Drawing inspiration from a recent construction of a polyhedral structure associated with an icosahedrally-symmetric map on the Riemann sphere, the article shows how to build such "dynamical polyhedra" for other icosahedral maps. First, icosahedral algebra is used to determine a special family of maps with 60 periodic critical points. The topological behavior of each map is worked out and results in a geometric algorithm that constructs a system of edges---the dynamical polyhedron---in natural correspondence to a map's topology. It turns out that the maps' descriptions fall into classes the presentation of which concludes the paper.

Ligand-based virtual screening (LBVS) is a promising approach for rapid and low-cost screening of potentially bioactive molecules in the early stage of drug discovery. Compared with traditional similarity-based machine learning methods, deep learning frameworks for LBVS can more effectively extract high-order molecule structure representations from molecular fingerprints or structures. However, the 3D conformation of a molecule largely influences its bioactivity and physical properties, and has rarely been considered in previous deep learning-based LBVS methods. Moreover, the relative bioactivity benchmark dataset is still lacking. To address these issues, we introduce a novel end-to-end deep learning architecture trained from molecular conformers for LBVS. We first extracted molecule conformers from multiple public molecular bioactivity data and consolidated them into a large-scale bioactivity benchmark dataset, which totally includes millions of endpoints and molecules corresponding to 954 targets. Then, we devised a deep learning-based LBVS called EquiVS to learn molecule representations from conformers for bioactivity prediction. Specifically, graph convolutional network (GCN) and equivariant graph neural network (EGNN) are sequentially stacked to learn high-order molecule-level and conformer-level representations, followed by attention-based deep multiple-instance learning (MIL) to aggregate these representations and then predict the potential bioactivity for the query molecule on a given target. We conducted various experiments to validate the data quality of our benchmark dataset, and confirmed EquiVS achieved better performance compared with 10 traditional machine learning or deep learning-based LBVS methods. Further ablation studies demonstrate the significant contribution of molecular conformation for bioactivity prediction, as well as the reasonability and non-redundancy of deep learning architecture in EquiVS. Finally, a model interpretation case study on CDK2 shows the potential of EquiVS in optimal conformer discovery. The overall study shows that our proposed benchmark dataset and EquiVS method have promising prospects in virtual screening applications.

We introduce poly-symplectic extension of Souriau Lie groups Thermodynamics based on higher-order model of statistical physics introduced by R.S. Ingarden. This extended model could be used for small data analytics and Machine Learning on Lie groups. Souriau Geometric Theory of Heat is well adapted to describe density of probability (Maximum Entropy Gibbs density) of data living on groups or on homogeneous manifolds. For Small Data Analytics (Rarified Gases , sparse statistical survey,…), density of maximum entropy should consider Higher Order Moments constraints (Gibbs density is not only defined by first moment but fluctuations request 2nd order and higher moments) as introduced by R.S. Ingarden. We use Poly-sympletic model introduced by Christian Günther, replacing the symplectic form by a vector-valued form. The poly-symplectic approach generalizes the Noether theorem, the existence of momentum mappings, the Lie algebra structure of the space of currents, the (non-)equivariant cohomology and the classification of G-homogeneous systems. The formalism is covariant, i.e. no special coordinates or coordinate systems on the parameter space are used to construct the Hamiltonian equations. We underline the contextures of these models, and the process to build these generic structures.