Network interoperability is crucial for achieving seamless communication across Internet of Things (IoT) environments. IoT comprises heterogeneous devices and systems supporting diverse technologies, protocols, and manufacturers. Enabling devices to communicate and exchange data effectively, regardless of underlying protocols, is key to building cohesive and integrated IoT networks. IoT has transformed multiple sectors ranging from home automation to healthcare—by harnessing a vast array of sensors and actuators that communicate through cloud, fog, and edge layers. However, the variety in device manufacturing and communication standards demands interoperable interfaces, and most current solutions depend on cloud-based centralised architectures. These architectures introduce latency and scalability challenges, particularly for resource-constrained IoT devices that often struggle to communicate with the cloud due to limited resources. This paper addresses network interoperability at the IoT edge level, focusing on resource-efficient communication by integrating Wi-Fi and Bluetooth, two commonly used protocols in IoT ecosystems. We have implemented a network edge interoperability solution that supports effective data exchange between devices operating on these distinct protocols, enhancing the overall efficiency, flexibility, and scalability of IoT systems. Our approach allows devices interoperate by addressing network latency and bandwidth limitations, incorporating an integrated controller to facilitate broader applications and enhance performance across IoT networks. Our findings illustrate how bridging protocol differences can foster more resilient and adaptable IoT solutions, advancing the deployment of IoT applications across various domains and use cases.

As Autonomous Vehicles (AVs) rapidly progress and become widely deployed, governments worldwide grapple with addressing the ethical challenges associated with AVs in dilemma situations that result in loss of human life. They are tackling these issues through the formulation of policies and guidelines, the establish-ment of dedicated research centres exploring the ethical implications of AVs, and seeking public opinions on how self-driving cars should handle such moral dilemmas. In this paper, we will evaluate the Australian government’s strategies for addressing the ethical issues related to AV accidents. We will critique the Decision Regulation Impact Statement (DRIS) released by the National Transport Commission (NTC) in 2018, which assessed the safety assurance options for Automated Driving Systems (ADSs). We will critically examine the NTC’s decision to exclude ethical considerations for AVs from the DRIS and the Automated Driving System Entity’s (ADSE) Statement of Compliance. W e will contend that safety and ethics are intrinsically linked. Furthermore, we argue that relying solely on the safety criteria may prove inadequate when addressing ethical dilemmas. Consequently, we advocate for the inclusion of AV ethical considerations, especially in complex ethical dilemmas, in future dialogues, even if a clear consensus on ethical decision-making by ADSs remains elusive. In conclusion, we will propose recommendations for the Australian government to enhance the development, deployment, and acceptance of AV technology.

The Internet of Things (IoT) has many important applications in multiple domains that include home automation, smart cites, healthcare, agriculture, and environment. IoT comprises a wide range of sensors and actuators that communicate with each other over cloud, fog and edge level networks. Moreover, these devices use various communication protocols and are made by different manufactures. To deal with these diversities, IoT essentially needs interoperable communication interfaces among devices. Unfortunately, existing interoperability solutions are centralised and use fog or cloud level computing resources, making IoT communications latency-prone and poorly scalable. These issues could be handled effectively, if edge level devices could be made interoperable within the edge level and without needing fog or cloud level access. This paper proposes a decentralized interoperability solution that stays fully within the edge level. The solution relies on controller devices that work on the interface boundaries of the edge devices. Unlike existing solutions, the proposed solution adopts a hierarchical interoperability model to handle interoperability at network, syntactical, semantic, and organizational levels. Our solution is non-proprietary, generic over vendors and platforms, and easily extendable to new devices. We compare our proposed solution with existing interoperability solutions for edge devices and show its mobility, efficiency and flexibility.

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. It plays an important role in various applications ranging from social network analysis to bioinformatic network interactions. However, existing alignment models either cannot handle large-scale graphs or fail to leverage different types of network information or modalities. In this paper, we propose a novel end-to-end alignment framework that can leverage different modalities to compare and align network nodes in an efficient way. In order to exploit the richness of the network context, our model constructs multiple embeddings for each node, each of which captures one modality or type of network information. We then design a late-fusion mechanism to combine the learned embeddings based on the importance of the underlying information. Our fusion mechanism allows our model to be adapted to various types of structure of the input network. Experimental results show that our technique outperforms state-of-the-art approaches in terms of accuracy on real and synthetic datasets, while being robust against various noise factors.

Network alignment is the task of identifying topo-logically and semantically similar nodes across (two) different networks. However, existing alignment models either cannot handle large-scale graphs or fail to leverage different types of network information or modalities. In this paper, we pro-pose a novel end-to-end alignment framework that can lever-age different modalities to compare and align network nodes in an efficient way. A comprehensive evaluation on various datasets shows that our technique outperforms state-of-the-art approaches. Our source code is available at https://github.com/thanhtrunghuynh93/holisticEmbeddingsNA.

MOTIVATION: Protein backbone angle prediction has achieved significant accuracy improvement with the development of deep learning methods. Usually the same deep learning model is used in making prediction for all residues regardless of the categories of secondary structures they belong to. In this paper, we propose to train separate deep learning models for each category of secondary structures. Machine learning methods strive to achieve generality over the training examples and consequently loose accuracy. In this work, we explicitly exploit classification knowledge to restrict generalisation within the specific class of training examples. This is to compensate the loss of generalisation by exploiting specialisation knowledge in an informed way. RESULTS: The new method named SAP4SS obtains mean absolute error (MAE) values of 15.59, 18.87, 6.03, and 21.71 respectively for four types of backbone angles [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]. Consequently, SAP4SS significantly outperforms existing state-of-the-art methods SAP, OPUS-TASS, and SPOT-1D: the differences in MAE for all four types of angles are from 1.5 to 4.1% compared to the best known results. AVAILABILITY: SAP4SS along with its data is available from https://gitlab.com/mahnewton/sap4ss .

This paper develops a new comprehensive computational framework for reasoning about private international law that encompasses the reasoning patterns modeled by previous works [3,8,9]. The framework is a multi-modal extension of [10] preserving some nice properties of the original system, including some efficient algorithms to compute the extensions of normative theories representing legal systems.

The travelling thief problem (TTP) is a multi-component optimisation problem involving two interdependent NP-hard components: the travelling salesman problem (TSP) and the knapsack problem (KP). Recent state-of-the-art TTP solvers modify the underlying TSP and KP solutions in an iterative and interleaved fashion. The TSP solution (cyclic tour) is typically changed in a deterministic way, while changes to the KP solution typically involve a random search, effectively resulting in a quasi-meandering exploration of the TTP solution space. Once a plateau is reached, the iterative search of the TTP solution space is restarted by using a new initial TSP tour. We propose to make the search more efficient though an adaptive surrogate model (based on a customised form of Support Vector Regression) that learns the characteristics of initial TSP tours that lead to good TTP solutions. The model is used to filter out non-promising initial TSP tours, in effect reducing the amount of time spent to find a good TTP solution. Experiments on a broad range of benchmark TTP instances indicate that the proposed approach filters out a considerable number of non-promising initial tours, at the cost of missing only a small number of the best TTP solutions.

Abstract Dropout has been proven to be an effective technique for regularizing and preventing the co-adaptation of neurons in deep neural networks (DNN). It randomly drops units with a probability of p during the training stage of DNN to avoid overfitting. The working mechanism of dropout can be interpreted as approximately and exponentially combining many different neural network architectures efficiently, leading to a powerful ensemble. In this work, we propose a novel diversification strategy for dropout, which aims at generating more different neural network architectures in less numbers of iterations. The dropped units in the last forward propagation will be marked. Then the selected units for dropping in the current forward propagation will be retained if they have been marked in the last forward propagation, i.e., we only mark the units from the last forward propagation. We call this new regularization scheme Tabu dropout, whose significance lies in that it does not have extra parameters compared with the standard dropout strategy and is computationally efficient as well. Experiments conducted on four public datasets show that Tabu dropout improves the performance of the standard dropout, yielding better generalization capability.

The travelling thief problem (TTP) is a combination of two interdependent NP-hard components: travelling salesman problem (TSP) and knapsack problem (KP). Existing approaches for TTP typically solve the TSP and KP components in an interleaved fashion, where the solution to one component is held fixed while the other component is changed. This indicates poor coordination between solving the two components and may lead to poor quality TTP solutions. For solving the TSP component, the 2-OPT segment reversing heuristic is often used for modifying the tour. We propose an extended and modified form of the reversing heuristic in order to concurrently consider both the TSP and KP components. Items deemed as less profitable and picked in cities earlier in the reversed segment are replaced by items that tend to be equally or more profitable and not picked in the later cities. Comparative evaluations on a broad range of benchmark TTP instances indicate that the proposed approach outperforms existing state-of-the-art TTP solvers.

Deep Belief Networks (DBN) have been successful in classification especially image recognition tasks. However, the performance of a DBN is often highly dependent on settings in particular the combination of runtime parameter values. In this work, we propose a hyper-heuristic based framework which can optimise DBNs independent from the problem domain. It is the first time hyper-heuristic entering this domain. The framework iteratively selects suitable heuristics based on a heuristic set, apply the heuristic to tune the DBN to better fit with the current search space. Under this framework the setting of DBN learning is adaptive. Three well-known image reconstruction benchmark sets were used for evaluating the performance of this new approach. Our experimental results show this hyper-heuristic approach can achieve high accuracy under different scenarios on diverse image sets. In addition state-of-the-art meta-heuristic methods for tuning DBN were introduced for comparison. The results illustrate that our hyper-heuristic approach can obtain better performance on almost all test cases.

Organisations typically have to cope with large numbers of business rules and existing regulations governing the business in which they operate. Due to the size and complexity of those rules, maintenance is difficult and it is increasingly complicated to ensure that each business process adheres to those rules. As such, automated extraction of business processes from rules has a number of clear advantages: (1) visualisation of all possible executions allowed by the rules, (2) automated execution and compliance by design, (3) identification of "inefficiencies" in the business rules. Existing approaches, however, only allow to generate partial traces based on input specifications and cannot handle many different input cases resulting in a full process. This paper presents a formal method to visualise and operationalise such sets of rules as a verifiable business process that is compliant by design and allows us to analyse all possible execution paths. In addition, it maintains information of all distinct input cases, to preserve dependencies between consecutive exclusive paths.

In this paper we provide a general, unifying framework for probabilistic belief revision. We first introduce a probabilistic logic called p-logic that is capable of representing and reasoning with basic probabilistic information. With p-logic as the background logic, we define a revision function called p-revision that resembles partial meet revision in the AGM framework. We provide a representation theorem for p-revision which shows that it can be characterised by the set of basic AGM revision postulates. P-revision represents an "all purpose" method for revising probabilistic information that can be used for, but not limited to, the revision problems behind Bayesian conditionalisation, Jeffrey conditionalisation, and Lewis's imaging. Importantly, p-revision subsumes all three approaches indicating that Bayesian conditionalisation, Jeffrey conditionalisation, and Lewis' imaging all obey the basic principles of AGM revision. As well our investigation sheds light on the corresponding operation of AGM expansion in the probabilistic setting.

We describe a constraint-based automated planner named Transition Constraints for Parallel Planning (TCPP). TCPP constructs its constraint model from a redefined version of the domain transition graphs (DTG) of a given planning problem. TCPP encodes state transitions in the redefined DTGs by using table constraints with cells containing don't cares or wild cards. TCPP uses Minion the constraint solver to solve the constraint model and returns a parallel plan. We empirically compare TCPP with the other state-of-the-art constraint-based parallel planner PaP2. PaP2 encodes action successions in the finite state automata (FSA) as table constraints with cells containing sets of values. PaP2 uses SICStus Prolog as its constraint solver. We also improve PaP2 by using don’t cares and mutex constraints. Our experiments on a number of standard classical planning benchmark domains demonstrate TCPP's efficiency over the original PaP2 running on SICStus Prolog and our reconstructed and enhanced versions of PaP2 running on Minion.

Belief revision has been studied mainly with respect to background logics that are monotonic in character. In this paper we study belief revision when the underlying logic is non-monotonic instead—an inherently interesting problem that is under explored. In particular, we will focus on the revision of a body of beliefs that is represented as a logic program under the answer set semantics, while the new information is also similarly represented as a logic program. Our approach is driven by the observation that unlike in a monotonic setting where, when necessary, consistency in a revised body of beliefs is maintained by jettisoning some old beliefs, in a non-monotonic setting consistency can be restored by adding new beliefs as well. We will define two revision functions through syntactic and model-theoretic methods respectively and subsequently provide representation theorems for characterising them.

The problem of finding a minimum vertex cover (MinVC) in a graph is a prominent NP-hard problem of great importance in both theory and application. During recent decades, there has been much interest in finding optimal or near-optimal solutions to this problem. Many existing heuristic algorithms for MinVC are based on local search strategies. Recently, an algorithm called FastVC takes a first step towards solving the MinVC problem for large real-world graphs. However, FastVC may be trapped by local minima during the local search stage due to the lack of suitable diversification mechanisms. In this work, we design a new random walk strategy to help FastVC escape from local minima. Experiments conducted on a broad range of large real-world graphs show that our algorithm outperforms state-of-the-art algorithms on most classes of the benchmark and finds smaller vertex covers on a considerable portion of the graphs.

MOTIVATION: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ. RESULTS: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction. AVAILABILITY AND IMPLEMENTATION: The method is available at http://sparks-lab.org CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

In-vitro methods for protein structure determination are time-consuming, cost-intensive, and failure-prone. Because of these expenses, alternative computer-based predictive methods have emerged. Predicting a protein's 3-D structure from only its amino acid sequence-also known as ab initio protein structure prediction (PSP)-is computationally demanding because the search space is astronomically large and energy models are extremely complex. Some successes have been achieved in predictive methods but these are limited to small sized proteins (around 100 amino acids); thus, developing efficient algorithms, reducing the search space, and designing effective search guidance heuristics are necessary to study large sized proteins. An on-lattice model can be a better ground for rapidly developing and measuring the performance of a new algorithm, and hence we consider this model for larger proteins (>150 amino acids) to enhance the genetic algorithms (GAs) framework. In this paper, we formulate PSP as a combinatorial optimization problem that uses 3-D face-centered-cubic lattice coordinates to reduce the search space and hydrophobic-polar energy model to guide the search. The whole optimization process is controlled by an enhanced GA framework with four enhanced features: 1) an exhaustive generation approach to diversify the search; 2) a novel hydrophobic core-directed macro-mutation operator to intensify the search; 3) a per-generation duplication elimination strategy to prevent early convergence; and 4) a random-walk technique to recover from stagnation. On a set of standard benchmark proteins, our algorithm significantly outperforms state-of-the-art algorithms. We also experimentally show that our algorithm is robust enough to produce very similar results regardless of different parameter settings.

Now-related temporal data play an important role in many applications. Clifford et al.'s approach is a milestone to model the semantics of `now' in temporal relational databases. Several relational representation models for now-related data have been presented; however, the semantics of such representations has not been explicitly studied. Additionally, the definition of a relational algebra to query now-related data is an open problem. We propose the first integrated approach that provides both a neat semantics for now-related data and a compact 1NF representation (data model and relational algebra) for them. Additionally, our approach also extends current approaches to consider (i) domains where it is not always possible to know when changes in the world are recorded in the database and (ii) now-related data with a bound on their persistency in the future. To do so, we explicitly model the notion of temporal indeterminacy in the future for now-related data. The properties of our approach are also analyzed both from a theoretical (semantic correctness and reducibility of the algebra) and from an experimental point of view. Experiments show that, despite the fact that our approach is a major extension to current temporal relational approaches, no significant overhead is added to deal with `now'.

We present a planner named Transition Constraints for Parallel Planning (TCPP). TCPP constructs a new constraint model from domain transition graphs (DTG) of a given planning problem. TCPP encodes the constraint model by using table constraints that allow don't cares or wild cards as cell values. TCPP uses Minion the constraint solver to solve the constraint model and returns the parallel plan. Empirical results exhibit the efficiency of our planning system over state-of-the-art constraint-based planners.

In this paper, we present a semantic network model (SNM) as a reasoning engine for the requirements models. The SNM consists of the vertices and the edges, in which they store information of the models and their interrelations. The SNM, through a semi-automated normalisation process, helps the user (1) to assign states to the models and their relations as to whether they can be included, excluded, or undecided, (2) to eliminate redundant interrelations, (3) to avoid over-specification, and (4) to visualise a simplified overview of the whole system. Finally, we formulate the well-formedness of the SNM, which indicates whether the given models can produce a formal specification. We also evaluate our techniques using several case studies.

Abstract Motivation: Frameshifting (FS) indels and nonsense (NS) variants disrupt the protein-coding sequence downstream of the mutation site by changing the reading frame or introducing a premature termination codon, respectively. Despite such drastic changes to the protein sequence, FS indels and NS variants have been discovered in healthy individuals. How to discriminate disease-causing from neutral FS indels and NS variants is an understudied problem. Results: We have built a machine learning method called DDIG-in (FS) based on real human genetic variations from the Human Gene Mutation Database (inherited disease-causing) and the 1000 Genomes Project (GP) (putatively neutral). The method incorporates both sequence and predicted structural features and yields a robust performance by 10-fold cross-validation and independent tests on both FS indels and NS variants. We showed that human-derived NS variants and FS indels derived from animal orthologs can be effectively employed for independent testing of our method trained on human-derived FS indels. DDIG-in (FS) achieves a Matthews correlation coefficient (MCC) of 0.59, a sensitivity of 86%, and a specificity of 72% for FS indels. Application of DDIG-in (FS) to NS variants yields essentially the same performance (MCC of 0.43) as a method that was specifically trained for NS variants. DDIG-in (FS) was shown to make a significant improvement over existing techniques. Availability and implementation: The DDIG-in web-server for predicting NS variants, FS indels, and non-frameshifting (NFS) indels is available at http://sparks-lab.org/ddig. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

BACKGROUND: The functioning of a protein relies on its location in the cell. Therefore, predicting protein subcellular localization is an important step towards protein function prediction. Recent studies have shown that relying on Gene Ontology (GO) for feature extraction can improve the prediction performance. However, for newly sequenced proteins, the GO is not available. Therefore, for these cases, the prediction performance of GO based methods degrade significantly. RESULTS: In this study, we develop a method to effectively employ physicochemical and evolutionary-based information in the protein sequence. To do this, we propose segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids to tackle Gram-positive and Gram-negative subcellular localization. We explore our proposed feature extraction techniques using 10 attributes that have been experimentally selected among a wide range of physicochemical attributes. Finally by applying the Rotation Forest classification technique to our extracted features, we enhance Gram-positive and Gram-negative subcellular localization accuracies up to 3.4% better than previous studies which used GO for feature extraction. CONCLUSION: By proposing segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids as well as using Rotation Forest classification technique, we are able to enhance the Gram-positive and Gram-negative subcellular localization prediction accuracies, significantly.

In this paper, we present a formal definition of the integration of the requirements modeling language Behavior Trees (BTs). We first provide the semantic integration of two interrelated BTs using an extended version of Communicating Sequential Processes. We then use a Semantic Network Model to capture a set of interrelated BTs, and develop algorithm to integrate them all into one BT. This formalisation facilitates developing (semi-)automated tools for modeling the requirements of large-scale software intensive systems.

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.

Protein structure prediction is an unsolved problem in computational biology. One great difficulty is due to the unknown factors in the actual energy function. Moreover, the energy models available are often not very informative particularly when spatially similar structures are compared during search. We introduce several novel heuristics to augment the energy model and present a new local search algorithm that exploits these heuristics in a mixed fashion. Although the heuristics individually are weaker in performance than the energy function, their combination interestingly produces stronger results. For standard benchmark proteins on the face centered cubic lattice and a realistic 20x20 energy model, we obtain structures with significantly lower energy than those obtained by the state-of-the-art algorithms. We also report results for these proteins using the same energy model on the cubic lattice.

In this paper, we present a local search framework for lattice fit problem of proteins. Our algorithm significantly improves state-of-the-art results and justifies the significance of the lattice models. In addition to these, our analysis reveals the weakness of several energy functions used.

No single algorithm suits the best for the protein structure prediction problem. Therefore, researchers have tried hybrid techniques to mix the power of different strategies to gain improvements. In this paper, we present a hybrid search framework that embeds a tabu-based local search within a population based genetic algorithm. We applied our hybrid algorithm on simplified protein structure prediction problem. We use a low-resolution ab initio search method with the hydrophobic-polar energy model and face-centred-cubic lattice. Within the genetic algorithm, we apply local search in two different situations: i) only once at the beginning and ii) every time at search stagnation. At the beginning, we apply local search to improve the randomly generated individuals and use them as an initial population for the genetic algorithm. Later, we apply local search after applying a random-walk at situations where the genetic algorithm gets stuck. In both cases, the use of local search is to improve the randomised solutions quickly. We experimentally show that our hybrid approach outperforms the state-of-the-art approaches.

Protein structure prediction is one of the most challenging problems in computational biology and remains unsolved for many decades. In a simplified version of the problem, the task is to find a self-avoiding walk with the minimum free energy assuming a discrete lattice and a given energy matrix. Genetic algorithms currently produce the state-of-the-art results for simplified protein structure prediction. However, performance of the genetic algorithms largely depends on the encodings they use in representing protein structures and the twin removal technique they use in eliminating duplicate solutions from the current population. In this paper, we present a new efficient encoding for protein structures. Our encoding is nonisomorphic in nature and results into efficient twin removal. This helps the search algorithm diversify and explore a larger area of the search space. In addition to this, we also propose an approximate matching scheme for removing near-similar solutions from the population. Our encoding algorithm is generic and applicable to any lattice type. On the standard benchmark proteins, our techniques significantly improve the state-of-the-art genetic algorithm for hydrophobic-polar (HP) energy model on face-centered-cubic (FCC) lattice.

In the last decade, Stream Processing Engines (SPEs) have emerged as a new processing paradigm that can process huge amounts of data while retaining low latency and high-throughputs. Yet, it is often necessary to join streaming data with traditional databases to provide more contextual information for the end-users and applications. The major problem that we confront is to join the fast arriving stream tuples with the static relation tuples that are on a slow database. This is what we call the Stream-Relation Join (SRJ) problem. Currently, SPEs use a naive tuple-by-tuple approach for SRJ processing where the SPE accesses the database for every incoming tuple. Some SPEs use cache to avoid accessing the database for every incoming tuple, while others do not because of the stochastic nature of streaming data. In this paper, we propose a new SRJ operator to facilitate SRJ processing regardless of the cache performance using two techniques: batching and out-of-order processing. The proposed operator provides an effective generic solution to the SRJ problem and the cost of incorporating our operator into different SPEs is minimal. Our experiments use a variety of synthetic and real data sets demonstrating that our operator outperforms the state-of-the-art tuple-by-tuple approach in terms of maximizing the throughput under ordering and memory constraints.

BACKGROUND: Even a single amino acid substitution in a protein sequence may result in significant changes in protein stability, structure, and therefore in protein function as well. In the post-genomic era, computational methods for predicting stability changes from only the sequence of a protein are of importance. While evolutionary relationships of protein mutations can be extracted from large protein databases holding millions of protein sequences, relevant evolutionary features for the prediction of stability changes have not been proposed. Also, the use of predicted structural features in situations when a protein structure is not available has not been explored. RESULTS: We proposed a number of evolutionary and predicted structural features for the prediction of stability changes and analysed which of them capture the determinants of protein stability the best. We trained and evaluated our machine learning method on a non-redundant data set of experimentally measured stability changes. When only the direction of the stability change was predicted, we found that the best performance improvement can be achieved by the combination of the evolutionary features mutation likelihood and SIFT score in conjunction with the predicted structural feature secondary structure. The same two evolutionary features in the combination with the predicted structural feature accessible surface area achieved the lowest error when the prediction of actual values of stability changes was assessed. Compared to similar studies, our method achieved improvements in prediction performance. CONCLUSION: Although the strongest feature for the prediction of stability changes appears to be the vector of amino acid identities in the sequential neighbourhood of the mutation, the most relevant combination of evolutionary and predicted structural features further improves prediction performance. Even the predicted structural features, which did not perform well on their own, turn out to be beneficial when appropriately combined with evolutionary features. We conclude that a high prediction accuracy can be achieved knowing only the sequence of a protein when the right combination of both structural and evolutionary features is used.

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 3-dimensional 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.

BACKGROUND: Given a protein's amino acid sequence, the protein structure prediction problem is to find a three dimensional structure that has the native energy level. For many decades, it has been one of the most challenging problems in computational biology. A simplified version of the problem is to find an on-lattice self-avoiding walk that minimizes the interaction energy among the amino acids. Local search methods have been preferably used in solving the protein structure prediction problem for their efficiency in finding very good solutions quickly. However, they suffer mainly from two problems: re-visitation and stagnancy. RESULTS: In this paper, we present an efficient local search algorithm that deals with these two problems. During search, we select the best candidate at each iteration, but store the unexplored second best candidates in a set of elite conformations, and explore them whenever the search faces stagnation. Moreover, we propose a new non-isomorphic encoding for the protein conformations to store the conformations and to check similarity when applied with a memory based search. This new encoding helps eliminate conformations that are equivalent under rotation and translation, and thus results in better prevention of re-visitation. CONCLUSION: On standard benchmark proteins, our algorithm significantly outperforms the state-of-the art approaches for Hydrophobic-Polar energy models and Face Centered Cubic Lattice.

The Minimum Vertex Cover (MVC) problem is a prominent NP-hard combinatorial optimization problem of great importance in both theory and application. Local search has proved successful for this problem. However, there are two main drawbacks in state-of-the-art MVC local search algorithms. First, they select a pair of vertices to exchange simultaneously, which is time-consuming. Secondly, although using edge weighting techniques to diversify the search, these algorithms lack mechanisms for decreasing the weights. To address these issues, we propose two new strategies: two-stage exchange and edge weighting with forgetting. The two-stage exchange strategy selects two vertices to exchange separately and performs the exchange in two stages. The strategy of edge weighting with forgetting not only increases weights of uncovered edges, but also decreases some weights for each edge periodically. These two strategies are used in designing a new MVC local search algorithm, which is referred to as NuMVC. We conduct extensive experimental studies on the standard benchmarks, namely DIMACS and BHOSLIB. The experiment comparing NuMVC with state-of-the-art heuristic algorithms show that NuMVC is at least competitive with the nearest competitor namely PLS on the DIMACS benchmark, and clearly dominates all competitors on the BHOSLIB benchmark. Also, experimental results indicate that NuMVC finds an optimal solution much faster than the current best exact algorithm for Maximum Clique on random instances as well as some structured ones. Moreover, we study the effectiveness of the two strategies and the run-time behaviour through experimental analysis.

In this paper, we propose two new strategies to design efficient local search algorithms for the minimum vertex cover (MVC) problem. There are two main drawbacks in state-of-the-art MVC local search algorithms: First, they select a pair of vertices to be exchanged simultaneously, which is time consuming; Second, although they use edge weighting techniques, they do not have a strategy to decrease the weights. To address these drawbacks, we propose two new strategies: two stage exchange and edge weighting with forgetting. The two stage exchange strategy selects two vertices to be exchanged separately and performs the exchange in two stages. The strategy of edge weighting with forgetting not only increases weights of uncovered edges, but also decreases some weights for each edge periodically. We utilize these two strategies to design a new algorithm dubbed NuMVC. The experimental results show that NuMVC significantly outperforms existing state-of-the-art heuristic algorithms on most of the hard DIMACS instances and all instances in the hard random BHOSLIB benchmark.

A key challenge in developing efficient local search solvers is to effectively minimise search stagnation (i.e. avoiding traps or local minima). A majority of the state-of-the-art local search solvers perform random and/or Novelty-based walks to overcome search stagnation. Although such strategies are effective in diversifying a search from its current local minimum, they do not actively prevent the search from visiting previously encountered local minima. In this paper, we propose a new preventative strategy to effectively minimise search stagnation using pseudo-conflict learning. We define a pseudo-conflict as a derived path from the search trajectory that leads to a local minimum. We then introduce a new variable selection scheme that penalises variables causing those pseudo-conflicts. Our experimental results show that the new preventative approach significantly improves the performance of local search solvers on a wide range of structured and random benchmarks.

To gain a better understanding of how proteins function a process known as protein structure prediction (PSP) is carried out. However, experimental PSP methods, such as X-ray crystallography and Nuclear Magnetic Resonance (NMR), can be time-consuming and inaccurate. This has given rise to numerous computational PSP approaches to try and elicit a protein's three-dimensional conformation. A popular PSP search strategy is Genetic Algorithms (GA). GAs allow for a generic search approach, which can provide a generic improvement to alleviate the need to redefine the search strategies for separate sequences. Though GA's working principles are remarkable, a serious problem that is inherent in the GA search process is the growth of twins or identical chromosomes. Therefore, enhanced twin removal strategies are crucial for any GA search solving hard-optimisation problems like PSP. In this paper we explain our high-resolution GA feature-based resampling PSP approach and propose a twin removal strategy to further enhance its prediction accuracy. This includes investigating the optimal chromosome correlation factor (CCF) for our approach and defining a pre-built structure library for twin removal. We have also compared our GA approach with the popular Monte Carlo (MC) method for PSP. Our results indicate that out of all the CCF values we tested a CCF value of 0.8 provided the best level of diversity within our GA population. It also generated, on average, more native-like structures than any of the other CCF values, and clearly demonstrated that twin removal is needed in PSP when using GAs to obtain more accurate results.

The Minimum Vertex Cover (MVC) problem is a well-known combinatorial optimization problem of great importance in theory and applications. In recent years, local search has been shown to be an effective and promising approach to solve hard problems, such as MVC. In this paper, we introduce two new local search algorithms for MVC, called EWLS (Edge Weighting Local Search) and EWCC (Edge Weighting Configuration Checking). The first algorithm EWLS is an iterated local search algorithm that works with a partial vertex cover, and utilizes an edge weighting scheme which updates edge weights when getting stuck in local optima. Nevertheless, EWLS has an instance-dependent parameter. Further, we propose a strategy called Configuration Checking for handling the cycling problem in local search. This is used in designing a more efficient algorithm that has no instance-dependent parameters, which is referred to as EWCC. Unlike previous vertex-based heuristics, the configuration checking strategy considers the induced subgraph configurations when selecting a vertex to add into the current candidate solution. A detailed experimental study is carried out using the well-known DIMACS and BHOSLIB benchmarks. The experimental results conclude that EWLS and EWCC are largely competitive on DIMACS benchmarks, where they outperform other current best heuristic algorithms on most hard instances, and dominate on the hard random BHOSLIB benchmarks. Moreover, EWCC makes a significant improvement over EWLS, while both EWLS and EWCC set a new record on a twenty-year challenge instance. Further, EWCC performs quite well even on structured instances in comparison to the best exact algorithm we know. We also study the run-time behavior of EWLS and EWCC which shows interesting properties of both algorithms.

Radio Frequency Identification (RFID) technology allows wireless interaction between tagged objects and readers to automatically identify large groups of items. This technology is widely accepted in a number of application domains, however, it suffers from data anomalies such as false-positive obse rvations. Existing methods, such as manual tools, user specified rules and filtering algorithms, lack the automation and intelligence to effectively remove ambiguous false-positive readings. In this paper, we propose a methodology which incorporates a highly intelligent feature set definition utilised in conjunction with various state-of-the-art classifying techniques to correctly determine if a reading flagged as a potential false-positive anomaly should be discarded. Through experimental study we have shown that our approach cleans highly ambiguous false-positive observational data effectively. We have also discovered that the Non-Monotonic Reasoning classifier obtained the highest cleaning rate when handling false-positive RFID readings.

This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.

Proteins carry out the majority of functionality on a cellular level. Computational protein structure prediction (PSP) methods have been introduced to speed up the PSP process due to manual methods, like nuclear magnetic resonance (NMR) and x-ray crystallography (XC) taking numerous months even years to produce a predicted structure for a target protein. A lot of work in this area is focused on the type of search strategy to employ. Two popular methods in the literature are: Monte Carlo based algorithms and Genetic Algorithms. Genetic Algorithms (GA) have proven to be quite useful in the PSP field, as they allow for a generic search approach, which alleviates the need to redefine the search strategies for separate sequences. They also lend themselves well to feature-based resampling techniques. Feature-based resampling works by taking previously computed local minima and combining features from them to create new structures that are more uniformly low in free energy. In this work we present a feature-based resampling genetic algorithm to refine structures that are outputted by PSP software. Our results indicate that our approach performs well, and produced an average 9.5% root mean square deviation (RMSD) improvement and a 17.36% template modeling score (TM-Score) improvement.

In this paper, we present a trust establishment and management framework for hierarchical wireless sensor networks. The wireless sensor network architecture we consider consists of a collection of sensor nodes, cluster heads and a base station arranged hierarchically. The framework encompasses schemes for establishing and managing trust between these different entities. We demonstrate that the proposed framework helps to minimize the memory, computation and communication overheads involved in trust management in wireless sensor networks. Our framework takes into account direct and indirect (group) trust in trust evaluation as well as the energy associated with sensor nodes in service selection. It also considers the dynamic aspect of trust by introducing a trust varying function which could be adjusted to give greater weight to the most recently obtained trust values in the trust calculation. The architecture also has the ability to deal with the inter-cluster movement of sensor nodes using a combination of certificate based trust and behaviour based trust.

Security and trust are fundamental challenges when it comes to the deployment of large wireless sensor networks. In this paper, we propose a novel hierarchical trust management scheme that minimizes communication and storage overheads. Our scheme takes into account direct and indirect (group) trust in trust evaluation as well as the energy associated with sensor nodes in service selection. It also considers the dynamic aspect of trust by introducing a trust varying function which could give greater weight to the most recently obtained trust values in the trust calculation. The proposed framework can be extended to such dynamic mobile inter-cluster wireless sensor network environments.

The inherent freedom in self-organized mobile ad-hoc networks (MANETs) introduces challenges for trust management; particularly when nodes do not have any prior knowledge of each other. Furthermore in MANETs, the nodes themselves should be responsible for their own security. We propose a novel approach for trust management in MANETs that is based on the nodes' own responsibility of building their trust level and node-level trust monitoring. The main contribution of this work is in the introduction of a Node based Trust Management (NTM) scheme in MANET based on the assumption that individual nodes are themselves responsible for their own trust level. We explore and develop the mathematical framework of trust in NTM. Finally, in this context, we demonstrate our scheme with notations, algorithms, analytical model and prove of its correctness.

The current search engine model considers users not trustworthy, so no tools are provided to let them specify what they are looking for or in what context, which severely limits what they are able to achieve. Instead, search engines try to guess that, which is currently done using "implicit feedback''. In this paper we propose a "web exploration engine'' - a model where users can use the search engine as their tool and explicitly specify the context of their search. Information about the web has been pre-classified in a large number of categories; users can explore this hierarchy by providing relevance feedback or search within a particular category. Search is truly ``local'' in the sense that keyword relevance is not global, but specific to the category. In contrast to using a search engine, users can guide the exploration engine with relevance feedback alone without entering keywords.

In this paper, we investigate knowledge reasoning within a simple framework called knowledge structure. We use variable forgetting as a basic operation for one agent to reason about its own or other agents\' knowledge. In our framework, two notions namely agents\' observable variables and the weakest sufficient condition play important roles in knowledge reasoning. Given a background knowledge base and a set of observable variables for each agent, we show that the notion of an agent knowing a formula can be defined as a weakest sufficient condition of the formula under background knowledge base. Moreover, we show how to capture the notion of common knowledge by using a generalized notion of weakest sufficient condition. Also, we show that public announcement operator can be conveniently dealt with via our notion of knowledge structure. Further, we explore the computational complexity of the problem whether an epistemic formula is realized in a knowledge structure. In the general case, this problem is PSPACE-hard; however, for some interesting subcases, it can be reduced to co-NP. Finally, we discuss possible applications of our framework in some interesting domains such as the automated analysis of the well-known muddy children puzzle and the verification of the revised Needham-Schroeder protocol. We believe that there are many scenarios where the natural presentation of the available information about knowledge is under the form of a knowledge structure. What makes it valuable compared with the corresponding multi-agent S5 Kripke structure is that it can be much more succinct.

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.

In most of the successful real protein structure prediction (PSP) problem, lattice models have been essentially utilized to have the folding backbone sampling at the top of the hierarchical approach. A three dimensional face-centred-cube (FCC), with the provision for providing the most compact core, can map closest to the folded protein in reality. Hence, our successful hybrid genetic algorithms (HGA) proposed earlier for a square and cube lattice model is being extended in this paper for a 3D FCC model. Furthermore, twins (conformations having similarity with each other), in GA population have also been considered for removal from the search space for improving the effectiveness of GA The HGA combined with the twin removal (TR) strategy showed best performance when compared with the simple GA (SGA), SGA with TR, and HGA only versions. Experiments were carried out on the publicly available benchmark HP sequences and results are expressed based on the fitness of the corresponding applied lattice model, which will help any future novel approach to be compared.

Model checking is a promising approach to automatic verification, which has concentrated on specification expressed in temporal logics. Comparatively little attention has been given to temporal logics of knowledge, although such logics have been proven to be very useful in the specifications of protocols for distributed systems. In this paper, we addressed the model checking problem for a temporal logic of knowledge (Halpern and Vardi's logic of CKLn). Based on the semantics of interpreted systems with local propositions, we developed an approach to symbolic CKLn model checking via Ordered Binary decision diagrams and implemented the corresponding symbolic model checker MCTK. In our approach to model checking specifications involving agents' knowledge, the knowledge modalities are eliminated via quantifiers over agents' non-observable variables. We then modelled the Dining Cryptographers protocol and the five-hands protocol for Russian Cards problem in MCTK. Via these two examples, we compare MCTK's empirical performance with two different state-of-the-art epistemic model checkers, MCK and MCMAS.

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.

Most existing formalizations treat belief change as a single‐step process, and ignore several problems that become important when a theory, or belief state, is revised over several steps. This paper identifies these problems, and argues for the need to retain all of the multiple possible outcomes of a belief change step, and for a framework in which the effects of a belief change step persist as long as is consistently possible. To demonstrate that such a formalization is indeed possible, we develop a framework, which uses the language of PJ‐default logic (Delgrande and Jackson 1991) to represent a belief state, and which enables the effects of a belief change step to persist by propagating belief constraints. Belief change in this framework maps one belief state to another, where each belief state is a collection of theories given by the set of extensions of the PJ‐default theory representing that belief state. Belief constraints do not need to be separately recorded; they are encoded as clearly identifiable components of a PJ‐default theory. The framework meets the requirements for iterated belief change that we identify and satisfies most of the AGM postulates (Alchourrón, Gärdenfors, and Makinson 1985) as well.

Local search techniques have attracted considerable interest in the artificial intelligence community since the development of GSAT and the min-conflicts heuristic for solving propositional satisfiability (SAT) problems and binary constraint satisfaction problems (CSPs) respectively. Newer techniques, such as the discrete Langrangian method (DLM), have significantly improved on GSAT and can also be applied to general constraint satisfaction and optimization. However, local search has yet to be successfully employed in solving temporal constraint satisfaction problems (TCSPs). This paper argues that current formalisms for representing TCSPs are inappropriate for a local search approach, and proposes an alternative CSP-based end-point ordering model for temporal reasoning. The paper looks at modelling and solving problems formulated using Allen's interval algebra (IA) and proposes a new constraint weighting algorithm derived from DLM. Using a set of randomly generated IA problems, it is shown that local search outperforms existing consistency-enforcing algorithms on those problems that the existing techniques find most difficult.

We introduce a new model, MPDN, for quantitative temporal reasoning with points and durations, that supposes an extension of the TCSP formalism and previous point-duration network models. The problem of deciding consistency for a MPDN is shown to be NP-complete. So, we identify a tractable fragment, named simple MPDN, that subsumes the STP model and allows for duration reasoning. Necessary and sufficient conditions for deciding consistency of a simple MPDN are used to design an algorithm for consistency checking, whose time complexity is cubic in the number of variables. This is a significant improvement, not only in computational complexity but also in simplicity, over previous non-specific algorithms that can be applied to solve the consistency problem.

In bitemporal databases, current facts and transaction states are modeled using a special value to represent the current time (such as a minimum or maximum timestamp or NULL). Previous studies indicate that the choice of value for now (i.e. the current time) significantly influences the efficiency of accessing bitemporal data. This paper introduces a new approach to represent now, in which current tuples and facts are represented as points on the transaction time and valid time line respectively. This allows us to exploit the computational advantages of point-based query languages. Via an empirical study, we demonstrate that our new approach to representing now offers considerable performance benefits over existing techniques for accessing bitemporal data.

Many extensions to existing binary constraint satisfaction algorithms have been proposed that directly deal with nonbinary constraints. Another choice is to perform a structural transformation of the representation of the problem, so that the resulting problem is a binary CSP except that now the original constraints which were nonbinary are replaced by binary compatibility constraints between relations. A lot of recent work has focussed on comparing different levels of local consistency enforceable in the nonbinary representation with the dual representation. In this paper we present extensions to the standard dual encoding that can compactly represent the given CSP using an equivalent dual encoding that contains all the original solutions to the CSP, using constraint coverings. We show how enforcing arc consistency in these constraint covering based encodings, strictly dominates enforcement of generalized arc consistency (GAC) on the primal nonbinary encoding.

Local search techniques have attracted considerable interest in the artificial intelligence (AI) community since the development of GSAT (Selman et al., 1992) and the min-conflicts heuristic (Minton et al., 1992) for solving large propositional satisfiability (SAT) problems and binary constraint satisfaction problems (CSPs) respectively. Newer SAT techniques, such as the Discrete Langrangian Method (DLM) (Shang and Wah, 1998), have significantly improved on GSAT and can also be applied to general constraint satisfaction and optimisation. However, local search has yet to be successfully employed in solving temporal constraint satisfaction problems (TCSPs). We argue that current formalisms for representing TCSPs are inappropriate for a local search approach, and we propose an alternative CSP-based end-point ordering model for temporal reasoning. In particular we look at modelling and solving problems formulated using Allen's (1983) interval algebra (IA) and propose a new constraint weighting algorithm derived from DLM. Using a set of randomly generated IA problems, we show that our local search outperforms Nebel's (1997) backtracking algorithm on larger and more difficult consistent problems.

This paper proposes a transparent selective sequential consistency approach to distributed shared memory (DSM) systems. First, three basic techniques-time selection, processor selection, and data selection-are analyzed for improving the performance of strictly sequential consistency DSM systems, and a transparent approach to achieving these selections is proposed. Then, this paper focuses on the protocols and techniques devised to achieve transparent data selection, including a novel selective lazy/eager updates propagation protocol for propagating updates on shared data objects, and the critical region updated pages set scheme to automatically detect the associations between shared data objects and synchronization objects. The proposed approach is able to offer the same potential performance advantages as the entry consistency model or the scope consistency model, but it imposes no extra burden to programmers and never fails to execute programs correctly. The devised protocols and techniques have been implemented and experimented with in the context of the TreadMarks DSM system. Performance results have shown that for many applications, our transparent data selection approach outperforms the lazy release consistency model using a lazy or eager updates propagation protocol.

Texture image segmentation plays an important role in texture analysis. This paper presents an approach to image segmentation by texture classification based on fractional discrimination functions. The idea behind this method is to enhance the texture edge points by means of image decomposition and contextual filtering in terms of the proposed fractional function. In addition, the function is described in a unified form with three-parameters. The parameters determine the global scale in conjunction with local scales for feature identification. Our experimental results show that texture features can be effectively extracted on the basis of the selective fractional discrimination function.

An incremental compilation approach to meta-reasoning is presented together with a method to update dynamically changing knowledge bases. The compilation process translates meta-level specification of facts and hypotheses into sentences of clausal logic. It then incrementally computes inconsistent sets of instances of hypotheses and records potential crucial literals. The extra information computed during compilation enables the theorem prover to avoid redundant computations and to efficiently update the compiled knowledge. Whenever a new fact is learned the effects of the fact are computed incrementally, without recompiling. A relationship between potential crucial literals and Reiter and de Kleer's prime implicants shows that this approach may be useful in incrementally computing and maintaining the prime implicants, as well.>

When Horn clause theories are combined with integrity constraints to produce potentially refutable theories, Seki and Takeuchi have shown how crucial literals can be used to discriminate two mutually incompatible theories. A literal is crucial with respect to two theories if only one of the two theories supports the derivation of that literal. In other words, actually determining the truth value of the crucial literal will refute one of the two incompatible theories. This paper presents an integration of the idea of crucial literal with Theorist, a logic‐based system for hypothetical reasoning. Theorist is a goal‐directed nonmonotonic reasoning system that classifies logical formulas as possible hypotheses, facts, and observations. As Theorist uses full clausal logic, it does not require Seki and Takeuchi's notion of integrity constraint to define refutable theories. In attempting to deduce observation sentences, Theorist identifies instances of possible hypotheses as nomological explanations: consistent sets of hypothesis instances required to deduce observations. As multiple and mutually incompatible explanations are possible, the notion of crucial literal provides the basis for proposing experiments that distinguish competing explanations. We attempt to make three contributions. First, we adapt Seki and Takeuchi's method for Theorist. To do so, we incrementally use crucial literals as experiments, whose results are used to reduce the total number of explanations generated for a given set of observations. Next, we specify an extension which incrementally constructs a table of all possible crucial literals for any pair of theories. This extension is more efficient and provides the user with greater opportunity to conduct experiments to eliminate falsifiable theories. A prototype is implemented in CProlog, and several examples of diagnosis are considered to show its empirical efficiency. Finally, we point out that assumption‐based truth maintenance systems (ATMS), as used in the multiple fault diagnosis system of de Kleer and Williams, are interesting special cases of this more general method of distinguishing explanatory theories.