Long Short-Term Memory Recurrent Neural Networks (LSTM-RNN) are one of the most powerful dynamic classifiers publicly known. The network itself and the related learning algorithms are reasonably well documented to get an idea how it works. This paper will shed more light into understanding how LSTM-RNNs evolved and why they work impressively well, focusing on the early, ground-breaking publications. We significantly improved documentation and fixed a number of errors and inconsistencies that accumulated in previous publications. To support understanding we as well revised and unified the notation used.
Interaction computing is inspired by the observation that cell metabolic/regulatory systems construct order dynamically, through constrained interactions between their components and based on a wide range of possible inputs and environmental conditions. The goals of this work are to (i) identify and understand mathematically the natural subsystems and hierarchical relations in natural systems enabling this and (ii) use the resulting insights to define a new model of computation based on interactions that is useful for both biology and computation. The dynamical characteristics of the cellular pathways studied in systems biology relate, mathematically, to the computational characteristics of automata derived from them, and their internal symmetry structures to computational power. Finite discrete automata models of biological systems such as the lac operon, the Krebs cycle and p53-mdm2 genetic regulation constructed from systems biology models have canonically associated algebraic structures (their transformation semigroups). These contain permutation groups (local substructures exhibiting symmetry) that correspond to 'pools of reversibility'. These natural subsystems are related to one another in a hierarchical manner by the notion of 'weak control'. We present natural subsystems arising from several biological examples and their weak control hierarchies in detail. Finite simple non-Abelian groups are found in biological examples and can be harnessed to realize finitary universal computation. This allows ensembles of cells to achieve any desired finitary computational transformation, depending on external inputs, via suitably constrained interactions. Based on this, interaction machines that grow and change their structure recursively are introduced and applied, providing a natural model of computation driven by interactions.In the 21st century, algebra will be as important for biology as chemistry was in the 20th century.-Günter P. Wagner
In a software system it is possible to quantify the amount of information that is leaked or corrupted by analysing the flows of information present in the source code. In a cyber-physical system, information flows are not only present at the digital level, but also at a physical level, and to and fro the two levels. In this work, we provide a methodology to formally analyse a Cyber-Physical System composite model (combining physics and control) using an information flow-theoretic approach. We use this approach to quantify the level of vulnerability of a system with respect to attackers with different capabilities. We illustrate our approach by means of a water distribution case study.
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