INESC-ID

About: INESC-ID is a nonprofit organization based out in Lisbon, Portugal. It is known for research contribution in the topics: Computer science & Context (language use). The organization has 932 authors who have published 2618 publications receiving 37658 citations.

Metagenome Fragment Classification Using N-Mer Frequency Profiles

Abstract: A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique N-mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC) that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable to identify any fragment from hundreds of genomes. It also performs quite well at the strain, species, and genera levels and achieves strain resolution despite classifying ubiquitous genomic fragments (gene and nongene regions). Cross-validation analysis demonstrates that species-accuracy achieves 90% for highly-represented species containing an average of 8 strains. We demonstrate that such a tool can be used on the Sargasso Sea dataset, and our analysis shows that NBC can be further enhanced.

When Scalability Meets Consistency: Genuine Multiversion Update-Serializable Partial Data Replication

Abstract: In this article we introduce GMU, a genuine partial replication protocol for transactional systems, which exploits an innovative, highly scalable, distributed multiversioning scheme. Unlike existing multiversion-based solutions, GMU does not rely on a global logical clock, which represents a contention point and can limit system scalability. Also, GMU never aborts read-only transactions and spares them from distributed validation schemes. This makes GMU particularly efficient in presence of read-intensive workloads, as typical of a wide range of real-world applications. GMU guarantees the Extended Update Serializability (EUS) isolation level. This consistency criterion is particularly attractive as it is sufficiently strong to ensure correctness even for very demanding applications (such as TPC-C), but is also weak enough to allow efficient and scalable implementations, such as GMU. Further, unlike several relaxed consistency models proposed in literature, EUS has simple and intuitive semantics, thus being an attractive, scalable consistency model for ordinary programmers. We integrated the GMU protocol in a popular open source in-memory transactional data grid, namely Infinispan. On the basis of a large scale experimental study performed on heterogeneous experimental platforms and using industry standard benchmarks (namely TPC-C and YCSB), we show that GMU achieves linear scalability and that it introduces negligible overheads (less than 10%), with respect to solutions ensuring non-serializable semantics, in a wide range of workloads.

SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Abstract: Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. Results: We present the System Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the cooperative development of the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyze qualitative models. Conclusion: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.

But that was in another country: agents and intercultural empathy

Abstract: This paper discusses the development of a believable agent-based educational application designed to develop inter-cultural empathy for 13--14 year old students. It considers relevant work in cultural taxonomy and adaptation to other cultures as well as work showing that users are sensitive to the perceived culture of believable interactive characters. It discusses how an existing affective agent architecture was developed to model culturally-specific agent behaviour. Finally, it considers the role of interaction modalities in supporting an empathic engagement with culturally-specific characters.