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//! Truncated singular value decomposition
//!
//! This module computes the k largest/smallest singular values/vectors for a dense matrix.
use crate::{
lobpcg::{lobpcg, random, Lobpcg},
Order, Result,
};
use ndarray::prelude::*;
use num_traits::NumCast;
use std::iter::Sum;
use rand::Rng;
/// The result of a eigenvalue decomposition, not yet transformed into singular values/vectors
///
/// Provides methods for either calculating just the singular values with reduced cost or the
/// vectors with additional cost of matrix multiplication.
#[derive(Debug, Clone)]
pub struct TruncatedSvdResult<A> {
eigvals: Array1<A>,
eigvecs: Array2<A>,
problem: Array2<A>,
order: Order,
ngm: bool,
}
impl<A: NdFloat + 'static + MagnitudeCorrection> TruncatedSvdResult<A> {
/// Returns singular values ordered by magnitude with indices.
fn singular_values_with_indices(&self) -> (Array1<A>, Vec<usize>) {
// numerate eigenvalues
let mut a = self.eigvals.iter().enumerate().collect::<Vec<_>>();
let (values, indices) = if self.order == Order::Largest {
// sort by magnitude
a.sort_by(|(_, x), (_, y)| x.partial_cmp(y).unwrap().reverse());
// calculate cut-off magnitude (borrowed from scipy)
let cutoff = A::epsilon() * // float precision
A::correction() * // correction term (see trait below)
*a[0].1; // max eigenvalue
// filter low singular values away
let (values, indices): (Vec<A>, Vec<usize>) = a
.into_iter()
.filter(|(_, x)| *x > &cutoff)
.map(|(a, b)| (b.sqrt(), a))
.unzip();
(values, indices)
} else {
a.sort_by(|(_, x), (_, y)| x.partial_cmp(y).unwrap());
let (values, indices) = a.into_iter().map(|(a, b)| (b.sqrt(), a)).unzip();
(values, indices)
};
(Array1::from(values), indices)
}
/// Returns singular values ordered by magnitude
pub fn values(&self) -> Array1<A> {
let (values, _) = self.singular_values_with_indices();
values
}
/// Returns singular values, left-singular vectors and right-singular vectors
pub fn values_vectors(&self) -> (Array2<A>, Array1<A>, Array2<A>) {
let (values, indices) = self.singular_values_with_indices();
// branch n > m (for A is [n x m])
#[allow(clippy::branches_sharing_code)]
let (u, v) = if self.ngm {
let vlarge = self.eigvecs.select(Axis(1), &indices);
let mut ularge = self.problem.dot(&vlarge);
ularge
.columns_mut()
.into_iter()
.zip(values.iter())
.for_each(|(mut a, b)| a.mapv_inplace(|x| x / *b));
(ularge, vlarge)
} else {
let ularge = self.eigvecs.select(Axis(1), &indices);
let mut vlarge = self.problem.t().dot(&ularge);
vlarge
.columns_mut()
.into_iter()
.zip(values.iter())
.for_each(|(mut a, b)| a.mapv_inplace(|x| x / *b));
(ularge, vlarge)
};
(u, values, v.reversed_axes())
}
}
#[derive(Debug, Clone)]
/// Truncated singular value decomposition
///
/// Wraps the LOBPCG algorithm and provides convenient builder-pattern access to
/// parameter like maximal iteration, precision and constrain matrix.
pub struct TruncatedSvd<A: NdFloat, R: Rng> {
order: Order,
problem: Array2<A>,
precision: f32,
maxiter: usize,
rng: R,
}
impl<A: NdFloat + Sum, R: Rng> TruncatedSvd<A, R> {
/// Create a new truncated SVD problem
///
/// # Parameters
/// * `problem`: rectangular matrix which is decomposed
/// * `order`: whether to return large or small (close to zero) singular values
/// * `rng`: random number generator
pub fn new_with_rng(problem: Array2<A>, order: Order, rng: R) -> TruncatedSvd<A, R> {
TruncatedSvd {
precision: 1e-5,
maxiter: problem.len_of(Axis(0)) * 2,
order,
problem,
rng,
}
}
}
impl<A: NdFloat + Sum, R: Rng> TruncatedSvd<A, R> {
/// Set the required precision of the solution
///
/// The precision is, in the context of SVD, the square-root precision of the underlying
/// eigenproblem solution. The eigenproblem-precision is used to check the L2 error of each
/// eigenvector and stops its optimization when the required precision is reached.
pub fn precision(mut self, precision: f32) -> Self {
self.precision = precision;
self
}
/// Set the maximal number of iterations
///
/// The LOBPCG is an iterative approach to eigenproblems and stops when this maximum
/// number of iterations are reached
pub fn maxiter(mut self, maxiter: usize) -> Self {
self.maxiter = maxiter;
self
}
/// Calculate the singular value decomposition
///
/// # Parameters
///
/// * `num`: number of singular-value/vector pairs, ordered by magnitude
///
/// # Example
///
/// ```rust
/// use ndarray::{arr1, Array2};
/// use linfa_linalg::{Order, lobpcg::TruncatedSvd};
/// use rand::SeedableRng;
/// use rand_xoshiro::Xoshiro256Plus;
///
/// let diag = arr1(&[1., 2., 3., 4., 5.]);
/// let a = Array2::from_diag(&diag);
///
/// let eig = TruncatedSvd::new_with_rng(a, Order::Largest, Xoshiro256Plus::seed_from_u64(42))
/// .precision(1e-4)
/// .maxiter(500);
///
/// let res = eig.decompose(3);
/// ```
pub fn decompose(mut self, num: usize) -> Result<TruncatedSvdResult<A>> {
if num == 0 {
// return empty solution if requested eigenvalue number is zero
return Ok(TruncatedSvdResult {
eigvals: Array1::zeros(0),
eigvecs: Array2::zeros((0, 0)),
problem: Array2::zeros((0, 0)),
order: self.order,
ngm: false,
});
}
let (n, m) = (self.problem.nrows(), self.problem.ncols());
// generate initial matrix
let x: Array2<f32> = random((usize::min(n, m), num), &mut self.rng);
let x = x.mapv(|x| NumCast::from(x).unwrap());
// square precision because the SVD squares the eigenvalue as well
let precision = self.precision * self.precision;
// use problem definition with less operations required
let res = if n > m {
lobpcg(
|y| self.problem.t().dot(&self.problem.dot(&y)),
x,
|_| {},
None,
precision,
self.maxiter,
self.order,
)
} else {
lobpcg(
|y| self.problem.dot(&self.problem.t().dot(&y)),
x,
|_| {},
None,
precision,
self.maxiter,
self.order,
)
};
// convert into TruncatedSvdResult
match res {
Ok(Lobpcg {
eigvals, eigvecs, ..
})
| Err((
_,
Some(Lobpcg {
eigvals, eigvecs, ..
}),
)) => Ok(TruncatedSvdResult {
problem: self.problem,
eigvals,
eigvecs,
order: self.order,
ngm: n > m,
}),
Err((err, None)) => Err(err),
}
}
}
/// Magnitude Correction
///
/// The magnitude correction changes the cut-off point at which an eigenvector belongs to the
/// null-space and its eigenvalue is therefore zero. The correction is multiplied by the floating
/// point epsilon and therefore dependent on the floating type.
pub trait MagnitudeCorrection {
fn correction() -> Self;
}
impl MagnitudeCorrection for f32 {
fn correction() -> Self {
1.0e3
}
}
impl MagnitudeCorrection for f64 {
fn correction() -> Self {
1.0e6
}
}
#[cfg(test)]
mod tests {
use super::Order;
use super::TruncatedSvd;
use approx::assert_abs_diff_eq;
use ndarray::{arr1, arr2, s, Array1, Array2, NdFloat};
use ndarray_rand::{rand_distr::StandardNormal, RandomExt};
use rand::distributions::{Distribution, Standard};
use rand::SeedableRng;
use rand_xoshiro::Xoshiro256Plus;
/// Generate random array
fn random<A>(sh: (usize, usize)) -> Array2<A>
where
A: NdFloat,
Standard: Distribution<A>,
{
let rng = Xoshiro256Plus::seed_from_u64(3);
super::random(sh, rng)
}
#[test]
fn test_truncated_svd() {
let a = arr2(&[[3., 2., 2.], [2., 3., -2.]]);
let res = TruncatedSvd::new_with_rng(a, Order::Largest, Xoshiro256Plus::seed_from_u64(42))
.precision(1e-5)
.maxiter(10)
.decompose(2)
.unwrap();
let (_, sigma, _) = res.values_vectors();
assert_abs_diff_eq!(&sigma, &arr1(&[5.0, 3.0]), epsilon = 1e-5);
}
#[test]
fn test_truncated_svd_random() {
let a: Array2<f64> = random((50, 10));
let res = TruncatedSvd::new_with_rng(
a.clone(),
Order::Largest,
Xoshiro256Plus::seed_from_u64(42),
)
.precision(1e-5)
.maxiter(10)
.decompose(10)
.unwrap();
let (u, sigma, v_t) = res.values_vectors();
let reconstructed = u.dot(&Array2::from_diag(&sigma).dot(&v_t));
assert_abs_diff_eq!(&a, &reconstructed, epsilon = 1e-5);
}
/// Eigenvalue structure in high dimensions
///
/// This test checks that the eigenvalues are following the Marchensko-Pastur law. The data is
/// standard uniformly distributed (i.e. E(x) = 0, E^2(x) = 1) and we have twice the amount of
/// data when compared to features. The probability density of the eigenvalues should then follow
/// a special densitiy function, described by the Marchenko-Pastur law.
///
/// See also https://en.wikipedia.org/wiki/Marchenko%E2%80%93Pastur_distribution
#[test]
fn test_marchenko_pastur() {
// create random number generator
let mut rng = Xoshiro256Plus::seed_from_u64(3);
// generate normal distribution random data with N >> p
let data = Array2::random_using((1000, 500), StandardNormal, &mut rng) / 1000f64.sqrt();
let res =
TruncatedSvd::new_with_rng(data, Order::Largest, Xoshiro256Plus::seed_from_u64(42))
.precision(1e-3)
.decompose(500)
.unwrap();
let sv = res.values().mapv(|x: f64| x * x);
// we have created a random spectrum and can apply the Marchenko-Pastur law
// with variance 1 and p/n = 0.5
let (a, b) = (
1. * (1. - 0.5f64.sqrt()).powf(2.0),
1. * (1. + 0.5f64.sqrt()).powf(2.0),
);
// check that the spectrum has correct boundaries
assert_abs_diff_eq!(b, sv[0], epsilon = 0.1);
assert_abs_diff_eq!(a, sv[sv.len() - 1], epsilon = 0.1);
// estimate density empirical and compare with Marchenko-Pastur law
let mut i = 0;
'outer: for th in Array1::linspace(0.1f64, 2.8, 28).slice(s![..;-1]) {
let mut count = 0;
while sv[i] >= *th {
count += 1;
i += 1;
if i == sv.len() {
break 'outer;
}
}
let x = th + 0.05;
let mp_law = ((b - x) * (x - a)).sqrt() / std::f64::consts::PI / x;
let empirical = count as f64 / 500. / ((2.8 - 0.1) / 28.);
assert_abs_diff_eq!(mp_law, empirical, epsilon = 0.05);
}
}
}