STAPLE: An agent programming language based on the joint intention theory
Joint intention theory has been used for rule based creation of teams and to provide a formal semantics for communicative acts but there were no agent programming languages linked to this theory. We proposed a declarative agent programming language called STAPLE whose logical semantics is given by the joint intention theory. This paper illustrates the STAPLE support for communication and teamwork in a unified framework.

title: Toward A Formalism for Conversation Protocols Using Joint Intention Theory
abstract: Conversation protocols are meant to achieve certain tasks or to bring about certain state of affairs in the world. Therefore, one may identify the landmarks or the state of affairs that must be brought about during the execution of a protocol in order to achieve its goal. Accordingly, the most important aspect of protocols is these landmarks rather than the communicative actions needed to achieve the landmarks. We show that families of conversation protocols can be expressed formally as partially ordered landmarks where each landmark is characterized by propositions that are true in the state represented by that landmark. Dialogue in natural languages is regarded as joint activity. Conversation protocols in multi-agent systems are treated as dialogue templates and are composed using speech acts from natural language dialogues. As such, we treat conversation protocols as joint action expressions and gainfully apply existing formal theories of dialogue, specifically the Joint Intention Theory, to protocols and their compositions. Conversation protocols may require agents to communicate with groups as well as individuals. However, most contemporary agent communication languages, notably FIPA and KQML, have either no provision or no well-defined semantics for group communication. Furthermore, the research on protocols so far does not correctlymore » incorporate groups into the protocols. We give a formal semantics to group communicative acts and use it to handle group communication in a formal treatment of protocols.« less

title: Direct execution of team specifications in STAPLE
abstract: Formal theories of teamwork are typically treated as software design specifications of team behavior. We take a different approach to programming teamwork by directly executing logical specifications of joint commitment and joint intention. This approach leads to a domain-independent framework for programming teamwork where one can modify (or add new) behavior for a team of agents just by modifying (or adding) logical sentences. One may also be able to predict the behavior of an agent team offline using its team intention specification and verify it by running the actual system.

title: Distributive and Collective Readings in Group Protocols
abstract: Collaborative applications require protocols that specify how distributed entities interact with one another in order to achieve a specified behavior. Many different kinds of relationships can be established between these entities as a result of such interactions. Distributive and Collective readings are two important ways to characterize group interaction. Starting from an attempt-based semantics of group communicative acts, we distinguish between these two concepts and evaluate group protocols with respect to formation of different types of teams during the interaction.

title: Dynamic tracking of page miss ratio curve for memory management
abstract: Memory can be efficiently utilized if the dynamic memory demands of applications can be determined and analyzed at run-time. The page miss ratio curve(MRC), i.e. page miss rate vs. memory size curve, is a good performance-directed metric to serve this purpose. However, dynamically tracking MRC at run time is challenging in systems with virtual memory because not every memory reference passes through the operating system (OS).This paper proposes two methods to dynamically track MRC of applications at run time. The first method is using a hardware MRC monitor that can track MRC at fine time granularity. Our simulation results show that this monitor has negligible performance and energy overheads. The second method is an OS-only implementation that can track MRC at coarse time granularity. Our implementation results on Linux show that it adds only 7--10% overhead.We have also used the dynamic MRC to guide both memory allocation for multiprogramming systems and memory energy management. Our real system experiments on Linux with applications including Apache Web Server show that the MRC-directed memory allocation can speed up the applications' execution/response time by up to a factor of 5.86 and reduce the number of page faults by up to 63.1%. Our execution-driven simulation results with SPEC2000 benchmarks show that the MRC-directed memory energy management can improve the Energy * Delay metric by 27--58% over previously proposed static and dynamic schemes.

title: Discriminative Fields for Modeling Spatial Dependencies in Natural Images
abstract: In this paper we present Discriminative Random Fields (DRF), a discriminative framework for the classification of natural image regions by incorporating neighborhood spatial dependencies in the labels as well as the observed data. The proposed model exploits local discriminative models and allows to relax the assumption of conditional independence of the observed data given the labels, commonly used in the Markov Random Field (MRF) framework. The parameters of the DRF model are learned using penalized maximum pseudo-likelihood method. Furthermore, the form of the DRF model allows the MAP inference for binary classification problems using the graph min-cut algorithms. The performance of the model was verified on the synthetic as well as the real-world images. The DRF model outperforms the MRF model in the experiments.

title: NAMD: Biomolecular Simulation on Thousands of Processors
abstract: NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.

title: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
abstract: With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

title: ESP: a language for programmable devices
abstract: This paper presents the design and implementation of Event-driven State-machines Programming (ESP)—a language for programmable devices. In traditional languages, like C, using event-driven state-machine forces a tradeoff that requires giving up ease of development and reliability to achieve high performance. ESP is designed to provide all of these three properties simultaneously.
ESP provides a comprehensive set of features to support development of compact and modular programs. The ESP compiler compiles the programs into two targets—a C file that can be used to generate efficient firmware for the device; and a specification that can be used by a verifier like SPlN to extensively test the firmware.
As a case study, we reimplemented VMMC firmware that runs on Myrinet network interface cards using ESP. We found that ESP simplifies the task of programming with event-driven state machines. It required an order of magnitude fewer lines of code than the previous implementation. We also found that model-checking verifiers like SPIN can be used to effectively debug the firmware. Finally, our measurements indicate that the performance overhead of using ESP is relatively small.