Decision trees, monotone functions, and semimatroids

We define decision trees for monotone functions on a simplicial complex. We define homology decidability of monotone functions, and show that various monotone functions related to semimatroids are homology decidable. Homology decidability is a generalization of semi-nonevasiveness, a notion due to Jonsson. The motivating example is the complex of bipartite graphs, whose Betti numbers are unknown in general. We show that these monotone functions have optimum decision trees, from which we can compute relative Betti numbers of related pairs of simplicial complexes. Moreover, these relative Betti numbers are coefficients of evaluations of the Tutte polynomial, and every semimatroid collapses onto its broken circuit complex.Comment: 16 page

Avoiding the Global Sort: A Faster Contour Tree Algorithm

We revisit the classical problem of computing the \emph{contour tree} of a scalar field $f:\mathbb{M} \to \mathbb{R}$, where $\mathbb{M}$ is a triangulated simplicial mesh in $\mathbb{R}^d$. The contour tree is a fundamental topological structure that tracks the evolution of level sets of $f$ and has numerous applications in data analysis and visualization. All existing algorithms begin with a global sort of at least all critical values of $f$, which can require (roughly) $\Omega(n\log n)$ time. Existing lower bounds show that there are pathological instances where this sort is required. We present the first algorithm whose time complexity depends on the contour tree structure, and avoids the global sort for non-pathological inputs. If $C$ denotes the set of critical points in $\mathbb{M}$, the running time is roughly $O(\sum_{v \in C} \log \ell_v)$, where $\ell_v$ is the depth of $v$ in the contour tree. This matches all existing upper bounds, but is a significant improvement when the contour tree is short and fat. Specifically, our approach ensures that any comparison made is between nodes in the same descending path in the contour tree, allowing us to argue strong optimality properties of our algorithm. Our algorithm requires several novel ideas: partitioning $\mathbb{M}$ in well-behaved portions, a local growing procedure to iteratively build contour trees, and the use of heavy path decompositions for the time complexity analysis

Building Efficient and Compact Data Structures for Simplicial Complexes

The Simplex Tree (ST) is a recently introduced data structure that can represent abstract simplicial complexes of any dimension and allows efficient implementation of a large range of basic operations on simplicial complexes. In this paper, we show how to optimally compress the Simplex Tree while retaining its functionalities. In addition, we propose two new data structures called the Maximal Simplex Tree (MxST) and the Simplex Array List (SAL). We analyze the compressed Simplex Tree, the Maximal Simplex Tree, and the Simplex Array List under various settings.Comment: An extended abstract appeared in the proceedings of SoCG 201

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. Multicomponent persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for chemical and biological problems. Extensive numerical experiments involving more than 4,000 protein-ligand complexes from the PDBBind database and near 100,000 ligands and decoys in the DUD database are performed to test respectively the scoring power and the virtual screening power of the proposed topological approaches. It is demonstrated that the present approaches outperform the modern machine learning based methods in protein-ligand binding affinity predictions and ligand-decoy discrimination