OBIKmers/obikmer
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 9 Wiki Activity

feat: implement parallel pairwise distance matrices

Browse Source 
Introduces parallelized pairwise distance matrix computation for Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger metrics across `Columnar`, `Packed`, and `Implicit` matrix variants. Adds trait methods and convenience wrappers, safely handles normalization and zero-denominator edge cases, and updates test suites to import required traits for validation.
This commit is contained in:
Eric Coissac
2026-06-08 20:04:51 +02:00
parent 09d9e21744
commit 1ec65922df
5 changed files with 6 additions and 163 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/obicompactvec/src/intmatrix.rs
-108
View File
@@ -54,23 +54,6 @@ impl ColumnarCompactIntMatrix {
Array1::from_vec(sums)
}
pub(crate) fn bray_dist_matrix(&self) -> Array2<f64> {
let sum_min = self.partial_bray_dist_matrix();
let col_sums = self.sum();
let n = self.n_cols();
let mut m = Array2::zeros((n, n));
for i in 0..n {
for j in 0..n {
if i != j {
let denom = col_sums[i] + col_sums[j];
m[[i, j]] = if denom == 0 { 0.0 }
else { 1.0 - 2.0 * sum_min[[i, j]] as f64 / denom as f64 };
}
}
}
m
}
pub(crate) fn partial_bray_dist_matrix(&self) -> Array2<u64> {
self.pairwise_u64(|i, j| self.col(i).partial_bray_dist(self.col(j)))
}
@@ -119,30 +102,6 @@ impl ColumnarCompactIntMatrix {
})
}
pub(crate) fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).relfreq_bray_dist(self.col(j)))
}
pub(crate) fn euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).euclidean_dist(self.col(j)))
}
pub(crate) fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).relfreq_euclidean_dist(self.col(j)))
}
pub(crate) fn hellinger_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).hellinger_dist(self.col(j)))
}
pub(crate) fn jaccard_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).jaccard_dist(self.col(j)))
}
pub(crate) fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).threshold_jaccard_dist(self.col(j), threshold))
}
pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
let mut meta = MatrixMeta::load(dir)?;
let mut b = PersistentCompactIntVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
@@ -343,29 +302,11 @@ impl PackedCompactIntMatrix {
self.pairwise_u64(|i, j| self.pair_partial_bray(i, j))
}
pub(crate) fn bray_dist_matrix(&self) -> Array2<f64> {
let col_sums = self.sum();
let sum_min = self.partial_bray_dist_matrix();
let n = self.n_cols;
let mut m = Array2::zeros((n, n));
for i in 0..n { for j in 0..n {
if i != j {
let denom = col_sums[i] + col_sums[j];
m[[i, j]] = if denom == 0 { 0.0 }
else { 1.0 - 2.0 * sum_min[[i, j]] as f64 / denom as f64 };
}
}}
m
}
pub(crate) fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.pair_partial_euclidean(i, j))
}
pub(crate) fn euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.pair_partial_euclidean(i, j).sqrt())
}
pub(crate) fn partial_threshold_jaccard_dist_matrix(&self, t: u32) -> (Array2<u64>, Array2<u64>) {
let n = self.n_cols;
let results: Vec<(usize, usize, u64, u64)> = upper_pairs(n)
@@ -381,46 +322,18 @@ impl PackedCompactIntMatrix {
(inter_m, union_m)
}
pub(crate) fn jaccard_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| {
let (inter, union) = self.pair_partial_threshold_jaccard(i, j, 1);
if union == 0 { 0.0 } else { 1.0 - inter as f64 / union as f64 }
})
}
pub(crate) fn threshold_jaccard_dist_matrix(&self, t: u32) -> Array2<f64> {
self.pairwise(|i, j| {
let (inter, union) = self.pair_partial_threshold_jaccard(i, j, t);
if union == 0 { 0.0 } else { 1.0 - inter as f64 / union as f64 }
})
}
pub(crate) fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
self.pairwise(|i, j| self.pair_partial_relfreq_bray(i, j, col_sums[i] as f64, col_sums[j] as f64))
}
pub(crate) fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
let col_sums = self.sum();
self.partial_relfreq_bray_dist_matrix(&col_sums)
}
pub(crate) fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
self.pairwise(|i, j| self.pair_partial_relfreq_euclidean(i, j, col_sums[i] as f64, col_sums[j] as f64))
}
pub(crate) fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
let col_sums = self.sum();
self.partial_relfreq_euclidean_dist_matrix(&col_sums)
}
pub(crate) fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
self.pairwise(|i, j| self.pair_partial_hellinger(i, j, col_sums[i] as f64, col_sums[j] as f64))
}
pub(crate) fn hellinger_dist_matrix(&self) -> Array2<f64> {
let col_sums = self.sum();
self.partial_hellinger_euclidean_dist_matrix(&col_sums)
}
}
/// Build `counts/matrix.pcmx` from existing `col_*.pciv` files.
@@ -508,27 +421,6 @@ impl PersistentCompactIntMatrix {
match self { Self::Columnar(m) => m.sum(), Self::Packed(m) => m.sum() }
}
pub fn bray_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.bray_dist_matrix(), Self::Packed(m) => m.bray_dist_matrix() }
}
pub fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.relfreq_bray_dist_matrix(), Self::Packed(m) => m.relfreq_bray_dist_matrix() }
}
pub fn euclidean_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.euclidean_dist_matrix(), Self::Packed(m) => m.euclidean_dist_matrix() }
}
pub fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.relfreq_euclidean_dist_matrix(), Self::Packed(m) => m.relfreq_euclidean_dist_matrix() }
}
pub fn hellinger_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.hellinger_dist_matrix(), Self::Packed(m) => m.hellinger_dist_matrix() }
}
pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.jaccard_dist_matrix(), Self::Packed(m) => m.jaccard_dist_matrix() }
}
pub fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
match self { Self::Columnar(m) => m.threshold_jaccard_dist_matrix(threshold), Self::Packed(m) => m.threshold_jaccard_dist_matrix(threshold) }
}
pub fn partial_bray_dist_matrix(&self) -> Array2<u64> {
match self { Self::Columnar(m) => m.partial_bray_dist_matrix(), Self::Packed(m) => m.partial_bray_dist_matrix() }
}