Articles de revista
http://hdl.handle.net/2117/3093
2016-02-11T00:28:39ZRTL synthesis: From logic synthesis to automatic pipelining
http://hdl.handle.net/2117/82027
RTL synthesis: From logic synthesis to automatic pipelining
Cortadella Fortuny, Jordi; Galceran Oms, Marc; Kishinevsky, Mike; Sapatnekar, Sachin S.
Design automation has been one of the main propellers of the semiconductor industry with logic synthesis being one of the core technologies in this field. This article reviews the evolution of logic synthesis until the advent of techniques for automatic pipelining based on elastic timing, either synchronous or asynchronous. The emergence of these techniques can enable a productive interaction with tools that can do microarchitectural exploration of complex designs.
2016-01-26T10:28:37ZCortadella Fortuny, JordiGalceran Oms, MarcKishinevsky, MikeSapatnekar, Sachin S.Design automation has been one of the main propellers of the semiconductor industry with logic synthesis being one of the core technologies in this field. This article reviews the evolution of logic synthesis until the advent of techniques for automatic pipelining based on elastic timing, either synchronous or asynchronous. The emergence of these techniques can enable a productive interaction with tools that can do microarchitectural exploration of complex designs.A MOOC on approaches to machine translation
http://hdl.handle.net/2117/81278
A MOOC on approaches to machine translation
Ruiz Costa-Jussà, Marta; Formiga, Lluís; Torrillas Tostado, Oriol; Petit Silvestre, Jordi; Rodríguez Fonollosa, José Adrián
This paper describes the design, development, and analysis of a MOOC entitled “Approaches to Machine Translation: Rule-based, statistical and hybrid”, and provides lessons learned and conclusions to be taken into account in the future. The course was developed within the Canvas platform, used by recognized European universities. It contains video-lectures, quizzes, and laboratory assignments. Evaluation was through on-line quizzes, programming assignments assessed by means of a specific code evaluation, and peer-to-peer strategies. This MOOC allowed people from various fields to be introduced to the theory and practice of Machine Translation. It also enabled us to internationally publicize various tools developed at the Universitat Politècnica de Catalunya.
2016-01-12T13:04:11ZRuiz Costa-Jussà, MartaFormiga, LluísTorrillas Tostado, OriolPetit Silvestre, JordiRodríguez Fonollosa, José AdriánThis paper describes the design, development, and analysis of a MOOC entitled “Approaches to Machine Translation: Rule-based, statistical and hybrid”, and provides lessons learned and conclusions to be taken into account in the future. The course was developed within the Canvas platform, used by recognized European universities. It contains video-lectures, quizzes, and laboratory assignments. Evaluation was through on-line quizzes, programming assignments assessed by means of a specific code evaluation, and peer-to-peer strategies. This MOOC allowed people from various fields to be introduced to the theory and practice of Machine Translation. It also enabled us to internationally publicize various tools developed at the Universitat Politècnica de Catalunya.SafeRazor: Metastability-robust adaptive clocking in resilient circuits
http://hdl.handle.net/2117/78809
SafeRazor: Metastability-robust adaptive clocking in resilient circuits
Cannizzaro, Marco; Beer, Salomon; Cortadella Fortuny, Jordi; Ginosar, Ran; Lavagno, Luciano
Razor-based circuits can run faster or at a lower voltage than those designed to work at the worst case corner. However, all known implementations are prone to failures due to the non-deterministic timing behavior introduced by metastability, even in the case where sufficient time is left for resolution. This paper analyzes the causes why Razor-based circuits fail and proposes a new scheme combining the Razor principle with stoppable clocks in a GALS setting. This scheme avoids any timing failure due to metastability and does not require any checkpointing or pipeline restarting logic, other than the usual auxiliary latch to store valid data. The experiments show how the Razor principle can be extended to any generic logic circuit, and not just to microprocessors with sophisticated pipeline flush/recovery mechanisms. In this way, the performance/power benefits of Razor can be adopted without the complex architectural changes required by the various Razor schemes in the literature.
2015-11-05T09:20:57ZCannizzaro, MarcoBeer, SalomonCortadella Fortuny, JordiGinosar, RanLavagno, LucianoRazor-based circuits can run faster or at a lower voltage than those designed to work at the worst case corner. However, all known implementations are prone to failures due to the non-deterministic timing behavior introduced by metastability, even in the case where sufficient time is left for resolution. This paper analyzes the causes why Razor-based circuits fail and proposes a new scheme combining the Razor principle with stoppable clocks in a GALS setting. This scheme avoids any timing failure due to metastability and does not require any checkpointing or pipeline restarting logic, other than the usual auxiliary latch to store valid data. The experiments show how the Razor principle can be extended to any generic logic circuit, and not just to microprocessors with sophisticated pipeline flush/recovery mechanisms. In this way, the performance/power benefits of Razor can be adopted without the complex architectural changes required by the various Razor schemes in the literature.High evolutionary turnover of satellite families in Caenorhabditis
http://hdl.handle.net/2117/78807
High evolutionary turnover of satellite families in Caenorhabditis
Subirana Torrent, Juan A.; Albà, M. Mar; Messeguer Peypoch, Xavier
Background: The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the evolutionary dynamics and the functional role of these sequences. We take advantage of the previously developed SATFIND program to study the satellites in four Caenorhabditis species and investigate these questions.; Methods: The identification and comparison of satellites is carried out in three steps. First we find all the satellites present in each species with the SATFIND program. Each satellite is defined by its length, number of repeats, and repeat sequence. Only satellites with at least ten repeats are considered. In the second step we build satellite families with a newly developed alignment program. Satellite families are defined by a consensus sequence and the number of satellites in the family. Finally we compare the consensus sequence of satellite families in different species.; Results: We give a catalog of individual satellites in each species. We have also identified satellite families with a related sequence and compare them in different species. We analyze the turnover of satellites: they increased in size through duplications of fragments of 100-300 bases. It appears that in many cases they have undergone an explosive expansion. In C. elegans we have identified a subset of large satellites that have strong affinity for the centromere protein CENP-A. We have also compared our results with those obtained from other species, including one nematode and three mammals.; Conclusions: Most satellite families found in Caenorhabditis are species-specific; in particular those with long repeats. A subset of these satellites may facilitate the formation of kinetochores in mitosis. Other satellite families in C. elegans are either related to Helitron transposons or to meiotic pairing centers.
2015-11-05T09:02:56ZSubirana Torrent, Juan A.Albà, M. MarMesseguer Peypoch, XavierBackground: The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the evolutionary dynamics and the functional role of these sequences. We take advantage of the previously developed SATFIND program to study the satellites in four Caenorhabditis species and investigate these questions.; Methods: The identification and comparison of satellites is carried out in three steps. First we find all the satellites present in each species with the SATFIND program. Each satellite is defined by its length, number of repeats, and repeat sequence. Only satellites with at least ten repeats are considered. In the second step we build satellite families with a newly developed alignment program. Satellite families are defined by a consensus sequence and the number of satellites in the family. Finally we compare the consensus sequence of satellite families in different species.; Results: We give a catalog of individual satellites in each species. We have also identified satellite families with a related sequence and compare them in different species. We analyze the turnover of satellites: they increased in size through duplications of fragments of 100-300 bases. It appears that in many cases they have undergone an explosive expansion. In C. elegans we have identified a subset of large satellites that have strong affinity for the centromere protein CENP-A. We have also compared our results with those obtained from other species, including one nematode and three mammals.; Conclusions: Most satellite families found in Caenorhabditis are species-specific; in particular those with long repeats. A subset of these satellites may facilitate the formation of kinetochores in mitosis. Other satellite families in C. elegans are either related to Helitron transposons or to meiotic pairing centers.FrogCOL and FrogMIS: new decentralized algorithms for finding large independent sets in graphs
http://hdl.handle.net/2117/77894
FrogCOL and FrogMIS: new decentralized algorithms for finding large independent sets in graphs
Blum, Christian; Calvo, Borja; Blesa Aguilera, Maria Josep
Finding large (and generally maximal) independent sets of vertices in a given graph is a fundamental problem in distributed computing. Applications include, for example, facility location and backbone formation in wireless ad hoc networks. In this paper, we study a decentralized (or distributed) algorithm inspired by the calling behavior of male Japanese tree frogs, originally introduced for the graph-coloring problem, for its potential usefulness in the context of finding large independent sets. Moreover, we adapt this algorithm to directly produce maximal independent sets without the necessity of first producing a graph-coloring solution. Both algorithms are compared to a wide range of decentralized algorithms from the literature on a diverse set of benchmark instances for the maximal independent set problem. The results show that both algorithms compare very favorably to their competitors.
2015-10-19T14:33:02ZBlum, ChristianCalvo, BorjaBlesa Aguilera, Maria JosepFinding large (and generally maximal) independent sets of vertices in a given graph is a fundamental problem in distributed computing. Applications include, for example, facility location and backbone formation in wireless ad hoc networks. In this paper, we study a decentralized (or distributed) algorithm inspired by the calling behavior of male Japanese tree frogs, originally introduced for the graph-coloring problem, for its potential usefulness in the context of finding large independent sets. Moreover, we adapt this algorithm to directly produce maximal independent sets without the necessity of first producing a graph-coloring solution. Both algorithms are compared to a wide range of decentralized algorithms from the literature on a diverse set of benchmark instances for the maximal independent set problem. The results show that both algorithms compare very favorably to their competitors.BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS
http://hdl.handle.net/2117/77809
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS
Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente Feruglio, Gabriel Alejandro; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano
Background: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.; Results: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).; Conclusion: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.
2015-10-16T11:36:17ZFosso, BrunoSantamaria, MonicaMarzano, MarinellaAlonso-Alemany, DanielValiente Feruglio, Gabriel AlejandroDonvito, GiacintoMonaco, AlfonsoNotarangelo, PasqualePesole, GrazianoBackground: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.; Results: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).; Conclusion: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.Forms of representation for simple games: Sizes, conversions and equivalences
http://hdl.handle.net/2117/77521
Forms of representation for simple games: Sizes, conversions and equivalences
Molinero Albareda, Xavier; Riquelme Csori, Fabián; Serna Iglesias, María José
Simple games are cooperative games in which the benefit that a coalition may have is always binary, i.e., a coalition may either win or loose. This paper surveys different forms of representation of simple games, and those for some of their subfamilies like regular games and weighted games. We analyze the forms of representations that have been proposed in the literature based on different data structures for sets of sets. We provide bounds on the computational resources needed to transform a game from one form of representation to another one. This includes the study of the problem of enumerating the fundamental families of coalitions of a simple game. In particular we prove that several changes of representation that require exponential time can be solved with polynomial-delay and highlight some open problems.
2015-10-08T14:51:25ZMolinero Albareda, XavierRiquelme Csori, FabiánSerna Iglesias, María JoséSimple games are cooperative games in which the benefit that a coalition may have is always binary, i.e., a coalition may either win or loose. This paper surveys different forms of representation of simple games, and those for some of their subfamilies like regular games and weighted games. We analyze the forms of representations that have been proposed in the literature based on different data structures for sets of sets. We provide bounds on the computational resources needed to transform a game from one form of representation to another one. This includes the study of the problem of enumerating the fundamental families of coalitions of a simple game. In particular we prove that several changes of representation that require exponential time can be solved with polynomial-delay and highlight some open problems.Analysing web-orchestrations under stress using uncertainty profiles
http://hdl.handle.net/2117/77274
Analysing web-orchestrations under stress using uncertainty profiles
Gabarró Vallès, Joaquim; Serna Iglesias, María José; Stewart, Alan
An orchestration is a multi-threaded computation that invokes a number of remote services. In practice, the responsiveness of a web-service fluctuates with demand; during surges in activity service responsiveness may be degraded, perhaps even to the point of failure. An uncertainty profile formalizes a user's perception of the effects of stress on an orchestration of web-services; it describes a strategic situation, modelled by a zero-sum angel-daemon game. Stressed web-service scenarios are analysed, using game theory, in a realistic way, lying between over-optimism (services are entirely reliable) and over-pessimism (all services are broken). The 'resilience' of an uncertainty profile can be assessed using the valuation of its associated zero-sum game. In order to demonstrate the validity of the approach, we consider two measures of resilience and a number of different stress models. It is shown how (i) uncertainty profiles can be ordered by risk (as measured by game valuations) and (ii) the structural properties of risk partial orders can be analysed.
2015-10-01T17:57:49ZGabarró Vallès, JoaquimSerna Iglesias, María JoséStewart, AlanAn orchestration is a multi-threaded computation that invokes a number of remote services. In practice, the responsiveness of a web-service fluctuates with demand; during surges in activity service responsiveness may be degraded, perhaps even to the point of failure. An uncertainty profile formalizes a user's perception of the effects of stress on an orchestration of web-services; it describes a strategic situation, modelled by a zero-sum angel-daemon game. Stressed web-service scenarios are analysed, using game theory, in a realistic way, lying between over-optimism (services are entirely reliable) and over-pessimism (all services are broken). The 'resilience' of an uncertainty profile can be assessed using the valuation of its associated zero-sum game. In order to demonstrate the validity of the approach, we consider two measures of resilience and a number of different stress models. It is shown how (i) uncertainty profiles can be ordered by risk (as measured by game valuations) and (ii) the structural properties of risk partial orders can be analysed.Abstract constraint data types
http://hdl.handle.net/2117/76978
Abstract constraint data types
Fiadeiro, Jose Luis; Orejas Valdés, Fernando
Martin Wirsing is one of the earliest contributors to the area of Algebraic Specification (e.g., [2]), which he explored in a variety of domains over many years. Throughout his career, he has also inspired countless researchers in related areas. This paper is inspired by one of the domains that he explored thirty years or so after his first contributions when leading the FET Integrated Project SENSORIA [14]: the use of constraint systems to deal with non-functional requirements and preferences [13,8]. Following in his footsteps, we provide an extension of the traditional notion of algebraic data type specification to encompass soft-constraints as formalised in [1]. Finally, we relate this extension with institutions [6] and recent work on graded consequence in institutions [3].
2015-09-21T09:39:30ZFiadeiro, Jose LuisOrejas Valdés, FernandoMartin Wirsing is one of the earliest contributors to the area of Algebraic Specification (e.g., [2]), which he explored in a variety of domains over many years. Throughout his career, he has also inspired countless researchers in related areas. This paper is inspired by one of the domains that he explored thirty years or so after his first contributions when leading the FET Integrated Project SENSORIA [14]: the use of constraint systems to deal with non-functional requirements and preferences [13,8]. Following in his footsteps, we provide an extension of the traditional notion of algebraic data type specification to encompass soft-constraints as formalised in [1]. Finally, we relate this extension with institutions [6] and recent work on graded consequence in institutions [3].Model synchronization based on triple graph grammars: correctness, completeness and invertibility
http://hdl.handle.net/2117/76970
Model synchronization based on triple graph grammars: correctness, completeness and invertibility
Hermann, Frank; Ehrig, Hartmut; Orejas Valdés, Fernando; Czarnecki, Krzysztof; Diskin, Zinovy; Xiong, Yingfei; Gottmann, Susann; Engel, Thomas
Triple graph grammars (TGGs) have been used successfully to analyze correctness and completeness of bidirectional model transformations, but a corresponding formal approach to model synchronization has been missing. This paper closes this gap by providing a formal synchronization framework with bidirectional update propagation operations. They are generated from a given TGG, which specifies the language of all consistently integrated source and target models. As our main result, we show that the generated synchronization framework is correct and complete, provided that forward and backward propagation operations are deterministic. Correctness essentially means that the propagation operations preserve and establish consistency while completeness ensures that the operations are defined for all possible inputs. Moreover, we analyze the conditions under which the operations are inverse to each other. All constructions and results are motivated and explained by a running example, which leads to a case study, using concrete visual syntax and abstract syntax notation based on typed attributed graphs.
2015-09-21T08:17:22ZHermann, FrankEhrig, HartmutOrejas Valdés, FernandoCzarnecki, KrzysztofDiskin, ZinovyXiong, YingfeiGottmann, SusannEngel, ThomasTriple graph grammars (TGGs) have been used successfully to analyze correctness and completeness of bidirectional model transformations, but a corresponding formal approach to model synchronization has been missing. This paper closes this gap by providing a formal synchronization framework with bidirectional update propagation operations. They are generated from a given TGG, which specifies the language of all consistently integrated source and target models. As our main result, we show that the generated synchronization framework is correct and complete, provided that forward and backward propagation operations are deterministic. Correctness essentially means that the propagation operations preserve and establish consistency while completeness ensures that the operations are defined for all possible inputs. Moreover, we analyze the conditions under which the operations are inverse to each other. All constructions and results are motivated and explained by a running example, which leads to a case study, using concrete visual syntax and abstract syntax notation based on typed attributed graphs.