Dev

.github/workflows/deploy.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Installing python
         run: |
           sudo apt-get update
-          sudo apt install python3.12
+          sudo apt install python3.10.11
           sudo apt-get install build-essential
 
       - name: Upgrading pip

.github/workflows/test.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9.13'
+          python-version: '3.10.11'
 
       # - name: Upgrading pip
       #   run: pip install --upgrade pip

docs/_toc.yml

@@ -34,6 +34,7 @@ parts:
   chapters:
   - file: higher-order/cebra_time.ipynb
   - file: higher-order/tca.ipynb
+  - file: higher-order/GLM_pynapple_nemos.ipynb
   - file: higher-order/glm.ipynb
   - file: higher-order/behavioral_state.ipynb
 - caption: Openscope Experimental Projects

docs/embargoed/cell_matching.ipynb

@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "e4511768",
    "metadata": {},
    "outputs": [],
@@ -82,7 +82,7 @@
     "# the subject ids should be the same, but the session ids should be different\n",
     "input_dandi_filepaths = [dandi_filepath_1, dandi_filepath_2]\n",
     "\n",
-    "dandi_api_key = \"f9459a77200783c455ec6f3cb0b6cd92fc9fe106\""
+    "dandi_api_key = os.environ['DANDI_API_KEY']"
    ]
   },
   {

docs/higher-order/compare_likelihood.py

@@ -0,0 +1,172 @@
+from time import perf_counter
+
+import jax
+
+import nemos as nmo
+import pynapple as nap
+import numpy as np
+from scipy.optimize import minimize
+
+jax.config.update("jax_enable_x64", True)
+
+def neg_log_lik_lnp(theta, X, y, Cinv):
+  # Compute the Poisson log likelihood
+  rate = np.exp(X @ theta)
+  log_lik = y @ np.log(rate) - rate.sum()
+  log_lik -= theta.T @ Cinv @ theta
+
+  return -log_lik
+
+def fit_lnp(X, y, lam=0):
+  filt_len = X.shape[1]
+  Imat = np.identity(filt_len) # identity matrix of size of filter + const
+  Imat[0,0] = 0
+  Cinv = lam*Imat
+
+  # Use a random vector of weights to start (mean 0, sd .2)
+  x0 = np.random.normal(0, .2, filt_len)
+  print("y:",y.shape,"X:",X.shape,"x0:",x0.shape)
+
+  # Find parameters that minimize the negative log likelihood function
+  res = minimize(neg_log_lik_lnp, x0, args=(X, y, Cinv))
+
+  return res["x"]
+
+def predict(X, weights, constant):
+    y = np.exp(X @ weights + constant)
+    return y
+
+def predict_spikes(X, weights, constant):
+    rate = predict(X, weights, constant)
+    spks = np.random.poisson(np.matrix.transpose(rate))
+    return spks
+
+def retrieve_stim_info(color_code, features, flashes):
+    """Retrieve stimulus information based on color code.
+
+    Parameters
+    ----------
+    color_code :
+        The color label (e.g., '-1.0' for black, '1.0 for white) to identify the stimulus.
+    features :
+        An array indicating which flash interval each timestamp belongs to.
+
+    Returns
+    ----------
+    color_feature:
+        A binary array where 1 indicates the timestamp falls within a flash
+        interval of the given color_code, and 0 otherwise.
+    """
+    # Get the indices of flash intervals where the color matches the given color_code
+    intervals = flashes.index[flashes["color"] == color_code]
+    # Initialize an array of zeros with the same length as the features array
+    color_feature = np.zeros(len(features))
+    # Create a boolean mask for entries in 'features' that match the target flash intervals
+    mask = np.isin(features, intervals)
+    # Mark the matching timestamps with 1
+    color_feature[mask] = 1
+
+    return color_feature
+
+
+
+dandiset_id = "000021"
+dandi_filepath = "sub-726298249/sub-726298249_ses-754829445.nwb"
+download_loc = "."
+
+path = "docs/higher-order/sub-726298249_ses-754829445.nwb"
+# t0 = perf_counter()
+# io = nmo.fetch.download_dandi_data(dandiset_id, dandi_filepath)
+# print(perf_counter() - t0)
+# nap_nwb = nap.NWBFile(io.read(), lazy_loading=True)
+#
+
+nap_nwb = nap.load_file(path)
+nwb = nap_nwb.nwb
+channel_probes = {}
+
+electrodes = nwb.electrodes
+for i in range(len(electrodes)):
+    channel_id = electrodes["id"][i]
+    location = electrodes["location"][i]
+    channel_probes[channel_id] = location
+
+# function aligns location information from electrodes table with channel id from the units table
+def get_unit_location(unit_id):
+    return channel_probes[int(units[unit_id].peak_channel_id)]
+
+units = nap_nwb["units"]
+units.brain_area = [channel_probes[int(ch_id)] for ch_id in units.peak_channel_id]
+
+units = units[(units.quality == "good") & (units.brain_area == "VISp") & (units.firing_rate > 2.)]
+
+
+
+flashes = nap_nwb["flashes_presentations"]
+
+# Set start, end and bin size
+start = nap_nwb["flashes_presentations"].start.min()
+end = nap_nwb["flashes_presentations"].end.max()
+bin_sz = 0.05
+
+counts = units.count(bin_sz, ep=nap.IntervalSet(start, end))
+
+# Create Tsd with timestamps corresponding to the desired time bins and bins sizes
+uniform = nap.Tsd(t=counts.t, d=np.ones(counts.t.shape[0]))
+
+# For each desired timestamp, find the index of the flash interval it falls into.
+# Returns NaN for timestamps outside all intervals, and an index for those within.
+features = flashes.in_interval(uniform)
+
+white_stimuli = retrieve_stim_info("1.0", features, flashes)
+black_stimuli = retrieve_stim_info("-1.0", features, flashes)
+
+history_size = int(0.25 / bin_sz)
+bas = nmo.basis.HistoryConv(history_size, label="w") + nmo.basis.HistoryConv(history_size, label="b")
+
+X = bas.compute_features(white_stimuli, black_stimuli)
+
+model = nmo.glm.GLM()
+model.fit(X, counts[:, 0])
+rate = model.predict(X)
+
+# first 5 of rate are nans (conv in mode valid + padding)
+intercept_plus_X = np.hstack((np.ones((X.shape[0], 1)), X))
+intercept_plus_coeff = np.hstack((model.intercept_, model.coef_))
+ll = model.observation_model._negative_log_likelihood(counts[5:,0], rate[5:], aggregate_sample_scores=np.sum)
+ll2 = neg_log_lik_lnp(
+    intercept_plus_coeff, intercept_plus_X[5:], counts[5:, 0], np.zeros((11, 11))
+)
+
+# if this is 0 or close it means that that we are computing the same un-regularized likelihood (modulo using the mean
+# instead of sum, so our likelihood used in the fit is theirs divided by the number of samples, which doesn't make a
+# difference).
+print(ll - ll2)
+
+# add regularization
+
+lam = 2**5  # their value for the regulariser
+
+# our penalized loss is  loss - 0.5 * lam * coef @ coeff, so 2**5 * 2 == 2**6
+model = nmo.glm.GLM(regularizer="Ridge", regularizer_strength= lam * 2 / (X.shape[0] - 5))
+reg = model.regularizer
+
+
+# instead of fitting attach coeff
+model.coef_ = intercept_plus_coeff[1:]
+model.intercept_ = intercept_plus_coeff[:1]
+# get the loss + penalty in nemos
+loss_with_penalty = model.regularizer.penalized_loss(
+                model._predict_and_compute_loss, model.regularizer_strength
+            )
+ll_penalised = (X.shape[0] - 5) * loss_with_penalty((model.coef_, model.intercept_), X[5:], counts[5:,0].d)
+
+Imat = np.identity(11)
+Imat[0, 0] = 0  # they do not regularise the intercept (same as as, good)
+Cinv = lam * Imat
+
+
+ll2_penalised = neg_log_lik_lnp(
+    intercept_plus_coeff, intercept_plus_X[5:], counts[5:, 0], Cinv
+)
+print(ll_penalised - ll2_penalised)

docs/references.bib

@@ -1,3 +1,56 @@
+@techreport{NeuropixelsWhitePaper2019,
+  title = {Allen Brain Observatory - Neuropixels Visual Coding - Technical White Paper},
+  author = {{Allen Institute for Brain Science}},
+  institution = {{Allen Institute for Brain Science}},
+  url = {https://brainmapportal-live-4cc80a57cd6e400d854-f7fdcae.divio-media.net/filer_public/80/75/8075a100-ca64-429a-b39a-569121b612b2/neuropixels_visual_coding_-_white_paper_v10.pdf},
+  year = {2019},
+  month = {October},
+}
+
+@misc{PillowCosyneTutorial,
+  title = { Jonathan Pillow - Tutorial: Statistical models for neural data - Part 1 (Cosyne 2018)},
+  author = {Jonathan Pillow},
+  howpublished = {YouTube},
+  url = {https://www.youtube.com/watch?v=NFeGW5ljUoI},
+  year = {2018},
+  month = {March},
+}
+
+@article{pillowPredictionDecodingRetinal2005,
+  title = {Prediction and {{Decoding}} of {{Retinal Ganglion Cell Responses}} with a {{Probabilistic Spiking Model}}},
+  author = {Pillow, Jonathan W. and Paninski, Liam and Uzzell, Valerie J. and Simoncelli, Eero P. and Chichilnisky, E. J.},
+  year = {2005},
+  journal = {Journal of Neuroscience},
+  volume = {25},
+  number = {47},
+  pages = {11003--11013},
+  publisher = {Society for Neuroscience},
+  issn = {0270-6474, 1529-2401},
+  doi = {10.1523/JNEUROSCI.3305-05.2005},
+  urldate = {2025-07-06},
+  chapter = {Behavioral/Systems/Cognitive},
+  copyright = {Copyright {\copyright} 2005 Society for Neuroscience 0270-6474/05/2511003-11.00/0},
+  langid = {english},
+  pmid = {16306413},
+  keywords = {computational model,decoding,integrate and fire,neural coding,precision,retinal ganglion cell,spike timing,spike trains,variability},
+}
+
+@article{pillowSpatiotemporalCorrelationsVisual2008,
+  title = {Spatio-Temporal Correlations and Visual Signalling in a Complete Neuronal Population},
+  author = {Pillow, Jonathan W. and Shlens, Jonathon and Paninski, Liam and Sher, Alexander and Litke, Alan M. and Chichilnisky, E. J. and Simoncelli, Eero P.},
+  year = {2008},
+  journal = {Nature},
+  volume = {454},
+  number = {7207},
+  pages = {995--999},
+  publisher = {Nature Publishing Group},
+  issn = {1476-4687},
+  doi = {10.1038/nature07140},
+  urldate = {2025-07-06},
+  copyright = {2008 Macmillan Publishers Limited. All rights reserved},
+  langid = {english},
+  keywords = {Humanities and Social Sciences,multidisciplinary,Science},
+}
 @article{Rubel2022
 ,	title	= {The Neurodata Without Borders ecosystem for neurophysiological data science}
 ,	author	= {Oliver Rübel and Andrew Tritt and Ryan Ly and Benjamin K Dichter and Satrajit Ghosh and Lawrence Niu and Pamela Baker and Ivan Soltesz and Lydia Ng and Karel Svoboda and Loren Frank and Kristofer E Bouchard}

requirements.txt

@@ -34,3 +34,9 @@ traitlets==5.6.0
 tqdm==4.66.2
 zarr==2.13.3
 ndx-harvey-swac @ git+https://github.com/sytseng/ndx-harvey-swac
+pooch >= 1.8.2
+jaxopt >= 0.8.5
+nemos >= 0.2.3
+pynapple >= 0.9.2
+seaborn >= 0.13.2
+scikit-learn>=1.7.0