Automated Reasoning for Systems Biology and Medici

文件名称: Automated Reasoning for Systems Biology and Medicine

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详细说明：Automated Reasoning for Systems Biology and Medicine，2019Endorsed by the International Society for Computational Biology, the Computational Biology series publishes the very latest, high-quality research devoted to specific issues in computer-assisted analysis of biological data. The main emphasis is on current scientific developments and innovative techniques in computational biology(bioinformatics), bringing to light methods from mathemat icS, statistics and computer science that directly address biological problems currently under investigation The series offers publications that present the state-of-the-art regarding the problems in question; show computational biology/bioinformatics methods at work: and finally discuss anticipated demands regarding developments in future methodology. Titles can range from focused monographs, to undergraduate and graduate textbooks, and professional text/reference works Moreinformationaboutthisseriesathttp://www.springer.com/series/5769 Pietro lio. Paolo zuliani Editors Automated reasoning for Systems Biology and medicine S pringer editors Pietro lio Paolo zulia Department of Computer Science School of computing and technology Newcastle University niversity of Cambridge Newcastle UK Cambridge UK ISSN1568-2684 Issn 2662-2432 (electronic) Computational Biology ISBN978-3-030-17296-1 ISBN978-3-030-17297-8( e Book) https://doi.org/10.1007/978-3-030-17297-8 C Springer nature Switzerland ag 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from he relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse ll, 6330 Cham, Switzerland Preface This book originates from the International Workshop on Automated Reasoning for Systems Biology and Medicine (arsbm 2016) that was held on 20 September 2016, at the Computer Laboratory of the University of Cambridge. This Institution truly a place of innovators-has a long, successful tradition for cultivating interdisciplinarity and multidisciplinarity. In the same spirit, this volume presents the very best research in an exciting new, multidisciplinary area: the application of formal, automated reasoning techniques for analysing complex models and data in Systems Biology and Systems Medicine Automated reasoning is the field of computer science devoted to the develop- ment of algorithms that return trusted answers, so that sound logical reasoning can be built upon. The main focus of the workshop was on the theory of delta-decidability (Gao, avigad, Clarke. Delta- Decidability over the reals, LICs 2012) and its biological and biomedical applications however, in reality, the variety of scientific topics discussed ranged from computational modelling,to formal methods, to machine learning and other fields of computer science. The workshop predated the conference CMSB 2016 so it generated cross-fertilisation and resonance particularly between fundamental issues and innovative applications Systems Biology and Systems Medicine started in the past 20 years as efforts to understand the enormous complexity of life from a computational point of view This has generated a wealth of new knowledge in the form of both computational models and data, whose staggering complexity makes manual analysis methods infeasible. Sound trusted and automated ways to analyse models and data are thus required in order to be able to trust the models' predictions and data analysis outcomes. Overall, this is crucial to engineering safe biomedical devices and safe linical protocols, and reducing our reliance on wet-lab experiments and clinical trials, thus reducing both economic and societal costs Some examples of the questions tackled in the area include: can we automati cally revise medications in patients with multiple chronic conditions? Again,can we verify that an artificial pancreas system delivers insulin in a way that type 1 diabetic patients never suffer from hyperglycaemia or hypoglycaemia? Finally, can we predict the effect of a mutation on cancer cells? Preface These aspects are clearly reflected in the book, which contains 17 high-quality hapters from world-leading researchers working on related fields. Each chapter has been peer-reviewed by at least two independent reviewers from an international pool of experts(see the Reviewers list below). The chapters are grouped in four different clusters based on the technique used Model Checking g Formal Methods and logic Stochastic Modelling and Analysis Machine Learning and Artificial Intelligence To help the reader with a life sciences background, another organisation of the chapters can be given in terms of application areas touched upon Application area Chapter(s) Artificial pancreas Autophagy/apoptosis Calcium dynamics 13 Cancer 5,7,10,15,17 Cardiac cells Cell cycle Clinical environments guidelines 8.9 Diabetes(see Artificial pancreas) epidemics Epidermal differentiation 2 Genetic circuits(see Synthetic biology) Iron homeostasis Metabolic networks 7.15 Myeloid differentiation narmacokinetics Remyelination 11 Signalling pathways 1,3,7,10,13 Stem cells Synthetic biology 12.16 This volume makes the most advanced contribution of the international commu nity to the research issues surrounding the fascinating world of automated reasoning in Systems Biology and Systems Medicine. We hope that you enjoy the chapters as much as we enjoyed organising the workshop and putting this collection together Preface We thank the invited speakers to the workshop and the authors who submitted their work to this volume. and we thank the reviewers for their hard work il reviewing the submissions and taking part in post-review discussions. Finally,we would like to express our sincere thanks to Springer for their support during the production of the volume Cambridge, UK Pietro lio Newcastle UK Paolo zuliani Contents Part I Model Checking Model Checking Approach to the Analysis of Biological Systems Nikola benes. Lubos brim Samuel Pastva and David Safranek 2 Automated Reasoning for the synthesis and analysis of Biological Programs 37 Sara-Jane dunn and Boyan Yordanov 3 Statistical Model Checking-Based Analysis of Biological Networks Bing Liu, Benjamin M. Gyori and P s. Thiagarajan 4 Models, Devices, Properties, and Verification of Artificial Pancreas Systems 93 Taisa Kushner, B. Wayne Bequette, Faye Cameron Gregory Forlenza, David Maahs and Sriram Sankaranarayanan 5 USing State Space Exploration to Determine How Gene Regulatory Networks Constrain Mutation Order in Cancer Evolution 133 Matthew A. Clarke, Steven Woodhouse, Nir Piterman Benjamin A. Hall and Jasmin Fisher Part Ii Formal Methods and logic 6 Set-Based Analysis for Biological Modeling 157 Thao Dang, Tommaso Dreossi, Eric Fanchon, Oded maler. Carla piazza and alexandre rocca 7 Logic and Linear Programs to Understand Cancer Response Misbah razzaq, Lokmane Chebouba, Pierre Le Jeune, Hanen mhamdi. Carito Guziolowski and jeremie bourdon Contents 8 Logic-Based Formalization of System Requirements for Integrated Clinical Environments 215 Cinzia bernardeschi. Andrea domenici and paolo masci 9 Balancing Prescriptions with Constraint Solvers ........ 243 Juliana K f bowles and marco b. caminati 10 Metastable Regimes and Tipping Points of Biochemical Networks with Potential Applications in Precision Medicine Satya Swarup Samal, Jeyashree Krishnan, Ali Hadizadeh esfahani Christoph luders Andreas weber and ovidiu radulescu Part Ili Stochastic Modelling and Analysis 11 Stochastic Spatial Modelling of the Remyelination Process in Multiple sclerosis Lesions 299 Ludovica luisa vissat, jane hillston and anna williams 12 Approximation Techniques for Stochastic Analysis of Biological Systems 327 Thakur Neupane, Zhen Zhang, Curtis Madsen, Hao Zheng and Chris j. myers 13 A Graphical Approach for Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets 349 Amr Ismail, Mostafa Herajy and monika Heiner 14 Methods for Personalised Delivery Rate Computation for IV Administered Anesthetic Propofol 369 Alena Simalatsar, Monia Guidi, Pierre Roduit and Thierry Buclin Part Iv Machine Learning and artificial Intelligence 15 Towards the Integration of Metabolic Network Modelling and Machine Learning for the routine analysis of High-Throughput Patient Dat Maria pires pacheco. Tamara bintener and Thomas sauter 16 Opportunities and Challenges in Applying Artificial Intelligence to Bioengineering Fusun yaman. aaron adler and jacob beal 17 Deep Learning with Convolutional Neural Networks for Histopathology Image analysis 453 Dragan bosnacki, Natal van riel and mitko veta Index...,,,.,...

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