Principal manifolds and graphs in practice: from molecular biology to dynamical systems

We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.Comment: 12 pages, 9 figure

Exploratory Analysis of Functional Data via Clustering and Optimal Segmentation

We propose in this paper an exploratory analysis algorithm for functional data. The method partitions a set of functions into $K$ clusters and represents each cluster by a simple prototype (e.g., piecewise constant). The total number of segments in the prototypes, $P$, is chosen by the user and optimally distributed among the clusters via two dynamic programming algorithms. The practical relevance of the method is shown on two real world datasets

Building Adaptive Basis Functions with a Continuous Self-Organizing Map

This paper introduces CSOM, a continuous version of the Self-Organizing Map (SOM). The CSOM network generates maps similar to those created with the original SOM algorithm but, due to the continuous nature of the mapping, CSOM outperforms the SOM on function approximation tasks. CSOM integrates self-organization and smooth prediction into a single process. This is a departure from previous work that required two training phases, one to self-organize a map using the SOM algorithm, and another to learn a smooth approximation of a function. System performance is illustrated with three examples.Office of Naval Research (N00014-95-10409, N00014-95-0657

A Neural Model of Visually Guided Steering, Obstacle Avoidance, and Route Selection

A neural model is developed to explain how humans can approach a goal object on foot while steering around obstacles to avoid collisions in a cluttered environment. The model uses optic flow from a 3D virtual reality environment to determine the position of objects based on motion discontinuities, and computes heading direction, or the direction of self-motion, from global optic flow. The cortical representation of heading interacts with the representations of a goal and obstacles such that the goal acts as an attractor of heading, while obstacles act as repellers. In addition the model maintains fixation on the goal object by generating smooth pursuit eye movements. Eye rotations can distort the optic flow field, complicating heading perception, and the model uses extraretinal signals to correct for this distortion and accurately represent heading. The model explains how motion processing mechanisms in cortical areas MT, MST, and posterior parietal cortex can be used to guide steering. The model quantitatively simulates human psychophysical data about visually-guided steering, obstacle avoidance, and route selection.Air Force Office of Scientific Research (F4960-01-1-0397); National Geospatial-Intelligence Agency (NMA201-01-1-2016); National Science Foundation (SBE-0354378); Office of Naval Research (N00014-01-1-0624

A self-organized model for cell-differentiation based on variations of molecular decay rates

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes). The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of this dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein) in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers) vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.Comment: 16 pages, 5 figure

Dimensionality Reduction Mappings

A wealth of powerful dimensionality reduction methods has been established which can be used for data visualization and preprocessing. These are accompanied by formal evaluation schemes, which allow a quantitative evaluation along general principles and which even lead to further visualization schemes based on these objectives. Most methods, however, provide a mapping of a priorly given finite set of points only, requiring additional steps for out-of-sample extensions. We propose a general view on dimensionality reduction based on the concept of cost functions, and, based on this general principle, extend dimensionality reduction to explicit mappings of the data manifold. This offers simple out-of-sample extensions. Further, it opens a way towards a theory of data visualization taking the perspective of its generalization ability to new data points. We demonstrate the approach based on a simple global linear mapping as well as prototype-based local linear mappings.

Artificial neural networks in geospatial analysis

Artificial neural networks are computational models widely used in geospatial analysis for data classification, change detection, clustering, function approximation, and forecasting or prediction. There are many types of neural networks based on learning paradigm and network architectures. Their use is expected to grow with increasing availability of massive data from remote sensing and mobile platforms