Transformation by example

La transformation de modèles consiste à transformer un modèle source en un modèle cible conformément à des méta-modèles source et cible. Nous distinguons deux types de transformations. La première est exogène où les méta-modèles source et cible représentent des formalismes différents et où tous les éléments du modèle source sont transformés. Quand elle concerne un même formalisme, la transformation est endogène. Ce type de transformation nécessite généralement deux étapes : l’identification des éléments du modèle source à transformer, puis la transformation de ces éléments. Dans le cadre de cette thèse, nous proposons trois principales contributions liées à ces problèmes de transformation. La première contribution est l’automatisation des transformations des modèles. Nous proposons de considérer le problème de transformation comme un problème d'optimisation combinatoire où un modèle cible peut être automatiquement généré à partir d'un nombre réduit d'exemples de transformations. Cette première contribution peut être appliquée aux transformations exogènes ou endogènes (après la détection des éléments à transformer). La deuxième contribution est liée à la transformation endogène où les éléments à transformer du modèle source doivent être détectés. Nous proposons une approche pour la détection des défauts de conception comme étape préalable au refactoring. Cette approche est inspirée du principe de la détection des virus par le système immunitaire humain, appelée sélection négative. L’idée consiste à utiliser de bonnes pratiques d’implémentation pour détecter les parties du code à risque. La troisième contribution vise à tester un mécanisme de transformation en utilisant une fonction oracle pour détecter les erreurs. Nous avons adapté le mécanisme de sélection négative qui consiste à considérer comme une erreur toute déviation entre les traces de transformation à évaluer et une base d’exemples contenant des traces de transformation de bonne qualité. La fonction oracle calcule cette dissimilarité et les erreurs sont ordonnées selon ce score. Les différentes contributions ont été évaluées sur d’importants projets et les résultats obtenus montrent leurs efficacités.

Query-by-Example Spoken Term Detection ALBAYZIN 2012 evaluation: overview, systems, results, and discussion

Query-by-Example Spoken Term Detection (QbE STD) aims at retrieving data from a speech data repository given an acoustic query containing the term of interest as input. Nowadays, it has been receiving much interest due to the high volume of information stored in audio or audiovisual format. QbE STD differs from automatic speech recognition (ASR) and keyword spotting (KWS)/spoken term detection (STD) since ASR is interested in all the terms/words that appear in the speech signal and KWS/STD relies on a textual transcription of the search term to retrieve the speech data. This paper presents the systems submitted to the ALBAYZIN 2012 QbE STD evaluation held as a part of ALBAYZIN 2012 evaluation campaign within the context of the IberSPEECH 2012 Conference(a). The evaluation consists of retrieving the speech files that contain the input queries, indicating their start and end timestamps within the appropriate speech file. Evaluation is conducted on a Spanish spontaneous speech database containing a set of talks from MAVIR workshops(b), which amount at about 7 h of speech in total. We present the database metric systems submitted along with all results and some discussion. Four different research groups took part in the evaluation. Evaluation results show the difficulty of this task and the limited performance indicates there is still a lot of room for improvement. The best result is achieved by a dynamic time warping-based search over Gaussian posteriorgrams/posterior phoneme probabilities. This paper also compares the systems aiming at establishing the best technique dealing with that difficult task and looking for defining promising directions for this relatively novel task.

Robotic Assembly of Naturally Varying Food Items via Teaching by Example

T. G. Williams, J.J. Rowland, and Lee M.H., Robotic Assembly of Naturally Varying Food Items via Teaching by Example, 9th Int. Symp. on Intelligent Robotic Systems (SIRS 2001), July 2001, France, pp133-142.

Teaching by Example in Food Assembly by Robot

T. G. Williams, J.J. Rowland, Lee M.H. and M.J. Neal Teaching by Example in Food Assembly by Robot, Proc. 2000 IEEE Int. Conf. On Robotics and Automation, San Francisco, April 2000, pp3247-52.

Squeak by Example

Squeak by Example, intended for both students and developers, will guide you gently through the Squeak language and environment by means of a series of examples and exercises. This book is made available under the Creative Commons Attribution-ShareAlike 3.0 license.

Pharo by Example

Pharo by Example, intended for both students and developers, will guide you gently through the Pharo language and environment by means of a series of examples and exercises. This book is made available under the Creative Commons Attribution-ShareAlike 3.0 license.

Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning

To accelerate gene isolation from plants by positional cloning, vector systems suitable for both chromosome walking and genetic complementation are highly desirable. Therefore, we developed a transformation-competent artificial chromosome (TAC) vector, pYLTAC7, that can accept and maintain large genomic DNA fragments stably in both Escherichia coli and Agrobacterium tumefaciens. Furthermore, it has the cis sequences required for Agrobacterium-mediated gene transfer into plants. We cloned large genomic DNA fragments of Arabidopsis thaliana into the vector and showed that most of the DNA fragments were maintained stably. Several TAC clones carrying 40- to 80-kb genomic DNA fragments were transferred back into Arabidopsis with high efficiency and shown to be inherited faithfully among the progeny. Furthermore, we demonstrated the practical utility of this vector system for positional cloning in Arabidopsis. A TAC contig was constructed in the region of the SGR1 locus, and individual clones with ca. 80-kb inserts were tested for their ability to complement the gravitropic defects of a homozygous mutant line. Successful complementation enabled the physical location of SGR1 to be delimited with high precision and confidence.

Picture analysis by graph transformation,

"Supported in part by the Department of Computer Science and the Atomic Energy Commission under contract US AEC AT(11-1)2118."

Structural synthesis by transformation of binary chains Strukturelle synthese durch umwandlung binaerer ketten

The paper presents a general method of structural synthesis which can be used to derive all possible simple- and multiple-jointed chains of positive, zero or negative degree-of-freedom. In this method all possible chains with N links and F degrees-of-freedom are derived by the transformation of the corresponding “binary chains” with N binary links and F degrees-of-freedom. The method is illustrated by applying to the case of chains with degrees-of-freedom 1,2,0 and −1.

Transformation field method for calculating the effective properties of isotropic graded composites having arbitrary shapes

A method of transformation field is developed to estimate the effective properties of graded composites whose inclusions have arbitrary shapes and gradient profiles by means of a periodic cell model. The boundary-value problem of graded composites having arbitrary inclusion shapes is solved by introducing the transformation field into the inclusion region. As an example, the effective dielectric response of isotropic graded composites having arbitrary shapes and gradient profiles is handled by the transformation field method (TFM). Moreover, TFM results are validated by the exact solutions of isotropic graded spherical inclusions having a power-law profile and good agreement is obtained in the dilute limit. Furthermore, it is found that the inclusion shapes and the parameters of the gradient profiles can have profound effect on the effective properties of composite systems at high concentration of inclusions.

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/.

Generation of millimeter-wave in optical pulse carrier by using an apodized Moire fiber grating

A novel scheme is proposed to transform a Gaussian pulse to a millimeter-wave frequency modulation pulse by using an apodized Moire fiber Bragg grating in radio-over-fiber system. The relation between the input and output pulses is analyzed theoretically by Fourier transformation method and the requirements for the proposed fiber grating are presented. An apodized Moire fiber Bragg grating is designed and its characteristics are studied. It is shown that the proposed device is feasible, and the new scheme is believed to be an effective solution for the generation of millimeter-wave sub-carrier in future radio-over-fiber systems. (c) 2006 Elsevier B.V. All rights reserved.

Mechanism-transformation synthesis and characterization of poly(styrene-b-2-ethyl-2-oxazoline) diblock copolymer

By mechanism-transformation (anionic --> cationic) poly(styrene-6-2-ethyl-2-oxazoline) diblock copolymer, PS-b-PEOx, was synthesized in two steps. The first step is the polymerization of styrene block capped with ethylene oxide and its tosylation; the second step is the cationic ring-opening polymerization of 2-ethyl-2-oxazoline. The products were thoroughly characterized by various methods, such as H-1-NMR, IR, DMA, TEM and SAXS. The results show that the copolymer obtained possesses high molecular weight and narrow molecular weight distribution.