multicell

package
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 Go to latest Published: Jan 28, 2025 License: MIT Imports: 13 Imported by: 0

Documentation

Index

Constants

View Source 
const (
	Left = iota
	Top
	Right
	Bottom
	NumFaces // Numbef of faces per cell
)

faces

View Source 
const (
	Sqrt3 = 1.7320508075688772
)

Variables

This section is empty.

Functions

func AStep3 

func AStep3(omega float64) func(float64) float64

abrupt three-step function

func Atan 

func Atan(omega float64) func(float64) float64

Simple arctan

func CStep1 

func CStep1(omega float64) func(float64) float64

degree-1 continuous step function

func ConservedGenomeSites 

func ConservedGenomeSites(mg1, vg1 Vec, gvecs []Vec) (map[int]int, []int)

func CorrVecs 

func CorrVecs(vs0, vs1 Vec) (float64, float64)

func CovarianceMatrix 

func CovarianceMatrix(xs []Vec, x0 Vec, ys []Vec, y0 Vec) *mat.Dense

func DotVecs 

func DotVecs(v0, v1 Vec) float64

func JustFail 

func JustFail(err error)

func LCatan 

func LCatan(omega float64) func(float64) float64

LeCun-inspired arctan function

func LCtanh 

func LCtanh(omega float64) func(float64) float64

LeCun tanh (without multiplying by Sqrt3).

func MatTotVar 

func MatTotVar(vecs []Vec, mv Vec) float64

Total variance of a matrix

func SCtanh 

func SCtanh(omega float64) func(float64) float64

Scaled tanh

func SStep3 

func SStep3(omega float64) func(float64) float64

smooth degree-3 step function

func SStep5 

func SStep5(omega float64) func(float64) float64

smooth degree-5 step function

func Tanh 

func Tanh(omega float64) func(float64) float64

func XPCA 

func XPCA(xs []Vec, x0 Vec, ys []Vec, y0 Vec) (Vec, []Vec, []Vec)

Get singular values, the first left and right singular vectors.

Types

type Cell 

type Cell struct {
	Id     int           // Identifier within an individual
	Facing [NumFaces]int // Facing Cell's Id; -1 if none.
	Cue    []Vec         // points to neighboring cell face or environment
	S      []Vec         // state vectors
	Pave   Vec
	Pvar   Vec
}

func (*Cell) Bottom 

func (c *Cell) Bottom(s *Setting) Vec

func (*Cell) DevStep 

func (c *Cell) DevStep(s *Setting, g Genome, istep int) float64

func (*Cell) Face 

func (c *Cell) Face(s *Setting, iface int) Vec

func (*Cell) Initialize 

func (c *Cell) Initialize(s *Setting)

func (*Cell) Left 

func (c *Cell) Left(s *Setting) Vec

func (*Cell) OppositeFace 

func (c *Cell) OppositeFace(s *Setting, iface int) Vec

func (*Cell) Right 

func (c *Cell) Right(s *Setting) Vec

func (*Cell) ToVec 

func (c *Cell) ToVec() Vec

all internal states into one vector.

func (*Cell) Top 

func (c *Cell) Top(s *Setting) Vec

type CellEnvs 

type CellEnvs struct {
	Tops    []Vec
	Bottoms []Vec
	Rights  []Vec
	Lefts   []Vec
}

type Environment 

type Environment = Vec

func (Environment) Bottom 

func (env Environment) Bottom(s *Setting) Vec

func (Environment) ChangeEnv 

func (env Environment) ChangeEnv(s *Setting, rng *rand.Rand) Environment

func (Environment) Face 

func (env Environment) Face(s *Setting, iface int) Vec

func (Environment) GenerateEnvs 

func (env Environment) GenerateEnvs(s *Setting, nepochs int) EnvironmentS

func (Environment) Left 

func (env Environment) Left(s *Setting) Vec

func (Environment) Len 

func (env Environment) Len() int

func (Environment) Right 

func (env Environment) Right(s *Setting) Vec

func (Environment) SelectingEnv 

func (env Environment) SelectingEnv(s *Setting) Vec

func (Environment) Top 

func (env Environment) Top(s *Setting) Vec

type EnvironmentS 

type EnvironmentS []Environment

func (EnvironmentS) DumpEnvs 

func (envs EnvironmentS) DumpEnvs(filename string)

type Genome 

type Genome struct {
	B []Vec
	SliceOfMaps[SpMat]
}

func (Genome) Clone 

func (genome Genome) Clone() Genome

func (Genome) Equal 

func (g0 Genome) Equal(g1 Genome) bool

func (Genome) MateWith 

func (g0 Genome) MateWith(g1 Genome) (Genome, Genome)

func (Genome) Mutate 

func (genome Genome) Mutate(s *Setting)

func (Genome) ToVec 

func (g Genome) ToVec(s *Setting) Vec

type Individual 

type Individual struct {
	Id      int
	MomId   int
	DadId   int
	Genome  Genome
	Cells   []Cell
	Ndev    int
	Align   float64
	Fitness float64
}

func (*Individual) Clone 

func (indiv *Individual) Clone(s *Setting, env Environment) Individual

func (*Individual) CueVec 

func (indiv *Individual) CueVec(s *Setting) Vec

func (*Individual) Develop 

func (indiv *Individual) Develop(s *Setting, selenv Vec) Individual

func (*Individual) Initialize 

func (indiv *Individual) Initialize(s *Setting, env Environment)

func (*Individual) NumCells 

func (indiv *Individual) NumCells() int

func (*Individual) Phenotype 

func (indiv *Individual) Phenotype(s *Setting) []Vec

func (*Individual) PhenotypeVec 

func (indiv *Individual) PhenotypeVec(s *Setting) Vec

func (*Individual) SelectedPhenotype 

func (indiv *Individual) SelectedPhenotype(s *Setting) []Vec

func (*Individual) SelectedPhenotypeVec 

func (indiv *Individual) SelectedPhenotypeVec(s *Setting) Vec

func (*Individual) SelectingCue 

func (indiv *Individual) SelectingCue(s *Setting) []Vec

func (*Individual) SelectingCueVec 

func (indiv *Individual) SelectingCueVec(s *Setting) Vec

func (*Individual) SetFitness 

func (indiv *Individual) SetFitness(s *Setting, selenv Vec, conv float64)

func (*Individual) StateVec 

func (indiv *Individual) StateVec() Vec

type PopStats 

type PopStats struct {
	Align    float64
	Fitness  float64
	Ndev     float64
	Nparents int
}

func (PopStats) Print 

func (stats PopStats) Print(iepoch, igen int)

type Population 

type Population struct {
	Iepoch int // epoch
	Igen   int // generation
	Indivs []Individual
}

func (*Population) AnalyzeVarEnvs 

func (pop *Population) AnalyzeVarEnvs(s *Setting, env0 Environment, n int)

Analyze adaptive plastic responses to various environmental changes.

func (*Population) Clone 

func (pop *Population) Clone(s *Setting, env Environment) Population

func (*Population) CueVecs 

func (pop *Population) CueVecs(s *Setting) []Vec

func (*Population) Develop 

func (pop *Population) Develop(s *Setting, env Environment)

func (*Population) Dump 

func (pop *Population) Dump(s *Setting) string

Dump the Population in a gzipped binary file.

func (*Population) DumpJSON 

func (pop *Population) DumpJSON(s *Setting) string

func (*Population) Evolve 

func (pop0 *Population) Evolve(s *Setting, env Environment) (Population, string)

func (*Population) GenoPhenoPlot 

func (pop *Population) GenoPhenoPlot(s *Setting, p0, paxis, g0, gaxis, env0 Vec)

func (*Population) GenomeVecs 

func (pop *Population) GenomeVecs(s *Setting) []Vec

func (*Population) GetMaxFitness 

func (pop *Population) GetMaxFitness() float64

func (*Population) GetPopStats 

func (pop *Population) GetPopStats() PopStats

func (*Population) GetProjected1 

func (pop *Population) GetProjected1(s *Setting, fout *os.File, label string, xs []Vec, x0 Vec, axis, ps Vec) (Vec, Vec)

func (*Population) GetProjected2 

func (pop *Population) GetProjected2(s *Setting, fout *os.File, label string, xs []Vec, x0 Vec, ys []Vec, y0 Vec, uaxis, vaxis, ps, gs Vec) (Vec, Vec)

func (*Population) Initialize 

func (pop *Population) Initialize(s *Setting, env Environment)

func (*Population) PGCov 

func (pop *Population) PGCov(s *Setting, p0, paxis, g0, gaxis, env0, env1 Vec)

func (*Population) PhenoVecs 

func (pop *Population) PhenoVecs(s *Setting) []Vec

func (*Population) PrintPopStats 

func (pop *Population) PrintPopStats(fout *os.File, gs, ps, ali0 Vec)

func (*Population) Reproduce 

func (pop *Population) Reproduce(s *Setting, env Environment) Population

func (*Population) SVDProject 

func (pop *Population) SVDProject(s *Setting, p0, paxis, g0, gaxis, c0, caxis Vec)

func (*Population) Select 

func (pop *Population) Select(s *Setting) Population

func (*Population) SelectedPhenoVecs 

func (pop *Population) SelectedPhenoVecs(s *Setting) []Vec

func (*Population) Sort 

func (pop *Population) Sort()

func (*Population) StateVecs 

func (pop *Population) StateVecs() []Vec

type Setting 

type Setting struct {
	Basename      string  // name of the model
	Seed          uint64  // random seed
	Outdir        string  // output directory for trajectory
	MaxPopulation int     // maximum population size
	MaxGeneration int     // maximum number of generations per epoch
	NumCellX      int     // number of cells in the x-axis
	NumCellY      int     // number of cells in the y-axis
	LenFace       int     // face length
	ProductionRun bool    // true if production run (i.e. "test" phase)
	EnvNoise      int     // flipped bits per face
	MutRate       float64 // mutation rate
	ConvDevelop   float64 // convergence limit
	Denv          int     // size of an environmental change
	SelStrength   float64 // selection strength
	CueScale      float64 // usually 1.0, 10 for the Null model.

	WithCue    bool                 // with cue or not
	MaxDevelop int                  // maximum number of developmental steps
	Alpha      float64              // weight for exponential moving average
	NumLayers  int                  // number of middle layers
	LenLayer   []int                // Length of each state vector
	Topology   SliceOfMaps[float64] // densities of genome matrices
	Omega      Vec                  // scaling factors of activation functions
}

various set-ups

func GetDefaultSetting 

func GetDefaultSetting(modelname string) *Setting

func LoadSetting 

func LoadSetting(filename string) *Setting

func (*Setting) AnalyzeAPRGeno 

func (s *Setting) AnalyzeAPRGeno(env0, env1 Environment, pop0, pop1 Population)

Comparing adaptive plastic response in env0 to evolutionary adaptation to env1

func (*Setting) CellId 

func (s *Setting) CellId(i, j int) int

func (*Setting) Dump 

func (s *Setting) Dump()

func (*Setting) GetCueAxis 

func (s *Setting) GetCueAxis(env0, env1 Environment) (Vec, Vec)

func (*Setting) GetGenomeAxis 

func (s *Setting) GetGenomeAxis(pop0, pop1 Population) (Vec, Vec)

func (*Setting) GetPhenoAxis 

func (s *Setting) GetPhenoAxis(pop0, pop1 Population, env0, env1 Environment) (Vec, Vec)

func (*Setting) GetSelectedPhenoAxis 

func (s *Setting) GetSelectedPhenoAxis(pop0, pop1 Population, env0, env1 Environment) (Vec, Vec)

func (*Setting) LoadEnvs 

func (s *Setting) LoadEnvs(filename string) []Environment

func (*Setting) LoadPopulation 

func (s *Setting) LoadPopulation(filename string) Population

func (*Setting) LoadPopulationJSON 

func (s *Setting) LoadPopulationJSON(filename string, env Environment) Population

func (*Setting) MateIndividuals 

func (s *Setting) MateIndividuals(indiv0, indiv1 Individual, env Environment) (Individual, Individual)

func (*Setting) NewCell 

func (s *Setting) NewCell(id int) Cell

func (*Setting) NewEnvironment 

func (s *Setting) NewEnvironment() Environment

func (*Setting) NewGenome 

func (s *Setting) NewGenome() Genome

func (*Setting) NewIndividual 

func (s *Setting) NewIndividual(id int, env Environment) Individual

func (*Setting) NewPopulation 

func (s *Setting) NewPopulation(env Environment) Population

func (*Setting) RandomGenomeVariance 

func (s *Setting) RandomGenomeVariance() float64

Expected variance of a random genome.

func (*Setting) SaveEnvs 

func (s *Setting) SaveEnvs(filename string, nepochs int) EnvironmentS

func (*Setting) SetCellEnv 

func (s *Setting) SetCellEnv(cells []Cell, env Environment)

func (*Setting) SetDevelop 

func (s *Setting) SetDevelop(flag bool)

func (*Setting) SetLayerM1 

func (s *Setting) SetLayerM1(n int)

Feedback loop to the previous layer

func (*Setting) SetLayerSL 

func (s *Setting) SetLayerSL(n int)

Self-loop for hidden layers

func (*Setting) SetModel 

func (s *Setting) SetModel(basename string)

func (*Setting) SetOmega 

func (s *Setting) SetOmega()

func (*Setting) TrajectoryFilename 

func (s *Setting) TrajectoryFilename(iepoch, igen int, suffix string) string

type SliceOfMaps 

type SliceOfMaps[T any] struct {
	M []map[int]T
}

sparse matrix of anything.

func NewSliceOfMaps 

func NewSliceOfMaps[T any](n int) SliceOfMaps[T]

func (SliceOfMaps[T]) At 

func (sm SliceOfMaps[T]) At(i, j int) T

func (SliceOfMaps[T]) Do 

func (sm SliceOfMaps[T]) Do(f func(i, j int, v T))

func (SliceOfMaps[T]) EachRow 

func (sm SliceOfMaps[T]) EachRow(f func(i int, mi map[int]T))

func (SliceOfMaps[T]) Set 

func (sm SliceOfMaps[T]) Set(i, j int, v T)

type SpMat 

type SpMat struct {
	Ncol int
	SliceOfMaps[float64]
}

sparse matrix

func NewSpMat 

func NewSpMat(nrow, ncol int) SpMat

Create a new sparse matrix

func (*SpMat) Clone 

func (sp *SpMat) Clone() SpMat

copy a sparse matrix

func (SpMat) Density 

func (sp SpMat) Density() float64

func (SpMat) Equal 

func (sp0 SpMat) Equal(sp1 SpMat) bool

func (SpMat) MateWith 

func (mat0 SpMat) MateWith(mat1 SpMat) (SpMat, SpMat)

func (SpMat) Mutate 

func (sp SpMat) Mutate(rate float64, density float64)

func (SpMat) Ncols 

func (sp SpMat) Ncols() int

func (SpMat) Nrows 

func (sp SpMat) Nrows() int

func (SpMat) PickRandomElements 

func (sp SpMat) PickRandomElements(n int) SliceOfMaps[float64]

func (SpMat) Randomize 

func (sp SpMat) Randomize(density float64)

random matrix

func (*SpMat) ToVec 

func (sp *SpMat) ToVec() Vec

type Vec 

type Vec []float64

vector

func DiffMats 

func DiffMats(vs1, vs0 []Vec) []Vec

func GetAxis 

func GetAxis(v0, v1 Vec) Vec

func MeanVecs 

func MeanVecs(vecs []Vec) Vec

func NewVec 

func NewVec(n int, v float64) Vec

Create a vector with initial values of "v".

func ProjectOnAxis 

func ProjectOnAxis(vecs []Vec, v0 Vec, axis Vec) Vec

func VarVecs 

func VarVecs(vecs []Vec, mv Vec) Vec

func (Vec) Acc 

func (vout Vec) Acc(vin Vec) Vec

Accumulate

func (Vec) Add 

func (vout Vec) Add(v0, v1 Vec) Vec

func (Vec) AddNoise 

func (vec Vec) AddNoise(lenface, nflip int) Vec

func (Vec) ApplyFVec 

func (vout Vec) ApplyFVec(f func(float64) float64, vin Vec)

func (Vec) Clone 

func (vec Vec) Clone() Vec

func (Vec) Diff 

func (vout Vec) Diff(v0, v1 Vec) Vec

func (Vec) MateWith 

func (vec0 Vec) MateWith(vec1 Vec) (Vec, Vec)

func (Vec) Mean 

func (vec Vec) Mean() float64

func (Vec) MultSpMatVec 

func (vout Vec) MultSpMatVec(sp SpMat, vin Vec)

multiply a sparse matrix to a vector. vout is NOT initialized!!

func (Vec) Mutate 

func (vec Vec) Mutate(rate float64)

func (Vec) Norm1 

func (v Vec) Norm1() float64

func (Vec) Norm2 

func (v Vec) Norm2() float64

func (Vec) NormInf 

func (v Vec) NormInf() float64

func (Vec) Normalize 

func (v Vec) Normalize() Vec

func (Vec) ScaleAcc 

func (vout Vec) ScaleAcc(s float64, vin Vec) Vec

Scale and Accumulate

func (Vec) ScaleBy 

func (vec Vec) ScaleBy(f float64) Vec

func (Vec) SetAll 

func (vec Vec) SetAll(v float64)

func (Vec) Sum 

func (vec Vec) Sum() float64

sum all elements.

Source Files

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