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Interval Represents an interval [a, b]. |
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FitnessResult Base class for results of objective (or fitness) functions. |
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LsysDisparityFitnessResult Result of a disparity objective evaluation. |
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Mutator | |||
TransformationFunction Base class for transformation functions. |
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ExponentialFunction Exponential parameter transformation. |
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ArctanFunction Arcus tangens transformation function. |
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LowerBoundedFunction A function asymptoting to a finite lower bound as x -> -Inf and linearly diverging as x -> +Inf. |
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SigmoidFunction Sigmoid parameter transformation. |
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ParameterTransformer Base class for parameter transformers. |
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TranssysTypedParameterTransformer Parameter transformer differentiating decay, diffusibility, constitutive, aspec, amax, rspec and rmax nodes. |
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OptimisationRecord Base class for optimisation records. |
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SimulatedAnnealingRecord Record containing data from a Simulated Annealing update. |
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GradientOptimisationRecord Record containing data from a step of gradient optimisation. |
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OptimisationResult Base class for returning results of an optimisation. |
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SimulatedAnnealingResult Result of optimisation by Simulated Annealing. |
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GradientOptimisationResult Result of optimisation by Simulated Annealing. |
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AbstractObjectiveFunction Base class for objective functions. |
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ExpressionSeriesObjective Abstract base class for objective functions based on comparing observed with desired expression profiles. |
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ExpressionSeriesSquareSumObjective The sum of squared Euclidean distances to a desired set of expression profiles as an objective function. |
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ExpressionSeriesCorrelationObjective Correlation based objective function. |
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AbstractOptimiser Abstract base class for optimisers. |
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SimulatedAnnealer Simple Simulated Annealing tool. |
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GradientOptimiser Gradient descent optimiser. |
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LsysObjectiveFunction |
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ParameterTransformer |
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Extract the set concentrations of a factor in instances that activated a rule (the active set), and the complement set (the inactive set). This method is rather specific to L-systems optimisation and should perhaps not be in this module. |
Standard deviation based disparity score. This function applies some tricks for preventing limitations of floating point precision from resulting in artificially low scores. See comments in source for details. |
Disparity of sign values of differences between expression levels in
symbols activating Evaluates to 0 if all signs are the same (and hence activating and
inactivating instances have expression levels of the factor specified by
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Objective function quantifying disparity of expression levels between instances that activate and that do not activate rules. This should be rewritten as a proper AbstractObjectiveFunction subclass. |
Get value expression nodes from a transsys program. Deprecated: use methods of TranssysProgram. |
Randomise values in value expressions. Deprecated: This functionality is now integrated into the optimising framework. |
Read a parameter transformer from a file. This function uses the "magic" first line to determine what subtype of ParameterTransformer is specified.
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