14,908 research outputs found
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
Static Analysis of Functional Programs
In this paper, the static analysis of programs in the functional programming language Miranda* is described based on two graph models. A new control-flow graph model of Miranda definitions is presented, and a model with four classes of callgraphs. Standard software metrics are applicable to these models. A Miranda front end for Prometrix, ¿, a tool for the automated analysis of flowgraphs and callgraphs, has been developed. This front end produces the flowgraph and callgraph representations of Miranda programs. Some features of the metric analyser are illustrated with an example program. The tool provides a promising access to standard metrics on functional programs
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