lazymatrix

Lazy column normalization for design matrices in Rust. lazymatrix presents

X̃ = (X − 1cᵀ) S⁻¹

as a linear operator without materializing the centered matrix. This matters for sparse matrices, where subtracting a column center would turn structural zeros into nonzeros. Matrix–vector products instead use the original matrix:

X̃v  = X(S⁻¹v) − 1(cᵀS⁻¹v)
X̃ᵀu = S⁻¹(Xᵀu − c Σu)

Centering and scaling are independently optional. The crate also provides borrowed logical column views and sparse column and row access for algorithms that work directly with stored entries.

Install

The core trait and operator API has no linear algebra dependency beyond num-traits. Enable a backend for ready-made matrix implementations:

cargo add lazymatrix --features faer
# or
cargo add lazymatrix --features nalgebra
# or, for dense arrays
cargo add lazymatrix --features ndarray
# or, for sprs sparse matrices
cargo add lazymatrix --features sprs
# or, for chunked Zarr arrays
cargo add lazymatrix --features zarrs

Unversioned features select the newest supported release. Use a versioned feature to stay on a particular release line:

For example, cargo add lazymatrix --features nalgebra_v0_34 enables nalgebra 0.34 and nalgebra-sparse 0.11. Set your direct backend dependency to the same release line. If Cargo enables multiple releases of one backend, lazymatrix implements traits only for the newest enabled release. The *_all features are internal markers, not entry points for selecting a backend.

The core and older backends support Rust 1.87. The nalgebra feature now selects nalgebra 0.35, which requires Rust 1.89. To retain the previous release and Rust 1.87 support, replace nalgebra with nalgebra_v0_34 in your feature list. The sprs backend supports Rust 1.87 with sprs 0.11.4 (used in the lockfile); sprs 0.11.5 requires Rust 1.88.

Example

use lazymatrix::{
    Centering, LazyMatrix, MatVec, Normalization, Scaling,
};
use nalgebra::{DMatrix, DVector};

let x = DMatrix::from_row_slice(
    3,
    2,
    &[1.0, 0.0, 2.0, 3.0, 0.0, 4.0],
);
let x = LazyMatrix::new(
    x,
    Normalization::new(Centering::Mean, Scaling::Sd),
).unwrap();

let y = x.matvec(&DVector::from_vec(vec![1.0, -1.0])).unwrap();

The same interface works with faer and nalgebra dense matrices, their borrowed views, and CSC sparse matrices. The ndarray backends support dense arrays, including borrowed, transposed, and strided views:

use lazymatrix::{Centering, LazyMatrix, MatVec, Normalization, Scaling};
use ndarray::array;

let x = array![[1.0, 0.0], [2.0, 3.0], [0.0, 4.0]];
let lazy = LazyMatrix::new(
    x.view(),
    Normalization::new(Centering::Mean, Scaling::Sd),
).unwrap();
let y = lazy.matvec(&array![1.0, -1.0]).unwrap();

Allocating ndarray products use Array1 vectors. Reusable-output products can write into mutable, strided vector views. A lazy forward product needs an owned input because it may clone and scale that input; call to_owned() on an immutable input view first. Logical-column operations and reusable transpose products accept immutable vector views directly. Borrowed column access preserves the original strides and takes O(1) time; dense logical-column operations take O(nrows) time.

The sprs backend supports owned CSC and CSR matrices and borrowed views. Use Vec for allocating products, or enable an ndarray feature to use that release's Array1. Reusable-output products accept any supported dense vector view, including strided ndarray inputs and destinations. The sprs feature does not select an ndarray backend version.

Wrap CSC storage in SprsCsc to borrow logical or sparse columns:

use lazymatrix::{Centering, LazyMatrix, MatVec, Normalization, Scaling, SprsCsc};
use sprs::CsMat;

let x = CsMat::new_csc(
    (3, 2),
    vec![0, 2, 3],
    vec![0, 2, 1],
    vec![1.0, 3.0, 2.0],
);
let csc = SprsCsc::try_new(x.view()).unwrap();
let lazy = LazyMatrix::new(csc, Normalization::new(Centering::Mean, Scaling::Sd)).unwrap();
let y = lazy.matvec(&vec![1.0, -1.0]).unwrap();
let column = lazy.sparse_column(0);
assert_eq!(column.row_indices(), &[0, 2]);

SprsCsc::try_new checks orientation in O(1) time and returns a CSR input unchanged as Err. Convert CSR explicitly with to_csc() or into_csc() when column access is needed. Products and statistics also work directly on CsMat or CsMatView in either orientation. They visit stored entries without materializing the normalized matrix. CSC statistics take O(ncols + nnz) time; CSR statistics take O(nrows + ncols + nnz) time and O(ncols) workspace.

Logical columns borrow sprs vector views for any supported index type. SparseColumns requires usize row indices so it can return slices without copying. A centered column dot takes O(nrows + nnz_column); dot_with_sum uses a caller-supplied vector sum to take O(nnz_column).

SparseRows borrows raw column-index and value slices from CSR storage in O(1) time, including explicitly stored zeros. It supports faer's SparseRowMat, SparseRowMatRef, and SparseRowMatMut with usize indices, and nalgebra-sparse's CsrMatrix. These CSR types currently provide shape and raw row access; their operator and column-statistics implementations remain future work.

For sprs, use the checked SprsCsr wrapper:

use lazymatrix::{SparseRows, SprsCsr};
use sprs::CsMat;

let x = CsMat::new(
    (2, 3),
    vec![0, 2, 3],
    vec![0, 2, 1],
    vec![1.0, 0.0, 2.0],
);
let csr = SprsCsr::try_new(x.view()).unwrap();
let (columns, values) = csr.sparse_row(0);
assert_eq!(columns, &[0, 2]);
assert_eq!(values, &[1.0, 0.0]);

SprsCsr::try_new checks orientation without copying and returns a CSC input unchanged as Err. The wrapper forwards products and statistics, so it can also be passed to LazyMatrix::new. Row borrowing requires usize column indices; pointer indices may use any supported width. The returned slices describe the original matrix, before normalization. Normalized row views remain future work.

Enable parallel alongside a backend to compute column statistics with Rayon. For sprs, CSC columns run independently in parallel; CSR statistics scan rows serially to accumulate columns without converting storage. See examples/ for complete solver examples that consume the operator.

Fallible operations

Matrix products, column statistics, and LazyMatrix::new now return Result. This is a breaking API change: use ? to propagate errors, or unwrap results when using an in-memory backend. Existing in-memory backends use std::convert::Infallible; storage backends can return read and decoding errors.

Custom backends implement MatrixErrorType once and use its associated Error type across all four operator traits and ColumnStats. Borrowing a matrix or wrapping it in LazyMatrix preserves that error type. Shape queries, borrowed column and row operations, and explicit-parameter construction remain infallible. Dimension mismatches still panic. After a failed reusable-output product, the output may be partial and must be discarded or overwritten by a successful call.

ColumnStats::normalization_stats computes the optional centers and raw scales as a NormalizationStats<F> pair. Its default dispatches to individual statistics. Storage backends can override it to share scans; LazyMatrix::new then replaces exact zero scales with one, preserving nonfinite values.

LazyMatrix::from_parts and LazyMatrix::with_scales reject explicit zero scales with a panic that reports the column index. Both positive and negative zero are rejected. Explicit parameters are otherwise preserved unchanged, including negative scales, tiny nonzero scales, and nonfinite centers or scales. These constructors do not guarantee finite arithmetic results.

Out-of-core matrices

A borrowed ndarray view can refer to a memory-mapped file. The ndarray_mmap example creates a private temporary .npy file in column-major order, fills it through a writable mapping, and normalizes a read-only ArrayView2 without allocating an owned matrix:

cargo run --locked --release --example ndarray_mmap --features ndarray -- 10000 32

This example requires ndarray 0.17. Memory mappings depend on the backing file remaining unmodified while views exist, including by other processes. Mapping a file lets the OS manage page residency; it does not impose a resident-memory limit. Column-major storage keeps this backend's column-statistics scans contiguous.

The zarrs feature supplies ZarrMatrix for synchronous, two-dimensional Zarr arrays with f32 or f64 elements. Enable zarrs 0.22 in your direct dependency as well. The adapter supports Rust 1.87 and does not select an ndarray backend.

use std::sync::Arc;
use lazymatrix::{Centering, LazyMatrix, MatVec, Normalization, Scaling, ZarrMatrix};
use zarrs::{array::Array, filesystem::FilesystemStore};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let store = Arc::new(FilesystemStore::new("data.zarr")?);
    let array = Array::open(store, "/matrix")?;
    let matrix = ZarrMatrix::<_, f64>::try_new(array)?;
    let lazy = LazyMatrix::new(matrix, Normalization::new(Centering::Mean, Scaling::Sd))?;
    let result = lazy.matvec(&vec![1.0; lazy.ncols()])?;
    println!("{} rows", result.len());
    Ok(())
}

Each product reads one chunk at a time. Normalization uses zero scans when inactive, one when sufficient, and at most two otherwise. Missing chunks retain the configured fill value, including nonzero or nonfinite values. Partial edge chunks contribute only entries inside the array. The array must remain unchanged throughout normalization and subsequent use; the adapter does not provide snapshot isolation.

Allocating products use Vec<F>. Reusable-output products accept the existing vector-view capabilities, including enabled backend vector types. The adapter provides no borrowed columns or rows. Working vectors and column statistics stay in RAM, together with chunk buffers and codec workspaces. Choose chunks that fit in memory; for sharded arrays, the relevant bound is the outer storage chunk. There is no byte budget, cache, prefetching, or parallel chunk scanning.

Filesystem and gzip support are enabled by this crate. Additional codecs can be enabled through your direct zarrs dependency. An unsupported codec is reported when zarrs opens the array.

The self-contained filesystem example creates data chunk by chunk:

cargo run --locked --release --example zarrs_chunked --features zarrs -- 10000 32

Both examples accept optional row and column counts and print operation timings. For larger-than-RAM measurements, first build the examples, then run the binaries with GNU time installed:

cargo build --locked --release --examples --features ndarray,zarrs
env time -v target/release/ndarray_mmap 1000000 256
env time -v target/release/zarrs_chunked 1000000 256

Increase dimensions so rows * cols * 8 exceeds available RAM, while vectors and chunks still fit. Set TMPDIR to a directory on disk and account for temporary disk space. Record peak RSS and timings separately from correctness tests, and distinguish page-cache effects from disk throughput: these examples generate their own files before reading them, so a run on data smaller than RAM is not a cold-I/O benchmark. CI uses small fixtures and verifies chunk-read counts without allocating a larger-than-RAM dataset.

License

Licensed under either the Apache License, Version 2.0 or the MIT license, at your option.