Predicting protein-protein interactions as a one-class classification problem

Protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been used to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. While it is easy to get a dataset of interacting protein as positive example, there is no experimentally confirmed non-interacting protein to be considered as a negative set. Therefore, in this paper we solve this problem as a one-class classification problem using One-Class SVM (OCSVM). Using only positive examples (interacting protein pairs) for training, the OCSVM achieves accuracy of 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with reliable accuracy

Protein sequences classification based on weighting scheme

We present a new technique to recognize remote protein homologies that rely on combining probabilistic modeling and supervised learning in high-dimensional feature spaces. The main novelty of our technique is the method of constructing feature vectors using Hidden Markov Model and the combination of this representation with a classifier capable of learning in very sparse high-dimensional spaces. Each feature vector records the sensitivity of each protein domain to a previously learned set of sub-sequences (strings). Unlike other previous methods, our method takes in consideration the conserved and non-conserved regions. The system subsequently utilizes Support Vector Machines (SVM) classifiers to learn the boundaries between structural protein classes. Experiments show that this method, which we call the String Weighting Scheme-SVM (SWS-SVM) method, significantly improves on previous methods for the classification of protein domains based on remote homologies. Our method is then compared to five existing homology detection methods

A component-oriented programming framework for developing embedded mobile robot software using PECOS model

A practical framework for component-based software engineering of embedded real-time systems, particularly for autonomous mobile robot embedded software development using PECOS component model is proposed The main features of this framework are: (1) use graphical representation for components definition and composition; (2) target C language for optimal code generation with small micro-controller; and (3) does not requires run-time support except for real-time kernel. Real-time implementation indicates that, the PECOS component model together with the proposed framework is suitable for resource constrained embedded systems

The importance of data classification using machine learning methods in microarray data

The detection of genetic mutations has attracted global attention. several methods have proposed to detect diseases such as cancers and tumours. One of them is microarrays, which is a type of representation for gene expression that is helpful in diagnosis. To unleash the full potential of microarrays, machine-learning algorithms and gene selection methods can be implemented to facilitate processing on microarrays and to overcome other potential challenges. One of these challenges involves high dimensional data that are redundant, irrelevant, and noisy. To alleviate this problem, this representation should be simplified. For example, the feature selection process can be implemented by reducing the number of features adopted in clustering and classification. A subset of genes can be selected from a pool of gene expression data recorded on DNA micro-arrays. This paper reviews existing classification techniques and gene selection methods. The effectiveness of emerging techniques, such as the swarm intelligence technique in feature selection and classification in microarrays, are reported as well. These emerging techniques can be used in detecting cancer. The swarm intelligence technique can be combined with other statistical methods for attaining better results

Recognition decision-making model using temporal data mining technique

An accurate and timely decision is crucial in any emergency situation. This paper presents a recognition decision making model that adopts the temporal data mining approach in making decisions. Reservoir water level and rainfall measurement were used as the case study to test the developed computational recognition-primed decision (RPD) model in predicting the amount of water to be dispatched represented by the number of spillway gates. Experimental results indicated that new events can be predicted from historical events. Patterns were extracted and can be transformed into readable and descriptive rule based form

A combination of PSO and local search in university course timetabling problem

The university course timetabling problem is a combinatorial optimization problem concerning the scheduling of a number of subjects into a finite number of timeslots in order to satisfy a set of specified constraints. The timetable problem can be very hard to solve, especially when attempting to find a near-optimal solutions, with a large number of instances. This paper presents a combination of particle swarm optimization and local search to effectively search the solution space in solving university course timetabling problem. Three different types of dataset range from small to large are used in validating the algorithm. The experiment results show that the combination of particle swarm optimization and local search is capable to produce feasible timetable with less computational time, comparable to other established algorithms

Non-Reshuffle-Based Approach for Rescheduling of Flexible Manufacturing System

Scheduling and rescheduling play vital roles in ensuring the effectiveness of the production control in flexible manufacturing system (FMS).  The failure of these systems may interrupt the efficiency of the production activities and thus may lessen the profit to be gained by the company. The FMS scheduling problem is considered as dynamic as new orders may get in every day. The new orders need to be immediately desegregated with the existing production schedule by preserving the efficiency and stability of the existing schedule. This research applies the non-reshuffle-based genetic match-up algorithms which admit new orders by manipulating available machine idle times to address rescheduling problem in a FMS that practises the pull strategy. The idea of the match-up approach is to update only a part of the initial schedule and genetic algorithms used to optimise the solution within the rescheduling horizon in such a way in order to preserve the efficiency and stability of the shop floor. The proposed methodology has been tested using different rescheduling parameters. The experiments show that the rescheduling method improves efficiency and stability of the new schedule