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macaque example
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@agosztolai
agosztolai committed Nov 28, 2023
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2 changes: 1 addition & 1 deletion MARBLE/geometry.py
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Expand Up @@ -671,7 +671,7 @@ def vector_diffusion(x, t, method="spectral", Lc=None):
return out


def compute_eigendecomposition(A, k=50, eps=1e-8):
def compute_eigendecomposition(A, k=None, eps=1e-8):
"""Eigendecomposition of a square matrix A.
Args:
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71 changes: 33 additions & 38 deletions examples/macaque_reaching/decoding.ipynb
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Expand Up @@ -9,55 +9,42 @@
"\n",
"This notebook takes the outputs from training MARBLE on macaque data with 20ms bin of spiking rates. It then performs decoding of the kinematic results provided publicly by the LFADS authors.\n",
"\n",
"\n",
"There are three main results files of interest, differing only in the output dimension of the MARBLE architecture:\n",
"1. Marble trained with 3-dim output dimension: marble_embeddings_20ms_out3.pkl - https://dataverse.harvard.edu/api/access/datafile/7062022 \n",
"2. Marble trained with 20-dim output dimension: marble_embeddings_20ms_out20.pkl - https://dataverse.harvard.edu/api/access/datafile/7062023 \n",
"3. Marble trained with 3-dim output dimension with rotation invariant features: marble_embeddings_20ms_rotation_invariant.pkl - https://dataverse.harvard.edu/api/access/datafile/7062087 \n",
"\n",
"\n",
"A fourth file containing the LFADS embeddings and the kinematics data:\n",
"1. kinematics.pkl - https://dataverse.harvard.edu/api/access/datafile/6969885 \n",
"\n",
"I'd like to thank the authors of LFADS for making this data accessible and answering our questions about the data!\n"
"We would like to thank the authors of LFADS for making this data accessible and answering our questions about the data!"
]
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 3,
"id": "cd350b67",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: statannotations in /Users/arnaudon/base/lib/python3.10/site-packages (0.5.0)\n",
"Requirement already satisfied: matplotlib>=2.2.2 in /Users/arnaudon/base/lib/python3.10/site-packages (from statannotations) (3.7.1)\n",
"Requirement already satisfied: seaborn<0.12,>=0.9.0 in /Users/arnaudon/base/lib/python3.10/site-packages (from statannotations) (0.11.2)\n",
"Requirement already satisfied: numpy>=1.12.1 in /Users/arnaudon/base/lib/python3.10/site-packages (from statannotations) (1.23.2)\n",
"Requirement already satisfied: scipy>=1.1.0 in /Users/arnaudon/base/lib/python3.10/site-packages (from statannotations) (1.9.0)\n",
"Requirement already satisfied: pandas>=0.23.0 in /Users/arnaudon/base/lib/python3.10/site-packages (from statannotations) (1.4.3)\n",
"Requirement already satisfied: packaging>=20.0 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (21.3)\n",
"Requirement already satisfied: pyparsing>=2.3.1 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (3.0.9)\n",
"Requirement already satisfied: cycler>=0.10 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (0.11.0)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (1.4.4)\n",
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"Requirement already satisfied: contourpy>=1.0.1 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (1.0.7)\n",
"Requirement already satisfied: pillow>=6.2.0 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (9.2.0)\n",
"Requirement already satisfied: python-dateutil>=2.7 in /Users/arnaudon/base/lib/python3.10/site-packages (from matplotlib>=2.2.2->statannotations) (2.8.2)\n",
"Requirement already satisfied: pytz>=2020.1 in /Users/arnaudon/base/lib/python3.10/site-packages (from pandas>=0.23.0->statannotations) (2022.2.1)\n",
"Requirement already satisfied: six>=1.5 in /Users/arnaudon/base/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib>=2.2.2->statannotations) (1.16.0)\n"
"Requirement already satisfied: statannotations in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (0.6.0)\n",
"Requirement already satisfied: matplotlib>=2.2.2 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from statannotations) (3.5.2)\n",
"Requirement already satisfied: pandas<2.0.0,>=0.23.0 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from statannotations) (1.5.3)\n",
"Requirement already satisfied: scipy>=1.1.0 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from statannotations) (1.9.3)\n",
"Requirement already satisfied: numpy>=1.12.1 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from statannotations) (1.23.3)\n",
"Requirement already satisfied: seaborn<0.12,>=0.9.0 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from statannotations) (0.11.2)\n",
"Requirement already satisfied: fonttools>=4.22.0 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (4.25.0)\n",
"Requirement already satisfied: cycler>=0.10 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (0.11.0)\n",
"Requirement already satisfied: pyparsing>=2.2.1 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (3.0.9)\n",
"Requirement already satisfied: packaging>=20.0 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (21.3)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (1.4.2)\n",
"Requirement already satisfied: python-dateutil>=2.7 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (2.8.2)\n",
"Requirement already satisfied: pillow>=6.2.0 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from matplotlib>=2.2.2->statannotations) (9.2.0)\n",
"Requirement already satisfied: pytz>=2020.1 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from pandas<2.0.0,>=0.23.0->statannotations) (2022.1)\n",
"Requirement already satisfied: six>=1.5 in /Users/gosztola/opt/anaconda3/envs/MARBLE/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=2.2.2->statannotations) (1.16.0)\n"
]
}
],
"source": [
"!pip install statannotations\n",
"import numpy as np\n",
"import pandas as pd\n",
"\n",
"import pickle\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import matplotlib.pylab as pl\n",
"\n",
Expand All @@ -66,7 +53,7 @@
"\n",
"from sklearn.model_selection import KFold\n",
"from sklearn.svm import SVC\n",
"from sklearn.preprocessing import StandardScaler\n"
"from sklearn.preprocessing import StandardScaler"
]
},
{
Expand All @@ -79,24 +66,32 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 4,
"id": "e9bc422a",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"File ‘data/marble_embeddings_20ms_out20.pkl’ already there; not retrieving.\n",
"File ‘data/kinematics.pkl’ already there; not retrieving.\n"
"File ‘marble_embeddings_20ms_out20.pkl’ already there; not retrieving.\n",
"File ‘kinematics.pkl’ already there; not retrieving.\n"
]
}
],
"source": [
"# load MARBLE embeddings\n",
"!wget -nc https://dataverse.harvard.edu/api/access/datafile/7062022 -O data/marble_embeddings_20ms_out20.pkl\n",
"!wget -nc https://dataverse.harvard.edu/api/access/datafile/6969885 -O data/kinematics.pkl\n",
"with open('data/marble_embeddings_20ms_out20.pkl', 'rb') as handle:\n",
"# Marble trained with 3-dim output dimension\n",
"!wget -nc https://dataverse.harvard.edu/api/access/datafile/7062022 -O marble_embeddings_20ms_out20.pkl\n",
"# Marble trained with 3-dim output dimension\n",
"#!wget -nc https://dataverse.harvard.edu/api/access/datafile/7062023 -O marble_embeddings_20ms_out3.pkl\n",
"# Marble trained with 3-dim output dimension with rotation invariant features\n",
"#!wget -nc https://dataverse.harvard.edu/api/access/datafile/7062087 -O marble_embeddings_20ms_out3_rotinv.pkl\n",
"\n",
"# kinematics\n",
"!wget -nc https://dataverse.harvard.edu/api/access/datafile/6969885 -O kinematics.pkl\n",
"\n",
"with open('marble_embeddings_20ms_out20.pkl', 'rb') as handle:\n",
" data = pickle.load(handle)\n",
"\n",
"distance_matrices = data[0]\n",
Expand All @@ -107,7 +102,7 @@
"sample_inds = data[5]\n",
"\n",
"# load kinematic data\n",
"kinematic_data = pickle.load(open('data/kinematics.pkl','rb')) \n",
"kinematic_data = pickle.load(open('kinematics.pkl','rb')) \n",
"\n",
"# define conditions of movement\n",
"conditions=['DownLeft','Left','UpLeft','Up','UpRight','Right','DownRight'] \n"
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