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Implements the kmeans++ algo to select the landmarks in the geometric method

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Former-commit-id: 732404a0dc6d7276e4e479dd2481aa4bd42d4ce5
This commit is contained in:
Eric Coissac
2023-12-11 16:07:03 +01:00
parent 37c3e16d5d
commit 2caaa62485
8 changed files with 259 additions and 140 deletions
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35
pkg/obitools/obilandmark/obilandmark.go
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@@ -109,43 +109,26 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
n_landmark := CLINCenter()
landmark_idx := obistats.SampleIntWithoutReplacement(n_landmark, library_size)
sort.IntSlice(landmark_idx).Sort()
log.Infof("Library contains %d sequence", len(library))
var seqworld obiutils.Matrix[float64]
for loop := 0; loop < 2; loop++ {
sort.IntSlice(landmark_idx).Sort()
log.Debugf("Selected indices : %v", landmark_idx)
seqworld = MapOnLandmarkSequences(library, landmark_idx)
initialCenters := obiutils.Make2DArray[float64](n_landmark, n_landmark)
for i, seq_idx := range landmark_idx {
initialCenters[i] = seqworld[seq_idx]
}
// classes, centers := obistats.Kmeans(&seqworld, n_landmark, &initialCenters)
classifier := obistats.MakeKmeansClustering(&seqworld, n_landmark, obistats.DefaultRG())
_, centers, inertia, converged := classifier.Run(1000, 0.001)
intertia := classifier.Inertia()
_, centers, inertia, converged := obistats.Kmeans(&seqworld, n_landmark, 0.001, &initialCenters)
converged := classifier.Run(1000, 0.001)
inertia := classifier.Inertia()
dist_centers := 0.0
for i := 0; i < n_landmark; i++ {
center := (*centers)[i]
icenter := initialCenters[i]
for j := 0; j < n_landmark; j++ {
diff := center[j] - icenter[j]
dist_centers += diff * diff
}
}
landmark_idx = obistats.KmeansBestRepresentative(&seqworld, centers)
log.Infof("Inertia: %f, Dist centers: %f, converged: %t", inertia, dist_centers, converged)
log.Infof("Inertia: %f, converged: %t", inertia, converged)
landmark_idx = classifier.CentersIndices()
sort.IntSlice(landmark_idx).Sort()
}
sort.IntSlice(landmark_idx).Sort()
log.Debugf("Selected indices : %v", landmark_idx)
seqworld = MapOnLandmarkSequences(library, landmark_idx)
@@ -159,12 +142,14 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
initialCenters[i] = seqworld[seq_idx]
}
classes := obistats.AssignToClass(&seqworld, &initialCenters)
// classes := obistats.AssignToClass(&seqworld, &initialCenters)
for i, seq := range library {
ic, _ := obiutils.InterfaceToIntSlice(seqworld[i])
seq.SetCoordinate(ic)
seq.SetAttribute("landmark_class", classes[i])
// seq.SetAttribute("landmark_class", classes[i])
// if the sequence is a landmark sequence
if i, ok := seq_landmark[i]; ok {
seq.SetAttribute("landmark_id", i)
}