{ "cells": [ { "cell_type": "markdown", "id": "a6b9d9f4", "metadata": {}, "source": [ "## Using `cz-benchmarks`\n", "\n", "You may duplicate this notebook and replace the simulated model execution cell with your own model code.\n", "\n", "This notebook guides you through loading single-cell datasets, running your model, and evaluating results using standardized tasks and metrics.\n", "\n", "All you need to do is swap in your model’s output—no extra setup required.\n", "Use the provided examples as templates for your workflow." ] }, { "cell_type": "code", "execution_count": null, "id": "977eebcb", "metadata": {}, "outputs": [], "source": [ "# Setup you notebook kernel and install the package\n", "# Install czbenchmarks for the selected Jupyter kernel\n", "!pip install czbenchmarks" ] }, { "cell_type": "markdown", "id": "07679138", "metadata": {}, "source": [ "### 1. Datasets\n", "\n", "Datasets are wrapped for consistent loading and compatibility:\n", "\n", "- `SingleCellLabeledDataset`: Gene expression data with cell labels (supports clustering, embedding, label prediction).\n", "- `SingleCellPerturbationDataset`: Perturbation datasets with control and perturbed cells." ] }, { "cell_type": "code", "execution_count": 1, "id": "1f6678a2", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "from czbenchmarks.datasets import load_dataset\n", "from czbenchmarks.datasets.single_cell_labeled import SingleCellLabeledDataset" ] }, { "cell_type": "markdown", "id": "497e612a", "metadata": {}, "source": [ "#### List Available Datasets \n", "\n", "This code snippet lists all available datasets in the czbenchmarks library." ] }, { "cell_type": "code", "execution_count": 2, "id": "acefbc6a", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | Dataset | \n", "
---|---|
chicken_spermatogenesis | \n", "{'organism': 'gallus_gallus', 'url': 's3://cz-... | \n", "
chimpanzee_spermatogenesis | \n", "{'organism': 'pan_troglodytes', 'url': 's3://c... | \n", "
gorilla_spermatogenesis | \n", "{'organism': 'gorilla_gorilla', 'url': 's3://c... | \n", "
human_spermatogenesis | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
marmoset_spermatogenesis | \n", "{'organism': 'callithrix_jacchus', 'url': 's3:... | \n", "
mouse_spermatogenesis | \n", "{'organism': 'mus_musculus', 'url': 's3://cz-b... | \n", "
opossum_spermatogenesis | \n", "{'organism': 'monodelphis_domestica', 'url': '... | \n", "
platypus_spermatogenesis | \n", "{'organism': 'ornithorhynchus_anatinus', 'url'... | \n", "
replogle_k562_essential_perturbpredict | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
rhesus_macaque_spermatogenesis | \n", "{'organism': 'macaca_mulatta', 'url': 's3://cz... | \n", "
tsv2_bladder | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_blood | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_bone_marrow | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_ear | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_eye | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_fat | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_heart | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_large_intestine | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_liver | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_lung | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_lymph_node | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_mammary | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_muscle | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_ovary | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_prostate | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_salivary_gland | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_skin | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_small_intestine | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_spleen | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_stomach | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_testis | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_thymus | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_tongue | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_trachea | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_uterus | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "
tsv2_vasculature | \n", "{'organism': 'homo_sapiens', 'url': 's3://cz-b... | \n", "