LNCS

We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements

Memristive Learning Cellular Automata: Theory and Applications

Memristors are novel non volatile devices that manage to combine storing and processing capabilities in the same physical place.Their nanoscale dimensions and low power consumption enable the further design of various nanoelectronic processing circuits and corresponding computing architectures, like neuromorhpic, in memory, unconventional, etc.One of the possible ways to exploit the memristor's advantages is by combining them with Cellular Automata (CA).CA constitute a well known non von Neumann computing architecture that is based on the local interconnection of simple identical cells forming N-dimensional grids.These local interconnections allow the emergence of global and complex phenomena.In this paper, we propose a hybridization of the CA original definition coupled with memristor based implementation, and, more specifically, we focus on Memristive Learning Cellular Automata (MLCA), which have the ability of learning using also simple identical interconnected cells and taking advantage of the memristor devices inherent variability.The proposed MLCA circuit level implementation is applied on optimal detection of edges in image processing through a series of SPICE simulations, proving its robustness and efficacy

On the development of slime mould morphological, intracellular and heterotic computing devices

The use of live biological substrates in the fabrication of unconventional computing (UC) devices is steadily transcending the barriers between science fiction and reality, but efforts in this direction are impeded by ethical considerations, the field’s restrictively broad multidisciplinarity and our incomplete knowledge of fundamental biological processes. As such, very few functional prototypes of biological UC devices have been produced to date. This thesis aims to demonstrate the computational polymorphism and polyfunctionality of a chosen biological substrate — slime mould Physarum polycephalum, an arguably ‘simple’ single-celled organism — and how these properties can be harnessed to create laboratory experimental prototypes of functionally-useful biological UC prototypes. Computing devices utilising live slime mould as their key constituent element can be developed into a) heterotic, or hybrid devices, which are based on electrical recognition of slime mould behaviour via machine-organism interfaces, b) whole-organism-scale morphological processors, whose output is the organism’s morphological adaptation to environmental stimuli (input) and c) intracellular processors wherein data are represented by energetic signalling events mediated by the cytoskeleton, a nano-scale protein network. It is demonstrated that each category of device is capable of implementing logic and furthermore, specific applications for each class may be engineered, such as image processing applications for morphological processors and biosensors in the case of heterotic devices. The results presented are supported by a range of computer modelling experiments using cellular automata and multi-agent modelling. We conclude that P. polycephalum is a polymorphic UC substrate insofar as it can process multimodal sensory input and polyfunctional in its demonstrable ability to undertake a variety of computing problems. Furthermore, our results are highly applicable to the study of other living UC substrates and will inform future work in UC, biosensing, and biomedicine

Computational Modeling, Formal Analysis, and Tools for Systems Biology.

As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science

Computer-Aided Clinical Trials For Medical Devices

Life-critical medical devices require robust safety and efficacy to treat patient populations with potentially large patient heterogeneity. Today, the de facto standard for evaluating medical devices is the randomized controlled trial. However, even after years of device development many clinical trials fail. For example, in the Rhythm ID Goes Head to Head Trial (RIGHT) the risk for inappropriate therapy by implantable cardioverter defibrillators (ICDs) actually increased relative to control treatments. With recent advances in physiological modeling and devices incorporating more complex software components, population-level device outcomes can be obtained with scalable simulations. Consequently, there is a need for data-driven approaches to provide early insight prior to the trial, lowering the cost of trials using patient and device models, and quantifying the robustness of the outcome. This work presents a clinical trial modeling and statistical framework which utilizes simulation to improve the evaluation of medical device software, such as the algorithms in ICDs. First, a method for generating virtual cohorts using a physiological simulator is introduced. Next, we present our framework which combines virtual cohorts with real data to evaluate the efficacy and allows quantifying the uncertainty due to the use of simulation. Results predicting the outcome of RIGHT and improving statistical power while reducing the sample size are shown. Finally, we improve device performance with an approach using Bayesian optimization. Device performance can degrade when deployed to a general population despite success in clinical trials. Our approach improves the performance of the device with outcomes aligned with the MADIT-RIT clinical trial. This work provides a rigorous approach towards improving the development and evaluation of medical treatments