multicell

package
v0.0.0-...-f60d257 Latest Latest
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 Go to latest Published: May 19, 2023 License: GPL-3.0 Imports: 13 Imported by: 12

Documentation

Index

Constants

View Source 
const (
	IAncEnv = iota // Previous env
	INovEnv        // Current env
	NBodies
)
View Source 
const (
	CellE = iota
	CellF
	CellG
	CellH
	CellP
)

Variables

View Source 
var DensityE float64 = defaultDensity
View Source 
var DensityF float64 = defaultDensity
View Source 
var DensityG float64 = defaultDensity
View Source 
var DensityH float64 = defaultDensity
View Source 
var DensityJ float64 = defaultDensity
View Source 
var DensityP float64 = defaultDensity

Functions

func AddNoise2CueFlip 

func AddNoise2CueFlip(cue_out, cue Cue, eta float64)

func AddNoise2CueNormal 

func AddNoise2CueNormal(cue_out, cue Cue, eta float64)

func AddVecs 

func AddVecs(vout, v0, v1 Vec)

func CheckCPD 

func CheckCPD(ten Tensor3, cpd []ElemsCPD) (float64, float64)

func CopyDmat 

func CopyDmat(mat1, mat0 Dmat)

func CrossoverSpmats 

func CrossoverSpmats(mat0, mat1 Spmat)

func DOT_Genealogy 

func DOT_Genealogy(genfilename, popfilename string, ngen, npop int)

Dumps genealogy of population for an epoch into a dot file, going backwards in time. Returns number of reproducing population

func DeepVec2Test 

func DeepVec2Test(v1, v2 [][]float64) float64

func DeepVec3NovTest 

func DeepVec3NovTest(v [][]float64, vv [][][]float64) error

func DiffGenomes 

func DiffGenomes(Gout, G1, G0 *Genome)

func DiffVecs 

func DiffVecs(vout, v0, v1 Vec)

func Dist2Vecs 

func Dist2Vecs(v0, v1 Vec) float64

func DistVecs 

func DistVecs(v0, v1 Vec) float64

func DistVecs1 

func DistVecs1(v0, v1 Vec) float64

func DotSpmats 

func DotSpmats(mat0, mat1 Spmat) float64

func DotVecs 

func DotVecs(v0, v1 Vec) float64

func GetCrossCov 

func GetCrossCov(vecs0, vecs1 []Vec, submean0, submean1 bool) (Vec, Vec, Dmat)

func GetCrossCov3 

func GetCrossCov3(vecs0, vecs1, vecs2 []Vec, submean0, submean1, submean2 bool) (Vec, Vec, Vec, Tensor3)

func GetCueVar 

func GetCueVar(cues Cues) float64

func GetMaxPop 

func GetMaxPop() int

func GetNcells 

func GetNcells() int

func GetNenv 

func GetNenv() int

func GetNsel 

func GetNsel() int

func GetSVD 

func GetSVD(ccmat Dmat) (*mat.Dense, []float64, *mat.Dense)

func GetSVD_opt 

func GetSVD_opt(ccmat Dmat, flag mat.SVDKind) (*mat.Dense, []float64, *mat.Dense)

expect flag = mat.SVDThin or mat.SVDThinU

func Hammingdist 

func Hammingdist(v0, v1 Vec) float64

func Mate 

func Mate(dad, mom *Indiv) (Indiv, Indiv)

func MinInt 

func MinInt(x, y int) int

func MultMatVec 

func MultMatVec(vout Vec, mat Spmat, vin Vec)

func MultMatVec_T 

func MultMatVec_T(vout Vec, mat Spmat, vin Vec)

func Norm2 

func Norm2(v Vec) float64

func Norm2Sq 

func Norm2Sq(v Vec) float64

func NormalizeVec 

func NormalizeVec(v Vec)

func ProjectSVD 

func ProjectSVD(label string, dirE, dirP *mat.VecDense, data0, data1 Dmat, mean0, mean1 Vec, ccmat Dmat, vals Vec, U, V *mat.Dense)

func RandomInit 

func RandomInit(a Dmat, maxcol int)

func ResetDmat 

func ResetDmat(mat Dmat)

func ScaleVec 

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

func SetParams 

func SetParams(s Settings)

func SetSeed 

func SetSeed(seed int64)

func SetSeedCue 

func SetSeedCue(seed int64)

func SumVec 

func SumVec(v Vec) float64

func TestEqualGenomes 

func TestEqualGenomes(G0, G1 Genome) float64

func TestEqualPopGenomes 

func TestEqualPopGenomes(pop0, pop1 Population) float64

func WAddVecs 

func WAddVecs(vout Vec, sca float64, v0, v1 Vec)

Types

type Body 

type Body struct {
	Genome   Genome
	Cells    []Cell // Array of cells of different types
	PErr     float64
	NDevStep int
}

func NewBody 

func NewBody(ncells int) Body

func (*Body) Copy 

func (body *Body) Copy() Body

func (*Body) DevBody 

func (body *Body) DevBody(envs Cues) Body

type CPDArray 

type CPDArray []ElemsCPD

type Cell 

type Cell struct {
	Id       int
	E        Vec     // Env + noise
	F        Vec     // Epigenetic markers
	G        Vec     // Gene expression
	H        Vec     // Higher order complexes
	P, Pvar  Vec     // moving average and variance of P (P is already EMA)
	PErr     float64 // ||e - p||_1
	NDevStep int     // Developmental path length

}

func NewCell 

func NewCell(id int) Cell

func (*Cell) Copy 

func (cell *Cell) Copy() Cell

func (*Cell) DevCell 

func (cell *Cell) DevCell(G Genome, env Cue) Cell

func (*Cell) GetState 

func (cell *Cell) GetState(ivec string, ibeg, iend int) Vec

type CoreTensor3 

type CoreTensor3 []elem_tensor3

func GetFastHOSVD 

func GetFastHOSVD(ten Tensor3) (CoreTensor3, *mat.Dense, *mat.Dense, *mat.Dense)

Interlaced Computation; supposed to be significantly faster. Should be len0 <= len1 <= len2

type Cue 

type Cue = Vec //Environment cue is a special kind of vector

func ChangeEnv 

func ChangeEnv(cue Cue, n int) Cue

Mutate precisely n bits of environment cue; ignore id part

func ChangeEnv2 

func ChangeEnv2(cue Cue, n int) Cue

make sure to change env(1:nsel) if n < nsel/2

func RandomEnv 

func RandomEnv(density float64) Cue

type Cues 

type Cues = []Cue //Cue array object

func ChangeEnvs 

func ChangeEnvs(cues Cues, n int) Cues

func CopyCues 

func CopyCues(cues Cues) Cues

func GetSelEnvs 

func GetSelEnvs(cues Cues) Cues

func NewCues 

func NewCues(ncells, nenv int) Cues

func RandomEnvs 

func RandomEnvs(ncells int, density float64) Cues

Randomly generate cue array

type Dmat 

type Dmat = []Vec

func FlattenTensor3 

func FlattenTensor3(ten Tensor3, ind int) Dmat

func KR_Product 

func KR_Product(a, b Dmat) Dmat

The Khatri-Rao Product between KxN and KxN matrices

func MultDmats 

func MultDmats(mat0, mat1 Dmat) Dmat

func NewDmat 

func NewDmat(nrow, ncol int) Dmat

type ElemsCPD 

type ElemsCPD struct {
	SVal float64
	Axes []Vec
}

func GetCPDO 

func GetCPDO(ten Tensor3, dir1, dir2 Vec, maxiter, rank int) []ElemsCPD

Canonical Polyadic Decomposition X = S*(A1 x A2 x A3) where A3 is orthogonal.

type Genome 

type Genome struct {
	E Spmat //Environment cue effect on epigenome
	F Spmat //Regulatory effect of epigenetic markers on gene expression
	G Spmat //Regulatory effect of gene expression on epigenetic markers
	H Spmat //Contribution of gene expression on higher order complexes
	J Spmat //Interaction between higher order complexes
	P Spmat //Resulting expressed phenotype
}

func NewGenome 

func NewGenome() Genome

func (*Genome) Clear 

func (G *Genome) Clear()

func (*Genome) Copy 

func (parent *Genome) Copy() Genome

func (*Genome) FlatVec 

func (genome *Genome) FlatVec() Vec

func (*Genome) Mutate 

func (genome *Genome) Mutate()

func (*Genome) NormalizeGenome 

func (G *Genome) NormalizeGenome() Genome

func (*Genome) Randomize 

func (G *Genome) Randomize()

type Indiv 

type Indiv struct {
	Id         int
	DadId      int
	MomId      int
	Bodies     []Body  //IAncEnv, INovEnv (see above const.)
	Fit        float64 //Fitness with cues
	WagFit     float64 //Wagner relative fitness
	Plasticity float64 //Observed Plasticity
	Dp1e1      float64 // ||p(e1) - e1||
	Dp0e0      float64 // ||p(e0) - e0||
	Dp1e0      float64 // ||p(e1) - e0||
	Dp0e1      float64 // ||p(e0) - e1||
}

func NewIndiv 

func NewIndiv(id int) Indiv

func (*Indiv) Copy 

func (indiv *Indiv) Copy() Indiv

func (*Indiv) Develop 

func (indiv *Indiv) Develop(ancenvs, novenvs Cues) Indiv

type PopStats 

type PopStats struct {
	PEDot      float64 // (delta P, delta E) dot product
	PErr1      float64 // <|| p(e1) - e1 ||> (Nov)
	PErr0      float64 // <|| p(e0) - e0 ||> (Anc)
	PED10      float64 // <|| p(e1) - e0 ||> (Nov-Anc)
	PED01      float64 // <|| p(e0) - e1 ||> (Anc-Nov)
	WagFit     float64
	Fitness    float64
	Plasticity float64
	Div        float64
	NDevStep   float64
}

type Population 

type Population struct {
	Params  Settings
	Gen     int
	NovEnvs Cues //Novel Environment
	AncEnvs Cues // Ancestral Environment
	Indivs  []Indiv
}

func NewPopulation 

func NewPopulation(s Settings) Population

func (*Population) ChangeEnvs 

func (pop *Population) ChangeEnvs(denv int)

func (*Population) ClearGenome 

func (pop *Population) ClearGenome()

func (*Population) Copy 

func (pop *Population) Copy() Population

func (*Population) DevPop 

func (pop *Population) DevPop(gen int) Population

func (*Population) Evolve 

func (pop0 *Population) Evolve(test bool, ftraj *os.File, jsonout string, nstep, epoch int) Population

Records population trajectory and writes files

func (*Population) ExportPopGz 

func (pop *Population) ExportPopGz(filename string)

func (*Population) GetFlatGenome 

func (pop *Population) GetFlatGenome(IEnv int) Dmat

func (*Population) GetFlatStateVec 

func (pop *Population) GetFlatStateVec(istate string, ienv, ibeg, iend int) Dmat

func (*Population) GetMeanPhenotype 

func (pop *Population) GetMeanPhenotype(gen int) Cues

func (*Population) GetStats 

func (pop *Population) GetStats() PopStats

func (*Population) ImportPopGz 

func (pop *Population) ImportPopGz(filename string)

func (*Population) PairReproduce 

func (pop *Population) PairReproduce(nNewPop int) Population

func (*Population) RandomizeGenome 

func (pop *Population) RandomizeGenome()

func (*Population) Reproduce 

func (pop *Population) Reproduce(nNewPop int) Population

func (*Population) Selection 

func (pop *Population) Selection(nNewPop int) []Indiv

func (*Population) SetRandomNovEnvs 

func (pop *Population) SetRandomNovEnvs()

func (*Population) SetWagnerFitness 

func (pop *Population) SetWagnerFitness()

func (*Population) SortPopIndivs 

func (pop *Population) SortPopIndivs()

type Settings 

type Settings struct {
	MaxPop     int // Maximum number of individuals in population
	MaxDevStep int // Maximum steps for development.
	NGenes     int
	NEnv       int
	NSel       int
	NCells     int     // Number of cell types
	WithCue    bool    // With cue?
	FLayer     bool    // f present?
	HLayer     bool    // h present?
	JLayer     bool    //  J present?
	Pfback     bool    // P feedback to E layer
	SDNoise    float64 // probability (or stdev) of environmental noise
	MutRate    float64 // mutation rate
	TauF       float64
	TauG       float64
	TauH       float64
	DensityE   float64
	DensityF   float64
	DensityG   float64
	DensityH   float64
	DensityJ   float64
	DensityP   float64
}

func CurrentSettings 

func CurrentSettings() Settings

type Spmat 

type Spmat struct {
	Ncol int                 // number of columns
	Mat  [](map[int]float64) // Sparse matrix is an array of maps.
}

func DiffSpmat 

func DiffSpmat(m1, m2 *Spmat) Spmat

func NewSpmat 

func NewSpmat(nrow, ncol int) Spmat

func (*Spmat) Copy 

func (sp *Spmat) Copy() Spmat

func (*Spmat) Randomize 

func (sp *Spmat) Randomize(density float64)

func (*Spmat) Scale 

func (sp *Spmat) Scale(c float64)

type Tensor3 

type Tensor3 []Dmat

func GetHOSVD 

func GetHOSVD(ten Tensor3) (Tensor3, *mat.Dense, *mat.Dense, *mat.Dense)

Returns a compact core tensor and orthonormal basis.

func NewTensor3 

func NewTensor3(n0, n1, n2 int) Tensor3

type Vec 

type Vec = []float64 //Vector is a slice

func CopyVec 

func CopyVec(v Vec) Vec

func FlattenEnvs 

func FlattenEnvs(cues Cues) Vec

func GetMeanVec 

func GetMeanVec(vecs []Vec) Vec

func GetVarVec 

func GetVarVec(vecs []Vec) Vec

func NewVec 

func NewVec(len int) Vec

func NormDiag2 

func NormDiag2(a Dmat) Vec

func Ones 

func Ones(len int) Vec

func UnitVec 

func UnitVec(len, dir int) Vec

func Zeroes 

func Zeroes(len int) Vec

Source Files

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