Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Biological Systems Workbook: Data modelling and simulations at molecular level

Nowadays, there are huge quantities of data surrounding the different fields of biology derived from experiments and theoretical simulations, where results are often stored in biological databases that are growing at a vertiginous rate every year. Therefore, there is an increasing research interest in the application of mathematical and physical models able to produce reliable predictions and explanations to understand and rationalize that information. All these investigations are helping to overcome biological questions pushing forward in the solution of problems faced by our society. In this Biological Systems Workbook, we aim to introduce the basic pieces allowing life to take place, from the 3D structural point of view. We will start learning how to look at the 3D structure of molecules from studying small organic molecules used as drugs. Meanwhile, we will learn some methods that help us to generate models of these structures. Then we will move to more complex natural organic molecules as lipid or carbohydrates, learning how to estimate and reproduce their dynamics. Later, we will revise the structure of more complex macromolecules as proteins or DNA. Along this process, we will refer to different computational tools and databases that will help us to search, analyze and model the different molecular systems studied in this course

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Simulation Intelligence: Towards a New Generation of Scientific Methods

The original "Seven Motifs" set forth a roadmap of essential methods for the field of scientific computing, where a motif is an algorithmic method that captures a pattern of computation and data movement. We present the "Nine Motifs of Simulation Intelligence", a roadmap for the development and integration of the essential algorithms necessary for a merger of scientific computing, scientific simulation, and artificial intelligence. We call this merger simulation intelligence (SI), for short. We argue the motifs of simulation intelligence are interconnected and interdependent, much like the components within the layers of an operating system. Using this metaphor, we explore the nature of each layer of the simulation intelligence operating system stack (SI-stack) and the motifs therein: (1) Multi-physics and multi-scale modeling; (2) Surrogate modeling and emulation; (3) Simulation-based inference; (4) Causal modeling and inference; (5) Agent-based modeling; (6) Probabilistic programming; (7) Differentiable programming; (8) Open-ended optimization; (9) Machine programming. We believe coordinated efforts between motifs offers immense opportunity to accelerate scientific discovery, from solving inverse problems in synthetic biology and climate science, to directing nuclear energy experiments and predicting emergent behavior in socioeconomic settings. We elaborate on each layer of the SI-stack, detailing the state-of-art methods, presenting examples to highlight challenges and opportunities, and advocating for specific ways to advance the motifs and the synergies from their combinations. Advancing and integrating these technologies can enable a robust and efficient hypothesis-simulation-analysis type of scientific method, which we introduce with several use-cases for human-machine teaming and automated science

An Evolutionary Algorithm to Generate Ellipsoid Detectors for Negative Selection

Negative selection is a process from the biological immune system that can be applied to two-class (self and nonself) classification problems. Negative selection uses only one class (self) for training, which results in detectors for the other class (nonself). This paradigm is especially useful for problems in which only one class is available for training, such as network intrusion detection. Previous work has investigated hyper-rectangles and hyper-spheres as geometric detectors. This work proposes ellipsoids as geometric detectors. First, the author establishes a mathematical model for ellipsoids. He develops an algorithm to generate ellipsoids by training on only one class of data. Ellipsoid mutation operators, an objective function, and a convergence technique are described for the evolutionary algorithm that generates ellipsoid detectors. Testing on several data sets validates this approach by showing that the algorithm generates good ellipsoid detectors. Against artificial data sets, the detectors generated by the algorithm match more than 90% of nonself data with no false alarms. Against a subset of data from the 1999 DARPA MIT intrusion detection data, the ellipsoids generated by the algorithm detected approximately 98% of nonself (intrusions) with an approximate 0% false alarm rate

Laboratory Directed Research and Development FY2010 Annual Report

A premier applied-science laboratory, Lawrence Livermore National Laboratory (LLNL) has at its core a primary national security mission - to ensure the safety, security, and reliability of the nation's nuclear weapons stockpile without nuclear testing, and to prevent and counter the spread and use of weapons of mass destruction: nuclear, chemical, and biological. The Laboratory uses the scientific and engineering expertise and facilities developed for its primary mission to pursue advanced technologies to meet other important national security needs - homeland defense, military operations, and missile defense, for example - that evolve in response to emerging threats. For broader national needs, LLNL executes programs in energy security, climate change and long-term energy needs, environmental assessment and management, bioscience and technology to improve human health, and for breakthroughs in fundamental science and technology. With this multidisciplinary expertise, the Laboratory serves as a science and technology resource to the U.S. government and as a partner with industry and academia. This annual report discusses the following topics: (1) Advanced Sensors and Instrumentation; (2) Biological Sciences; (3) Chemistry; (4) Earth and Space Sciences; (5) Energy Supply and Use; (6) Engineering and Manufacturing Processes; (7) Materials Science and Technology; Mathematics and Computing Science; (8) Nuclear Science and Engineering; and (9) Physics

BIOLOGICAL INSPIRED INTRUSION PREVENTION AND SELF-HEALING SYSTEM FOR CRITICAL SERVICES NETWORK

With the explosive development of the critical services network systems and Internet, the need for networks security systems have become even critical with the enlargement of information technology in everyday life. Intrusion Prevention System (IPS) provides an in-line mechanism focus on identifying and blocking malicious network activity in real time. This thesis presents new intrusion prevention and self-healing system (SH) for critical services network security. The design features of the proposed system are inspired by the human immune system, integrated with pattern recognition nonlinear classification algorithm and machine learning. Firstly, the current intrusions preventions systems, biological innate and adaptive immune systems, autonomic computing and self-healing mechanisms are studied and analyzed. The importance of intrusion prevention system recommends that artificial immune systems (AIS) should incorporate abstraction models from innate, adaptive immune system, pattern recognition, machine learning and self-healing mechanisms to present autonomous IPS system with fast and high accurate detection and prevention performance and survivability for critical services network system. Secondly, specification language, system design, mathematical and computational models for IPS and SH system are established, which are based upon nonlinear classification, prevention predictability trust, analysis, self-adaptation and self-healing algorithms. Finally, the validation of the system carried out by simulation tests, measuring, benchmarking and comparative studies. New benchmarking metrics for detection capabilities, prevention predictability trust and self-healing reliability are introduced as contributions for the IPS and SH system measuring and validation. Using the software system, design theories, AIS features, new nonlinear classification algorithm, and self-healing system show how the use of presented systems can ensure safety for critical services networks and heal the damage caused by intrusion. This autonomous system improves the performance of the current intrusion prevention system and carries on system continuity by using self-healing mechanism