hsp90 posterior calc and moving things around

flatironinstitute · Sep 13, 2023 · 6af4b30 · 6af4b30
1 parent 51db67f
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diff --git a/Lukes_folder/6wxb/6wxb_MMD.ipynb b/Lukes_folder/6wxb/6wxb_MMD.ipynb
diff --git a/Lukes_folder/6wxb/6wxb_MMD_bandwidths.ipynb b/Lukes_folder/6wxb/6wxb_MMD_bandwidths.ipynb
diff --git a/Lukes_folder/6wxb/6wxb_MMD_index.ipynb b/Lukes_folder/6wxb/6wxb_MMD_index.ipynb
diff --git a/Lukes_folder/6wxb/6wxb_distances_boot_nonrandom_params.npz b/Lukes_folder/6wxb/6wxb_distances_boot_nonrandom_params.npz
diff --git a/Lukes_folder/6wxb/6wxb_distances_boot_nonrandom_params_no_whiten.npz b/Lukes_folder/6wxb/6wxb_distances_boot_nonrandom_params_no_whiten.npz
diff --git a/Lukes_folder/6wxb/6wxb_experimental_data.ipynb b/Lukes_folder/6wxb/6wxb_experimental_data.ipynb
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params_no_whiten.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params_no_whiten.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params_no_whiten_test.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params_no_whiten_test.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params_test.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_hypothesis_nonrandom_params_test.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_index_mmd_no_whiten.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_index_mmd_no_whiten.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_mmd_comparison_nonrandom_params.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_mmd_comparison_nonrandom_params.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_mmd_comparison_nonrandom_params_no_whiten.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_mmd_comparison_nonrandom_params_no_whiten.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_mmd_comparison_random_params.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_mmd_comparison_random_params.png
diff --git a/Lukes_folder/6wxb/6wxb_figures/6wxb_posterior_means_no_whiten.png b/Lukes_folder/6wxb/6wxb_figures/6wxb_posterior_means_no_whiten.png
diff --git a/Lukes_folder/6wxb/6wxb_images.ipynb b/Lukes_folder/6wxb/6wxb_images.ipynb
diff --git a/Lukes_folder/6wxb/6wxb_loss b/Lukes_folder/6wxb/6wxb_loss
diff --git a/Lukes_folder/6wxb/6wxb_no_fft_loss b/Lukes_folder/6wxb/6wxb_no_fft_loss
diff --git a/...s_folder/image_params_mixed_training.json → ...b_params/image_params_mixed_training.json b/...s_folder/image_params_mixed_training.json → ...b_params/image_params_mixed_training.json
@@ -3,9 +3,11 @@
     "PIXEL_SIZE": 2.06,
     "SIGMA": [0.5, 5.0],
     "MODEL_FILE": "../data/protein_models/6wxb_mixed_models.npy",
-    "SHIFT": 40,
+    "SHIFT": true,
     "DEFOCUS": [0.5, 5.0],
-    "SNR": [0.01,1.0],
+    "SNR": [0.001, 0.1],
+    "RADIUS_MASK": 100,
     "AMP": 0.1,
-    "B_FACTOR": [1.0, 100.0]
+    "B_FACTOR": [1.0, 100.0],
+    "ELECWAVE": 0.019866
 }
diff --git a/Lukes_folder/6wxb/6wxb_params/resnet18_encoder.json b/Lukes_folder/6wxb/6wxb_params/resnet18_encoder.json
@@ -0,0 +1,12 @@
+{"EMBEDDING": "RESNET18",
+"OUT_DIM": 256,
+"NUM_TRANSFORM": 5,
+"NUM_HIDDEN_FLOW": 10,
+"HIDDEN_DIM_FLOW": 256,
+"MODEL": "NSF",
+"LEARNING_RATE": 0.0005,
+"CLIP_GRADIENT": 5.0,
+"THETA_SHIFT": 9.5,
+"THETA_SCALE": 9.5,
+"BATCH_SIZE": 256
+}
diff --git a/Lukes_folder/6wxb/6wxb_params/resnet18_fft_encoder.json b/Lukes_folder/6wxb/6wxb_params/resnet18_fft_encoder.json
@@ -0,0 +1,12 @@
+{"EMBEDDING": "RESNET18_FFT_FILTER",
+"OUT_DIM": 256,
+"NUM_TRANSFORM": 5,
+"NUM_HIDDEN_FLOW": 10,
+"HIDDEN_DIM_FLOW": 256,
+"MODEL": "NSF",
+"LEARNING_RATE": 0.0003,
+"CLIP_GRADIENT": 5.0,
+"THETA_SHIFT": 50,
+"THETA_SCALE": 50,
+"BATCH_SIZE": 256
+}
diff --git a/Lukes_folder/6wxb/6wxb_prior_to_posterior.ipynb b/Lukes_folder/6wxb/6wxb_prior_to_posterior.ipynb
diff --git a/Lukes_folder/6wxb/distance_boot.npz b/Lukes_folder/6wxb/distance_boot.npz
diff --git a/Lukes_folder/6wxb/distances_boot.npz b/Lukes_folder/6wxb/distances_boot.npz
diff --git a/Lukes_folder/6wxb/distances_boot_nonrandom_params.npz b/Lukes_folder/6wxb/distances_boot_nonrandom_params.npz
diff --git a/Lukes_folder/6wxb/posterior_samples_exp.npz b/Lukes_folder/6wxb/posterior_samples_exp.npz
diff --git a/Lukes_folder/6wxb/test_log_posteriors.ipynb b/Lukes_folder/6wxb/test_log_posteriors.ipynb
diff --git a/Lukes_folder/6wxb/train_6xwb.ipynb b/Lukes_folder/6wxb/train_6xwb.ipynb
@@ -0,0 +1,123 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "from cryo_sbi import CryoEmSimulator\n",
+    "#from cryo_sbi import gen_training_set\n",
+    "from cryo_sbi.inference.train_npe_model import npe_train_no_saving\n",
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Creating particles and then training with them"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Training neural network:\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "  5%|▍         | 28/600 [10:54<3:41:57, 23.28s/epoch, loss=-.243] "
+     ]
+    }
+   ],
+   "source": [
+    "#torch.cuda.empty_cache()\n",
+    "#npe_train_no_saving(\n",
+    "#    image_config=\"6wxb/image_params_mixed_training.json\",\n",
+    "#    train_config=\"6wxb/resnet18_fft_encoder.json\",\n",
+    "#    epochs=600,\n",
+    "#    estimator_file=\"estimator_6wxb.estimator\",\n",
+    "#    loss_file=\"6wxb_loss\",\n",
+    "#    device=\"cuda\",\n",
+    "#    simulation_batch_size=1024\n",
+    "#)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Training neural network:\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "  0%|          | 0/600 [00:00<?, ?epoch/s]/mnt/ceph/users/levans/cryo_em_SBI/.venv/lib/python3.9/site-packages/torch/nn/modules/conv.py:459: UserWarning: Applied workaround for CuDNN issue, install nvrtc.so (Triggered internally at ../aten/src/ATen/native/cudnn/Conv_v8.cpp:80.)\n",
+      "  return F.conv2d(input, weight, bias, self.stride,\n",
+      "100%|██████████| 600/600 [7:17:29<00:00, 43.75s/epoch, loss=12.6]  \n"
+     ]
+    }
+   ],
+   "source": [
+    "torch.cuda.empty_cache()\n",
+    "npe_train_no_saving(\n",
+    "    image_config=\"/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/6wxb/image_params_mixed_training.json\",\n",
+    "    train_config=\"/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/6wxb/resnet18_encoder.json\",\n",
+    "    epochs=600,\n",
+    "    estimator_file= \"/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/estimator_6xwb_no_fft.estimator\",\n",
+    "    loss_file=\"/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/6wxb_no_fft_loss\",\n",
+    "    device=\"cuda\",\n",
+    "    simulation_batch_size=1024\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.15 64-bit",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.15"
+  },
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "7b7fbdd20bcc2083504065e64dd68e11295ac29c39a09e225403f090756a3e6a"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/Lukes_folder/6wxb/train_6xwb.py b/Lukes_folder/6wxb/train_6xwb.py
@@ -0,0 +1,19 @@
+import torch
+import matplotlib.pyplot as plt
+
+from cryo_sbi import CryoEmSimulator
+#from cryo_sbi import gen_training_set
+from cryo_sbi.inference.train_npe_model import npe_train_no_saving
+print(torch.version.cuda)
+
+torch.cuda.empty_cache()
+npe_train_no_saving(
+    image_config="/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/6wxb/image_params_mixed_training.json",
+    train_config="/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/6wxb/resnet18_encoder.json",
+    epochs=600,
+    estimator_file= "/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/estimator_6xwb_no_fft.estimator",
+    loss_file="/mnt/ceph/users/levans/cryo_em_SBI/Lukes_folder/6wxb_no_fft_loss",
+    device="cuda",
+    simulation_batch_size=1024
+)
+
diff --git a/Lukes_folder/6wxb_prior_to_posterior.ipynb b/Lukes_folder/6wxb_prior_to_posterior.ipynb
diff --git a/Lukes_folder/comparing_estimator_posteriors.ipynb b/Lukes_folder/comparing_estimator_posteriors.ipynb
@@ -244,7 +244,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3.9.15 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -260,7 +260,12 @@
    "pygments_lexer": "ipython3",
    "version": "3.9.15"
   },
-  "orig_nbformat": 4
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "7b7fbdd20bcc2083504065e64dd68e11295ac29c39a09e225403f090756a3e6a"
+   }
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2

diff --git a/Lukes_folder/hsp90_posterior_mat.npz b/Lukes_folder/hsp90_posterior_mat.npz
diff --git a/Lukes_folder/hsp90_prior_to_posterior.ipynb b/Lukes_folder/hsp90_prior_to_posterior.ipynb
diff --git a/Lukes_folder/hsp90_test_log_posteriors copy.ipynb b/Lukes_folder/hsp90_test_log_posteriors copy.ipynb
diff --git a/Lukes_folder/hsp90_test_log_posteriors.ipynb b/Lukes_folder/hsp90_test_log_posteriors.ipynb
diff --git a/Lukes_folder/jupyter_ASPIRE_config.yaml b/Lukes_folder/jupyter_ASPIRE_config.yaml