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Publications about 'geometry'
Books and proceedings
  1. E.D. Sontag. Polynomial Response Maps, volume 13 of Lecture Notes in Control and Information Sciences. Springer-Verlag, Berlin, 1979. [PDF] Keyword(s): realization theory, discrete-time, real algebraic geometry.
    Abstract:
    (This is a monograph based upon Eduardo Sontag's Ph.D. thesis. The contents are basically the same as the thesis, except for a very few revisions and extensions.) This work deals the realization theory of discrete-time systems (with inputs and outputs, in the sense of control theory) defined by polynomial update equations. It is based upon the premise that the natural tools for the study of the structural-algebraic properties (in particular, realization theory) of polynomial input/output maps are provided by algebraic geometry and commutative algebra, perhaps as much as linear algebra provides the natural tools for studying linear systems. Basic ideas from algebraic geometry are used throughout in system-theoretic applications (Hilbert's basis theorem to finite-time observability, dimension theory to minimal realizations, Zariski's Main Theorem to uniqueness of canonical realizations, etc). In order to keep the level elementary (in particular, not utilizing sheaf-theoretic concepts), certain ideas like nonaffine varieties are used only implicitly (eg., quasi-affine as open sets in affine varieties) or in technical parts of a few proofs, and the terminology is similarly simplified (e.g., "polynomial map" instead of "scheme morphism restricted to k-points", or "k-space" instead of "k-points of an affine k-scheme").


Articles in journal or book chapters
  1. S. Wang, E.D. Sontag, and D.A. Lauffenburger. What cannot be seen correctly in 2D visualizations of single-cell 'omics data?. Cell Systems, 14:723-731, 2023. [WWW] [PDF] Keyword(s): visualization, single-cell data, tSNE, UMAP.
    Abstract:
    Single-cell -omics datasets are high-dimensional and difficult to visualize. A common strategy for exploring such data is to create and analyze 2D projections. Such projections may be highly nonlinear, and implementation algorithms are designed with the goal of preserving aspects of the original high-dimensional shape of data such as neighborhood relationships or metrics. However, important aspects of high-dimensional geometry are known from mathematical theory to have no equivalent representation in 2D, or are subject to large distortions, and will therefore be misrepresented or even invisible in any possible 2D representation. We show that features such as quantitative distances, relative positioning, and qualitative neighborhoods of high-dimensional data points will always be misrepresented in 2D projections. Our results rely upon concepts from differential geometry, combinatorial geometry, and algebraic topology. As an illustrative example, we show that even a simple single-cell RNA sequencing dataset will always be distorted, no matter what 2D projection is employed. We also discuss how certain recently developed computational tools can help describe the high-dimensional geometric features that will be necessarily missing from any possible 2D projections.


  2. M. Chaves, A. M. Sengupta, and E.D. Sontag. Geometry and topology of parameter space: investigating measures of robustness in regulatory networks. J. of Mathematical Biology, 59:315-358, 2009. [PDF] Keyword(s): identifiability, robust, robustness, geometry.
    Abstract:
    The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this robustness property is a challenging task, but mathematical models have often associated it to the volume of the space of admissible parameters. Not only the volume of the space but also its topology and geometry contain information on essential aspects of the network, including feasible pathways, switching between two parallel pathways or distinct/disconnected active regions of parameters. A method is presented here to characterize the space of admissible parameters, by writing it as a semi-algebraic set, and then theoretically analyzing its topology and geometry, as well as volume. This method provides a more objective and complete measure of the robustness of a developmental module. As a detailed case study, the segment polarity gene network is analyzed.


  3. A. Dayarian, M. Chaves, E.D. Sontag, and A. M. Sengupta. Shape, Size and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks. PLoS Computational Biology, 5:e10000256, 2009. [PDF] Keyword(s): identifiability, robust, robustness, geometry.
    Abstract:
    The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the region in the parameter space in which the system is functional. In recent work, we emphasized that topology and geometry matter, as well as volume. In this paper, and using the segment polarity gene network to illustrate our approach, we show that random walks in parameter space and how they exit the feasible region provide a rich perspective on the different modes of failure of a model. In particular, for the segment polarity network, we found that, between two alternative ways of activating Wingless, one is more robust. Our method provides a more complete measure of robustness to parameter variation. As a general modeling strategy, our approach is an interesting alternative to Boolean representation of biochemical networks.


  4. M. Chaves, E.D. Sontag, and R. Albert. Methods of robustness analysis for Boolean models of gene control networks. IET Systems Biology, 153:154-167, 2006. [PDF] Keyword(s): systems biology, biochemical networks, boolean systems, identifiability, robust, robustness, geometry, Boolean, segment polarity network, gene and protein networks, hybrid systems.
    Abstract:
    As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states (expressed or not expressed) for each gene or protein in the network as well as a high level of synchronization among the various regulatory processes. In this paper, we discuss and compare two possible methods of adapting qualitative models to incorporate the continuous-time character of regulatory networks. The first method consists of introducing asynchronous updates in the Boolean model. In the second method, we adopt the approach introduced by L. Glass to obtain a set of piecewise linear differential equations which continuously describe the states of each gene or protein in the network. We apply both methods to a particular example: a Boolean model of the segment polarity gene network of Drosophila melanogaster. We analyze the dynamics of the model, and provide a theoretical characterization of the model's gene pattern prediction as a function of the timescales of the various processes.


Conference articles
  1. T. Asano, J. Hershberger, J. Pach, E.D. Sontag, D. Souivaine, and S. Suri. Separating bi-chromatic points by parallel lines. In Proceedings of the Second Canadian Conf. on Computational Geometry, Ottawa, Canada, 1990, pages 46-49, 1990. [PDF] Keyword(s): computational geometry.
    Abstract:
    Given a 2-coloring of the vertices of a regular n-gon P, how many parallel lines are needed to separate the vertices into monochromatic subsets? We prove that floor(n/2) is a tight upper bound, and also provide an O(n log n) time algorithm to determine the direction that gives the minimum number of lines. If the polygon is a non-regular convex polygon, then n-3 lines may be necessary, while n-2 lines always suffice. This problem arises in machine learning and has implications about the representational capabilities of some neural networks.


Miscellaneous
  1. M. D. Kvalheim and E. D. Sontag. Why do autoencoders work?, 2023. Note: Preprint in https://arxiv.org/abs/2310.02250 (see linked pdf). [PDF]
    Abstract:
    Deep neural network autoencoders are routinely used computationally for model reduction. They allow recognizing the intrinsic dimension of data that lie in a k-dimensional subset K of an input Euclidean space $\R^n$. The underlying idea is to obtain both an encoding layer that maps $\R^n$ into $\R^k$ (called the bottleneck layer or the space of latent variables) and a decoding layer that maps $\R^k$ back into $\R^n$, in such a way that the input data from the set K is recovered when composing the two maps. This is achieved by adjusting parameters (weights) in the network to minimize the discrepancy between the input and the reconstructed output. Since neural networks (with continuous activation functions) compute continuous maps, the existence of a network that achieves perfect reconstruction would imply that K is homeomorphic to a k-dimensional subset of $\R^k$, so clearly there are topological obstructions to finding such a network. On the other hand, in practice the technique is found to "work" well, which leads one to ask if there is a way to explain this effectiveness. We show that, up to small errors, indeed the method is guaranteed to work. This is done by appealing to certain facts from differential geometry. A computational example is also included to illustrate the ideas.



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