5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011)

The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘11 hopes to contribute to this effort promoting this fruitful interaction. PACBB'11 technical program included 50 papers from a submission pool of 78 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants

Notas sobre Soft Sets - Preliminaries

[ES]Muchos problemas de la vida real requieren el uso de datos imprecisos o inciertos. Su análisis debe implicar la aplicación de principios matemáticos capaces de captar estas características. La teoría de los conjuntos difusos supuso un cambio paradigmático en las Matemáticas al permitir la pertenencia parcial. Para una definición y argumentos acerca de su aplicabilidad a varios campos, nos interesa especialmente una generalización de los conjuntos difusos: la aplicación de la teoría de los soft sets y sus extensiones a los problemas de toma de decisiones

Modeling Cellular Signaling Systems: An Abstraction-Refinement Approach

International audienceThe molecular mechanisms of cell communication with the environment involve many concurrent processes governing dynamically the cell function. This concurrent behavior makes traditional methods, such as differential equations, unsatisfactory as a modeling strategy since they do not scale well when a more detailed view of the system is required. Concurrent Constraint Programming (CCP) is a declarative model of concurrency closely related to logic for specifying reactive systems, i.e., systems that continuously react with the environment. Agents in CCP interact by telling and asking information represented as constraints (e.g., x > 42). In this paper we describe a modeling strategy for cellular signaling systems based on a temporal and probabilistic extension of CCP. Starting from an abstract model, we build refinements adding further details coming from experimentation or abstract assumptions. The advantages of our approach are: due to the notion of partial information as constraints in CCP, the model can be straightforwardly extended when more information is available; qualitative and quantitative information can be represented by means of probabilistic constructs of the language; finally, the model is a runnable specification and can be executed, thus allowing for the simulation of the system. We outline the use of this methodology to model the interaction of G-protein-coupled receptors with their respective G-proteins that activates signaling pathways inside the cell. We also present simulation results obtained from an implementation of the framewor

SAMasGC: Sequencing Analysis with a Multiagent System and Grid Computing

Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms

Learning AI with deepint.net

This keynote will examine the evolution of intelligent computer systems over the last years, underscoring the need for human capital in this field, so that further progress can be made. In this regard, learning about AI through experience is a big challenge, but it is possible thanks to tools such as deepint.net, which enable anyone to develop AI systems; knowledge of programming is no longer necessary

Smart Buildings

This talk presents an efficient cyberphysical platform for the smart management of smart buildings http://www.deepint.net. It is efficient because it facilitates the implementation of data acquisition and data management methods, as well as data representation and dashboard configuration. The platform allows for the use of any type of data source, ranging from the measurements of a multi-functional IoT sensing devices to relational and non-relational databases. It is also smart because it incorporates a complete artificial intelligence suit for data analysis; it includes techniques for data classification, clustering, forecasting, optimization, visualization, etc. It is also compatible with the edge computing concept, allowing for the distribution of intelligence and the use of intelligent sensors. The concept of smart building is evolving and adapting to new applications; the trend to create intelligent neighbourhoods, districts or territories is becoming increasingly popular, as opposed to the previous approach of managing an entire megacity. In this paper, the platform is presented, and its architecture and functionalities are described. Moreover, its operation has been validated in a case study at Salamanca - Ecocasa. This platform could enable smart building to develop adapted knowledge management systems, adapt them to new requirements and to use multiple types of data, and execute efficient computational and artificial intelligence algorithms. The platform optimizes the decisions taken by human experts through explainable artificial intelligence models that obtain data from IoT sensors, databases, the Internet, etc. The global intelligence of the platform could potentially coordinate its decision-making processes with intelligent nodes installed in the edge, which would use the most advanced data processing techniques

Intelligent Models in Complex Problem Solving

Artificial Intelligence revived in the last decade. The need for progress, the growing processing capacity and the low cost of the Cloud have facilitated the development of new, powerful algorithms. The efficiency of these algorithms in Big Data processing, Deep Learning and Convolutional Networks is transforming the way we work and is opening new horizons

Case-Based Reasoning to Classify Endodontic Retreatments

Within the field of odontology, an analysis of the probability of success of endodontic retreatment facilitates the diagnostic and decision-making process of medical personnel. This study presents a case-based reasoning system that predicts the probability of success and failure of retreatments to avoid extraction. Different classifiers were applied during the reuse phase of the case-based reasoning process. The system was tested on a set of patients who received retreatments, and a set of variables considered to be of particular interest, were selected

Managing smart cities with deepint.net

In this keynote, the evolution of intelligent computer systems will be examined. The need for human capital will be emphasised, as well as the need to follow one’s “gut instinct” in problem-solving. We will look at the benefits of combining information and knowledge to solve complex problems and will examine how knowledge engineering facilitates the integration of different algorithms. Furthermore, we will analyse the importance of complementary technologies such as IoT and Blockchain in the development of intelligent systems. It will be shown how tools like "Deep Intelligence" make it possible to create computer systems efficiently and effectively. "Smart" infrastructures need to incorporate all added-value resources so they can offer useful services to the society, while reducing costs, ensuring reliability and improving the quality of life of the citizens. The combination of AI with IoT and with blockchain offers a world of possibilities and opportunities

Efficient Deployment of DeepTech AI Models in Engineering Solutions

The blockchain system, appeared in 2009 together with the virtual currency bitcoin, is a record of digital transactions based on a huge database in which all financial operations carried out with electronic currency are registered. The Blockchain (or chain of blocks) is a shared database that works as a book for the record of purchase-sale operations or any other transaction. It is the technological base of the operation of bitcoin, for example. It consists of a set of notes that are in a shared online database in which operations, quantities, dates and participants are registered by means of codes. By using cryptographic keys and being distributed by many computers (people), it presents security advantages against manipulation and fraud. A modification in one of the copies would be useless, but the change must be made in all the copies because the database is open and public