Pablo Rodríguez-Mier

The growing availability of single-cell and spatially resolved transcriptomics has led to the development of many approaches to infer cell-cell communication, each capturing only a partial view of the complex landscape of intercellular signalling. Here we present LIANA+, a scalable framework built around a rich knowledge base to decode coordinated inter- and intracellular signalling events from single- and multi-condition datasets in both single-cell and spatially resolved data. By extending and unifying established methodologies, LIANA+ provides a comprehensive set of synergistic components to study cell-cell communication via diverse molecular mediators, including those measured in multi-omics data. LIANA+ is accessible at https://github.com/saezlab/liana-py with extensive vignettes ( https://liana-py.readthedocs.io/ ) and provides an all-in-one solution to intercellular communication inference.

Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention. Using five publicly available datasets, we demonstrated that changes in parameters such as the background set, differential metabolite selection methods, and pathway database used can result in profoundly different ORA results. The use of a non-assay-specific background set, for example, resulted in large numbers of false-positive pathways. Pathway database choice, evaluated using three of the most popular metabolic pathway databases (KEGG, Reactome, and BioCyc), led to vastly different results in both the number and function of significantly enriched pathways. Factors that are specific to metabolomics data, such as the reliability of compound identification and the chemical bias of different analytical platforms also impacted ORA results. Simulated metabolite misidentification rates as low as 4% resulted in both gain of false-positive pathways and loss of truly significant pathways across all datasets. Our results have several practical implications for ORA users, as well as those using alternative pathway analysis methods. We offer a set of recommendations for the use of ORA in metabolomics, alongside a set of minimal reporting guidelines, as a first step towards the standardisation of pathway analysis in metabolomics.

Abstract—In this paper we present a theoretical analysis of graph-based service composition in terms of its dependency with service discovery. Driven by this analysis we define a composition framework by means of integration with fine-grained I/O service discovery that enables the generation of a graph-based composition which contains the set of services that are semantically relevant for an input-output request. The proposed framework also includes an optimal composition search algorithm to extract the best composition from the graph minimising the length and the number of services, and different graph optimisations to improve the scalability of the system. A practical implementation used for the empirical analysis is also provided. This analysis proves the scalability and flexibility of our proposal and provides insights on how integrated composition systems can be designed in order to achieve good performance in real scenarios for the Web.

Service Oriented Architectures and web service technology are becoming popular in recent years. As more web services can be used over the Internet, the need to find efficient algorithms for web services composition that can deal with large amounts of services becomes important. These algorithms must deal with different issues like performance, semantics or user restrictions. In this paper we present an A* algorithm which solves the problem of semantic input-output message structure matching for web service composition. Given are quest, a service dependency graph with a subset of the original services from an external repository is dynamically generated. Then, the A* search algorithm is used to find a minimal composition that satisfies the user request. Moreover, in order to improve the performance, a set of dynamic optimization techniques has been implemented over the search process. A full experimental validation with eight different public repositories has been done showing a good performance as in all tests as the algorithm finds a valid solution with minimal number of services and execution path.

In this paper we present a hybrid approach for automatic composition of Web services that generates semantic input-output based compositions with optimal end-to-end QoS, minimizing the number of services of the resulting composition. The proposed approach has four main steps: (1) generation of the composition graph for a request; (2) computation of the optimal composition that minimizes a single objective QoS function; (3) multi-step optimizations to reduce the search space by identifying equivalent and dominated services; and (4) hybrid local-global search to extract the optimal QoS with the minimum number of services. An extensive validation with the datasets of the Web Service Challenge 2009-2010 and randomly generated datasets shows that: (1) the combination of local and global optimization is a general and powerful technique to extract optimal compositions in diverse scenarios; and (2) the hybrid strategy performs better than the state-of-the-art, obtaining solutions with less services and optimal QoS.