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00000000..0de38a2e --- /dev/null +++ b/_sources/arg.rst.txt @@ -0,0 +1,7 @@ +Arg +====== + +.. automodule:: neuromancer.arg + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/blocks.rst.txt b/_sources/blocks.rst.txt new file mode 100644 index 00000000..604a7671 --- /dev/null +++ b/_sources/blocks.rst.txt @@ -0,0 +1,7 @@ +Blocks +====== + +.. automodule:: neuromancer.blocks + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/bounds.rst.txt b/_sources/bounds.rst.txt new file mode 100644 index 00000000..d986db0d --- /dev/null +++ b/_sources/bounds.rst.txt @@ -0,0 +1,7 @@ +Bounds +====== + +.. automodule:: neuromancer.bounds + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/callbacks.rst.txt b/_sources/callbacks.rst.txt new file mode 100644 index 00000000..c398eabb --- /dev/null +++ b/_sources/callbacks.rst.txt @@ -0,0 +1,7 @@ +Callbacks +========= + +.. automodule:: neuromancer.callbacks + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/component.rst.txt b/_sources/component.rst.txt new file mode 100644 index 00000000..84e55900 --- /dev/null +++ b/_sources/component.rst.txt @@ -0,0 +1,7 @@ +Component +========= + +.. automodule:: neuromancer.component + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/constraint.rst.txt b/_sources/constraint.rst.txt new file mode 100644 index 00000000..50de6f9e --- /dev/null +++ b/_sources/constraint.rst.txt @@ -0,0 +1,7 @@ +Constraint +========== + +.. automodule:: neuromancer.constraint + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/dataset.rst.txt b/_sources/dataset.rst.txt new file mode 100644 index 00000000..2542564c --- /dev/null +++ b/_sources/dataset.rst.txt @@ -0,0 +1,7 @@ +Dataset +========= + +.. automodule:: neuromancer.dataset + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/dynamics.rst.txt b/_sources/dynamics.rst.txt new file mode 100644 index 00000000..df34ab20 --- /dev/null +++ b/_sources/dynamics.rst.txt @@ -0,0 +1,7 @@ +Dynamics +======== + +.. automodule:: neuromancer.dynamics + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/estimators.rst.txt b/_sources/estimators.rst.txt new file mode 100644 index 00000000..c3b2528b --- /dev/null +++ b/_sources/estimators.rst.txt @@ -0,0 +1,7 @@ +Estimators +========== + +.. automodule:: neuromancer.estimators + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/gnn.rst.txt b/_sources/gnn.rst.txt new file mode 100644 index 00000000..ecc681b9 --- /dev/null +++ b/_sources/gnn.rst.txt @@ -0,0 +1,7 @@ +GNN +====== + +.. automodule:: neuromancer.gnn + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/gradients.rst.txt b/_sources/gradients.rst.txt new file mode 100644 index 00000000..3f868ebe --- /dev/null +++ b/_sources/gradients.rst.txt @@ -0,0 +1,7 @@ +Gradients +========= + +.. automodule:: neuromancer.gradients + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 00000000..bb8a2492 --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,327 @@ +.. SLiM documentation master file, created by + sphinx-quickstart on Sat Nov 7 06:40:51 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. +.. _Aaron Tuor: http://sw.cs.wwu.edu/~tuora/aarontuor/ + +NeuroMANCER +============================ + +.. image:: _static/class_diagram.png + +Additional Documentation +------------------------ +Additional documentation for the library can be found in the `pdf +form `__. +There is also an `introduction +video `__ covering core +features of the library. + +Getting Started +--------------- + +Below is a Neuromancer syntax example for differentiable parametric programming + +.. code:: python + + import neuromancer as nm + + # primal solution map to be trained + func = nm.blocks.MLP(insize=2, outsize=2, hsizes=[80] * 4) + sol_map = nm.maps.Map(func, + input_keys=["a", "p"], + output_keys=["x"], + name='primal_map') + + # problem primal variables + x = nm.constraints.variable("x")[:, [0]] + y = nm.constraints.variable("x")[:, [1]] + + # sampled problem parameters + p = nm.constraints.variable('p') + a = nm.constraints.variable('a') + + # nonlinear objective function + f = (1-x)**2 + a*(y-x**2)**2 + obj = f.minimize(weight=1., name='obj') + + # constraints + con_1 = 100*(x >= y) + con_2 = 100*((p/2)**2 <= x**2+y**2) + con_3 = 100*(x**2+y**2 <= p**2) + + # create constrained optimization loss + objectives = [obj] + constraints = [con_1, con_2, con_3] + loss = nm.loss.PenaltyLoss(objectives, constraints) + # construct constrained optimization problem + components = [sol_map] + problem = nm.problem.Problem(components, loss) + +Conda install +------------- + +First clone the neuromancer library. +Conda install is recommended for GPU acceleration. +In many cases the following simple install should work for the specified OS + + +.. code:: bash + + + user@machine:~$ git clone -b master https://github.com/pnnl/neuromancer.git --single-branch + +Install dependencies +-------------------- + +Ubuntu +~~~~~~ + +.. code:: bash + + $ conda env create -f linux_env.yml + $ conda activate neuromancer + +Windows +~~~~~~~ + +.. code:: bash + + $ conda env create -f windows_env.yml + $ conda activate neuromancer + (neuromancer) $ conda install -c defaults intel-openmp -f + +MacOS (Apple M1) +~~~~~~~~~~~~~~~~ + +.. code:: bash + + $ conda env create -f osxarm64_env.yml + $ conda activate neuromancer + +Other operating system +~~~~~~~~~~~~~~~~~~~~~~ + +.. code:: bash + + $ conda create -n neuromancer python=3.10.4 + $ conda activate neuromancer + (neuromancer) $ conda install pytorch pytorch-cuda=11.6 -c pytorch -c nvidia + ## OR (for Mac): conda install pytorch -c pytorch + (neuromancer) $ conda config --append channels conda-forge + (neuromancer) $ conda install scipy numpy matplotlib scikit-learn pandas dill mlflow pydot=1.4.2 pyts numba + (neuromancer) $ conda install networkx=3.0 plum-dispatch + (neuromancer) $ conda install -c anaconda pytest hypothesis + (neuromancer) $ conda install cvxpy cvxopt casadi seaborn imageio + (neuromancer) $ conda install tqdm torchdiffeq toml + ## (for Windows): conda install -c defaults intel-openmp -f + +Install neuromancer ecosystem +----------------------------- + +.. code:: bash + + (neuromancer) $ pip install -e . --no-deps + +Pip install +----------- + +.. code :: bash + + python3 -m pip install -e.[docs,tests,examples] + +See the `pyproject.toml` file for reference. + +.. code:: + [project.optional-dependencies] + tests = ["pytest", "hypothesis"] + examples = ["casadi", "cvxpy", "imageio"] + docs = ["sphinx", "sphinx-rtd-theme"] + +Test NeuroMANCER install +------------------------ + +Run pytest on the test folder. It should take about 2 minutes to run the +tests on CPU. There will be a lot of warnings that you can safely +ignore. These warnings will be cleaned up in a future release. + +Examples +-------- + +For detailed examples of NeuroMANCER usage for control, system +identification, and parametric programming as well as tutorials for +basic usage, see the scripts in the examples folder. + +Community +--------- + +Contributing examples +~~~~~~~~~~~~~~~~~~~~~ + +If you have an example of using NeuroMANCER to solve an interesting +problem, or of using NeuroMANCER in a unique way, we would love to see +it incorporated into our current library of examples. To submit an +example, create a folder for your example/s in the example folder if +there isn’t currently and applicable folder and place either your +executable python file or notebook file there. Push your code back to +github and then submit a pull request. Please make sure to note in a +comment at the top of your code if there are additional dependencies to +run your example and how to install those dependencies. + +Contributing code +~~~~~~~~~~~~~~~~~ + +We welcome contributions to NeuroMANCER. Please accompany contributions +with some lightweight unit tests via pytest (see test/ folder for some +examples of easy to compose unit tests using pytest). In addition to +unit tests a script utilizing introduced new classes or modules should +be placed in the examples folder. To contribute a new feature please +submit a pull request. + +Reporting issues or bugs +~~~~~~~~~~~~~~~~~~~~~~~~ + +If you find a bug in the code or want to request a new feature, please +open an issue. + +NeuroMANCER development plan +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Here are some upcoming features we plan to develop. Please let us know +if you would like to get involved and contribute so we may be able to +coordinate on development. If there is a feature that you think would be +highly valuable but not included below, please open an issue and let us +know your thoughts. + +- Faster dynamics modeling via Torchscript +- Control and modelling for networked systems +- Easy to implement modeling and control with uncertainty + quantification +- Online learning examples +- Benchmark examples of DPC compared to deep RL +- Conda and pip package distribution +- CVXPY-like interface for optimization via Problem.solve method +- More versatile and simplified time series dataloading +- Pytorch Lightning trainer compatibility + +Publications +------------ + +- `James Koch, Zhao Chen, Aaron Tuor, Jan Drgona, Draguna Vrabie, + Structural Inference of Networked Dynamical Systems with Universal + Differential Equations, arXiv:2207.04962, + (2022) `__ +- `Ján Drgoňa, Sayak Mukherjee, Aaron Tuor, Mahantesh Halappanavar, + Draguna Vrabie, Learning Stochastic Parametric Differentiable + Predictive Control Policies, IFAC ROCOND conference + (2022) `__ +- `Sayak Mukherjee, Ján Drgoňa, Aaron Tuor, Mahantesh Halappanavar, + Draguna Vrabie, Neural Lyapunov Differentiable Predictive Control, + IEEE Conference on Decision and Control Conference + 2022 `__ +- `Wenceslao Shaw Cortez, Jan Drgona, Aaron Tuor, Mahantesh + Halappanavar, Draguna Vrabie, Differentiable Predictive Control with + Safety Guarantees: A Control Barrier Function Approach, IEEE + Conference on Decision and Control Conference + 2022 `__ +- `Ethan King, Jan Drgona, Aaron Tuor, Shrirang Abhyankar, Craig + Bakker, Arnab Bhattacharya, Draguna Vrabie, Koopman-based + Differentiable Predictive Control for the Dynamics-Aware Economic + Dispatch Problem, 2022 American Control Conference + (ACC) `__ +- `Drgoňa, J., Tuor, A. R., Chandan, V., & Vrabie, D. L., + Physics-constrained deep learning of multi-zone building thermal + dynamics. Energy and Buildings, 243, 110992, + (2021) `__ +- `E. Skomski, S. Vasisht, C. Wight, A. Tuor, J. Drgoňa and D. Vrabie, + “Constrained Block Nonlinear Neural Dynamical Models,” 2021 American + Control Conference (ACC), 2021, pp. 3993-4000, doi: + 10.23919/ACC50511.2021.9482930. `__ +- `Skomski, E., Drgoňa, J., & Tuor, A. (2021, May). Automating + Discovery of Physics-Informed Neural State Space Models via Learning + and Evolution. In Learning for Dynamics and Control (pp. 980-991). + PMLR. `__ +- `Drgoňa, J., Tuor, A., Skomski, E., Vasisht, S., & Vrabie, D. (2021). + Deep Learning Explicit Differentiable Predictive Control Laws for + Buildings. IFAC-PapersOnLine, 54(6), + 14-19. `__ +- `Tuor, A., Drgona, J., & Vrabie, D. (2020). Constrained neural + ordinary differential equations with stability guarantees. arXiv + preprint arXiv:2004.10883. `__ +- `Drgona, Jan, et al. “Differentiable Predictive Control: An MPC + Alternative for Unknown Nonlinear Systems using Constrained Deep + Learning.” Journal of Process Control Volume 116, August 2022, Pages + 80-92 `__ +- `Drgona, J., Skomski, E., Vasisht, S., Tuor, A., & Vrabie, D. (2020). + Dissipative Deep Neural Dynamical Systems, in IEEE Open Journal of + Control Systems, vol. 1, pp. 100-112, + 2022 `__ +- `Drgona, J., Tuor, A., & Vrabie, D., Learning Constrained Adaptive + Differentiable Predictive Control Policies With Guarantees, arXiv + preprint arXiv:2004.11184, + (2020) `__ + +Cite as +------- + +.. code:: bib + + @article{Neuromancer2022, + title={{NeuroMANCER: Neural Modules with Adaptive Nonlinear Constraints and Efficient Regularizations}}, + author={Tuor, Aaron and Drgona, Jan and Skomski, Mia and Koch, James and Chen, Zhao and Dernbach, Stefan and Legaard, Christian Møldrup and Vrabie, Draguna}, + Url= {https://github.com/pnnl/neuromancer}, + year={2022} + } + + +Authors: Authors: Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, +Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro + +Acknowledgements +----------------- +This research was partially supported by the Mathematics for Artificial Reasoning in Science (MARS) and Data Model Convergence (DMC) initiatives via the Laboratory Directed Research and Development (LDRD) investments at Pacific Northwest National Laboratory (PNNL), by the U.S. Department of Energy, through the Office of Advanced Scientific Computing Research's “Data-Driven Decision Control for Complex Systems (DnC2S)” project, and through the Energy Efficiency and Renewable Energy, Building Technologies Office under the “Dynamic decarbonization through autonomous physics-centric deep learning and optimization of building operations” and the “Advancing Market-Ready Building Energy Management by Cost-Effective Differentiable Predictive Control” projects. +PNNL is a multi-program national laboratory operated for the U.S. Department of Energy (DOE) by Battelle Memorial Institute under Contract No. DE-AC05-76RL0-1830. + +Documentation +------------------------ +.. image:: _static/class_diagram.png + +.. toctree:: + :maxdepth: 2 + :caption: Modules: + + dynamics.rst + activations.rst + blocks.rst + dataset.rst + estimators.rst + loggers.rst + operators.rst + plot.rst + problem.rst + rnn.rst + simulators.rst + trainer.rst + visuals.rst + arg.rst + callbacks.rst + component.rst + constraint.rst + gradients.rst + bounds.rst + gnn.rst + integrators.rst + interpolation.rst + loss.rst + maps.rst + ode.rst + pwa_maps.rst + solvers.rst + simulator.rst + physics.rst + + psl/index.rst + slim/index.rst + + + diff --git a/_sources/integrators.rst.txt b/_sources/integrators.rst.txt new file mode 100644 index 00000000..b6fd8b82 --- /dev/null +++ b/_sources/integrators.rst.txt @@ -0,0 +1,7 @@ +Integrators +=========== + +.. automodule:: neuromancer.integrators + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/interpolation.rst.txt b/_sources/interpolation.rst.txt new file mode 100644 index 00000000..b4a0ac0e --- /dev/null +++ b/_sources/interpolation.rst.txt @@ -0,0 +1,7 @@ +Interpolation +============= + +.. automodule:: neuromancer.interpolation + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/loggers.rst.txt b/_sources/loggers.rst.txt new file mode 100644 index 00000000..c3ef9231 --- /dev/null +++ b/_sources/loggers.rst.txt @@ -0,0 +1,7 @@ +Loggers +======= + +.. automodule:: neuromancer.loggers + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/loss.rst.txt b/_sources/loss.rst.txt new file mode 100644 index 00000000..57a4e851 --- /dev/null +++ b/_sources/loss.rst.txt @@ -0,0 +1,7 @@ +Loss +====== + +.. automodule:: neuromancer.loss + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/maps.rst.txt b/_sources/maps.rst.txt new file mode 100644 index 00000000..41a0b886 --- /dev/null +++ b/_sources/maps.rst.txt @@ -0,0 +1,7 @@ +Maps +====== + +.. automodule:: neuromancer.maps + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/ode.rst.txt b/_sources/ode.rst.txt new file mode 100644 index 00000000..6e9c977e --- /dev/null +++ b/_sources/ode.rst.txt @@ -0,0 +1,7 @@ +ODE +====== + +.. automodule:: neuromancer.ode + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/operators.rst.txt b/_sources/operators.rst.txt new file mode 100644 index 00000000..65207dca --- /dev/null +++ b/_sources/operators.rst.txt @@ -0,0 +1,7 @@ +Operators +========= + +.. automodule:: neuromancer.operators + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/physics.rst.txt b/_sources/physics.rst.txt new file mode 100644 index 00000000..7f55f871 --- /dev/null +++ b/_sources/physics.rst.txt @@ -0,0 +1,7 @@ +Physics +======= + +.. automodule:: neuromancer.physics + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/plot.rst.txt b/_sources/plot.rst.txt new file mode 100644 index 00000000..cbf1abab --- /dev/null +++ b/_sources/plot.rst.txt @@ -0,0 +1,7 @@ +Plot +====== + +.. automodule:: plot + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/problem.rst.txt b/_sources/problem.rst.txt new file mode 100644 index 00000000..d817da67 --- /dev/null +++ b/_sources/problem.rst.txt @@ -0,0 +1,7 @@ +Problem +======= + +.. automodule:: neuromancer.problem + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/psl/autonomous.rst.txt b/_sources/psl/autonomous.rst.txt new file mode 100644 index 00000000..5bb5df43 --- /dev/null +++ b/_sources/psl/autonomous.rst.txt @@ -0,0 +1,7 @@ +Autonomous +================== + +.. automodule:: neuromancer.psl.autonomous + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/psl/emulator.rst.txt b/_sources/psl/emulator.rst.txt new file mode 100644 index 00000000..7c80968b --- /dev/null +++ b/_sources/psl/emulator.rst.txt @@ -0,0 +1,7 @@ +Emulator +======== + +.. automodule:: neuromancer.psl.emulator + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/psl/index.rst.txt b/_sources/psl/index.rst.txt new file mode 100644 index 00000000..8fb3e166 --- /dev/null +++ b/_sources/psl/index.rst.txt @@ -0,0 +1,17 @@ +.. PSL documentation master file, created by + sphinx-quickstart on Thu Jan 7 12:20:09 2021. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +PSL: Python Systems Library v1.2 +================================ + +.. toctree:: + :maxdepth: 2 + :caption: Docs: + + autonomous.rst + emulator.rst + nonautonomous.rst + perturb.rst + diff --git a/_sources/psl/nonautonomous.rst.txt b/_sources/psl/nonautonomous.rst.txt new file mode 100644 index 00000000..79a09981 --- /dev/null +++ b/_sources/psl/nonautonomous.rst.txt @@ -0,0 +1,7 @@ +Nonautonomous +============= + +.. automodule:: neuromancer.psl.nonautonomous + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/psl/perturb.rst.txt b/_sources/psl/perturb.rst.txt new file mode 100644 index 00000000..99920e90 --- /dev/null +++ b/_sources/psl/perturb.rst.txt @@ -0,0 +1,7 @@ +Perturb +================================== + +.. automodule:: psl.perturb + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/pwa_maps.rst.txt b/_sources/pwa_maps.rst.txt new file mode 100644 index 00000000..334af697 --- /dev/null +++ b/_sources/pwa_maps.rst.txt @@ -0,0 +1,7 @@ +PWA Maps +======== + +.. automodule:: neuromancer.pwa_maps + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/rnn.rst.txt b/_sources/rnn.rst.txt new file mode 100644 index 00000000..00b89c30 --- /dev/null +++ b/_sources/rnn.rst.txt @@ -0,0 +1,7 @@ +RNN +====== + +.. automodule:: neuromancer.rnn + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/simulator.rst.txt b/_sources/simulator.rst.txt new file mode 100644 index 00000000..73183b88 --- /dev/null +++ b/_sources/simulator.rst.txt @@ -0,0 +1,7 @@ +Simulator +========= + +.. automodule:: neuromancer.simulator + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/simulators.rst.txt b/_sources/simulators.rst.txt new file mode 100644 index 00000000..7deb65ff --- /dev/null +++ b/_sources/simulators.rst.txt @@ -0,0 +1,7 @@ +Simulators +========== + +.. automodule:: neuromancer.simulators + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/slim/benchmarks.rst.txt b/_sources/slim/benchmarks.rst.txt new file mode 100644 index 00000000..efa07be1 --- /dev/null +++ b/_sources/slim/benchmarks.rst.txt @@ -0,0 +1,7 @@ +Benchmarks +========== + +.. automodule:: slim.butterfly.benchmark + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/slim/index.rst.txt b/_sources/slim/index.rst.txt new file mode 100644 index 00000000..af2599c1 --- /dev/null +++ b/_sources/slim/index.rst.txt @@ -0,0 +1,86 @@ +.. SLiM documentation master file, created by + sphinx-quickstart on Sat Nov 7 06:40:51 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. +.. _Aaron Tuor: http://sw.cs.wwu.edu/~tuora/aarontuor/ +.. _Orthogonal: https://arxiv.org/abs/1612.00188 +.. _Butterfly: https://github.com/HazyResearch/learning-circuits +.. _L0: https://arxiv.org/pdf/1712.01312.pdf +.. _Spectral: https://arxiv.org/pdf/1803.09327.pdf +.. _`Schur Decomposition`: https://papers.nips.cc/paper/9513-non-normal-recurrent-neural-network-nnrnn-learning-long-time-dependencies-while-improving-expressivity-with-transient-dynamics.pdf +.. _Lasso: https://leon.bottou.org/publications/pdf/compstat-2010.pdf +.. _Symplectic: https://arxiv.org/abs/1705.03341 +.. _AntiSymmetric: https://arxiv.org/abs/1705.03341 + +.. _`Concentric Ellipses`: https://arxiv.org/pdf/1705.03341.pdf +.. _`Swiss Roll`: https://arxiv.org/pdf/1705.03341.pdf +.. _Peaks: https://arxiv.org/pdf/1705.03341.pdf +.. _Add: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.676.4320&rep=rep1&type=pdf +.. _Multiply: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.676.4320&rep=rep1&type=pdf +.. _XOR: https://icml.cc/Conferences/2011/papers/532_icmlpaper.pdf +.. _Ackley: https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.71.2526&rep=rep1&type=pdf +.. _MNIST: https://ieeexplore.ieee.org/abstract/document/6296535 + + +SLiM: Structured Linear Maps +============================ + + +This package provides a suite of structured linear maps which can be used as drop-in replacements for PyTorch's nn.Linear module. Recent work viewing neural networks from a dynamical systems perspective has introduced a host of parametrizations for the basic linear maps which are subcomponents of neural networks. Such parametrizations may enhance the stability of learning, and embed models with inductive priors that encode domain application knowledge. This package is an effort to collect these all in one place with a common API to facilitate rapid exploration. + +.. note:: We encourage folks to contribute any new structured linear maps as feature requests. + ++---------------------------------------+---------------------------------------+ +| Linear Map | class | ++=======================================+=======================================+ +| Orthogonal_ |:any:`OrthogonalLinear` | ++---------------------------------------+---------------------------------------+ +| L0_ |:any:`L0Linear` | ++---------------------------------------+---------------------------------------+ +| Butterfly_ |:any:`ButterflyLinear` | ++---------------------------------------+---------------------------------------+ +| Spectral_ |:any:`SpectralLinear` | ++---------------------------------------+---------------------------------------+ +| `Schur Decomposition`_ |:any:`SchurDecompositionLinear` | ++---------------------------------------+---------------------------------------+ +| Lasso_ |:any:`LassoLinear` | ++---------------------------------------+---------------------------------------+ +| Symplectic_ |:any:`SymplecticLinear` | ++---------------------------------------+---------------------------------------+ +| AntiSymmetric_ |:any:`SkewSymmetricLinear` | ++---------------------------------------+---------------------------------------+ + +Benchmarks +---------- +Sequence to Classification: + +- MNIST_ +- XOR_ + +Point to Classification: + +- `Concentric Ellipses`_ +- `Swiss Roll`_ +- Peaks_ + +Sequence to Regression: + +- Add_ +- Multiply_ + +Point to Regression: + +- Ackley_ + +Dynamics: + +- Building models + + +.. toctree:: + :maxdepth: 2 + :caption: Docs: + + linear.rst + rnn.rst + benchmarks.rst diff --git a/_sources/slim/linear.rst.txt b/_sources/slim/linear.rst.txt new file mode 100644 index 00000000..19611a55 --- /dev/null +++ b/_sources/slim/linear.rst.txt @@ -0,0 +1,7 @@ +Linear +====== + +.. automodule:: neuromancer.slim.linear + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/slim/rnn.rst.txt b/_sources/slim/rnn.rst.txt new file mode 100644 index 00000000..2a7a85bf --- /dev/null +++ b/_sources/slim/rnn.rst.txt @@ -0,0 +1,7 @@ +RNN +====== + +.. automodule:: neuromancer.slim.rnn + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/solvers.rst.txt b/_sources/solvers.rst.txt new file mode 100644 index 00000000..d8deb867 --- /dev/null +++ b/_sources/solvers.rst.txt @@ -0,0 +1,7 @@ +Solvers +======== + +.. automodule:: neuromancer.solvers + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/trainer.rst.txt b/_sources/trainer.rst.txt new file mode 100644 index 00000000..968ad9a3 --- /dev/null +++ b/_sources/trainer.rst.txt @@ -0,0 +1,7 @@ +Trainer +======= + +.. automodule:: neuromancer.trainer + :members: + :undoc-members: + :special-members: __call__ diff --git a/_sources/visuals.rst.txt b/_sources/visuals.rst.txt new file mode 100644 index 00000000..8c9dfdd9 --- /dev/null +++ b/_sources/visuals.rst.txt @@ -0,0 +1,7 @@ +Visuals +======= + +.. automodule:: neuromancer.visuals + :members: + :undoc-members: + :special-members: __call__ diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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font-weight: bold } /* Literal.String.Escape */ +.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */ +.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */ +.highlight .sx { color: #008000 } /* Literal.String.Other */ +.highlight .sr { color: #A45A77 } /* Literal.String.Regex */ +.highlight .s1 { color: #BA2121 } /* Literal.String.Single */ +.highlight .ss { color: #19177C } /* Literal.String.Symbol */ +.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */ +.highlight .fm { color: #0000FF } /* Name.Function.Magic */ +.highlight .vc { color: #19177C } /* Name.Variable.Class */ +.highlight .vg { color: #19177C } /* Name.Variable.Global */ +.highlight .vi { color: #19177C } /* Name.Variable.Instance */ +.highlight .vm { color: #19177C } /* Name.Variable.Magic */ +.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 00000000..7918c3fa --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/tiny_dadaist.ico b/_static/tiny_dadaist.ico new file mode 100644 index 00000000..9198b38a Binary files /dev/null and b/_static/tiny_dadaist.ico differ diff --git a/activations.html b/activations.html new file mode 100644 index 00000000..4fa90c1f --- /dev/null +++ b/activations.html @@ -0,0 +1,144 @@ + + + + + + + Activations — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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+ +
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+

Activations

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/arg.html b/arg.html new file mode 100644 index 00000000..df491747 --- /dev/null +++ b/arg.html @@ -0,0 +1,144 @@ + + + + + + + Arg — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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+ +
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+ +
+

Arg

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+ + +
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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/blocks.html b/blocks.html new file mode 100644 index 00000000..18a78779 --- /dev/null +++ b/blocks.html @@ -0,0 +1,144 @@ + + + + + + + Blocks — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Blocks

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/bounds.html b/bounds.html new file mode 100644 index 00000000..a7e9bd5e --- /dev/null +++ b/bounds.html @@ -0,0 +1,144 @@ + + + + + + + Bounds — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Bounds

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/callbacks.html b/callbacks.html new file mode 100644 index 00000000..6068b610 --- /dev/null +++ b/callbacks.html @@ -0,0 +1,144 @@ + + + + + + + Callbacks — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Callbacks

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/component.html b/component.html new file mode 100644 index 00000000..1a0bc24a --- /dev/null +++ b/component.html @@ -0,0 +1,144 @@ + + + + + + + Component — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Component

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/constraint.html b/constraint.html new file mode 100644 index 00000000..1e8ebe6d --- /dev/null +++ b/constraint.html @@ -0,0 +1,144 @@ + + + + + + + Constraint — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Constraint

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/dataset.html b/dataset.html new file mode 100644 index 00000000..7ccca541 --- /dev/null +++ b/dataset.html @@ -0,0 +1,144 @@ + + + + + + + Dataset — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Dataset

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/dynamics.html b/dynamics.html new file mode 100644 index 00000000..4400ca41 --- /dev/null +++ b/dynamics.html @@ -0,0 +1,144 @@ + + + + + + + Dynamics — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Dynamics

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/estimators.html b/estimators.html new file mode 100644 index 00000000..7e5b8285 --- /dev/null +++ b/estimators.html @@ -0,0 +1,144 @@ + + + + + + + Estimators — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Estimators

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 00000000..4c53ef61 --- /dev/null +++ b/genindex.html @@ -0,0 +1,140 @@ + + + + + + Index — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/gnn.html b/gnn.html new file mode 100644 index 00000000..db9b60a4 --- /dev/null +++ b/gnn.html @@ -0,0 +1,144 @@ + + + + + + + GNN — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

GNN

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/gradients.html b/gradients.html new file mode 100644 index 00000000..bffe930b --- /dev/null +++ b/gradients.html @@ -0,0 +1,144 @@ + + + + + + + Gradients — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Gradients

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 00000000..238e6d43 --- /dev/null +++ b/index.html @@ -0,0 +1,439 @@ + + + + + + + NeuroMANCER — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

NeuroMANCER

+_images/class_diagram.png +
+

Additional Documentation

+

Additional documentation for the library can be found in the pdf +form. +There is also an introduction +video covering core +features of the library.

+
+
+

Getting Started

+

Below is a Neuromancer syntax example for differentiable parametric programming

+
import neuromancer as nm
+
+# primal solution map to be trained
+func = nm.blocks.MLP(insize=2, outsize=2, hsizes=[80] * 4)
+sol_map = nm.maps.Map(func,
+        input_keys=["a", "p"],
+        output_keys=["x"],
+        name='primal_map')
+
+# problem primal variables
+x = nm.constraints.variable("x")[:, [0]]
+y = nm.constraints.variable("x")[:, [1]]
+
+# sampled problem parameters
+p = nm.constraints.variable('p')
+a = nm.constraints.variable('a')
+
+# nonlinear objective function
+f = (1-x)**2 + a*(y-x**2)**2
+obj = f.minimize(weight=1., name='obj')
+
+# constraints
+con_1 = 100*(x >= y)
+con_2 = 100*((p/2)**2 <= x**2+y**2)
+con_3 = 100*(x**2+y**2 <= p**2)
+
+# create constrained optimization loss
+objectives = [obj]
+constraints = [con_1, con_2, con_3]
+loss = nm.loss.PenaltyLoss(objectives, constraints)
+# construct constrained optimization problem
+components = [sol_map]
+problem = nm.problem.Problem(components, loss)
+
+
+
+
+

Conda install

+

First clone the neuromancer library. +Conda install is recommended for GPU acceleration. +In many cases the following simple install should work for the specified OS

+
user@machine:~$ git clone -b master https://github.com/pnnl/neuromancer.git --single-branch
+
+
+
+
+

Install dependencies

+
+

Ubuntu

+
$ conda env create -f linux_env.yml
+$ conda activate neuromancer
+
+
+
+
+

Windows

+
$ conda env create -f windows_env.yml
+$ conda activate neuromancer
+(neuromancer) $ conda install -c defaults intel-openmp -f
+
+
+
+
+

MacOS (Apple M1)

+
$ conda env create -f osxarm64_env.yml
+$ conda activate neuromancer
+
+
+
+
+

Other operating system

+
$ conda create -n neuromancer python=3.10.4
+$ conda activate neuromancer
+(neuromancer) $ conda install pytorch pytorch-cuda=11.6 -c pytorch -c nvidia
+## OR (for Mac): conda install pytorch -c pytorch
+(neuromancer) $ conda config --append channels conda-forge
+(neuromancer) $ conda install scipy numpy matplotlib scikit-learn pandas dill mlflow pydot=1.4.2 pyts numba
+(neuromancer) $ conda install networkx=3.0 plum-dispatch
+(neuromancer) $ conda install -c anaconda pytest hypothesis
+(neuromancer) $ conda install cvxpy cvxopt casadi seaborn imageio
+(neuromancer) $ conda install tqdm torchdiffeq toml
+## (for Windows): conda install -c defaults intel-openmp -f
+
+
+
+
+
+

Install neuromancer ecosystem

+
(neuromancer) $ pip install -e . --no-deps
+
+
+
+
+

Pip install

+
python3 -m pip install -e.[docs,tests,examples]
+
+
+

See the pyproject.toml file for reference.

+
+
+

Test NeuroMANCER install

+

Run pytest on the test folder. It should take about 2 minutes to run the +tests on CPU. There will be a lot of warnings that you can safely +ignore. These warnings will be cleaned up in a future release.

+
+
+

Examples

+

For detailed examples of NeuroMANCER usage for control, system +identification, and parametric programming as well as tutorials for +basic usage, see the scripts in the examples folder.

+
+
+

Community

+
+

Contributing examples

+

If you have an example of using NeuroMANCER to solve an interesting +problem, or of using NeuroMANCER in a unique way, we would love to see +it incorporated into our current library of examples. To submit an +example, create a folder for your example/s in the example folder if +there isn’t currently and applicable folder and place either your +executable python file or notebook file there. Push your code back to +github and then submit a pull request. Please make sure to note in a +comment at the top of your code if there are additional dependencies to +run your example and how to install those dependencies.

+
+
+

Contributing code

+

We welcome contributions to NeuroMANCER. Please accompany contributions +with some lightweight unit tests via pytest (see test/ folder for some +examples of easy to compose unit tests using pytest). In addition to +unit tests a script utilizing introduced new classes or modules should +be placed in the examples folder. To contribute a new feature please +submit a pull request.

+
+
+

Reporting issues or bugs

+

If you find a bug in the code or want to request a new feature, please +open an issue.

+
+
+

NeuroMANCER development plan

+

Here are some upcoming features we plan to develop. Please let us know +if you would like to get involved and contribute so we may be able to +coordinate on development. If there is a feature that you think would be +highly valuable but not included below, please open an issue and let us +know your thoughts.

+
    +

  • Faster dynamics modeling via Torchscript

    • +

  • Control and modelling for networked systems

    • +

  • Easy to implement modeling and control with uncertainty +quantification

    • +

  • Online learning examples

    • +

  • Benchmark examples of DPC compared to deep RL

    • +

  • Conda and pip package distribution

    • +

  • CVXPY-like interface for optimization via Problem.solve method

    • +

  • More versatile and simplified time series dataloading

    • +

  • Pytorch Lightning trainer compatibility

    • +
+
+
+
+

Publications

+ +
+
+

Cite as

+
@article{Neuromancer2022,
+  title={{NeuroMANCER: Neural Modules with Adaptive Nonlinear Constraints and Efficient Regularizations}},
+  author={Tuor, Aaron and Drgona, Jan and Skomski, Mia and Koch, James and Chen, Zhao and Dernbach, Stefan and Legaard, Christian Møldrup and Vrabie, Draguna},
+  Url= {https://github.com/pnnl/neuromancer},
+  year={2022}
+}
+
+
+

Authors: Authors: Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, +Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro

+
+
+

Acknowledgements

+

This research was partially supported by the Mathematics for Artificial Reasoning in Science (MARS) and Data Model Convergence (DMC) initiatives via the Laboratory Directed Research and Development (LDRD) investments at Pacific Northwest National Laboratory (PNNL), by the U.S. Department of Energy, through the Office of Advanced Scientific Computing Research’s “Data-Driven Decision Control for Complex Systems (DnC2S)” project, and through the Energy Efficiency and Renewable Energy, Building Technologies Office under the “Dynamic decarbonization through autonomous physics-centric deep learning and optimization of building operations” and the “Advancing Market-Ready Building Energy Management by Cost-Effective Differentiable Predictive Control” projects. +PNNL is a multi-program national laboratory operated for the U.S. Department of Energy (DOE) by Battelle Memorial Institute under Contract No. DE-AC05-76RL0-1830.

+
+
+

Documentation

+_images/class_diagram.png +
+

Modules:

+ +
+
+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/integrators.html b/integrators.html new file mode 100644 index 00000000..519d96e9 --- /dev/null +++ b/integrators.html @@ -0,0 +1,144 @@ + + + + + + + Integrators — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Integrators

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/interpolation.html b/interpolation.html new file mode 100644 index 00000000..d2f4e356 --- /dev/null +++ b/interpolation.html @@ -0,0 +1,144 @@ + + + + + + + Interpolation — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Interpolation

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/loggers.html b/loggers.html new file mode 100644 index 00000000..f9066f08 --- /dev/null +++ b/loggers.html @@ -0,0 +1,144 @@ + + + + + + + Loggers — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Loggers

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/loss.html b/loss.html new file mode 100644 index 00000000..6a387184 --- /dev/null +++ b/loss.html @@ -0,0 +1,144 @@ + + + + + + + Loss — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Loss

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/maps.html b/maps.html new file mode 100644 index 00000000..5dcc64de --- /dev/null +++ b/maps.html @@ -0,0 +1,144 @@ + + + + + + + Maps — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Maps

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 00000000..d63f1607 Binary files /dev/null and b/objects.inv differ diff --git a/ode.html b/ode.html new file mode 100644 index 00000000..8d1fc211 --- /dev/null +++ b/ode.html @@ -0,0 +1,144 @@ + + + + + + + ODE — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

ODE

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/operators.html b/operators.html new file mode 100644 index 00000000..940806cc --- /dev/null +++ b/operators.html @@ -0,0 +1,144 @@ + + + + + + + Operators — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Operators

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/physics.html b/physics.html new file mode 100644 index 00000000..9cc42ebd --- /dev/null +++ b/physics.html @@ -0,0 +1,144 @@ + + + + + + + Physics — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Physics

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/plot.html b/plot.html new file mode 100644 index 00000000..41221f7a --- /dev/null +++ b/plot.html @@ -0,0 +1,144 @@ + + + + + + + Plot — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Plot

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/problem.html b/problem.html new file mode 100644 index 00000000..1f835651 --- /dev/null +++ b/problem.html @@ -0,0 +1,144 @@ + + + + + + + Problem — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Problem

+
+ + +
+
+
+ +
+ +
+

© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
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+ + + + \ No newline at end of file diff --git a/slim/benchmarks.html b/slim/benchmarks.html new file mode 100644 index 00000000..a4db766c --- /dev/null +++ b/slim/benchmarks.html @@ -0,0 +1,151 @@ + + + + + + + Benchmarks — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + +
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Benchmarks

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

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+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file diff --git a/slim/index.html b/slim/index.html new file mode 100644 index 00000000..cc325df7 --- /dev/null +++ b/slim/index.html @@ -0,0 +1,225 @@ + + + + + + + SLiM: Structured Linear Maps — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
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SLiM: Structured Linear Maps

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This package provides a suite of structured linear maps which can be used as drop-in replacements for PyTorch’s nn.Linear module. Recent work viewing neural networks from a dynamical systems perspective has introduced a host of parametrizations for the basic linear maps which are subcomponents of neural networks. Such parametrizations may enhance the stability of learning, and embed models with inductive priors that encode domain application knowledge. This package is an effort to collect these all in one place with a common API to facilitate rapid exploration.

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Note

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We encourage folks to contribute any new structured linear maps as feature requests.

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Linear Map

class

Orthogonal

OrthogonalLinear

L0

L0Linear

Butterfly

ButterflyLinear

Spectral

SpectralLinear

Schur Decomposition

SchurDecompositionLinear

Lasso

LassoLinear

Symplectic

SymplecticLinear

AntiSymmetric

SkewSymmetricLinear

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Benchmarks

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Sequence to Classification:

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Point to Classification:

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Sequence to Regression:

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Point to Regression:

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Dynamics:

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  • Building models

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Docs:

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

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+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file diff --git a/slim/linear.html b/slim/linear.html new file mode 100644 index 00000000..8f6ce37f --- /dev/null +++ b/slim/linear.html @@ -0,0 +1,153 @@ + + + + + + + Linear — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
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Linear

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file diff --git a/slim/rnn.html b/slim/rnn.html new file mode 100644 index 00000000..9cf70e1a --- /dev/null +++ b/slim/rnn.html @@ -0,0 +1,153 @@ + + + + + + + RNN — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
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RNN

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file diff --git a/solvers.html b/solvers.html new file mode 100644 index 00000000..e95dce6a --- /dev/null +++ b/solvers.html @@ -0,0 +1,144 @@ + + + + + + + Solvers — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
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Solvers

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

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+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file diff --git a/trainer.html b/trainer.html new file mode 100644 index 00000000..4f23958e --- /dev/null +++ b/trainer.html @@ -0,0 +1,144 @@ + + + + + + + Trainer — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
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Trainer

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file diff --git a/visuals.html b/visuals.html new file mode 100644 index 00000000..f60d8976 --- /dev/null +++ b/visuals.html @@ -0,0 +1,144 @@ + + + + + + + Visuals — NeuroMANCER 1.3.3 documentation + + + + + + + + + + + + + + + + + + + + + +
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Visuals

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© Copyright 2023, Aaron Tuor, Jan Drgona, Mia Skomski, Stefan Dernbach, James Koch, Zhao Chen, Christian Møldrup Legaard, Draguna Vrabie, Madelyn Shapiro.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + \ No newline at end of file