Aspect] is a simple and practical aspect-oriented extension to Java With just a few new constructs, AspectJ provides support for modular implementation of a range of crosscutting concerns. In AspectJ's dynamic join point model, join points are well-defined points in the execution of the program; pointcuts are collections of join points; advice are special method-like constructs that can be attached to pointcuts; and aspects are modular units of crosscutting implementation, comprising pointcuts, advice, and ordinary Java member declarations. AspectJ code is compiled into standard Java bytecode. Simple extensions to existing Java development environments make it possible to browse the crosscutting structure of aspects in the same kind of way as one browses the inheritance structure of classes. Several examples show that AspectJ is powerful, and that programs written using it are easy to understand.

An overview of AspectJ

Approximate Bayesian computation (ABC) techniques permit inferences in complex demographic models, but are computationally inefficient. A Markov chain Monte Carlo (MCMC) approach has been proposed (Marjoram et al. 2003), but it suffers from computational problems and poor mixing. We propose several methodological developments to overcome the shortcomings of this MCMC approach and hence realize substantial computational advances over standard ABC. The principal idea is to relax the tolerance within MCMC to permit good mixing, but retain a good approximation to the posterior by a combination of subsampling the output and regression adjustment. We also propose to use a partial least-squares (PLS) transformation to choose informative statistics. The accuracy of our approach is examined in the case of the divergence of two populations with and without migration. In that case, our ABC–MCMC approach needs considerably lower computation time to reach the same accuracy than conventional ABC. We then apply our method to a more complex case with the estimation of divergence times and migration rates between three African populations.

https://www.genetics.org/content/genetics/182/4/1207.full.pdf

Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood

Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association. We shall show that Bayesian models are able to use prior information and model measurements with various distributions; tree-based methods can either build a tree with all features or collectively make a final decision based on trees learned from each view; kernel methods fuse the similarity matrices learned from individual views together for a final similarity matrix or learning model; network-based fusion methods are capable of inferring direct and indirect associations in a heterogeneous network; matrix factorization models have potential to learn interactions among features from different views; and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.

A review on machine learning principles for multi-view biological data integration.

Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

/pdf/genome-interplay-in-the-grain-transcriptome-of-hexaploid-24rdustedf.pdf

Genome interplay in the grain transcriptome of hexaploid bread wheat

The morphological and biochemical properties of plant canopies are strong predictors of photosynthetic capacity and nutrient cycling. Remote sensing research at the leaf and canopy scales has demonstrated the ability to characterize the biochemical status of vegetation canopies using reflectance spectroscopy, including at the leaf level and canopy level from air- and spaceborne imaging spectrometers. We developed a set of accurate and precise spectroscopic calibrations for the determination of leaf chemistry (contents of nitrogen, carbon, and fiber constituents), morphology (leaf mass per area, Marea), and isotopic composition (δ15N) of temperate and boreal tree species using spectra of dried and ground leaf material. The data set consisted of leaves from both broadleaf and needle-leaf conifer species and displayed a wide range in values, determined with standard analytical approaches: 0.7–4.4% for nitrogen (Nmass), 42–54% for carbon (Cmass), 17–58% for fiber (acid-digestible fiber, ADF), 7–44% for lignin (acid-digestible lignin, ADL), 3–31% for cellulose, 17–265 g/m2 for Marea, and −9.4‰ to 0.8‰ for δ15N. The calibrations were developed using a partial least-squares regression (PLSR) modeling approach combined with a novel uncertainty analysis. Our PLSR models yielded model calibration (independent validation shown in parentheses) R2 and the root mean square error (RMSE) values, respectively, of 0.98 (0.97) and 0.10% (0.13%) for Nmass, R2 = 0.77 (0.73) and RMSE = 0.88% (0.95%) for Cmass, R2 = 0.89 (0.84) and RMSE = 2.8% (3.4%) for ADF, R2 = 0.77 (0.69) and RMSE = 2.4% (3.9%) for ADL, R2 = 0.77 (0.72) and RMSE = 1.4% (1.9%) for leaf cellulose, R2 = 0.62 (0.60) and RMSE = 0.91‰ (1.5‰) for δ15N, and R2 = 0.88 (0.87) with RMSE = 17.2 g/m2 (22.8 g/m2) for Marea. This study demonstrates the potential for rapid and accurate estimation of key foliar traits of forest canopies that are important for ecological research and modeling activities, with a single calibration equation valid over a wide range of northern temperate and boreal species and leaf physiognomies. The results provide the basis to characterize important variability between and within species, and across ecological gradients using a rapid, cost-effective, easily replicated method.

/pdf/spectroscopic-determination-of-leaf-morphological-and-47icthwhup.pdf

Spectroscopic determination of leaf morphological and biochemical traits for northern temperate and boreal tree species

Performance and cost analysis are the two main purposes of business process modeling, where the Petri net extended with time information is an effective tool for performance analysis, but not for cost analysis. This paper proposes a time Petri net extended with price information—Price Time Petri Net. Firstly, this paper associates a price with a time transition, and gives the semantics for price time Petri net in terms of priced timed transition systems. Then it defines a priced state class as an extension of state class, and discusses the soundness and completeness for this extension. An algorithm is given to prove that the minimum-cost reachability problem for bounded price time Petri net is decidable. Finally, this paper gives an example and draws a conclusion that incorporating price information in time Petri net and applying price time Petri net to business process management

/pdf/a-time-petri-net-extended-with-price-information-3os5kmtrky.pdf

A Time Petri Net Extended with Price Information

Web applications are the legacy software of the future. The Web application reverse-engineering process becomes necessary in order to facilitate the maintenance and evolution. This paper presents an approach to recover the architecture of web applications. The approach generates UML models from existing web applications through static and dynamic techniques. UML diagrams are extracted to depict the static, dynamic and behavioral aspect of Web applications. Finally, the architecture of the tool is described.

An Approach for Reverse Engineering of Web Applications

Improve the semantic interoperability of information

This paper discusses the needs of the portlets' semantic interoperability. It shows the drawbacks of current specifications of portlets such as JSR168 and WSRP. The paper suggests using ontology to support semantic interoperability of portlets. It proposes a scheme of ontology as a remote portlet service to illustrate the semantic interoperability of portlets.

Using Ontology to Support Portlet Semantic Interoperability

Web portals are integration of enterprise applications and services. The further integration of applications in portal context is actually the problem of portlet interoperation. However, there is not yet a definitive answer to portlet interoperation. This paper focuses on using ontology to support portlet semantic interoperability based on new features of JSR268. The proposed approach maps the portlets to concepts in ontology, and then constructs semantic data associations between such concepts, and finally achieves portlet interoperation based on the data associations. Experimental results show that this proposed approach can achieve application integration in portal without modifications to the applications.

Li Shixian

Papers

A Time Petri Net Extended with Price Information

An Approach for Reverse Engineering of Web Applications

Improve the semantic interoperability of information

Using Ontology to Support Portlet Semantic Interoperability

An Approach to Support Portlet Semantic Interoperation by Using Ontology Based on JSR268