Probabilistic Approximations of Signaling Pathway Dynamics
Systems of ordinary differential equations (ODEs) are often used to model the dynamics of complex biological pathways. We construct a discrete state model as a probabilistic approximation of the ODE dynamics by discretizing the value space and the time domain. We then sample a representative set of trajectories and exploit the discretization and the structure of the signaling pathway to encode these trajectories compactly as a dynamic Bayesian network. As a result, many interesting pathway properties can be analyzed efficiently through standard Bayesian inference techniques. We have tested our method on a model of EGF-NGF signaling pathway [1] and the results are very promising in terms of both accuracy and efficiency.

title: Opinion Mining
abstract: Описанл процедуру формування інтегрального показника об’єкта згідно з відгуками користувачів під час застосування методів оцінювання опінії текстової інформації у web-документах. Запропоновано використання лінгвістичних змінних та застосування вагових коефіцієнтів для достовірнішого результату оцінювання емоційного забарвлення текстової інформації. Ключові слова: опінія, емоційне забарвлення, об’єкт, інтегральний показник, лінгвістична змінна, ваговий коефіцієнт.

title: Finding Actionable Knowledge via Automated Comparison
abstract: The problem of finding interesting and actionable patterns is a major challenge in data mining. It has been studied by many data mining researchers. The issue is that data mining algorithms often generate too many patterns, which make it very hard for the user to find those truly useful ones. Over the years many techniques have been proposed. However, few have made it to real-life applications. At the end of 2005, we built a data mining system for Motorola (called Opportunity Map) to enable the user to explore the space of a large number of rules in order to find actionable knowledge. The approach is based on the concept of rule cubes and operations on rule cubes. A rule cube is similar to a data cube, but stores rules. Since its deployment, some issues have also been identified during the regular use of the system in Motorola. One of the key issues is that although the operations on rule cubes are flexible, each operation is primitive and has to be initiated by the user. Finding a piece of actionable knowledge typically involves many operations and intense visual inspections, which are labor-intensive and time-consuming. From interactions with our users, we identified a generic problem that is crucial for finding actionable knowledge. The problem involves extensive comparison of sub-populations and identification of the cause of their differences. This paper first defines the problem and then proposes an effective method to solve the problem automatically. To the best of our knowledge, there is no reported study of this problem. The new method has been added to the Opportunity Map system and is now in daily use in Motorola.

title: Entity discovery and assignment for opinion mining applications
abstract: Opinion mining became an important topic of study in recent years due to its wide range of applications. There are also many companies offering opinion mining services. One problem that has not been studied so far is the assignment of entities that have been talked about in each sentence. Let us use forum discussions about products as an example to make the problem concrete. In a typical discussion post, the author may give opinions on multiple products and also compare them. The issue is how to detect what products have been talked about in each sentence. If the sentence contains the product names, they need to be identified. We call this problem entity discovery. If the product names are not explicitly mentioned in the sentence but are implied due to the use of pronouns and language conventions, we need to infer the products. We call this problem entity assignment. These problems are important because without knowing what products each sentence talks about the opinion mined from the sentence is of little use. In this paper, we study these problems and propose two effective methods to solve the problems. Entity discovery is based on pattern discovery and entity assignment is based on mining of comparative sentences. Experimental results using a large number of forum posts demonstrate the effectiveness of the technique. Our system has also been successfully tested in a commercial setting.

title: Dealing with different distributions in learning from
abstract: In the problem of learning with positive and unlabeled examples, existing research all assumes that positive examples P and the hidden positive examples in the unlabeled set U are generated from the same distribution. This assumption may be violated in practice. In such cases, existing methods perform poorly. This paper proposes a novel technique A-EM to deal with the problem. Experimental results with product page classification demonstrate the effectiveness of the proposed technique.

title: Speed-up iterative frequent itemset mining with constraint changes
abstract: Mining of frequent itemsets is a fundamental data mining task. Past research has proposed many efficient algorithms for this purpose. Recent work also highlighted the importance of using constraints to focus the mining process to mine only those relevant itemsets. In practice, data mining is often an interactive and iterative process. The user typically changes constraints and runs the mining algorithm many times before being satisfied with the final results. This interactive process is very time consuming. Existing mining algorithms are unable to take advantage of this iterative process to use previous mining results to speed up the current mining process. This results in an enormous waste of time and computation. In this paper, we propose an efficient technique to utilize previous mining results to improve the efficiency of current mining when constraints are changed. We first introduce the concept of tree boundary to summarize useful information available from previous mining. We then show that the tree boundary provides an effective and efficient framework for the new mining. The proposed technique has been implemented in the context of two existing frequent itemset mining algorithms, FP-tree and tree projection. Experiment results on both synthetic and real-life datasets show that the proposed approach achieves a dramatic saving of computation.

title: An Effective PSO-Based Hybrid Algorithm for Multiobjective Permutation Flow Shop Scheduling
abstract: This paper proposes a hybrid algorithm based on particle swarm optimization (PSO) for a multiobjective permutation flow shop scheduling problem, which is a typical NP-hard combinatorial optimization problem with strong engineering backgrounds. Not only does the proposed multiobjective algorithm (named MOPSO) apply the parallel evolution mechanism of PSO characterized by individual improvement, population cooperation, and competition to effectively perform exploration but it also utilizes several adaptive local search methods to perform exploitation. First, to make PSO suitable for solving scheduling problems, a ranked-order value (ROV) rule based on a random key technique to convert the continuous position values of particles to job permutations is presented. Second, a multiobjective local search based on the Nawaz-Enscore-Ham heuristic is applied to good solutions with a specified probability to enhance the exploitation ability. Third, to enrich the searching behavior and to avoid premature convergence, a multiobjective local search based on simulated annealing with multiple different neighborhoods is designed, and an adaptive meta-Lamarckian learning strategy is employed to decide which neighborhood will be used. Due to the fusion of multiple different searching operations, good solutions approximating the real Pareto front can be obtained. In addition, MOPSO adopts a random weighted linear sum function to aggregate multiple objectives to a single one for solution evaluation and for guiding the evolution process in the multiobjective sense. Due to the randomness of weights, searching direction can be enriched, and solutions with good diversity can be obtained. Simulation results and comparisons based on a variety of instances demonstrate the effectiveness, efficiency, and robustness of the proposed hybrid algorithm.

title: A Scalable Peer-to-Peer Overlay for Applications with Time Constraints
abstract: With the development of Internet, p2p is increasingly receiving attention in research. Recently, a class of p2p applications with time constraints appear. These applications require a short time to locate the resource and(or) a low transit delay between the resource user and the resource holder, such as Skype, MSN. In this paper we propose a scalable p2p overlay for applications with time constraints. Our system provides supports for just two operations for uplayered p2p applications: (1) Given a resource key and the node's IP who holds the resource, it registers the resource information to the associated node in at most two overlay hops; and (2) Given a resource key and a time constraint(0 for no constraint), it returns if possible a path(one or two overlay hops) to the resource holder, and the transit delay of the path is lower than the time constraint. Results from theoretical analysis and simulations show that our system is viable and scalable.

title: Dynamic Complexities in a Lotka-volterra Predator-prey Model Concerning impulsive Control Strategy
abstract: Based on the classical Lotka–Volterra predator–prey system, an impulsive differential equation to model the process of periodically releasing natural enemies and spraying pesticides at different fixed times for pest control is proposed and investigated. It is proved that there exists a globally asymptotically stable pest-eradication periodic solution when the impulsive period is less than some critical value. Otherwise, the system can be permanent. We observe that our impulsive control strategy is more effective than the classical one if we take chemical control efficiently. Numerical results show that the system we considered has more complex dynamics including period-doubling bifurcation, symmetry-breaking bifurcation, period-halving bifurcation, quasi-periodic oscillation, chaos and nonunique dynamics, meaning that several attractors coexist. Finally, a pest–predator stage-structured model for the pest concerning this kind of impulsive control strategy is proposed, and we also show that there exists a ...

title: DE and NLP Based QPLS Algorithm
abstract: As a novel evolutionary computing technique, Differential Evolution (DE) has been considered to be an effective optimization method for complex optimization problems, and achieved many successful applications in engineering. In this paper, a new algorithm of Quadratic Partial Least Squares (QPLS) based on Nonlinear Programming (NLP) is presented. And DE is used to solve the NLP so as to calculate the optimal input weights and the parameters of inner relationship. The simulation results based on the soft measurement of diesel oil solidifying point on a real crude distillation unit demonstrate that the superiority of the proposed algorithm to linear PLS and QPLS which is based on Sequential Quadratic Programming (SQP) in terms of fitting accuracy and computational costs.

title: Entropy-based metrics in swarm clustering
abstract: Ant-based clustering methods have received significant attention as robust methods for clustering. Most ant-based algorithms use local density as a metric for determining the ants' propensities to pick up or deposit a data item; however, a number of authors in classical clustering methods have pointed out the advantages of entropy-based metrics for clustering. We introduced an entropy metric into an ant-based clustering algorithm and compared it with other closely related algorithms using local density. The results strongly support the value of entropy metrics, obtaining faster and more accurate results. Entropy governs the pickup and drop behaviors, while movement is guided by the density gradient. Entropy measures also require fewer training parameters than density-based clustering. The remaining parameters are subjected to robustness studies, and a detailed analysis is performed. 
 
In the second phase of the study, we further investigated Ramos and Abraham's ( Proc 2003   2003. pp 1370–1375) contention that ant-based methods are particularly suited to incremental clustering. Contrary to expectations, we did not find substantial differences between the efficiencies of incremental and nonincremental approaches to data clustering.