Prioritized nonlinear modeling of shared dynamics across neural populations.
The 7 matches
- [1] § Methods › Testing the nonlinearity in cross-population model components ↔ CroP-DYNO/source/CroPDYNO/example/CroPDYNO_tutorial.ipynb, lines 246 to 273 · score 0.84 · candidate configurations, fold inner cross, nonlinearity configuration, hidden layer, cross population prediction, validation · Report a mismatch
- [2] § Methods › Testing the nonlinearity in cross-population model components ↔ CroP-DYNO/source/DPAD/example/DPAD_tutorial2.ipynb, lines 1 to 329 · score 0.73 · fold inner cross, selected configuration, inner validation, nonlinearity configuration, hidden layer, hidden units · Report a mismatch
- [3] § Methods › Testing the nonlinearity in cross-population model components ↔ CroP-DYNO/source/DPAD/tools/flexible.py, lines 4736 to 4807 · score 0.71 · multilayer perceptrons, hidden layer, hidden units, MLPs, linear, DYNO · Report a mismatch
- [4] § Methods › Testing the nonlinearity in cross-population model components ↔ CroP-DYNO/source/CroPDYNO/example/CroPDYNO_tutorial.ipynb, lines 246 to 273 · score 0.60 · inner cross validation, nonlinearity configuration, candidate, flexible, fold, CroP · Report a mismatch
- [5] § Methods › Neural recordings, behavioral tasks, and data preprocessing ↔ CroP-DYNO/source/DPAD/tools/GaussianSmoother.py, lines 7 to 54 · score 0.58 · Gaussian kernel, standard deviation, smoothed · Report a mismatch
- [6] § Methods › Neural recordings, behavioral tasks, and data preprocessing ↔ CroP-DYNO/source/DPAD/example/DPAD_tutorial2.ipynb, lines 535 to 649 · score 0.53 · Gaussian kernel, downsampled, bins, spiking, smoothed, behavioral · Report a mismatch
- [7] § Methods › Testing the nonlinearity in cross-population model components ↔ CroP-DYNO/source/DPAD/example/DPAD_tutorial.ipynb, lines 210 to 257 · score 0.53 · hidden layer, hidden units, MLPs, nonlinear, training, neural · Report a mismatch
Paper
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The authors' code
Jupyter notebook · 323 lines · 14 KB · no license · 2 matches
- # %% [markdown]
- # Written by: Trisha Jha
- #
- # Last update: Jul, 2026
- # %% [markdown]
- # # CroP-DYNO Tutorial
- #
- # ## Overview
- # CroP-DYNO (cross-population prioritized dynamical nonlinear interaction model) is a method for nonlinear dynamical modeling of interactions between two simultaneously recorded neural populations. Given the activity of a source population Y and a target population Z, CroP-DYNO learns a dynamical model of population Y while prioritizing the dynamics that are shared with population Z. For more details, see our manuscript: Jha T, Song D and Shanechi M M 2026 Prioritized nonlinear
- # modeling of shared dynamics across neural populations *J. Neural Eng.*
- # https://doi.org/10.1088/1741-2552/ae9bee
- #
- # CroP-DYNO's implementation is derived from the [DPAD](https://github.com/ShanechiLab/DPAD) codebase (Sani, Pesaran, and Shanechi, *Nature Neuroscience*, 2024).
- #
- # ## Model
- # Given the activity of a source population, $y_k$, and a target population, $z_k$, CroP-DYNO learns a latent state $x_k$, composed of two components: $x_k^{(1)}$, the dynamics shared between populations Y and Z, and $x_k^{(2)}$, the within-population Y dynamics not shared with population Z. The model is formulated as:
- #
- # $$ x_{k+1} = A'(x_k) + K(y_k) $$
- #
- # $$ y_k = C_y(x_k) + e_k $$
- #
- # $$ z_k = C_z(x_k) + \epsilon_k $$
- #
- # Multi-input multi-output functions $A'$ (latent state dynamics), $K$ (mapping from source population Y activity to latent states), $C_y$ (source population Y readout), and $C_z$ (target population Z readout) define the model. CroP-DYNO allows the user to flexibly set any of these four mappings to be linear or nonlinear, which in turn enables testing hypotheses about where nonlinearity in the cross-population interaction originates.
- #
- # *Note: in the CroP-DYNO paper these two populations are referred to as population A and population B; here we call them population Y and population Z to match the naming used in the code below.*
- # %% [markdown]
- # # Using CroP-DYNO
- # ## Modeling data
- # To use CroP-DYNO, import the model class:
- # ```python
- # from CroPDYNO.CroPDYNOModel import CroPDYNOModel
- # ```
- #
- # You can then use it to model cross-population data as:
- # ```python
- # idSys = CroPDYNOModel()
- # methodCode = 'CroPDYNO_Cz1HL64U' # Only Cz (the target-population Z readout) will be nonlinear, 1 Hidden layer with 64 Units.
- # args = CroPDYNOModel.prepare_args(methodCode)
- # idSys.fit(Y=yTrain, Z=zTrain, nx=6, n1=2, **args)
- # ```
- #
- # With the following arguments:
- # - `Y`: Source population Y activity. Dimensions are: data x time.
- # - `Z`: Target population Z activity, i.e. the cross-population prediction objective. Dimensions are: data x time.
- # - `nx`: the total dimension of the latent state in the model.
- # - `n1`: the number of latent state dimensions dedicated to shared cross-population dynamics ($x_k^{(1)}$).
- # - `args`: other arguments specifying which mappings are linear vs. nonlinear.
- #
- # `CroPDYNOModel.prepare_args` takes a `methodCode` string and returns the arguments to pass to `idSys.fit`. In the example above, `methodCode` is `'CroPDYNO_Cz1HL64U'`, which makes only $C_z$ nonlinear while $A'$, $K$, and $C_y$ remain linear. You can inspect the output of `CroPDYNOModel.prepare_args` to see how the architecture of each mapping is specified.
- #
- # After running the above, the learned model is stored in the object `idSys`.
- #
- # ## Using the model for cross-population prediction and self-prediction
- # For a learned model `idSys`, use `predict` to extract the latent state and predict both populations' activity given new source population Y activity:
- # ```python
- # zPred, yPred, xPred = idSys.predict(yTest)
- # ```
- # With the argument:
- # - `yTest`: Source population Y activity in the test data. Dimensions are: time x data dimension.
- #
- # And with outputs (all dimensions are time x data dimension):
- # - `zPred`: Prediction of target population Z activity from past source population Y activity (i.e., cross-population prediction).
- # - `yPred`: Self-prediction of source population Y activity from its own past.
- # - `xPred`: The latent state extracted at each time point.
- #
- # Note that inference only requires source population Y activity, consistent with CroP-DYNO's design for settings where only one population is accessible at inference time.
- #
- # We next go through a complete worked example on simulated data.
- # %% [markdown]
- # # Example: CroP-DYNO on simulated cross-population data
- # In this example, we use CroP-DYNO to model simulated data from a system with a known ground-truth model, and evaluate cross-population prediction performance against that ground truth. We use a simulated dataset where only $C_z$ is nonlinear. Both populations are multi-channel (3 channels each).
- #
- # First, we import CroP-DYNO and a few other useful tools.
- # %%
- # CroP-DYNO requires Python 3.11 (see the repository README for setup).
- # This prints your Python version as a quick check.
- !python --version
- # %%
- import logging
- import os
- import sys
- sys.path.insert(0, os.path.join("..", ".."))
- sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath("")), "..", ".."))
- # Setting up logs
- logging.basicConfig(level=logging.INFO)
- logger = logging.getLogger(__name__)
- import coloredlogs
- coloredlogs.install(
- level=logging.INFO,
- fmt="%(asctime)s %(name)s [%(filename)s > %(lineno)s] %(levelname)s %(message)s",
- datefmt="%Y-%m-%d %H:%M:%S",
- logger=logger,
- )
- # Prepare plots
- import matplotlib
- import matplotlib.pyplot as plt
- import numpy as np
- matplotlib.rcParams["figure.facecolor"] = "w"
- matplotlib.rcParams["axes.facecolor"] = "w"
- matplotlib.rcParams.update(
- {"font.size": 16, "axes.titlesize": 14, "axes.labelsize": 14}
- )
- # Import CroP-DYNO and supporting tools
- import CroPDYNO
- from CroPDYNO.CroPDYNOModel import CroPDYNOModel
- from CroPDYNO.tools.evaluation import evalPrediction
- from CroPDYNO.tools.file_tools import pickle_load
- # Set random seeds for exact reproducibility
- seed = 42
- import random
- import tensorflow as tf
- random.seed(seed)
- np.random.seed(seed)
- tf.random.set_seed(seed)
- # %% [markdown]
- # Let's load data from an example ground-truth model where $C_z$ is nonlinear. We treat the first signal as source population Y activity ($y_k$) and the second signal as target population Z activity ($z_k$):
- # %%
- # Load data
- data_dir = os.path.join(os.path.dirname(CroPDYNO.__file__), "..", "..", "data")
- fName = "sample_data.p"
- sample_data_path = os.path.join(data_dir, fName)
- print("Loading example data from {}".format(sample_data_path))
- data = pickle_load(sample_data_path)
- # This data is from a ground-truth model with a nonlinear Cz.
- maxN = int(2 * 1e4) # Number of time points to use in this notebook
- N = np.min((maxN, data["y"].shape[0]))
- y = data["y"][:N, :] # Source population Y activity
- z = data["z"][:N, :] # Target population Z activity
- trueModel = data["csys"] # The object containing the true simulated model
- n1 = len(
- trueModel.zDims
- ) # The number of latent state dimensions shared with population Z (cross-population states)
- nx = n1 # Only running stage 1 (extract cross-population states); set nx > n1 to also learn residual within-population Y dynamics
- allYData, allZData = y, z
- # %% [markdown]
- # Let's separate the data into training and test segments.
- # %%
- # Separate data into training and test data:
- trainInds = np.arange(np.round(0.9 * allYData.shape[0]), dtype=int)
- testInds = np.arange(1 + trainInds[-1], allYData.shape[0])
- yTrain = allYData[trainInds, :]
- yTest = allYData[testInds, :]
- zTrain = allZData[trainInds, :]
- zTest = allZData[testInds, :]
- # %% [markdown]
- # ## Section 1: Ideal vs. nonlinear $C_z$ vs. linear CroP-DYNO
- #
- # Training the model. We fit CroP-DYNO with the ground-truth latent dimensions, using a nonlinear readout for population Z ($C_z$) and keeping the other three mappings linear:
- # %%
- # Fit CroP-DYNO to the training data:
- idSys = CroPDYNOModel()
- methodCode = "CroPDYNO_Cz1HL64U_ErSV16_skipCy"
- #ErSV16: changes early stopping to 16 epochs, based on an inner validation set (last 20% of the training data). Without this, by default early stopping is 3 epochs and based on training loss.
- #skipCy: skip fitting Cy parameter as it is not relevant to cross-region prediction (save time for this tutorial)
- args = CroPDYNOModel.prepare_args(methodCode)
- epochs = 2000
- idSys.fit(Y=yTrain.T, Z=zTrain.T, nx=nx, n1=n1, epochs=epochs, **args)
- # %% [markdown]
- # Inference on test data and computing cross-population prediction performance. Inference uses only source population Y activity, consistent with CroP-DYNO's causal inference from the source population:
- # %%
- # Inference:
- print("Computing predictions for the learned model")
- zTestPred, yTestPred, xTestPred = idSys.predict(yTest)
- # Compute CC of cross-population prediction (z from y)
- zCC = evalPrediction(zTest, zTestPred, "CC")
- # For comparison, do the same using the true model
- print("Computing predictions for the true model (slower due to the analytical symbolic implementation of nonlinearity)")
- zTestPredIdeal, yTestPredIdeal, xTestPredIdeal = trueModel.predict(yTest)
- zCCIdeal = evalPrediction(zTest, zTestPredIdeal, "CC")
- print(
- f"Cross-population prediction (Z from Y) CC:\n"
- f" CroP-DYNO (Cz nonlinear) => {np.mean(zCC):.3g}\n"
- f" Ideal using true model => {np.mean(zCCIdeal):.3g}"
- )
- # %% [markdown]
- # ## Comparison to a fully linear CroP-DYNO model
- #
- # As a baseline, we also fit a fully linear CroP-DYNO model (all mappings linear) to see how much the nonlinear $C_z$ actually helps cross-population prediction.
- # %%
- # Fit a fully linear CroP-DYNO model
- methodCode = "CroPDYNO_ErSV16_skipCy" # No nonlinearity terms; ErSV16 (early stopping) and skipCy still apply
- idSysLin = CroPDYNOModel()
- argsLin = CroPDYNOModel.prepare_args(methodCode)
- idSysLin.fit(Y=yTrain.T, Z=zTrain.T, nx=nx, n1=n1, epochs=epochs, **argsLin)
- # Inference and cross-population prediction CC
- print("Computing predictions for the linear model")
- zTestPredLin, yTestPredLin, xTestPredLin = idSysLin.predict(yTest)
- zCCLin = evalPrediction(zTest, zTestPredLin, "CC")
- print(
- f"Cross-population prediction (Z from Y) CC:\n"
- f" Linear CroP-DYNO => {np.mean(zCCLin):.3g}\n"
- f" CroP-DYNO (Cz nonlinear) => {np.mean(zCC):.3g}"
- )
- # %% [markdown]
- # ## Section 2: Flexible CroP-DYNO — automatically searching for the best nonlinearity
- #
- # Above, we manually chose `'CroPDYNO_Cz1HL64U_ErSV16_skipCy'`, i.e., we assumed only $C_z$ should be nonlinear. Instead of guessing, flexible CroP-DYNO can search over which of the three mappings relevant to cross-population prediction ($A'$, $K$, $C_z$) should be linear vs. nonlinear. It does so by using an inner cross-validation on the training data, and picks the configuration that best predicts population Z. This runs in two steps: (1) search for the best nonlinearity configuration, then (2) fit one final model on all training data using that configuration.
- # %%
- # Step 1: search for the best nonlinearity configuration via inner cross-validation
- from CroPDYNO.tools.flexible import fitCroPDYNOWithFlexibleNonlinearity
- settings = {}
- settings["min_cores_to_enable_parallelization"] = 100 # If fewer cores than this are available, runs will not be parallelized
- settings["fit_epochs"] = 2000 # Same max-epochs cap as above; fitting stops early upon convergence
- # Search space: A', K, and Cz each tried as linear (0 hidden layers) or nonlinear (1 hidden layer, 64 units) => 2^3 = 8 cases
- # (Cy is not searched here and is skipped as it is not relevant for cross-region prediction),
- # selected via 2-fold inner cross-validation (iCVF2) on cross-population (z) prediction
- methodCode = "CroPDYNO_GSUT_iCVF2_AKCz1HL64U_ErSV16_skipCy"
- saveDir = os.path.join("results") # Where the inner cross-validation results are saved
- # Typical runtime: sum (no parallelization) or max (full parallelization) of run time across the 8 candidate configurations
- selectedMethodCode, iCVRes = fitCroPDYNOWithFlexibleNonlinearity(
- yTrain, Z=zTrain, nx=nx, n1=n1, settings=settings, methodCode=methodCode, saveDir=saveDir
- )
- print(f"\n\nSelected nonlinearity setting: {selectedMethodCode}")
- # %% [markdown]
- # The flexible search found that $C_z$-only is the best nonlinearity configuration. This means the flexible search works as intended; it recovered the correct configuation. Next, we can fit a final model on all the training data using this selected configuration.
- # %%
- # Step 2: fit one final model on all training data using the selected nonlinearity configuration
- idSysFlex = CroPDYNOModel()
- argsFlex = CroPDYNOModel.prepare_args(selectedMethodCode)
- idSysFlex.fit(Y=yTrain.T, Z=zTrain.T, nx=nx, n1=n1, epochs=epochs, **argsFlex)
- # Inference and cross-population prediction CC
- print("Computing predictions for the flexible model")
- zTestPredFlex, yTestPredFlex, xTestPredFlex = idSysFlex.predict(yTest)
- zCCFlex = evalPrediction(zTest, zTestPredFlex, "CC")
- print(
- f"Cross-population prediction (Z from Y) CC:\n Flexible CroP-DYNO ({selectedMethodCode}) => {np.mean(zCCFlex):.3g}"
- )
- # %% [markdown]
- # ## Section 3: Causal vs. noncausal (smoothing) CroP-DYNO
- #
- # So far, every model has been causal in time: prediction of $z_k$ only uses past activity of population Y. CroP-DYNO can also run noncausally (smoothing), where the RNN is bidirectional and estimates $z_k$ using both past *and future* activity of population Y. This is no longer causal in time, as it requires the full Y activity, but it can improve prediction accuracy.
- #
- # Adding `_xSmth` to the `methodCode` string enables this bidirectional/noncausal mode. To isolate the effect of causal vs. noncausal on its own, we keep everything else the same as our original ground-truth-nonlinearity model (only $C_z$ nonlinear) and compare below.
- # %%
- # Fit the noncausal (smoothing) counterpart of our original nonlinear-Cz model:
- methodCode = "CroPDYNO_Cz1HL64U_ErSV16_skipCy_xSmth" # now noncausal (smoothing)
- idSysSmth = CroPDYNOModel()
- argsSmth = CroPDYNOModel.prepare_args(methodCode)
- idSysSmth.fit(Y=yTrain.T, Z=zTrain.T, nx=nx, n1=n1, epochs=epochs, **argsSmth)
- # %%
- # Inference and cross-population prediction CC
- print("Computing predictions for the noncausal (smoothing) model")
- zTestPredSmth, yTestPredSmth, xTestPredSmth = idSysSmth.predict(yTest)
- zCCSmth = evalPrediction(zTest, zTestPredSmth, "CC")
- print(
- f"Cross-population prediction (Z from Y) CC:\n"
- f" CroP-DYNO (Cz nonlinear, causal) => {np.mean(zCC):.3g}\n"
- f" CroP-DYNO (Cz nonlinear, noncausal/smoothing) => {np.mean(zCCSmth):.3g}"
- )
CroPDYNO_tutorial.ipynb at commit 762f351, no license · at the source
Overview
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States of America
- Department of Neurological Surgery, University of Southern California, Los Angeles, CA, United States of America
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, United States of America
- Thomas Lord Department of Computer Science, Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, United States of America
Abstract
Objective. Advances in neural recording technology enable simultaneous measurements across multiple brain regions, providing new opportunities to study inter-regional interactions. However, several challenges arise when developing nonlinear dynamical models of cross-region interactions. In particular, we identify three key desired properties for a nonlinear framework. First, it should prioritize extraction of cross-region dynamics to avoid confounds from within-region dynamics. Second, it should enable localization of nonlinear structure within the model to better interpret cross-regional interaction models. Third, it should support both temporally causal and non-causal inference of shared dynamics and do so using source region activity alone. Current cross-regional models do not satisfy all these properties. Approach. Here, we address these challenges by developing cross-population prioritized dynamical nonlinear interaction model (CroP-DYNO), a nonlinear dynamical framework that prioritizes the learning of shared cross-population dynamics to avoid confounds from within-population activity. Further, CroP-DYNO allows individual components of the dynamical model to be independently specified as nonlinear or linear. Finally, it supports both temporally causal and non-causal inference of latent states, using only source region activity. Main results. We validate our method on datasets across species and distinct brain regions. We find that both the prioritized learning and the nonlinear modeling in CroP-DYNO are important for accurately extracting cross-population dynamics. As such, CroP-DYNO outperforms baseline nonprioritized and linear prioritized models in predicting target neural population activity from source activity. Further, CroP-DYNO enables systematic localization of nonlinear structure and quantifies dominant predictive interactions between brain regions, with interaction strengths that align with known circuit anatomy. Significance. Overall, these results establish CroP-DYNO as a flexible nonlinear framework for studying interactions between neural populations and brain regions, enabling both accurate modeling and interpretable dissection of nonlinear structure in cross-regional communication models.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 7 matches between paragraphs and lines of code.
ShanechiLab/CroP
762f351a51b087e5b344d0a5a5d5b3506a619494, 8 September 2026Availability: 1 check, the latest on 24 October 2026: the link answers
- 24 October 2026: the link answers
90 files
- CroP-DYNO/
source/ , Python, 14 linesCroPDYNO/ CroPDYNOModel.py - CroP-DYNO/
source/ , Python, 3 linesCroPDYNO/ RNNModel.py - CroP-DYNO/
source/ , Python, 3 linesCroPDYNO/ RegressionModel.py - CroP-DYNO/
source/ , Python, 9 linesCroPDYNO/ __init__.py - CroP-DYNO/
source/ , Jupyter, 323 lines, 2 matchesCroPDYNO/ example/ CroPDYNO_tutorial.ipynb - CroP-DYNO/
source/ , Python, 1 lineCroPDYNO/ example/ __init__.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ GaussianSmoother.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ LinearMapping.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ SSM.py - CroP-DYNO/
source/ , Python, 1 lineCroPDYNO/ tools/ __init__.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ abstract_classes.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ evaluation.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ file_tools.py - CroP-DYNO/
source/ , Python, 59 linesCroPDYNO/ tools/ flexible.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ model_base_classes.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ parse_tools.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ plot.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ plot_model_params.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ sim_tools.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ tf_losses.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ tf_tools.py - CroP-DYNO/
source/ , Python, 2 linesCroPDYNO/ tools/ tools.py - CroP-DYNO/
source/ , Python, 4,615 linesDPAD/ DPADModel.py - CroP-DYNO/
source/ , Python, 2,630 linesDPAD/ RNNModel.py - CroP-DYNO/
source/ , Python, 736 linesDPAD/ RegressionModel.py - CroP-DYNO/
source/ , Python, 4 linesDPAD/ __init__.py - CroP-DYNO/
source/ , Jupyter, 663 lines, 1 matchDPAD/ example/ DPAD_tutorial.ipynb - CroP-DYNO/
source/ , Jupyter, 958 lines, 2 matchesDPAD/ example/ DPAD_tutorial2.ipynb - CroP-DYNO/
source/ , Python, 1 lineDPAD/ example/ __init__.py - CroP-DYNO/
source/ , Python, 1,819 linesDPAD/ tests/ test_DPADModel.py - CroP-DYNO/
source/ , Python, 491 linesDPAD/ tests/ test_RNNModel.py - CroP-DYNO/
source/ , Python, 54 lines, 1 matchDPAD/ tools/ GaussianSmoother.py - CroP-DYNO/
source/ , Python, 299 linesDPAD/ tools/ LinearMapping.py - CroP-DYNO/
source/ , Python, 502 linesDPAD/ tools/ SSM.py - CroP-DYNO/
source/ , Python, 1 lineDPAD/ tools/ __init__.py - CroP-DYNO/
source/ , Python, 16 linesDPAD/ tools/ abstract_classes.py - CroP-DYNO/
source/ , Python, 1,158 linesDPAD/ tools/ evaluation.py - CroP-DYNO/
source/ , Python, 140 linesDPAD/ tools/ file_tools.py - CroP-DYNO/
source/ , Python, 4,896 lines, 1 matchDPAD/ tools/ flexible.py - CroP-DYNO/
source/ , Python, 602 linesDPAD/ tools/ model_base_classes.py - CroP-DYNO/
source/ , Python, 422 linesDPAD/ tools/ parse_tools.py - CroP-DYNO/
source/ , Python, 1,710 linesDPAD/ tools/ plot.py - CroP-DYNO/
source/ , Python, 462 linesDPAD/ tools/ plot_model_params.py - CroP-DYNO/
source/ , Python, 91 linesDPAD/ tools/ sim_tools.py - CroP-DYNO/
source/ , Python, 50 linesDPAD/ tools/ tests/ test_LinearMapping.py - CroP-DYNO/
source/ , Python, 130 linesDPAD/ tools/ tests/ test_parse_tools.py - CroP-DYNO/
source/ , Python, 229 linesDPAD/ tools/ tests/ test_tf_losses.py - CroP-DYNO/
source/ , Python, 191 linesDPAD/ tools/ tests/ test_tools.py - CroP-DYNO/
source/ , Python, 303 linesDPAD/ tools/ tf_losses.py - CroP-DYNO/
source/ , Python, 120 linesDPAD/ tools/ tf_tools.py - CroP-DYNO/
source/ , Python, 939 linesDPAD/ tools/ tools.py - CroP-DYNO/
source/ , Python, 1 line__init__.py - CroP-DYNO/
source/ , Python, 21 linessetup.py - CroP-LDM/
source/ , Python, 75 linesCroPLDM/ CroPLDMModel.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ LSSM.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ MatHelper.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ PrepModel.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ ReducedRankRegressor.py - CroP-LDM/
source/ , Python, 6 linesCroPLDM/ __init__.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ evaluation.py - CroP-LDM/
source/ , Jupyter, 316 linesCroPLDM/ example/ CroPLDM_tutorial.ipynb - CroP-LDM/
source/ , Python, 1 lineCroPLDM/ example/ __init__.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ mode_tools.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ sim_tools.py - CroP-LDM/
source/ , Python, 3 linesCroPLDM/ tools.py - CroP-LDM/
source/ , Python, 962 linesPSID/ IPSID.py - CroP-LDM/
source/ , Python, 1,671 linesPSID/ LSSM.py - CroP-LDM/
source/ , Python, 78 linesPSID/ MatHelper.py - CroP-LDM/
source/ , Python, 503 linesPSID/ PSID.py - CroP-LDM/
source/ , Python, 798 linesPSID/ PSIDModel.py - CroP-LDM/
source/ , Python, 163 linesPSID/ PrepModel.py - CroP-LDM/
source/ , Python, 79 linesPSID/ ReducedRankRegressor.py - CroP-LDM/
source/ , Python, 4 linesPSID/ __init__.py - CroP-LDM/
source/ , Python, 388 linesPSID/ evaluation.py - CroP-LDM/
source/ , Python, 565 linesPSID/ example/ IPSID_example.py - CroP-LDM/
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Code availability statement
The code used to support the results is available at: https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 89 scripts, each with its path and the digest of its content;
- 7 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability statement
The main data supporting the results in this study are available within the paper. Raw data from Dataset 1 are publicly available as cited in the paper. Raw data from Dataset 2 are too large to be publicly shared, yet may be made available for research purposes from the corresponding author on reasonable request.
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
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Version 1, 24 October 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 5 keywords, 2 funders, 129 references.
Cite
This paper
Jha, T., Song, D., & Shanechi, M. M. (2026). Prioritized nonlinear modeling of shared dynamics across neural populations. Journal of neural engineering, 23(5), 056054. https://
BibTeX
@article{jha2026prioriti
author = {Jha, Trisha and Song, Dong and Shanechi, Maryam M},
title = {{Prioritized nonlinear modeling of shared dynamics across neural populations}},
journal = {Journal of neural engineering},
year = {2026},
month = oct,
volume = {23},
number = {5},
pages = {056054},
publisher = {IOP Publishing},
issn = {1741-2560},
doi = {10.1088/
url = {https://
pmid = {42617643},
pmcid = {PMC13673170}
}
RIS
TY - JOUR
AU - Jha, Trisha
AU - Song, Dong
AU - Shanechi, Maryam M
TI - Prioritized nonlinear modeling of shared dynamics across neural populations
T2 - Journal of neural engineering
J2 - J Neural Eng
PY - 2026
DA - 2026/
VL - 23
IS - 5
SP - 056054
SN - 1741-2560
PB - IOP Publishing
DO - 10.1088/
UR - https://
LA - en
ER -
CSL-JSON
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"id": "10.1088/
"type": "article-journal",
"title": "Prioritized nonlinear modeling of shared dynamics across neural populations",
"container-title": "Journal of neural engineering",
"author": [
{
"family": "Jha",
"given": "Trisha"
},
{
"family": "Song",
"given": "Dong"
},
{
"family": "Shanechi",
"given": "Maryam M"
}
],
"container-title-short":
"volume": "23",
"issue": "5",
"page": "056054",
"DOI": "10.1088/
"PMID": "42617643",
"PMCID": "PMC13673170",
"ISSN": "1741-2560",
"publisher": "IOP Publishing",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
10,
16
]
]
}
}
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