Automated parameter estimation for biological models using Bayesian statistical model checking
نویسندگان
چکیده
منابع مشابه
Parameter discovery in stochastic biological models using simulated annealing and statistical model checking
Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology ...
متن کاملAn LTL Model Checking Approach for Biological Parameter Inference
The identification of biological parameters governing dynamics of Genetic Regulatory Networks (GRN) poses a problem of combinatorial explosion, since the possibilities of parameter instantiation are numerous even for small networks. In this paper, we propose to adapt LTL model checking algorithms to infer biological parameters from biological properties given as LTL formulas. In order to reduce...
متن کاملParallelized Parameter Estimation of Biological Pathway Models
We develop a GPUs based technique to analyze bio-pathway models consisting of systems of ordinary differential equations (ODEs). A key component in our technique is an online procedure for verifying whether a numerically generated trajectory of a model satisfies a property expressed in bounded linear temporal logic. Using this procedure, we construct a statistical model checking algorithm which...
متن کاملParameter Estimation in Canonical Biological Systems Models
Dynamical models are the cornerstone of computational systems biology. While many methods are available for testing and simulating dynamical models, the estimation of their parameter values continues to be a difficult challenge. In recent years, this challenge has been addressed extensively for canonical models within Biochemical Systems Theory (BST), and while still no generally satisfactory s...
متن کاملUsing Statistical Model Checking for Measuring Systems
State spaces represent the way a system evolves through its different possible executions. Automatic verification techniques are used to check whether the system satisfies certain properties, expressed using automata or logic-based formalisms. This provides a Boolean indication of the system’s fitness. It is sometimes desirable to obtain other indications, measuring e.g., duration, energy or pr...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2015
ISSN: 1471-2105
DOI: 10.1186/1471-2105-16-s17-s8