207 research outputs found

    A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

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    Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the folding process. Coupled with high computing power and large scale storage, researchers now can computationally simulate the protein folding process in atomistic details at femtosecond temporal resolution. Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. As a result, effectively managing and analyzing such trajectories is becoming increasingly important. In this article, we present a spatio-temporal mining approach to analyze protein folding trajectories. It exploits the simplicity of contact maps, while also integrating 3D structural information in the analysis. It characterizes the dynamic folding process by first identifying spatio-temporal association patterns in contact maps, then studying how such patterns evolve along a folding trajectory. We demonstrate that such patterns can be leveraged to summarize folding trajectories, and to facilitate the detection and ordering of important folding events along a folding path. We also show that such patterns can be used to identify a consensus partial folding pathway across multiple folding trajectories. Furthermore, we argue that such patterns can capture both local and global structural topology in a 3D protein conformation, thereby facilitating effective structural comparison amongst conformations. We apply this approach to analyze the folding trajectories of two small synthetic proteins-BBA5 and GSGS (or Beta3S). We show that this approach is promising towards addressing the above issues, namely, folding trajectory summarization, folding events detection and ordering, and consensus partial folding pathway identification across trajectories

    Path finding on a spherical self-organizing map using distance transformations

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    Spatialization methods create visualizations that allow users to analyze high-dimensional data in an intuitive manner and facilitates the extraction of meaningful information. Just as geographic maps are simpli ed representations of geographic spaces, these visualizations are esssentially maps of abstract data spaces that are created through dimensionality reduction. While we are familiar with geographic maps for path planning/ nding applications, research into using maps of high-dimensional spaces for such purposes has been largely ignored. However, literature has shown that it is possible to use these maps to track temporal and state changes within a high-dimensional space. A popular dimensionality reduction method that produces a mapping for these purposes is the Self-Organizing Map. By using its topology preserving capabilities with a colour-based visualization method known as the U-Matrix, state transitions can be visualized as trajectories on the resulting mapping. Through these trajectories, one can gather information on the transition path between two points in the original high-dimensional state space. This raises the interesting question of whether or not the Self-Organizing Map can be used to discover the transition path between two points in an n-dimensional space. In this thesis, we use a spherically structured Self-Organizing Map called the Geodesic Self-Organizing Map for dimensionality reduction and the creation of a topological mapping that approximates the n-dimensional space. We rst present an intuitive method for a user to navigate the surface of the Geodesic SOM. A new application of the distance transformation algorithm is then proposed to compute the path between two points on the surface of the SOM, which corresponds to two points in the data space. Discussions will then follow on how this application could be improved using some form of surface shape analysis. The new approach presented in this thesis would then be evaluated by analyzing the results of using the Geodesic SOM for manifold embedding and by carrying out data analyses using carbon dioxide emissions data

    Path finding on a spherical self-organizing map using distance transformations

    Get PDF
    Spatialization methods create visualizations that allow users to analyze high-dimensional data in an intuitive manner and facilitates the extraction of meaningful information. Just as geographic maps are simpli ed representations of geographic spaces, these visualizations are esssentially maps of abstract data spaces that are created through dimensionality reduction. While we are familiar with geographic maps for path planning/ nding applications, research into using maps of high-dimensional spaces for such purposes has been largely ignored. However, literature has shown that it is possible to use these maps to track temporal and state changes within a high-dimensional space. A popular dimensionality reduction method that produces a mapping for these purposes is the Self-Organizing Map. By using its topology preserving capabilities with a colour-based visualization method known as the U-Matrix, state transitions can be visualized as trajectories on the resulting mapping. Through these trajectories, one can gather information on the transition path between two points in the original high-dimensional state space. This raises the interesting question of whether or not the Self-Organizing Map can be used to discover the transition path between two points in an n-dimensional space. In this thesis, we use a spherically structured Self-Organizing Map called the Geodesic Self-Organizing Map for dimensionality reduction and the creation of a topological mapping that approximates the n-dimensional space. We rst present an intuitive method for a user to navigate the surface of the Geodesic SOM. A new application of the distance transformation algorithm is then proposed to compute the path between two points on the surface of the SOM, which corresponds to two points in the data space. Discussions will then follow on how this application could be improved using some form of surface shape analysis. The new approach presented in this thesis would then be evaluated by analyzing the results of using the Geodesic SOM for manifold embedding and by carrying out data analyses using carbon dioxide emissions data

    Tour recommendation for groups

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    Consider a group of people who are visiting a major touristic city, such as NY, Paris, or Rome. It is reasonable to assume that each member of the group has his or her own interests or preferences about places to visit, which in general may differ from those of other members. Still, people almost always want to hang out together and so the following question naturally arises: What is the best tour that the group could perform together in the city? This problem underpins several challenges, ranging from understanding people’s expected attitudes towards potential points of interest, to modeling and providing good and viable solutions. Formulating this problem is challenging because of multiple competing objectives. For example, making the entire group as happy as possible in general conflicts with the objective that no member becomes disappointed. In this paper, we address the algorithmic implications of the above problem, by providing various formulations that take into account the overall group as well as the individual satisfaction and the length of the tour. We then study the computational complexity of these formulations, we provide effective and efficient practical algorithms, and, finally, we evaluate them on datasets constructed from real city data

    Unveiling the frontiers of deep learning: innovations shaping diverse domains

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    Deep learning (DL) enables the development of computer models that are capable of learning, visualizing, optimizing, refining, and predicting data. In recent years, DL has been applied in a range of fields, including audio-visual data processing, agriculture, transportation prediction, natural language, biomedicine, disaster management, bioinformatics, drug design, genomics, face recognition, and ecology. To explore the current state of deep learning, it is necessary to investigate the latest developments and applications of deep learning in these disciplines. However, the literature is lacking in exploring the applications of deep learning in all potential sectors. This paper thus extensively investigates the potential applications of deep learning across all major fields of study as well as the associated benefits and challenges. As evidenced in the literature, DL exhibits accuracy in prediction and analysis, makes it a powerful computational tool, and has the ability to articulate itself and optimize, making it effective in processing data with no prior training. Given its independence from training data, deep learning necessitates massive amounts of data for effective analysis and processing, much like data volume. To handle the challenge of compiling huge amounts of medical, scientific, healthcare, and environmental data for use in deep learning, gated architectures like LSTMs and GRUs can be utilized. For multimodal learning, shared neurons in the neural network for all activities and specialized neurons for particular tasks are necessary.Comment: 64 pages, 3 figures, 3 table

    Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

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    An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u
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