Approximation Algorithms for Reconstructing the Duplication History of Tandem Repeats

Computing the duplication history of a tandem repeated region is an important problem in computational biology (Fitch in Genetics 86:623–644, 1977; Jaitly et al. in J. Comput. Syst. Sci. 65:494–507, 2002; Tang et al. in J. Comput. Biol. 9:429–446, 2002). In this paper, we design a polynomial-time approximation scheme (PTAS) for the case where the size of the duplication block is 1. Our PTAS is faster than the previously best PTAS in Jaitly et al. (J. Comput. Syst. Sci. 65:494–507, 2002). For example, to achieve a ratio of 1.5, our PTAS takes O(n ⁵) time while the PTAS in Jaitly et al. (J. Comput. Syst. Sci. 65:494–507, 2002) takes O(n ¹¹) time. We also design a ratio-6 polynomial-time approximation algorithm for the case where the size of each duplication block is at most 2. This is the first polynomial-time approximation algorithm with a guaranteed ratio for this case. Part of work was done during a Z.-Z. Chen visit at City University of Hong Kong.     

On Total Variation Minimization and Surface Evolution Using Parametric Maximum Flows

In a recent paper Boykov et al. (LNCS, Vol. 3953, pp. 409–422, 2006) propose an approach for computing curve and surface evolution using a variational approach and the geo-cuts method of Boykov and Kolmogorov (International conference on computer vision, pp. 26–33, 2003). We recall in this paper how this is related to well-known approaches for mean curvature motion, introduced by Almgren et al. (SIAM Journal on Control and Optimization 31(2):387–438, 1993) and Luckhaus and Sturzenhecker (Calculus of Variations and Partial Differential Equations 3(2):253–271, 1995), and show how the corresponding problems can be solved with sub-pixel accuracy using Parametric Maximum Flow techniques. This provides interesting algorithms for computing crystalline curvature motion, possibly with a forcing term. A. Chambolle’s research supported by ANR project “MICA”, grant ANR-08-BLAN-0082. J. Darbon’s research supported by ONR grant N000140710810.     

Model Checking Weighted Integer Reset Timed Automata

Weighted timed automata (WTA), introduced in Alur et al. (Proceedings of HSCC’01, LNCS, vol. 2034, pp. 49–62, Springer, Berlin, 2001), Behrmann et al. (Proceedings of HSCC’01, LNCS, vol. 2034, pp. 147–161, Springer, Berlin, 2001) are an extension of Alur and Dill (Theor. Comput. Sci. 126(2):183–235, 1994) timed automata, a widely accepted formalism for the modelling and verification of real time systems. Weighted timed automata extend timed automata by allowing costs on the locations and edges. There has been a lot of interest Bouyer et al. (Inf. Process. Lett. 98(5):188–194, 2006), Bouyer et al. (Log. Methods Comput. Sci. 4(2):9, 2008), Brihaye et al. (Proceedings of FORMATS/FTRTFT’04, LNCS, vol. 3253, pp. 277–292, Springer, Berlin, 2004), Brihaye et al. (Inf. Comput. 204(3):408–433, 2006) in studying the model checking problem of weighted timed automata. The properties of interest are written using logic weighted CTL (WCTL), an extension of CTL with costs. It has been shown Bouyer et al. (Log. Methods Comput. Sci. 4(2):9, 2008) that the problem of model checking WTAs with a single clock using WCTL with no external cost variables is decidable, while 3 clocks render the problem undecidable Bouyer et al. (Inf. Process. Lett. 98(5):188–194, 2006). The question of 2 clocks is open. In this paper, we introduce a subclass of weighted timed automata called weighted integer reset timed automata (WIRTA) and study the model checking problem. We give a clock reduction technique for WIRTA. Given a WIRTA A\mathcal{A} with n≥1 clocks, we show that a single clock WIRTA A￠\mathcal{A}' preserving the paths and costs of A\mathcal{A} can be obtained. This gives us the decidability of model checking WIRTA with n≥1 clocks and m≥1 costs using WCTL with no external cost variables. We then show that for a restricted version of WCTL with external cost variables, the model checking problem is undecidable for WIRTA with 3 stopwatch costs and 1 clock. Finally, we show that model checking WTA with 2 clocks and 1 stopwatch cost against WCTL with no external cost variables is undecidable, thereby answering a question that has remained long open.     

Efficient RNTS system for privacy of banking off-line customer

With the development in IT technology and with growing demands of users, a ubiquitous environment is being made. Because individual identification is important in ubiquitous environment, RFID technology would be used frequently. RFID is a radio frequency identification technology to replace bar code. The reader transmits query (request of user information) and tag-provides user information. RFID has various advantages, such as high speed identification rates, mass memory storages. However, eavesdropping is possible as well as a problem that user information is exposed (Juels et al. in Conference on Computer and Communications Security—ACM CCS, pp. 103–111, 2003; Ohkubo et al. in RFID Privacy Workshop 2003; Weis et al. in International Conference on Security in Pervasive Computing, pp. 201–212, 2003; Weis et al. in Cryptographic Hardware and Embedded Systems—CHES, pp. 454–469, 2002). Therefore, when off-line customer had visited bank for banking service, RNTS (RFID number ticket service) system provides both anonymity in customer identification and efficiency of banking service. In addition, RNTS system protects privacy of an off-line user visiting the bank and it is an efficient method offering service in order of arriving in the bank.     

An improved data hiding approach for polygon meshes

We present an improved technique for data hiding in polygonal meshes, which is based on the work of Bogomjakov et al. (Comput. Graph. Forum 27(2):637–642, 2008). Like their method, we use an arrangement on primitives relative to a reference ordering to embed a message. But instead of directly interpreting the index of a primitive in the reference ordering as the encoded/decoded bits, our method slightly modifies the mapping so that our modification doubles the chance of encoding an additional bit compared to Bogomjakov et al.’s (Comput. Graph. Forum 27(2):637–642, 2008). We illustrate the inefficiency in the original mapping of Bogomjakov et al. (Comput. Graph. Forum 27(2):637–642, 2008) with an intuitive representation using a binary tree.     

Characteristic-Based Schemes for Multi-Class Lighthill-Whitham-Richards Traffic Models

In this paper we provide the full spectral decomposition of the Multi-Class Lighthill Whitham Richards (MCLWR) traffic models described in (Wong et al. in Transp. Res. Part A 36:827–841, 2002; Benzoni-Gavage and Colombo in Eur. J. Appl. Math. 14:587–612, 2003). Even though the eigenvalues of these models can only be found numerically, the knowledge of the spectral structure allows the use of characteristic-based High Resolution Shock Capturing (HRSC) schemes. We compare the characteristic-based approach to the component-wise schemes used in (Zhang et al. in J. Comput. Phys. 191:639–659, 2003), and propose two strategies to minimize the oscillatory behavior that can be observed when using the component-wise approach.     

A Unified Primal-Dual Algorithm Framework Based on Bregman Iteration

In this paper, we propose a unified primal-dual algorithm framework for two classes of problems that arise from various signal and image processing applications. We also show the connections to existing methods, in particular Bregman iteration (Osher et al., Multiscale Model. Simul. 4(2):460–489, 2005) based methods, such as linearized Bregman (Osher et al., Commun. Math. Sci. 8(1):93–111, 2010; Cai et al., SIAM J. Imag. Sci. 2(1):226–252, 2009, CAM Report 09-28, UCLA, March 2009; Yin, CAAM Report, Rice University, 2009) and split Bregman (Goldstein and Osher, SIAM J. Imag. Sci., 2, 2009). The convergence of the general algorithm framework is proved under mild assumptions. The applications to ℓ ¹ basis pursuit, TV−L ² minimization and matrix completion are demonstrated. Finally, the numerical examples show the algorithms proposed are easy to implement, efficient, stable and flexible enough to cover a wide variety of applications.     

On body shapes providing maximum depth of penetration

The problem of maximization of the depth of penetration of rigid impactor into semi-infinite solid media (concrete shield) is investigated analytically and numerically using two-stage model and experimental data of Forrestal and Tzou (Int J Solids Struct 34(31–32):4127–4146, 1997). The shape of the axisymmetric rigid impactor has been taken as an unknown design variable. To solve the formulated optimization problem for nonadditive functional, we expressed the depth of penetration (DOP) under some isoperimetric constraints. We apply approaches based on analytical and qualitative variational methods and numerical optimization algorithm of global search. Basic attention for considered optimization problem was given to constraints on the mass of penetrated bodies, expressed by the volume in the case of penetrated solid body and by the surface area in the case of penetrated thin-walled rigid shell. As a result of performed investigation, based on two-term and three-term two stage models proposed by Forrestal et al. (Int J Impact Eng 15(4):396–405, 1994), Forrestal and Tzou (Int J Solids Struct 34(31–32):4127–4146, 1997) and effectively developed by Ben-Dor et al. (Comp Struct 56:243–248, 2002, Comput Struct 81(1):9–14, 2003a, Int J Solids Struct 40(17):4487–4500, 2003b, Mech Des Struct Mach 34(2): 139–156, 2006), we found analytical and numerical solutions and analyzed singularities of optimal forms.     

On the air damping of flexible microbeam in free space at the free-molecule regime

Predicting air damping is crucial in the design of high Q microelectromechanical systems. In the past, air damping of rigid microbeam in free space at molecular regime is usually estimated using the free molecular model proposed by Christian (Vacuum 16:175–178, 1966), air damping of flexible microbeam is estimated using the model proposed by Blom (J Vac Sci Technol B 10:19–26, 1992). The relation between the two models is Q _Blom = 3Q _Christian. In this paper, a general proof is presented that shows the Christian’s model is valid for the air damping of flexible microbeam in free space at molecular regime. By comparing with the experimental results available in the literatures (Blom et al. in J Vac Sci Technol B 10:19–26, 1992; Yasumura et al. in J Micromech Syst 9:117–125, 2000), we conclude that the Christian’s model is the best choice in predicting the air damping of flexible microbeam in free space at the molecular regime.     

A posteriori error analysis of time-dependent Stokes problem by Chorin-Temam scheme

We present a posteriori-residual analysis for the approximate time-dependent Stokes model Chorin-Temam projection scheme (Chorin in Math. Comput. 23:341–353, 1969; Temam in Arch. Ration. Mech. Appl. 33:377–385, 1969). Based on the multi-step approach introduced in Bergam et al. (Math. Comput. 74(251):1117–1138, 2004), we derive error estimators, with respect to both time and space approximations, related to diffusive and incompressible parts of Stokes equations. Using a conforming finite element discretization, we prove the equivalence between error and estimators under specific conditions.     

A face emotion tree structure representation with probabilistic recursive neural network modeling

This paper describes a novel structural approach to recognize the human facial features for emotion recognition. Conventionally, features extracted from facial images are represented by relatively poor representations, such as arrays or sequences, with a static data structure. In this study, we propose to extract facial expression features vectors as Localized Gabor Features (LGF) and then transform these feature vectors into FacE Emotion Tree Structures (FEETS) representation. It is an extension of the Human Face Tree Structures (HFTS) representation presented in (Cho and Wong in Lecture notes in computer science, pp 1245–1254, 2005). This facial representation is able to simulate as human perceiving the real human face and both the entities and relationship could contribute to the facial expression features. Moreover, a new structural connectionist architecture based on a probabilistic approach to adaptive processing of data structures is presented. The so-called probabilistic based recursive neural network (PRNN) model extended from Frasconi et al. (IEEE Trans Neural Netw 9:768–785, 1998) is developed to train and recognize human emotions by generalizing the FEETS representation. For empirical studies, we benchmarked our emotion recognition approach against other well known classifiers. Using the public domain databases, such as Japanese Female Facial Expression (JAFFE) (Lyons et al. in IEEE Trans Pattern Anal Mach Intell 21(12):1357–1362, 1999; Lyons et al. in third IEEE international conference on automatic face and gesture recognition, 1998) database and Cohn–Kanade AU-Coded Facial Expression (CMU) Database (Cohn et al. in 7th European conference on facial expression measurement and meaning, 1997), our proposed system might obtain an accuracy of about 85–95% for subject-dependent and subject-independent conditions. Moreover, by testing images having artifacts, the proposed model significantly supports the robust capability to perform facial emotion recognition.     

Improved Approximation Results for the Minimum Energy Broadcasting Problem

In this paper we present new results on the performance of the Minimum Spanning Tree heuristic for the Minimum Energy Broadcast Routing (MEBR) problem. We first prove that, for any number of dimensions d≥2, the approximation ratio of the heuristic does not increase when the power attenuation coefficient α, that is the exponent to which the coverage distance must be raised to give the emission power, grows. Moreover, we show that, for any fixed instance, as a limit for α going to infinity, the ratio tends to the lower bound of Clementi et al. (Proceedings of the 18th annual symposium on theoretical aspects of computer science (STACS), pp. 121–131, 2001), Wan et al. (Wirel. Netw. 8(6):607–617, 2002) given by the d-dimensional kissing number, thus closing the existing gap between the upper and the lower bound. We then introduce a new analysis allowing to establish a 7.45-approximation ratio for the 2-dimensional case, thus significantly decreasing the previously known 12 upper bound (Wan et al. in Wirel. Netw. 8(6):607–617, 2002) (actually corrected to 12.15 in Klasing et al. (Proceedings of the 3rd IFIP-TC6 international networking conference, pp. 866–877, 2004)). Finally, we extend our analysis to any number of dimensions d≥2 and any α≥d, obtaining a general approximation ratio of 3 ^d −1, again independent of α. The improvements of the approximation ratios are specifically significant in comparison with the lower bounds given by the kissing numbers, as these grow at least exponentially with respect to d. The research was partially funded by the European project COST Action 293, “Graphs and Algorithms in Communication Networks” (GRAAL). Preliminary version of this paper appeared in Flammini et al. (Proceedings of ACM joint workshop on foundations of mobile computing (DIALM-POMC), pp. 85–91, 2004).     

Hybrid Extensional Prototype Compositionality

It has been argued that prototypes cannot compose, and that for this reason concepts cannot be prototypes (Osherson and Smith in Cognition 9:35–58, 1981; Fodor and Lepore in Cognition 58:253–270, 1996; Connolly et al. in Cognition 103:1–22, 2007). In this paper I examine the intensional and extensional approaches to prototype compositionality, arguing that neither succeeds in their present formulations. I then propose a hybrid extensional theory of prototype compositionality, according to which the extension of a complex concept is determined as a function of what triggers its constituent prototypes. I argue that the theory escapes the problems traditionally raised against extensional theories of compositionality.     

Ontology-driven coordination model for multiagent-based mobile workforce brokering systems

Coordination has been recognized by many researchers as the most important feature of multi-agent systems. Coordination is defined as managing interdependencies amongst activities (Malone and Crowston in ACM Comput. Surv. 26(1):87–119, 1994). The traditional approach of implementing a coordination mechanism is to hard-wire it into a coordination system at design time. However, in dynamic and open environments, many attributes of the system cannot be accurately identified at the design time. Therefore, dynamic coordination, capable of coordinating activities at run-time, has emerged. On the other hand, a successful dynamic coordination model for multi-agent systems requires knowledge sharing as well as common vocabulary. Therefore, an ontological approach is an appropriate way in proposing dynamic coordination models for multi-agent systems. In this paper, an Ontology-Driven Dynamic Coordination Model (O-DC) for Multiagent-Based Mobile Workforce Brokering Systems (MWBS) (Mousavi et al. in Int. J. Comput. Sci. 6:(5):557–565, 2010; Mousavi et al. in Proceedings of 4th IEEE international symposium on information technology, ITSim’10, Kuala Lumpur, Malaysia, 15–17 June 2010, vol. 3, pp. 1416–1421, 2010; Mousavi and Nordin in Proceedings of the IEEE international conference on electrical engineering and informatics, Bandung, Indonesia, 17–19 June 2007, pp. 294–297, 2007) is proposed and formulated. Subsequently, the applicability of O-DC is examined via simulation based on a real-world scenario.     

Feature subset selection based on fuzzy entropy measures for handling classification problems

In this paper, we present a new method for dealing with feature subset selection based on fuzzy entropy measures for handling classification problems. First, we discretize numeric features to construct the membership function of each fuzzy set of a feature. Then, we select the feature subset based on the proposed fuzzy entropy measure focusing on boundary samples. The proposed method can select relevant features to get higher average classification accuracy rates than the ones selected by the MIFS method (Battiti, R. in IEEE Trans. Neural Netw. 5(4):537–550, 1994), the FQI method (De, R.K., et al. in Neural Netw. 12(10):1429–1455, 1999), the OFEI method, Dong-and-Kothari’s method (Dong, M., Kothari, R. in Pattern Recognit. Lett. 24(9):1215–1225, 2003) and the OFFSS method (Tsang, E.C.C., et al. in IEEE Trans. Fuzzy Syst. 11(2):202–213, 2003).

Linear Time Algorithms for Exact Distance Transform

In 2003, Maurer et al. (IEEE Trans. Pattern Anal. Mach. Intell. 25:265–270, 2003) published a paper describing an algorithm that computes the exact distance transform in linear time (with respect to image size) for the rectangular binary images in the k-dimensional space ℝ ^k and distance measured with respect to L _p -metric for 1≤p≤∞, which includes Euclidean distance L ₂. In this paper we discuss this algorithm from theoretical and practical points of view. On the practical side, we concentrate on its Euclidean distance version, discuss the possible ways of implementing it as signed distance transform, and experimentally compare implemented algorithms. We also describe the parallelization of these algorithms and discuss the computational time savings associated with them. All these implementations will be made available as a part of the CAVASS software system developed and maintained in our group (Grevera et al. in J. Digit. Imaging 20:101–118, 2007). On the theoretical side, we prove that our version of the signed distance transform algorithm, GBDT, returns the exact value of the distance from the geometrically defined object boundary. We provide a complete proof (which was not given of Maurer et al. (IEEE Trans. Pattern Anal. Mach. Intell. 25:265–270, 2003) that all these algorithms work correctly for L _p -metric with 1<p<∞. We also point out that the precise form of the algorithm from Maurer et al. (IEEE Trans. Pattern Anal. Mach. Intell. 25:265–270, 2003) is not well defined for L ₁ and L _∞ metrics. In addition, we show that the algorithm can be used to find, in linear time, the exact value of the diameter of an object, that is, the largest possible distance between any two of its elements.     

Observing the observer: non-intrusive verbalisations using the Concurrent Observer Narrative Technique

This paper presents the application of, and a discussion about, a new method of information acquisition, the Concurrent Observer Narrative Technique (CONT), that requires an expert to narrate the work of experienced colleagues. The method is explored through a case study of instructors in a training simulation environment. The method involves multiple expert users of the system equally matched in experience; one or more of which perform the task at hand, namely running the training session, whilst another, not engaged in the training activity, provides verbal reports whilst observing task progression. All are situated in the work environment concurrently. The method is discussed in terms of the richness and detail of the data obtained from the reports and in terms of some advantages and disadvantages over other verbal reporting methods, specifically collegial verbalisation (Jansson et al. in Cogn Tech Work 8:41–49, 2006) and Elicitation By Critiquing (Miller et al. in Cogn Tech Work 8: 90–102, 2006). It is argued that the CONT provides a relatively easy, inexpensive, and non-intrusive method that can supply a wealth of information that does not require further interpretation and that the method is of particular applicability in domains where the subject matter expert is unable to provide concurrent verbalisations themselves and where the subject matter is too complex to be understood by a lay person.     

Large area micro hot embossing of Pyrex glass with GC mold machined by dicing

Micro/Nano imprinting or hot embossing is currently a target of interest for industrial production of micro and Nano devices for the low cost aspect. In Fluidic MEMS (Micro Electromechanical Systems) applications, polymer materials have been widely employed for their low cost to fabricate the economical products (Becker and Heim in Sens Acuators A 83:120–135, 2000; Becker and Gaertner in Mol Biotechnol 82:89–99, 2001). However glasses are much more suitable for the higher temperature applications or under the stronger chemical environments. Moreover UV absorption of glass materials is much less than that of polymers, which is the advantage for bio-analysis. In Optical MEMS as well, glasses are good candidate materials for the better optical properties, such as high refractive index, low UV absorption and others. Although wet etching of glasses is widely employed for fabrication of fluidic MEMS devices, the wet etching is not satisfactory for the low machining resolution, the isotropic etched profile and poor roughness of the fabricated structures. Dry etching of glasses is then an alternative for Micro/Nano structuring, but the etching rate is extremely low (order of 0.1 μm/min) and the cost is too high because of the expensive RIE (Reactive Ion Etching) facility. Above mentioned is the reason why we are interested in hot embossing or imprinting of glasses of Micro/Nano scale. In our previous study, Micro/Nano imprinting was developed for Pyrex glasses using GC (Glassy Carbon) mold prepared by FIB machining (Takahashi et al. in Symposium on DTIP 2004 pp 441–446, 2004). The disadvantage of FIB machining is limited area of etching. The typical area of FIB is less than several hundreds micrometer square. This is the reason why we tried the large area of embossing using GC mold fabricated by dicing machine. Micro hot embossed test structures were successfully demonstrated with good fidelity. Fabricated micro structures can be applied for fabrication of microchamber array for PCR (Akagi et al. in Sci Techol Adv Mater 5:343–349, 2004; Nagai et al. in Anal Chem 73:1043–1047, 2001).     

On truthfulness and approximation for scheduling selfish tasks

We consider the problem of designing truthful mechanisms for scheduling n tasks on a set of m parallel related machines in order to minimize the makespan. In what follows, we consider that each task is owned by a selfish agent. This is a variant of the KP-model introduced by Koutsoupias and Papadimitriou (Proc. of STACS 1999, pp. 404–413, 1999) (and of the CKN-model of Christodoulou et al. in Proc. of ICALP 2004, pp. 345–357, 2004) in which the agents cannot choose the machine on which their tasks will be executed. This is done by a centralized authority, the scheduler. However, the agents may manipulate the scheduler by providing false information regarding the length of their tasks. We introduce the notion of increasing algorithm and a simple reduction that transforms any increasing algorithm into a truthful one. Furthermore, we show that some of the classical scheduling algorithms are indeed increasing: the LPT algorithm, the PTAS of Graham (SIAM J. Appl. Math. 17(2):416–429, 1969) in the case of two machines, as well as a simple PTAS for the case of m machines, with m a fixed constant. Our results yield a randomized r(1+ε)-approximation algorithm where r is the ratio between the largest and the smallest speed of the related machines. Furthermore, by combining our approach with the classical result of Shmoys et al. (SIAM J. Comput. 24(6):1313–1331, 1995), we obtain a randomized 2r(1+ε)-competitive algorithm. It has to be noticed that these results are obtained without payments, unlike most of the existing works in the field of Mechanism Design. Finally, we show that if payments are allowed then our approach gives a (1+ε)-algorithm for the off-line case with related machines.     

Walrasian Equilibrium: Hardness,Approximations and Tractable Instances

We study the complexity issues for Walrasian equilibrium in a special case of combinatorial auction, called single-minded auction, in which every participant is interested in only one subset of commodities. Chen et al. (J. Comput. Syst. Sci. 69(4): 675–687, 2004) showed that it is NP-hard to decide the existence of a Walrasian equilibrium for a single-minded auction and proposed a notion of approximate Walrasian equilibrium called relaxed Walrasian equilibrium. We show that every single-minded auction has a relaxed Walrasian equilibrium that satisfies at least two-thirds of the participants, proving a conjecture posed in Chen et al. (J. Comput. Syst. Sci. 69(4): 675–687, 2004). Motivated by practical considerations, we introduce another concept of approximate Walrasian equilibrium called weak Walrasian equilibrium. We show NP-completeness and hardness of approximation results for weak Walrasian equilibria. In search of positive results, we restrict our attention to the tollbooth problem (Guruswami et al. in Proceedings of the Symposium on Discrete Algorithms (SODA), pp. 1164–1173, 2005), where every participant is interested in a single path in some underlying graph. We give a polynomial time algorithm to determine the existence of a Walrasian equilibrium and compute one (if it exists), when the graph is a tree. However, the problem is still NP-hard for general graphs.