A survey of simulation techniques in commerce and defence

Despite the developments in Modelling and Simulation (M&S) tools and techniques over the past years, there has been a gap in the M&S research and practice in healthcare on developing a toolkit to assist the modellers and simulation practitioners with selecting an appropriate set of techniques. This study is a preliminary step towards this goal. This paper presents some results from a systematic literature survey on applications of M&S in the commerce and defence domains that could inspire some improvements in the healthcare. Interim results show that in the commercial sector Discrete-Event Simulation (DES) has been the most widely used technique with System Dynamics (SD) in second place. However in the defence sector, SD has gained relatively more attention. SD has been found quite useful for qualitative and soft factors analysis. From both the surveys it becomes clear that there is a growing trend towards using hybrid M&S approaches

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

Topological descriptors for 3D surface analysis

We investigate topological descriptors for 3D surface analysis, i.e. the classification of surfaces according to their geometric fine structure. On a dataset of high-resolution 3D surface reconstructions we compute persistence diagrams for a 2D cubical filtration. In the next step we investigate different topological descriptors and measure their ability to discriminate structurally different 3D surface patches. We evaluate their sensitivity to different parameters and compare the performance of the resulting topological descriptors to alternative (non-topological) descriptors. We present a comprehensive evaluation that shows that topological descriptors are (i) robust, (ii) yield state-of-the-art performance for the task of 3D surface analysis and (iii) improve classification performance when combined with non-topological descriptors.Comment: 12 pages, 3 figures, CTIC 201

The wavelet transform for pre-processing IR spectra in the identification of mono- and di-substituted benzenes

This paper describes the wavelet transformation of IR spectra with the Daubechies analysing wavelet functions as a feature extracting method that successfully reduces the spectral data more than 20-fold with a significant improvement in the classification process