{ "cells": [ { "cell_type": "markdown", "id": "19375bf6", "metadata": {}, "source": [ "# The ANI-1 dataset in one line, and a paper-style correlation test\n", "\n", "The **ANI-1 dataset** (Smith, Isayev & Roitberg, *Sci. Data* **4**, 170193,\n", "2017) is the training set behind the ANI-1 potential: ~20 million\n", "off-equilibrium conformations of 57k small organic molecules (H, C, N, O) from\n", "GDB-11, each with a wB97X/6-31G(d) total energy, generated by Normal Mode\n", "Sampling. `xnn` serves it through the same one-liner hub as every other\n", "dataset:\n", "\n", "```python\n", "from xnn.common.data import load_dataset\n", "splits = load_dataset(\"ani1\", heavy_atoms=[2, 3, 4]) # pyanitools .h5 -> xnn dicts\n", "```\n", "\n", "The first call downloads the one 4.8 GB archive from figshare (cached and\n", "MD5-verified under `datasets/ani1/`); afterwards it is instant and offline. Here\n", "we load a **small subset**, train `xnn` ANI on it, and reproduce the paper's\n", "energy-correlation plot (Fig. 4A) at small scale.\n", "\n", "Run with the **`xnn`** kernel." ] }, { "cell_type": "markdown", "id": "2cf0f116", "metadata": {}, "source": [ "## 0. Load a subset of the ANI-1 dataset" ] }, { "cell_type": "code", "execution_count": 1, "id": "2ee865e1", "metadata": { "execution": { "iopub.execute_input": "2026-07-20T04:18:28.793869Z", "iopub.status.busy": "2026-07-20T04:18:28.793752Z", "iopub.status.idle": "2026-07-20T04:18:35.619554Z", "shell.execute_reply": "2026-07-20T04:18:35.612743Z" } }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "d8e58df4f2ba48eda589a8510498d1da", "version_major": 2, "version_minor": 0 }, "text/plain": [ "ani1:ani_gdb_s02: 0%| | 0/13 [00:00" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from torch.utils.data import DataLoader\n", "from xnn.common.data import collate\n", "\n", "model = trainer.model.eval(); device = trainer.device\n", "EV2KCAL = 23.060541945329334\n", "E_pred, E_ref = [], []\n", "for batch in DataLoader(test_ds, batch_size=64, collate_fn=collate):\n", " batch = batch.to(device)\n", " with torch.no_grad():\n", " E_pred.append(model(batch)[\"energy\"].cpu().numpy())\n", " E_ref.append(batch.energy.cpu().numpy())\n", "E_pred, E_ref = np.concatenate(E_pred), np.concatenate(E_ref)\n", "rmse = np.sqrt(np.mean((E_pred - E_ref) ** 2))\n", "print(f\"test energy RMSE: {rmse*1e3:.1f} meV = {rmse*EV2KCAL:.3f} kcal/mol\")\n", "\n", "fig, ax = plt.subplots(figsize=(4.6, 4.4))\n", "ax.scatter(E_ref, E_pred, s=8, alpha=0.5)\n", "lim = [min(E_ref.min(), E_pred.min()), max(E_ref.max(), E_pred.max())]\n", "ax.plot(lim, lim, \"k--\", lw=1)\n", "ax.set_xlabel(\"DFT residual energy (eV)\"); ax.set_ylabel(\"ANI residual energy (eV)\")\n", "ax.set_title(f\"ANI-1 subset RMSE {rmse*EV2KCAL:.3f} kcal/mol\")\n", "fig.tight_layout(); fig.savefig(\"ani1_correlation.png\", dpi=110); plt.show()" ] }, { "cell_type": "markdown", "id": "3c0ab6cc", "metadata": {}, "source": [ "## Summary\n", "\n", "`load_dataset(\"ani1\", ...)` brings the original 20 M-conformation ANI-1 training\n", "set into the same one-line hub as every other `xnn` dataset, with heavy-atom\n", "subset selection and conformation caps for tractable experiments. Trained on a\n", "small subset, `xnn` ANI already reproduces DFT energies to well within chemical\n", "accuracy, the paper's headline result. At full scale with the published\n", "`ANI.ani1x()` architecture this is the ANI-1x potential verified against\n", "torchani in `examples/fidelity_checks/ani_verification.ipynb`." ] } ], "metadata": { "kernelspec": { "display_name": "xnn (.venv)", "language": "python", "name": "xnn" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.13.12" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { "0d1861feb4624383abf7b7107d6a7ba5": { "model_module": "@jupyter-widgets/base", "model_module_version": "2.0.0", "model_name": "LayoutModel", "state": { "_model_module": "@jupyter-widgets/base", "_model_module_version": "2.0.0", "_model_name": "LayoutModel", "_view_count": null, "_view_module": "@jupyter-widgets/base", "_view_module_version": "2.0.0", "_view_name": "LayoutView", "align_content": null, 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