neuralrnn 0.3.5__tar.gz

neuralrnn-0.3.5/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+docs/
+docs/ARCHITECTURE.md
+docs/PORTING_GUIDE.md
+docs/papers/*_cn.md
+notebook/figs/
+notebook/models/
+notebook/test/
+notebook/test_analysis_fixes.py
+notebook/test.ipynb
+notebook/*.py
+notebook/**/*.py
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+# Redis
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+# Environments
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+
+# Streamlit
+.streamlit/secrets.toml

neuralrnn-0.3.5/LICENSE

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+MIT License
+
+Copyright (c) 2026 HH Chen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

neuralrnn-0.3.5/PKG-INFO

@@ -0,0 +1,156 @@
+Metadata-Version: 2.4
+Name: neuralrnn
+Version: 0.3.5
+Summary: A unified framework for implementing RNN methods in cognitive neuroscience
+Project-URL: Homepage, https://github.com/HHChen730/NeuralRNN
+Project-URL: Documentation, https://neuralrnn.readthedocs.io/
+Author-email: Honghua Chen <honghuachen69@gmail.com>
+License: MIT
+License-File: LICENSE
+Keywords: PLRNN,RNN,computational-neuroscience,dynamical-systems,dynamics-reconstruction,interpretability
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
+Requires-Dist: gym>=0.21
+Requires-Dist: ipykernel
+Requires-Dist: jupyter
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: neurogym>=0.0.1
+Requires-Dist: numpy>=1.23
+Requires-Dist: safetensors>=0.4
+Requires-Dist: scipy>=1.10
+Requires-Dist: torch>=2.0
+Requires-Dist: tqdm
+Description-Content-Type: text/markdown
+
+# NeuralRNN
+
+---
+
+**NeuralRNN is A unified framework for implementing RNN methods in cognitive neuroscience** — bringing two major paradigms under a single [Transformers](https://github.com/huggingface/transformers)-style interface:
+
+- **Paradigm A: Task Optimization**[^1]: Train RNNs on cognitive tasks, then reverse-engineer how they perform computation using analyses including fixed points, vector fields, dimensionality reduction, etc. The goal is to use RNNs as a proxy for cognitive computation.
+- **Paradigm B: Dynamical System Reconstruction (DSR)**[^2][^3]: Fit generative RNNs directly from neural/behavioral time series that can reproduce attractors, power spectra, and Lyapunov spectra of the target system.
+
+Both paradigms share a unified set of `model config`, `Trainer`, and `analysis` tools. **The only difference between the two paradigms is the `Objective`**: Paradigm A aims to optimize output for cognitive task performance, while Paradigm B aims to construct a dynamical system isomorphic to the target neural activity. Moreover, DSR can also be applied to reconstruct the dynamics of TBO-trained models for interpretability analysis[^4].
+
+---
+
+## Core Concept
+
+All models are viewed as "discrete dynamical systems with downstream readout" $z_t=F_\theta(z_{t-1},x_t),\;y_t=G_\phi(z_t)$.
+
+A model only needs to implement two methods:
+
+```python
+def recurrence(self, x_t, z_prev, *, inputs=None): ...  # single-step transition F
+def readout(self, z_t): ...                              # readout G
+```
+
+NeuralRNN provides an interface to automatically connect the model to the unified trainer and all analysis tools.
+
+## What NeuralRNN contains and not
+
+NeuralRNN contains the pipeline to model RNN for neuroscience research, including (1) constructing dataset, (2) building and configuring RNN models, (3) training, and (4) model analysis (see the full pipeline in **[`custom pipeline`](notebook/03_custom_pipeline.ipynb)**  and the documents in **[`docs`](docs/README.md)**). We also provide the guide to implement each built-in model through this framework (see **[`notebook`](notebook/README.md)**).
+
+However, there are others methods using dynamical system methods as well, including [MARBLE](https://www.nature.com/articles/s41592-024-02582-2), [FINDR](https://www.nature.com/articles/s41586-025-09528-4), [neuralflow](https://www.nature.com/articles/s41586-025-09199-1), and [SSMLearn](https://arxiv.org/abs/2510.13519). These model-agnostic methods aim to inference interpretable representations of neural population dynamics exactly from the neural response, which are not included in NeuralRNN but can be suitably combined for the further analysis of RNN models.
+
+
+## Install
+
+```bash
+$ git clone https://github.com/ChenHH730/NeuralRNN.git
+$ cd NeuralRNN
+$ pip install -e .
+```
+
+
+## Quickstart
+
+```python
+from neuralrnn import AutoConfig, AutoModel, Trainer, TrainingArguments
+from neuralrnn import TeacherForcingObjective, load_dataset
+
+# 1) dataset
+# use registered dataset or custom dataset
+ds = load_dataset("lorenz63", sequence_length=200, batch_size=16, normalize=True) 
+
+# 2) model (config) + objective (based on the paradigm) + training
+cfg = AutoConfig.for_model("shallow_plrnn", input_dim=0, latent_dim=3,
+        output_dim=3, hidden_dim=50, autonomous=True)  # model config
+model = AutoModel.from_config(cfg)  # load model
+Trainer(model, ds, TeacherForcingObjective(alpha=0.1),
+        TrainingArguments(max_steps=2000)).train()  # train model
+
+# 3) save and load (config.json + model.safetensors)
+model.save_pretrained("ckpt/")
+model = AutoModel.from_pretrained("ckpt/")
+
+# 4) analysis (model agnostic)
+from neuralrnn.analysis import find_fixed_points, max_lyapunov_exponent
+fps = find_fixed_points(model)
+```
+
+## Content Structure
+
+```
+src/neuralrnn/
+  configuration_utils.py   modeling_utils.py     # core contracts (Config / Model base classes)
+  auto/                    # AutoConfig / AutoModel registration & dispatch
+  models/                  # model zoo: ctrnn, ei_rnn, lowrank_rnn (Paradigm A), plrnn (Paradigm B), latent_circuit, tiny_rnn,
+                           #   constrained_rnn, multiarea_rnn, gain_rnn (gain_rnn + stp_rnn)
+  data/                    # unified batching, datasets, open data registry + download cache
+  train/                   # generic Trainer + paradigm Objectives + reusable loss terms /
+                           #   regularizers / metrics + nested cross-validation
+  analysis/                # fixed points / linearization / vector fields / dim reduction /
+                           #   Lyapunov / D_stsp, D_H / PLRNN invariant manifolds / sequentiality
+docs/                      # ARCHITECTURE.md · PORTING_GUIDE.md · theory/ · papers/
+notebook/                  # end-to-end tutorials for each paper
+```
+
+## Built-in Models
+
+| Model | Paradigm | Status (mostly used) |
+|---|---|---|
+| continuous time RNN | A | ✅ |
+| E-I RNN (Dale's principle) | A | ✅ |
+| Latent Circuit Model | B | ✅ |
+| piecewise linear RNN | B | ✅ |
+| Tiny RNN | B | ✅ |
+| low-rank RNN | AB | ✅ |
+| constrained RNN | A | ✅ |
+| seRNN | A | ✅ |
+| multi-area RNN | A | ✅ |
+| gain RNN | AB | ✅ |
+| STP RNN | A | ✅ |
+
+The second column shows the corresponding paradigm used in the original work.  
+
+## Porting New Papers into the Framework
+
+Core principle: **Porting = writing adapters (wrapping + verification), not rewriting mathematics**. Any model that implements `recurrence/readout` is plug-and-play; the analysis layer works only through the model's public contract and never imports specific model classes.
+
+## License
+
+MIT, see [LICENSE](LICENSE). Original code of ported papers belongs to their respective authors; please follow their individual licenses when porting.
+
+## References
+
+[^1]: [Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks](https://doi.org/10.1371/journal.pcbi.1004792). 
+Project: https://github.com/gyyang/nn-brain
+
+[^2]: [Reconstructing computational dynamics from neural measurements with RNN](https://www.nature.com/articles/s41583-023-00740-7)
+Project: https://github.com/DurstewitzLab/CNS-2023
+
+[^3]: [Discovering cognitive strategies with tiny-RNN](https://www.nature.com/articles/s41586-025-09142-4) 
+Project: https://github.com/jil095/tinyRNN
+
+[^4]: https://github.com/engellab/latentcircuit
+
+[^5]: https://github.com/Dynamics-of-Neural-Systems-Lab/MARBLE
+
+[^6]: https://github.com/NN4Neurosim/nn4n https://nn4n.org/
+[^7]: 

neuralrnn-0.3.5/README.md

@@ -0,0 +1,128 @@
+# NeuralRNN
+
+---
+
+**NeuralRNN is A unified framework for implementing RNN methods in cognitive neuroscience** — bringing two major paradigms under a single [Transformers](https://github.com/huggingface/transformers)-style interface:
+
+- **Paradigm A: Task Optimization**[^1]: Train RNNs on cognitive tasks, then reverse-engineer how they perform computation using analyses including fixed points, vector fields, dimensionality reduction, etc. The goal is to use RNNs as a proxy for cognitive computation.
+- **Paradigm B: Dynamical System Reconstruction (DSR)**[^2][^3]: Fit generative RNNs directly from neural/behavioral time series that can reproduce attractors, power spectra, and Lyapunov spectra of the target system.
+
+Both paradigms share a unified set of `model config`, `Trainer`, and `analysis` tools. **The only difference between the two paradigms is the `Objective`**: Paradigm A aims to optimize output for cognitive task performance, while Paradigm B aims to construct a dynamical system isomorphic to the target neural activity. Moreover, DSR can also be applied to reconstruct the dynamics of TBO-trained models for interpretability analysis[^4].
+
+---
+
+## Core Concept
+
+All models are viewed as "discrete dynamical systems with downstream readout" $z_t=F_\theta(z_{t-1},x_t),\;y_t=G_\phi(z_t)$.
+
+A model only needs to implement two methods:
+
+```python
+def recurrence(self, x_t, z_prev, *, inputs=None): ...  # single-step transition F
+def readout(self, z_t): ...                              # readout G
+```
+
+NeuralRNN provides an interface to automatically connect the model to the unified trainer and all analysis tools.
+
+## What NeuralRNN contains and not
+
+NeuralRNN contains the pipeline to model RNN for neuroscience research, including (1) constructing dataset, (2) building and configuring RNN models, (3) training, and (4) model analysis (see the full pipeline in **[`custom pipeline`](notebook/03_custom_pipeline.ipynb)**  and the documents in **[`docs`](docs/README.md)**). We also provide the guide to implement each built-in model through this framework (see **[`notebook`](notebook/README.md)**).
+
+However, there are others methods using dynamical system methods as well, including [MARBLE](https://www.nature.com/articles/s41592-024-02582-2), [FINDR](https://www.nature.com/articles/s41586-025-09528-4), [neuralflow](https://www.nature.com/articles/s41586-025-09199-1), and [SSMLearn](https://arxiv.org/abs/2510.13519). These model-agnostic methods aim to inference interpretable representations of neural population dynamics exactly from the neural response, which are not included in NeuralRNN but can be suitably combined for the further analysis of RNN models.
+
+
+## Install
+
+```bash
+$ git clone https://github.com/ChenHH730/NeuralRNN.git
+$ cd NeuralRNN
+$ pip install -e .
+```
+
+
+## Quickstart
+
+```python
+from neuralrnn import AutoConfig, AutoModel, Trainer, TrainingArguments
+from neuralrnn import TeacherForcingObjective, load_dataset
+
+# 1) dataset
+# use registered dataset or custom dataset
+ds = load_dataset("lorenz63", sequence_length=200, batch_size=16, normalize=True) 
+
+# 2) model (config) + objective (based on the paradigm) + training
+cfg = AutoConfig.for_model("shallow_plrnn", input_dim=0, latent_dim=3,
+        output_dim=3, hidden_dim=50, autonomous=True)  # model config
+model = AutoModel.from_config(cfg)  # load model
+Trainer(model, ds, TeacherForcingObjective(alpha=0.1),
+        TrainingArguments(max_steps=2000)).train()  # train model
+
+# 3) save and load (config.json + model.safetensors)
+model.save_pretrained("ckpt/")
+model = AutoModel.from_pretrained("ckpt/")
+
+# 4) analysis (model agnostic)
+from neuralrnn.analysis import find_fixed_points, max_lyapunov_exponent
+fps = find_fixed_points(model)
+```
+
+## Content Structure
+
+```
+src/neuralrnn/
+  configuration_utils.py   modeling_utils.py     # core contracts (Config / Model base classes)
+  auto/                    # AutoConfig / AutoModel registration & dispatch
+  models/                  # model zoo: ctrnn, ei_rnn, lowrank_rnn (Paradigm A), plrnn (Paradigm B), latent_circuit, tiny_rnn,
+                           #   constrained_rnn, multiarea_rnn, gain_rnn (gain_rnn + stp_rnn)
+  data/                    # unified batching, datasets, open data registry + download cache
+  train/                   # generic Trainer + paradigm Objectives + reusable loss terms /
+                           #   regularizers / metrics + nested cross-validation
+  analysis/                # fixed points / linearization / vector fields / dim reduction /
+                           #   Lyapunov / D_stsp, D_H / PLRNN invariant manifolds / sequentiality
+docs/                      # ARCHITECTURE.md · PORTING_GUIDE.md · theory/ · papers/
+notebook/                  # end-to-end tutorials for each paper
+```
+
+## Built-in Models
+
+| Model | Paradigm | Status (mostly used) |
+|---|---|---|
+| continuous time RNN | A | ✅ |
+| E-I RNN (Dale's principle) | A | ✅ |
+| Latent Circuit Model | B | ✅ |
+| piecewise linear RNN | B | ✅ |
+| Tiny RNN | B | ✅ |
+| low-rank RNN | AB | ✅ |
+| constrained RNN | A | ✅ |
+| seRNN | A | ✅ |
+| multi-area RNN | A | ✅ |
+| gain RNN | AB | ✅ |
+| STP RNN | A | ✅ |
+
+The second column shows the corresponding paradigm used in the original work.  
+
+## Porting New Papers into the Framework
+
+Core principle: **Porting = writing adapters (wrapping + verification), not rewriting mathematics**. Any model that implements `recurrence/readout` is plug-and-play; the analysis layer works only through the model's public contract and never imports specific model classes.
+
+## License
+
+MIT, see [LICENSE](LICENSE). Original code of ported papers belongs to their respective authors; please follow their individual licenses when porting.
+
+## References
+
+[^1]: [Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks](https://doi.org/10.1371/journal.pcbi.1004792). 
+Project: https://github.com/gyyang/nn-brain
+
+[^2]: [Reconstructing computational dynamics from neural measurements with RNN](https://www.nature.com/articles/s41583-023-00740-7)
+Project: https://github.com/DurstewitzLab/CNS-2023
+
+[^3]: [Discovering cognitive strategies with tiny-RNN](https://www.nature.com/articles/s41586-025-09142-4) 
+Project: https://github.com/jil095/tinyRNN
+
+[^4]: https://github.com/engellab/latentcircuit
+
+[^5]: https://github.com/Dynamics-of-Neural-Systems-Lab/MARBLE
+
+[^6]: https://github.com/NN4Neurosim/nn4n https://nn4n.org/
+[^7]: 

neuralrnn-0.3.5/pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "neuralrnn"
+version = "0.3.5"
+description = "A unified framework for implementing RNN methods in cognitive neuroscience"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT" }
+authors = [{ name = "Honghua Chen", email = "honghuachen69@gmail.com" }]
+keywords = ["RNN", "computational-neuroscience", "dynamical-systems",
+            "dynamics-reconstruction", "interpretability", "PLRNN"]
+
+dependencies = [
+    "torch>=2.0",
+    "numpy>=1.23",
+    "scipy>=1.10",        
+    "safetensors>=0.4",   
+    "neurogym>=0.0.1",
+    "gym>=0.21",
+    "matplotlib>=3.6",
+    "jupyter",
+    "ipykernel",
+    "tqdm",
+]
+
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+
+[project.urls]
+Homepage = "https://github.com/HHChen730/NeuralRNN"
+Documentation = "https://neuralrnn.readthedocs.io/"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/neuralrnn"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py39"
+
+[tool.pytest.ini_options]
+testpaths = ["test"]
+
+[tool.setuptools.exclude-package-data]
+"neuralrnn" = ["docs/*", "notebook/*", "*.ipynb"]

neuralrnn-0.3.5/src/neuralrnn/__init__.py

@@ -0,0 +1,79 @@
+"""NeuralRNN: a unified framework for RNN methods in cognitive neuroscience.
+
+Brings two front-line paradigms under one transformers-style API:
+  Paradigm A -- optimize and train RNNs on cognitive tasks, with interpretability analysis
+  (fixed points / vector fields / dimensionality reduction);
+  Paradigm B -- reconstruct dynamics directly from neural / behavioral data
+  (PLRNN / LFADS / low-rank / Tiny RNN).
+
+Core abstraction: every model is a "discrete dynamical system with readout". Implementing only
+`recurrence` and `readout` is enough to plug into the unified Trainer (paradigm differences are
+handled by Objective) and analysis modules.
+"""
+
+from __future__ import annotations
+
+__version__ = "0.3.5"
+
+# Core base classes / output container
+from .configuration_utils import (
+    NeuralRNNConfig, resolve_euler_alpha,
+    SUPPORTED_NONLINEARITY_MODES, validate_nonlinearity_mode,
+)
+from .modeling_utils import NeuralDynamicsModel, DynamicsModelOutput
+
+# Unified activation factory
+from .activations import get_activation, SUPPORTED_ACTIVATIONS
+
+# Auto factories
+from .auto import (
+    AutoConfig, AutoModel,
+    register_config, register_model,
+    CONFIG_REGISTRY, MODEL_REGISTRY,
+)
+
+# Data
+from .data import (
+    BaseDataset, StandardScaler, CustomDataset,
+    CognitiveTaskDataset, ReconstructionDataset,
+    DATASET_REGISTRY, DatasetSpec, load_dataset,
+)
+
+# Training
+from .train import (
+    Trainer, TrainingArguments,
+    Objective, SupervisedObjective, RegularizedSupervisedObjective,
+    TeacherForcingObjective, BehavioralObjective, VariationalObjective,
+    ReconstructionObjective, ConstrainedSupervisedObjective,
+    build_objective, register_objective, OBJECTIVE_REGISTRY, AutoObjective,
+    masked_mse, masked_cross_entropy, masked_nll, loss_mse,
+    activity_l2, weight_l2, weight_l1,
+    orthogonality_penalty, model_orthogonality_penalty,
+    accuracy_classification, accuracy_general,
+)
+
+# Visualization
+from . import visualization
+
+__all__ = [
+    "__version__",
+    "NeuralRNNConfig", "NeuralDynamicsModel", "DynamicsModelOutput",
+    "resolve_euler_alpha",
+    "SUPPORTED_NONLINEARITY_MODES", "validate_nonlinearity_mode",
+    "get_activation", "SUPPORTED_ACTIVATIONS",
+    "AutoConfig", "AutoModel", "register_config", "register_model",
+    "CONFIG_REGISTRY", "MODEL_REGISTRY",
+    "BaseDataset", "StandardScaler", "CustomDataset",
+    "CognitiveTaskDataset", "ReconstructionDataset",
+    "DATASET_REGISTRY", "DatasetSpec", "load_dataset",
+    "Trainer", "TrainingArguments",
+    "Objective", "SupervisedObjective", "RegularizedSupervisedObjective",
+    "TeacherForcingObjective", "BehavioralObjective", "VariationalObjective",
+    "ReconstructionObjective", "ConstrainedSupervisedObjective",
+    "build_objective", "register_objective", "OBJECTIVE_REGISTRY", "AutoObjective",
+    "masked_mse", "masked_cross_entropy", "masked_nll", "loss_mse",
+    "activity_l2", "weight_l2", "weight_l1",
+    "orthogonality_penalty", "model_orthogonality_penalty",
+    "accuracy_classification", "accuracy_general",
+]
+