Persistent Homology in Sparse Regression and its Application to Brain Morphometry

Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region.Comment: submitted to IEEE Transactions on Medical Imagin

Intrinsic Volumes of Random Cubical Complexes

Intrinsic volumes, which generalize both Euler characteristic and Lebesgue volume, are important properties of $d$-dimensional sets. A random cubical complex is a union of unit cubes, each with vertices on a regular cubic lattice, constructed according to some probability model. We analyze and give exact polynomial formulae, dependent on a probability, for the expected value and variance of the intrinsic volumes of several models of random cubical complexes. We then prove a central limit theorem for these intrinsic volumes. For our primary model, we also prove an interleaving theorem for the zeros of the expected-value polynomials. The intrinsic volumes of cubical complexes are useful for understanding the shape of random $d$-dimensional sets and for characterizing noise in applications.Comment: 17 pages with 7 figures; this version includes a central limit theore

Exploring the potential of 3D Zernike descriptors and SVM for protein\u2013protein interface prediction

Abstract Background The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. Results In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein–Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). Conclusions The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class

Searching high order invariants in computer imagery

In this paper, we present a direct computational application of Homological Perturbation Theory (HPT, for short) to computer imagery. More precisely, the formulas of the A ∞–coalgebra maps Δ 2 and Δ 3 using the notion of AT-model of a digital image, and the HPT technique are implemented. The method has been tested on some specific examples, showing the usefulness of this computational tool for distinguishing 3D digital images