A Greedy Algorithm for Optimal Recombination
Let Σ be an alphabet and Σn denote the collection of all sequences of length n over Σ. For any s1 = ajaj+1 . . . an+s2 = b1b2 . . . bj bj+1 . . . bn ∈ Σn, a recombination of s1 and s2 at position j is defined as an operation that crosses s1 and s2 at position j and generates t1 = a1a2 . . .  . bn and t2 = b1b2 . . .  Denote A and S two collections of sequences. In this paper, we discuss generating A from S by a series of recombinations in minimum number of steps. We present a greedy algorithm for finding the optimal recombination evolutionary history from S to any tree A of sequences when |S| = 2.

title: Functional Divergence in TGF-b Signaling Pathway

title: A programming framework for quality-aware ubiquitous multimedia applications
abstract: Ubiquitous computing promises a computing environment that seamlessly and pervasively delivers applications to the user, despite changes of resources, devices, and locations. However, few ubiquitous multimedia applications (UMAs) exist up-to-date. One of the main reasons lies in the fact that it is difficult and error-prone to build a UMA which is mobile and deployable in different ubiquitous environments, and still provides acceptable application-specific Quality-of-Service (QoS) guarantees. In this paper, we present the design and implementation of a novel programming framework, called 'QCompiler" to address the challenges. The framework includes (1) a high-level application specification for the application developer to easily write a UMA with specific quality, mobility, and ubiquity supports, (2) a meta-data compilation, which provides automated consistency checks, translations, and substitutions, to relieve the application developer from dealing with complex programming related to quality, mobility, and ubiquity, (3) a binding, which prepares a quality-aware specification to be executable, in a specific deployment environment, and (4)a run-time meta-data execution, utilizing the meta-data compilation's results, to manage and control a quality-aware multimedia application. As a case study, we apply the programming framework to build a mobile Video-on-Demand (VoD) application. The experimental results show tradeoffs between easiness and flexibility to develop and deploy UMA, and overheads during UMA instantiation and adaptation.

title: Polyhedral Geometry and the Two-Plane Parameterization
abstract: Recently the light-field and lumigraph systems have been proposed as general methods of representing the visual information present in a scene. These methods represent this information as a 4D function of light over the domain of directed lines. These systems use the intersection points of the lines on two planes to parameterize the lines in space. This paper explores the structure of the two-plane parameterization in detail. In particular we analyze the association between the geometry of the scene and subsets of the 4D data. The answers to these questions are essential to understanding the relationship between a lumigraph, and the geometry that it attempts to represent. This knowledge is potentially important for a variety of applications such as extracting shape from lumigraph data, and lumigraph compression.

title: An overlay based QoS-aware voice-over-IP conferencing system
abstract: Ubiquitous IP telephony has become a feasible Internet service, and it is expected to meet the quality standards of traditional telephone services. The work presents a distributed voice-over-IP (VoIP) conferencing system called Venus that is implemented as a composable application-level service overlay network. Compared to the traditional centralized approach, Venus achieves better scalability and resource utilization by efficiently aggregating resources across distributed voice mixers. Moreover, Venus provides multi-constrained quality-of-service (QoS) provisioning by establishing each conferencing session based on multiple QoS constraints (e.g., delay, loss rate) and resource requirements (e.g., bandwidth, audio channels). Venus provides a failure resilient VoIP conferencing service by leveraging the fast failure recovery capability of the application-level service overlay network. Large-scale simulation results illustrate the efficiency of the Venus system.

title: Performance evaluation of DCCP: A focus on smoothness and TCP-friendliness
abstract: Recent years have seen dramatic increases of the use of multimedia applications on the Internet, which typically either lack congestion control or use proprietary congestion control mechanisms. This can easily cause congestion collapse or compatibility problems. Datagram Congestion Control Protocol (Dccp) fills the gap betweenUdp andTcp, featuring congestion control rather than reliability for packet-switched rich content delivery with high degree of flexibility. We present aDccp model designed and implemented withOpnet Modeler, and the experiments and evaluation focused on largely the smoothness of the data rates, and the fairness between concurrentDccp flows andTcp flows. We foundDccp-ccid3 demonstrates stable data rates under different scenarios, and the fairness betweenDccp andTcp is only achieved under certain conditions. We also validated that the throughput ofDccp-Ccid3 is proportional to the average packet size, and relatively fixed packet size is critical for the optimal operation ofDccp. Problems in the slow start phase and insufficient receiver buffer size were identified and we hereby proposed solutions on this.RésuméLe nombre d’applications multimédias sur l’internet a considérablement augmenté ces dernières années. Ces applications généralement ne gèrent pas les congestions ou bien utilisent des mécanismes de contrôle propriétaires. Il peut en résulter facilement des congestions graves ou des problèmes d’incompatibilité. Le protocoleDccp (Datagram Congestion Control Protocol) se positionne entreUdp etTcp puisqu ’il fournit, pour des paquets multimédias, un contrôle de congestion hautement flexible mais sans la fiabilité de délivrance. Cet article présente un modèleDccp conçu et implémenté avec le simulateurOpnet. Les expérimentations et les analyses portent principalement sur le lissage des débits et l’équité entre des fluxDccp etTcp concurrents. On montre queDccp-Ccid3 affiche des débits stables sous divers scénarios et que l’équité entreDccp etTcp n’est atteinte que sous certaines conditions. On valide également que le débit deDccp-Ccid3 est proportionnel à la taille moyenne des paquets et que le fait d’avoir des paquets de taille relativement constante est un facteur essentiel pour un fonctionnement optimal deDccp. Les problèmes pendant la phase de démarrage lent et ceux dus à une mémoire tampon insuffisante côté récepteur sont également analysés et résolus.

title: On Composing Stream Applications in Peer-to-Peer Environments
abstract: Stream processing has become increasingly important as many emerging applications call for continuous real-time processing over data streams, such as voice-over-IP telephony, security surveillance, and sensor data analysis. In this paper, we propose a composable stream processing system for cooperative peer-to-peer environments. The system can dynamically select and compose stream processing elements located on different peers into user desired applications. We investigate multiple alternative approaches to composing stream applications: 1) global-state-based centralized versus local-state-based distributed algorithms for initially composing stream applications at setup phase. The centralized algorithm performs periodical global state maintenance while the distributed algorithm performs on-demand state collection. 2) Reactive versus proactive failure recovery schemes for maintaining composed stream applications during runtime. The reactive failure recovery algorithm dynamically recomposes a new stream application upon failures while the proactive approach maintains a number of backup compositions for failure recovery. We conduct both theoretical analysis and experimental evaluations to study the properties of different approaches. Our study illustrates the performance and overhead trade-offs among different design alternatives, which can provide important guidance for selecting proper algorithms to compose stream applications in cooperative peer-to-peer environments