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Implements a parallel version of Kmeans

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Former-commit-id: 58ab24b9b274451e00eea0275249234e2c2ea09b
This commit is contained in:
Eric Coissac
2023-08-26 01:26:40 +02:00
parent 077f3b5bb5
commit cbd42d5b30
3 changed files with 182 additions and 72 deletions
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38
pkg/obitools/obilandmark/obilandmark.go
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@@ -1,7 +1,6 @@
package obilandmark
import (
"math"
"os"
"sort"
"sync"
@@ -16,6 +15,18 @@ import (
log "github.com/sirupsen/logrus"
)
// MapOnLandmarkSequences performs sequence mapping on a given library of bio sequences.
//
// Computes for each sequence in the library a descriptor vector containing describing the sequence
// as the set of its distances to every landmark sequence.
//
// Parameters:
// - library: A slice of bio sequences to be mapped.
// - landmark_idx: A list of indices representing landmark sequences.
// - sizes: Optional argument specifying the number of workers to use.
//
// Returns:
// - seqworld: A matrix of float64 values representing the mapped coordinates.
func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int, sizes ...int) obiutils.Matrix[float64] {
nworkers := obioptions.CLIParallelWorkers()
@@ -73,6 +84,20 @@ func MapOnLandmarkSequences(library obiseq.BioSequenceSlice, landmark_idx []int,
return seqworld
}
// CLISelectLandmarkSequences selects landmark sequences from the given iterator and assigns attributes to the sequences.
//
// The fonction annotate the input set of sequences with two or three attributes:
// - 'landmark_id' indicating which sequence was selected and to which landmark it corresponds.
// - 'landmark_coord' indicates the coordinates of the sequence.
// - 'landmark_class' indicates to which landmark (landmark_id) the sequence is the closest.
//
// Parameters:
// - iterator: an object of type obiiter.IBioSequence representing the iterator to select landmark sequences from.
//
// Returns:
// - an object of type obiiter.IBioSequence providing the input sequence annotated with their coordinates respectively to
// each selected landmark sequences and with an attribute 'landmark_id' indicating which sequence was selected and to
// which landmark it corresponds.
func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSequence {
library := iterator.Load()
@@ -80,14 +105,14 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
library_size := len(library)
n_landmark := NCenter()
landmark_idx := obistats.SampleIntWithoutReplacemant(n_landmark, library_size)
landmark_idx := obistats.SampleIntWithoutReplacement(n_landmark, library_size)
log.Infof("Library contains %d sequence", len(library))
var seqworld obiutils.Matrix[float64]
for loop := 0; loop < 5; loop++ {
sort.IntSlice(landmark_idx).Sort()
log.Infof("Selected indices : %v", landmark_idx)
log.Debugf("Selected indices : %v", landmark_idx)
seqworld = MapOnLandmarkSequences(library, landmark_idx)
initialCenters := obiutils.Make2DArray[float64](n_landmark, n_landmark)
@@ -100,8 +125,11 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
dist_centers := 0.0
for i := 0; i < n_landmark; i++ {
center := (*centers)[i]
icenter := initialCenters[i]
for j := 0; j < n_landmark; j++ {
dist_centers += math.Pow((*centers)[i][j]-initialCenters[i][j], 2)
diff := center[j] - icenter[j]
dist_centers += diff * diff
}
}
@@ -112,7 +140,7 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
sort.IntSlice(landmark_idx).Sort()
log.Infof("Selected indices : %v", landmark_idx)
log.Debugf("Selected indices : %v", landmark_idx)
seqworld = MapOnLandmarkSequences(library, landmark_idx)
seq_landmark := make(map[int]int, n_landmark)