hpdex 1.0.1

High-Performance Parallel Differential Expression Analysis for Single-Cell Data

hpdex

High-performance differential expression analysis for single-cell data

Overview · Installation · Quick Start · API · Kernels · Benchmarks · FAQ · License

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🔎 Overview

hpdex now ships a C++ backend with careful memory layout and true multithreading, delivering large speedups for Mann–Whitney U–based DE on single-cell matrices:

• ⚡ Sparse CSC: in DE scenarios (gene × group pairs), the pure Mann–Whitney U kernel is often hundreds of times faster than SciPy when multi-threaded.
• 🧩 End-to-end DE (parallel_differential_expression): with scheduling and reuse, typical pipelines are 2–3 orders of magnitude faster than pdex-style Python loops.
• 📦 Dense: even single-thread is commonly ~3× faster than SciPy on dense inputs; multi-thread scales further.
• 📈 Statistical parity: tie-aware U, continuity correction, and asymptotic p-values match scipy.stats.mannwhitneyu under equivalent settings (within float tolerance).

Key capabilities:

• 🧵 C++ multithreading, per-thread workspaces, low allocator pressure
• 🧮 Float & histogram kernels (auto-selected by data type)
• 🧠 Tie & continuity corrections; exact or asymptotic p-values in backend
• 🧱 Robust sparse support (CSC highly recommended)
• 🧰 Drop-in friendly design & clean Python API

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⚙️ Installation

From PyPI

pip install hpdex

From source

git clone --recurse-submodules https://github.com/AI4Cell/hpdex.git # for highway submodule
cd hpdex
pip install -e .

Requirements

• Python ≥ 3.10
• numpy, scipy, pandas, anndata, tqdm
• Building from source requires a C++17 compiler; OpenMP recommended for threading

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🚀 Quick Start

import anndata as ad
from hpdex import parallel_differential_expression

adata = ad.read_h5ad("data.h5ad")

df = parallel_differential_expression(
    adata,
    groupby_key="perturbation",
    reference="control",
    threads=8,                 # C++ multithreading
    tie_correction=True,
    use_continuity=True,       # continuity correction for U -> Z
    show_progress=True,
)

df.to_csv("de_results.csv", index=False)

Output schema (DataFrame):

column	description
target	target group name
feature	gene / feature id
p_value	two-sided p-value from Mann–Whitney U
u_statistic	U₁ statistic (reference vs target)
fold_change	mean(target) / mean(reference)
log2_fold_change	log2(fold_change)
fdr	BH-adjusted p-value

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📚 API Reference

parallel_differential_expression

parallel_differential_expression(
    adata: ad.AnnData,
    groupby_key: str,
    reference: str | None,          # None -> treated as "non-targeting" baseline
    groups: list[str] | None = None,
    metric: str = "wilcoxon",       # currently only "wilcoxon" (Mann–Whitney U)
    tie_correction: bool = True,
    use_continuity: bool = True,
    min_samples: int = 2,
    threads: int = -1,              # -1 -> use all logical cores
    clip_value: float = 20.0,
    show_progress: bool = True,
) -> pd.DataFrame

Notes

• threads controls the C++ backend concurrency.
• reference=None creates a “non-targeting” baseline for missing labels.
• Internally the matrix is converted to CSC (scipy.sparse.csc_matrix) for best performance.
• The backend currently defaults to zero-handling = "min" (zeros at head), suitable for UMI counts.

Low-level backend (advanced)

from hpdex.backend import mannwhitneyu, group_mean

U1, P = mannwhitneyu(
    matrix_csc,           # scipy.sparse.csc_matrix or ndarray (dense handled internally)
    group_id_int32,       # shape: (n_cells,), 0=reference, 1..G-1=targets, -1=ignored
    n_targets: int,
    ref_sorted=False,     # set True if your ref slice is already sorted
    tar_sorted=False,     # set True if target slices are sorted
    use_continuity=True,
    tie_correction=True,
    zero_handling="min",  # "none" | "min" | "max" | "mix"
    threads=-1,
    show_progress=False,
)

means = group_mean(
    matrix_csc,
    group_id_int32,
    G,                    # total groups (reference + targets)
    include_zeros=True,
    threads=-1,
)  # returns array shape: (G, n_genes)

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🧪 Statistical Kernels

Float kernel

• Merge-rank U with tie tracking; contiguous slices; vector-friendly
• Memory: O(n) per slice; scales well with threads

Histogram kernel

• For integer/UMI counts with limited range
• Bucketized ranks reduce sorting; memory O(bins) (≪ n)

Common

• Exact/asymptotic p-values in backend
• Tie & continuity corrections
• Batch-wise scheduling across (gene × group)

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📈 Benchmarks

Typical observations (indicative; varies by CPU, threads, sparsity):

Scenario	Matrix	Speedup vs SciPy
Dense single-thread U per gene	dense	~3×
Sparse multi-thread U (DE setting)	CSC, 64T	100×–300×
End-to-end DE vs pdex-style baseline	CSC, 64T	10²–10³×

Why fast? Thread-local workspaces (no per-column allocations), cache-friendly slices, zero-aware rank merge, and reduced Python overhead.

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🧷 Testing

cd test && cat bench_mwu.txt | xargs python bench_mwu.py

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❓ FAQ

Do you correct for multiple testing?

Yes. The output fdr applies Benjamini–Hochberg (BH).

Why are p-values sometimes ~0?

Very large samples and strong effects can underflow in float. This is expected; prefer fdr for decisions.

How are zeros handled?

Backend supports "none", "min", "max", "mix". The high-level API currently uses "min" by default, which is suitable for UMI counts.

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📄 License

MIT — see LICENSE.

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_{Built for large-scale single-cell perturbation analysis, now powered by a C++ backend.}