ChemComp：基于化学反应网络计算的编译框架.pdf

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1、ChemComp:A Compilation Framework for Computing with Chemical Reaction NetworksAntonino TumeoComputer Scientist,PNNLAuthors:Nicolas Bohm AgostiniConnah G.M.JohnsonWilliam CannonAntonino Tumeo268 kJ/mol in one secondPotential of Biochemical PathwayOPS:1023Energy/s:68 kWFrontier(ORNL,2021)FLOPS:1018Ene

2、rgy/s:29,000 kWRules are simple compared to biologyPotential Gain in OPS/W4x107 xGlucosePyruvateATPADPATPADPATPATPATPADPADPADPGlucose+2 ATP 2 Pyruvate+6 ATP“Chemical advantage”meets the high-performance requirements for scientific workflows:-Scalable-Massively concurrent-Continuous(time)representati

3、on-“Low”energyChemistry conveys a“chemical advantage”for computationBeneficial to applications:-Continuous systems such as ODEs as natural representation-Neural networks/NLP as massively concurrent inferenceChemical reactions can be used for useful computation3Chemical ReactionsOrdinary Differential

4、 EquationsOrdinary Differential EquationsChemical ReactionsMass Action Kinetics LawCompilerD.Soloveichik,et.al.-Turing completeness Natural Computing 2008M.Matejak,et.al.Modelic Lib of Chem Processes Modelica Conf 2015W.Poole,et.al.-BioCRNpyler PLOS Computational Biology 2022R.Rendal,et.al.-Chemilan

5、g Github 2023S.Shah,et.al.-CCompiler arXiv 2008M.Vasic,et.al.-CRN+Natural Computing 2020RW does not consider:Concrete chemical reactionsTracking species over time4Chemical reaction can be mapped to ODEs()=():Number of input species in reaction :Number of output species in reaction():Propensity or Ra

6、te of the reaction Using the Law of Mass Action kinetics:Chemical concentrationTimek1A+BCCDr1:r2:k25Simulated TimeProblem SolutionOne reactionTwo reactionsThree reactionsFour reactionsa)c)b)5Fitting mathematical patterns into concrete CRs6Reservoir computing can harness real world systems for comput