randomly generated problems and problems based on realistic situations and assumptions. We find constraint weighting produces fairly consistent behaviour within problem domains, and is more influenced by the number and interconnectedness of constraints than the realism or randomness of a problem. We conclude that constraint weighting is better suited to smaller structured problems, where it is can clearly distinguish between different constraint groups. 1. MIN: Incrementing weights at each local minimum (based on [9]).

Research paper thumbnail of An Efficient Algorithm for Solving Dynamic Complex DCOP Problems

2009 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology, 2009

Multi Agent Systems and the Distributed Constraint Optimization Problem (DCOP) formalism offer se... more Multi Agent Systems and the Distributed Constraint Optimization Problem (DCOP) formalism offer several asynchronous and optimal algorithms for solving naturally distributed optimization problems efficiently. There has been good application of this technology in addressing real world problems in areas like Sensor Networks and Meeting Scheduling. Most of these algorithms however exploit static tree structures and are thus not well suited to modeling and solving problems in rapidly changing domains. Also, while in theory most DCOP algorithms can be extended to handle complex local sub-problems, we argue that this generally results in making their performance sub-optimal, and thus their application less suitable. In this paper we present new measures that emphasize the interconnectedness between each agent's local and inter-agent sub-problems and use these measures to guide dynamic agent ordering during distributed constraint reasoning. The resulting algorithm, DCDCOP, offers a robust, flexible, and efficient mechanism for modeling and solving dynamic complex problems. Experimental evaluation of the algorithm shows that DCD-COP significantly outperforms ADOPT, the gold standard in search-based DCOP algorithms.

Research paper thumbnail of GGA-AAM: Novel heuristic method of gradient driven Genetic Algorithm for Active Appearance Models

2008 Third International Conference on Digital Information Management, 2008

... Although this half of the population has fallen in the local minima, but still parameter ... ... more ... Although this half of the population has fallen in the local minima, but still parameter ... This section describes GGA-AAM (Gradient based Ge-netic Algorithm AAM) method by combining the subsec ... the newly born children to make half of a new population for segmentation phase. ...

Research paper thumbnail of Electrical signature of nanoscale coalescence in a percolating Bi nanocluster film

Physical Review B, 2010

We explore changes in the electrical conductance of a percolating Bi nanocluster film due to coal... more We explore changes in the electrical conductance of a percolating Bi nanocluster film due to coalescence. A power law increase in conductance is observed immediately after deposition and we show this corresponds to power law changes in the radius of the necks between clusters. The power-law exponent ͑Շ0.04͒ is much smaller than expected from classical models of microparticle coalescence. Atomistic kinetic Monte Carlo simulations reveal similar behavior during a late stage of coalescence where faceting near the necks slows the effects of surface diffusion.

Research paper thumbnail of A complete first-order temporal BDI logic for forest multi-agent systems

Knowledge-Based Systems, 2012

This paper presents a new complete first-order temporal BDI logic and forest multi-agent system. ... more This paper presents a new complete first-order temporal BDI logic and forest multi-agent system. The main characteristic of the logic is that its semantic model is based on the forest multi-agent system, which enables us to reason about beliefs, desires, and intentions between agents with different layers such as father agent and child agent. The logical reasoning and hierarchical structures of the forest multi-agent system can suitably capture the hierarchical property of the real systems and therefore is practically realistic. We propose further four classes of first-order BDI interpreted systems and four proof systems which are sound and complete with respect to corresponding classes of BDI interpreted systems. Finally, we give a case to show how to characterize the forest multi-agent system by using the hierarchical structure of modules, and to solve the model checking problem of first-order temporal BDI logic for the forest multi-agent system.

Research paper thumbnail of Power law fitting procedures: The electrical conductance of coalescing nanocluster films

Journal of Applied Physics, 2011

Power law fitting procedures: The electrical conductance of coalescing nanocluster films. [Journa... more Power law fitting procedures: The electrical conductance of coalescing nanocluster films. [Journal of Applied Physics 109, 014910 (2011)]. Pierre Y. Convers, Abdul Sattar, Simon A. Brown, Shaun C. Hendy. Abstract. The electrical ...

Research paper thumbnail of Levels of modality for BDI Logic

Journal of Applied Logic, 2011

The use of rational agents for modelling real world problems has both been heavily investigated a... more The use of rational agents for modelling real world problems has both been heavily investigated and become well accepted, with BDI (Beliefs, Desires, and Intentions) Logic being a widely used architecture to represent and reason about rational agency. However, in the real world, we often have to deal with different levels of confidence in the beliefs we hold, desires we have, and intentions that we commit to. This paper extends our previous framework that integrated qualitative levels of beliefs, desires, and intentions into BDI Logic. We describe an expanded set of axioms and properties of the extended logic. We present a modular structure for the semantics which involves a non-normal Kripke type semantics that may be used for other agent systems. Further, we demonstrate the usefulness of our framework with a scheduling task example.

Research paper thumbnail of Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011

Research paper thumbnail of A Segmentation-based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014

Protein fold recognition (PFR) is considered as an important step towards the protein structure p... more Protein fold recognition (PFR) is considered as an important step towards the protein structure prediction problem. Despite all the efforts that have been made so far, finding an accurate and fast computational approach to solve the PFR still remains a challenging problem for bioinformatics and computational biology. In this study, we propose the concept of segmented-based feature extraction technique to provide local evolutionary information embedded in position specific scoring matrix (PSSM) and structural information embedded in the predicted secondary structure of proteins using SPINE-X. We also employ the concept of occurrence feature to extract global discriminatory information from PSSM and SPINE-X. By applying a support vector machine (SVM) to our extracted features, we enhance the protein fold prediction accuracy for 7.4 percent over the best results reported in the literature. We also report 73.8 percent prediction accuracy for a data set consisting of proteins with less than 25 percent sequence similarity rates and 80.7 percent prediction accuracy for a data set with proteins belonging to 110 folds with less than 40 percent sequence similarity rates. We also investigate the relation between the number of folds and the number of features being used and show that the number of features should be increased to get better protein fold prediction results when the number of folds is relatively large.

Research paper thumbnail of Believing change and changing belief

IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans, 1996

We present a rst-order logic of time, chance, and probability that is capable of expressing the r... more We present a rst-order logic of time, chance, and probability that is capable of expressing the relation between subjective probability and objective c hance at di erent t i m e s. U sing this capability, w e show h o w the logic can distinguish between causal and evidential correlation by distinguishing between conditions, events, and actions that 1) in uence the agent's belief in chance and 2) the agent believes to in uence chance. Furthermore, the semantics of the logic captures commonsense inferences concerning objective c hance and causality. W e show that an agent's subjective probability is the expected value of its beliefs concerning objective c hance. We also prove that an agent using this representation believes with certainty that the past cannot be causally in uenced.

Research paper thumbnail of Analysis of Authentication Protocols in Agent-Based Systems Using Labeled Tableaux

IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics), 2009

The study of multiagent systems (MASs) focuses on systems in which many intelligent agents intera... more The study of multiagent systems (MASs) focuses on systems in which many intelligent agents interact with each other using communication protocols. For example, an authentication protocol is used to verify and authorize agents acting on behalf of users to protect restricted data and information. After authentication, two agents should be entitled to believe that they are communicating with each other and not with intruders. For specifying and reasoning about the security properties of authentication protocols, many researchers have proposed the use of belief logics. Since authentication protocols are designed to operate in dynamic environments, it is important to model the evolution of authentication systems through time in a systematic way. We advocate the systematic combinations of logics of beliefs and time for modeling and reasoning about evolving agent beliefs in MASs. In particular, we use a temporal belief logic called TML + for establishing trust theories for authentication systems and also propose a labeled tableau system for this logic. To illustrate the capabilities of TML + , we present trust theories for several well-known authentication protocols, namely, the Lowe modified wide-mouthed frog protocol, the amended Needham-Schroeder symmetric key protocol, and Kerberos. We also show how to verify certain security properties of those protocols. With the logic TML + and its associated modal tableaux, we are able to reason about and verify authentication systems operating in dynamic environments.

Research paper thumbnail of Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice

BMC Bioinformatics, 2013

Background: Protein structure prediction is an important but unsolved problem in biological scien... more Background: Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3dimensional face-centred-cubic lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (H-core) is essential for the progress of the search. The H-core helps find a stable structure with the lowest possible free energy. Results: In order to build H-cores, we present a new Spiral Search algorithm based on tabu-guided local search. Our algorithm uses a novel H-core directed guidance heuristic that squeezes the structure around a dynamic hydrophobic-core centre. We applied random walks to break premature H-cores and thus to avoid early convergence. We also used a novel relay-restart technique to handle stagnation. Conclusions: We have tested our algorithms on a set of benchmark protein sequences. The experimental results show that our spiral search algorithm outperforms the state-of-the-art local search algorithms for simplified protein structure prediction. We also experimentally show the effectiveness of the relay-restart.

Research paper thumbnail of Evolving algorithms for constraint satisfaction

Proceedings of the 2004 Congress on Evolutionary Computation (IEEE Cat. No.04TH8753)

This paper proposes a framework for automatically evolving constraint satisfaction algorithms usi... more This paper proposes a framework for automatically evolving constraint satisfaction algorithms using genetic programming. The aim is to overcome the difficulties associated with matching algorithms to specific constraint satisfaction problems. A representation is introduced that is suitable for genetic programming and that can handle both complete and local search heuristics. In addition, the representation is shown to have considerably more flexibility than existing alternatives, being able to discover entirely new heuristics and to exploit synergies between heuristics. In a preliminary empirical study, it is shown that the new framework is capable of evolving algorithms for solving the well-studied problem of boolean satisfiability testing.

Research paper thumbnail of On the efficiency of logic-based diagnosis

Proceedings of the third international conference on Industrial and engineering applications of artificial intelligence and expert systems - IEA/AIE '90, 1990

Diagnosis is a problem in which one must ex-plain the discrepancy between the observed and correc... more Diagnosis is a problem in which one must ex-plain the discrepancy between the observed and correct system behavior by assuming some component (possibly multiple components) of the system is functioning abnormally. A diag-nostic reasoning system must deal with two is- ...

Research paper thumbnail of Dual Encoding Using Constraint Coverings

Pacific Rim International Conference on Artificial Intelligence, 2000

Constraint satisfaction problems (CSPs) involve finding an assignment of values to variables that... more Constraint satisfaction problems (CSPs) involve finding an assignment of values to variables that satisfy a set of constraints between variables. Non-binary constraints have recently begun to attract more attention, since many real-life problems are naturally expressed as non-binary formulations. In order to solve a non-binary CSP, one either uses an algorithm that has been generalised for non-binary constraint satisfaction or

Research paper thumbnail of An apparent Effect of Immunopotentiation During Late Gestation on the Postpartum Reproductive Performance of Nili-Ravi Buffaloes ( Bubalus Bubalis )

Veterinary Research Communications, 1997

Thirty-two Nili-Ravi buffaloes were used to determine the effect of prepartum immunopotentiation ... more Thirty-two Nili-Ravi buffaloes were used to determine the effect of prepartum immunopotentiation in late gestation with levamisole hydrochloride (0.5 mg/kg), vitamin E+selenium (vitE-Se) (Etosol-SE, 10 ml intramuscularly) or Bacille Calmette Guerin (BCG) (0.5 ml/animal, subcutaneously) on postpartum reproductive performance. The immunopotentiating treatment was given twice, with treatments one week apart, approximately 80 days prior to the expected date of parturition.

Research paper thumbnail of Advances in Local Search for Satisfiability

AI 2007: Advances in Artificial Intelligence

In this paper we describe a stochastic local search (SLS) procedure for finding satisfying models... more In this paper we describe a stochastic local search (SLS) procedure for finding satisfying models of satisfiable propositional formulae. This new algorithm, gNovelty + , draws on the features of two other WalkSAT family algorithms: R+AdaptNovelty + and G 2 WSAT, while also successfully employing a dynamic local search (DLS) clause weighting heuristic to further improve performance. gNovelty + was a Gold Medal winner in the random category of the 2007 SAT competition. In this paper we present a detailed description of the algorithm and extend the SAT competition results via an empirical study of the effects of problem structure and parameter tuning on the performance of gNovelty +. The study also compares gNovelty + with two of the most representative WalkSAT-based solvers: G 2 WSAT, AdaptNovelty + , and two of the most representative DLS solvers: RSAPS and PAWS. Our new results augment the SAT competition results and show that gNovelty + is also highly competitive in the domain of solving structured satisfiability problems in comparison with other SLS techniques.

Research paper thumbnail of An integer programming-based nurse rostering system

Lecture Notes in Computer Science, 1996

Research paper thumbnail of GAGM-AAM: A genetic optimization with Gaussian mixtures for Active Appearance Models

2008 15th IEEE International Conference on Image Processing, 2008

Abstract This paper proposes an optimization technique of genetic algorithm (GA) combined with Ga... more Abstract This paper proposes an optimization technique of genetic algorithm (GA) combined with Gaussian mixtures (GAGM) to make a robust, efficient and real time face alignment application for embedded systems. It uses 2.5 D Active Appearance Model (AAM) for the ...

Research paper thumbnail of Solving Overconstrained Temporal Reasoning Problems

Lecture Notes in Computer Science, 2001

Representing and reasoning with temporal information is an essential part of many t a s k s i n A... more Representing and reasoning with temporal information is an essential part of many t a s k s i n A I s u c h a s s c heduling, planning and natural language processing. Two i n u e n tial frameworks for representing temporal information are: interval algebra and point algebra 1, 8]. Given a k n o wledge-base consisting of temporal relations, the main reasoning problem is to determine whether this knowledge-base is satis able, i.e., there is a scenario which is consistent with the information provided. However, when a given set of temporal relations is unsatis able, no further reasoning is performed. We argue that many real world problems are inherently overconstrained, and we can not just ignore them, we m ust address them. This paper investigates approaches for handling overconstrainedness in temporal reasoning. We a d a p t a w ell studied notion of partial satisfaction to de ne partial scenarios: an optimal partial solution. We propose two reasoning procedures for computing an optimal partial solution to a problem or a complete solution if it exists.

Research paper thumbnail of On the Behavior and Application of Constraint Weighting

Lecture Notes in Computer Science, 1999

In this paper we compare the performance of three constraint weighting schemes with one of the la... more In this paper we compare the performance of three constraint weighting schemes with one of the latest and fastest WSAT heuristics: rnovelty. We extend previous results from satisfiability testing by looking at the broader domain of constraint satisfaction and test for differences in performance using randomly generated problems and problems based on realistic situations and assumptions. We find constraint weighting produces fairly consistent behaviour within problem domains, and is more influenced by the number and interconnectedness of constraints than the realism or randomness of a problem. We conclude that constraint weighting is better suited to smaller structured problems, where it is can clearly distinguish between different constraint groups. 1. MIN: Incrementing weights at each local minimum (based on [9]).

Research paper thumbnail of An Efficient Algorithm for Solving Dynamic Complex DCOP Problems

2009 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology, 2009

Multi Agent Systems and the Distributed Constraint Optimization Problem (DCOP) formalism offer se... more Multi Agent Systems and the Distributed Constraint Optimization Problem (DCOP) formalism offer several asynchronous and optimal algorithms for solving naturally distributed optimization problems efficiently. There has been good application of this technology in addressing real world problems in areas like Sensor Networks and Meeting Scheduling. Most of these algorithms however exploit static tree structures and are thus not well suited to modeling and solving problems in rapidly changing domains. Also, while in theory most DCOP algorithms can be extended to handle complex local sub-problems, we argue that this generally results in making their performance sub-optimal, and thus their application less suitable. In this paper we present new measures that emphasize the interconnectedness between each agent's local and inter-agent sub-problems and use these measures to guide dynamic agent ordering during distributed constraint reasoning. The resulting algorithm, DCDCOP, offers a robust, flexible, and efficient mechanism for modeling and solving dynamic complex problems. Experimental evaluation of the algorithm shows that DCD-COP significantly outperforms ADOPT, the gold standard in search-based DCOP algorithms.

Research paper thumbnail of GGA-AAM: Novel heuristic method of gradient driven Genetic Algorithm for Active Appearance Models

2008 Third International Conference on Digital Information Management, 2008

... Although this half of the population has fallen in the local minima, but still parameter ... ... more ... Although this half of the population has fallen in the local minima, but still parameter ... This section describes GGA-AAM (Gradient based Ge-netic Algorithm AAM) method by combining the subsec ... the newly born children to make half of a new population for segmentation phase. ...

Research paper thumbnail of Electrical signature of nanoscale coalescence in a percolating Bi nanocluster film

Physical Review B, 2010

We explore changes in the electrical conductance of a percolating Bi nanocluster film due to coal... more We explore changes in the electrical conductance of a percolating Bi nanocluster film due to coalescence. A power law increase in conductance is observed immediately after deposition and we show this corresponds to power law changes in the radius of the necks between clusters. The power-law exponent ͑Շ0.04͒ is much smaller than expected from classical models of microparticle coalescence. Atomistic kinetic Monte Carlo simulations reveal similar behavior during a late stage of coalescence where faceting near the necks slows the effects of surface diffusion.

Research paper thumbnail of A complete first-order temporal BDI logic for forest multi-agent systems

Knowledge-Based Systems, 2012

This paper presents a new complete first-order temporal BDI logic and forest multi-agent system. ... more This paper presents a new complete first-order temporal BDI logic and forest multi-agent system. The main characteristic of the logic is that its semantic model is based on the forest multi-agent system, which enables us to reason about beliefs, desires, and intentions between agents with different layers such as father agent and child agent. The logical reasoning and hierarchical structures of the forest multi-agent system can suitably capture the hierarchical property of the real systems and therefore is practically realistic. We propose further four classes of first-order BDI interpreted systems and four proof systems which are sound and complete with respect to corresponding classes of BDI interpreted systems. Finally, we give a case to show how to characterize the forest multi-agent system by using the hierarchical structure of modules, and to solve the model checking problem of first-order temporal BDI logic for the forest multi-agent system.

Research paper thumbnail of Power law fitting procedures: The electrical conductance of coalescing nanocluster films

Journal of Applied Physics, 2011

Power law fitting procedures: The electrical conductance of coalescing nanocluster films. [Journa... more Power law fitting procedures: The electrical conductance of coalescing nanocluster films. [Journal of Applied Physics 109, 014910 (2011)]. Pierre Y. Convers, Abdul Sattar, Simon A. Brown, Shaun C. Hendy. Abstract. The electrical ...

Research paper thumbnail of Levels of modality for BDI Logic

Journal of Applied Logic, 2011

The use of rational agents for modelling real world problems has both been heavily investigated a... more The use of rational agents for modelling real world problems has both been heavily investigated and become well accepted, with BDI (Beliefs, Desires, and Intentions) Logic being a widely used architecture to represent and reason about rational agency. However, in the real world, we often have to deal with different levels of confidence in the beliefs we hold, desires we have, and intentions that we commit to. This paper extends our previous framework that integrated qualitative levels of beliefs, desires, and intentions into BDI Logic. We describe an expanded set of axioms and properties of the extended logic. We present a modular structure for the semantics which involves a non-normal Kripke type semantics that may be used for other agent systems. Further, we demonstrate the usefulness of our framework with a scheduling task example.

Research paper thumbnail of Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011

Research paper thumbnail of A Segmentation-based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2014

Protein fold recognition (PFR) is considered as an important step towards the protein structure p... more Protein fold recognition (PFR) is considered as an important step towards the protein structure prediction problem. Despite all the efforts that have been made so far, finding an accurate and fast computational approach to solve the PFR still remains a challenging problem for bioinformatics and computational biology. In this study, we propose the concept of segmented-based feature extraction technique to provide local evolutionary information embedded in position specific scoring matrix (PSSM) and structural information embedded in the predicted secondary structure of proteins using SPINE-X. We also employ the concept of occurrence feature to extract global discriminatory information from PSSM and SPINE-X. By applying a support vector machine (SVM) to our extracted features, we enhance the protein fold prediction accuracy for 7.4 percent over the best results reported in the literature. We also report 73.8 percent prediction accuracy for a data set consisting of proteins with less than 25 percent sequence similarity rates and 80.7 percent prediction accuracy for a data set with proteins belonging to 110 folds with less than 40 percent sequence similarity rates. We also investigate the relation between the number of folds and the number of features being used and show that the number of features should be increased to get better protein fold prediction results when the number of folds is relatively large.

Research paper thumbnail of Believing change and changing belief

IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans, 1996

We present a rst-order logic of time, chance, and probability that is capable of expressing the r... more We present a rst-order logic of time, chance, and probability that is capable of expressing the relation between subjective probability and objective c hance at di erent t i m e s. U sing this capability, w e show h o w the logic can distinguish between causal and evidential correlation by distinguishing between conditions, events, and actions that 1) in uence the agent's belief in chance and 2) the agent believes to in uence chance. Furthermore, the semantics of the logic captures commonsense inferences concerning objective c hance and causality. W e show that an agent's subjective probability is the expected value of its beliefs concerning objective c hance. We also prove that an agent using this representation believes with certainty that the past cannot be causally in uenced.

Research paper thumbnail of Analysis of Authentication Protocols in Agent-Based Systems Using Labeled Tableaux

IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics), 2009

The study of multiagent systems (MASs) focuses on systems in which many intelligent agents intera... more The study of multiagent systems (MASs) focuses on systems in which many intelligent agents interact with each other using communication protocols. For example, an authentication protocol is used to verify and authorize agents acting on behalf of users to protect restricted data and information. After authentication, two agents should be entitled to believe that they are communicating with each other and not with intruders. For specifying and reasoning about the security properties of authentication protocols, many researchers have proposed the use of belief logics. Since authentication protocols are designed to operate in dynamic environments, it is important to model the evolution of authentication systems through time in a systematic way. We advocate the systematic combinations of logics of beliefs and time for modeling and reasoning about evolving agent beliefs in MASs. In particular, we use a temporal belief logic called TML + for establishing trust theories for authentication systems and also propose a labeled tableau system for this logic. To illustrate the capabilities of TML + , we present trust theories for several well-known authentication protocols, namely, the Lowe modified wide-mouthed frog protocol, the amended Needham-Schroeder symmetric key protocol, and Kerberos. We also show how to verify certain security properties of those protocols. With the logic TML + and its associated modal tableaux, we are able to reason about and verify authentication systems operating in dynamic environments.

Research paper thumbnail of Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice

BMC Bioinformatics, 2013

Background: Protein structure prediction is an important but unsolved problem in biological scien... more Background: Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3dimensional face-centred-cubic lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (H-core) is essential for the progress of the search. The H-core helps find a stable structure with the lowest possible free energy. Results: In order to build H-cores, we present a new Spiral Search algorithm based on tabu-guided local search. Our algorithm uses a novel H-core directed guidance heuristic that squeezes the structure around a dynamic hydrophobic-core centre. We applied random walks to break premature H-cores and thus to avoid early convergence. We also used a novel relay-restart technique to handle stagnation. Conclusions: We have tested our algorithms on a set of benchmark protein sequences. The experimental results show that our spiral search algorithm outperforms the state-of-the-art local search algorithms for simplified protein structure prediction. We also experimentally show the effectiveness of the relay-restart.