nengo-dl 3.6.0

Deep learning integration for Nengo

Deep learning integration for Nengo

NengoDL is a simulator for Nengo models. That means it takes a Nengo network as input, and allows the user to simulate that network using some underlying computational framework (in this case, TensorFlow).

In practice, what that means is that the code for constructing a Nengo model is exactly the same as it would be for the standard Nengo simulator. All that changes is that we use a different Simulator class to execute the model.

For example:

import nengo
import nengo_dl
import numpy as np

with nengo.Network() as net:
    inp = nengo.Node(output=np.sin)
    ens = nengo.Ensemble(50, 1, neuron_type=nengo.LIF())
    nengo.Connection(inp, ens, synapse=0.1)
    p = nengo.Probe(ens)

with nengo_dl.Simulator(net) as sim: # this is the only line that changes
    sim.run(1.0)

print(sim.data[p])

However, NengoDL is not simply a duplicate of the Nengo simulator. It also adds a number of unique features, such as:

• optimizing the parameters of a model through deep learning training methods (using the Keras API)

• faster simulation speed, on both CPU and GPU

• automatic conversion from Keras models to Nengo networks

• inserting TensorFlow code (individual functions or whole network architectures) directly into a Nengo model

If you are interested in NengoDL you may also be interested in KerasSpiking, a companion project to NengoDL that has a more minimal feature set but integrates even more transparently with the Keras API. See this page for a more detailed comparison between the two projects.

Documentation

Check out the documentation for

• Installation instructions

• Details on the unique features of NengoDL

• Tutorial for new users with a TensorFlow background

• Tutorial for new users with a Nengo background

• More in-depth examples

• API reference

Release history

3.6.0 (January 26, 2023)

Compatible with Nengo 3.0 - 3.2

Compatible with TensorFlow 2.3 - 2.11

Added

• Included tensorflow-macos in the alternative tensorflow package names checked during installation. (#228)

• Added support for groups parameter to ConvertConv. (#223)

Changed

• Pinned TensorFlow version to <2.11 on Windows. As of 2.11 the TensorFlow package for Windows is maintained by a third party (Intel), and there are currently bugs in that package affecting functionality that is required by NengoDL. (#229)

Removed

• Removed support for “graph mode” (i.e., running with tf.compat.v1.disable_eager_execution()). TensorFlow is no longer supporting this functionality, and it is increasingly buggy. Graph mode may still be faster for some models; if you need this functionality, try using a previous version of NengoDL. (#229)

• Dropped support for TensorFlow 2.2. The minimum supported version is now 2.3.4 (earlier 2.3.x versions should work as well, but TensorFlow may install an incompatible protobuf version that the user will need to manually correct). (#228)

3.5.0 (May 18, 2022)

Compatible with Nengo 3.0 - 3.2

Compatible with TensorFlow 2.2 - 2.9

Changed

• Dropped support for Python 3.6 and added support for 3.9 and 3.10. (#224)

3.4.4 (February 10, 2022)

Compatible with Nengo 3.0 - 3.2

Compatible with TensorFlow 2.2 - 2.8

Added

• Added support for nengo.transforms.ConvolutionTranspose. (#183)

3.4.3 (November 9, 2021)

Compatible with Nengo 3.0.0 - 3.1.0

Compatible with TensorFlow 2.2.0 - 2.7.0

Added

• Added support for TensorFlow 2.7.0. (#218)

Changed

• Increased minimum keras-spiking version to 0.3.0. (#219)

3.4.2 (August 12, 2021)

Compatible with Nengo 3.0.0 - 3.1.0

Compatible with TensorFlow 2.2.0 - 2.6.0

Added

• Added support for TensorFlow 2.6.0. (#216)

3.4.1 (May 28, 2021)

Compatible with Nengo 3.0.0 - 3.1.0

Compatible with TensorFlow 2.2.0 - 2.5.0

Added

• Added support for TensorFlow 2.5.0. (#212)

Fixed

• A more informative error message will be raised if a custom neuron build function returns the wrong number of values. (#199)

Removed

• Dropped support for Python 3.5 (which reached its end of life in September 2020). (#184)

3.4.0 (November 26, 2020)

Compatible with Nengo 3.0.0 - 3.1.0

Compatible with TensorFlow 2.2.0 - 2.4.0

Added

• Added support for KerasSpiking layers in the Converter. (#182)

• Added support for tf.keras.layers.TimeDistributed in the Converter. (#182)

• Added support for TensorFlow 2.4. (#185)

• Added support for Nengo 3.1. (#187)

Changed

• Minor improvements to build speed by building constants outside of TensorFlow. (#173)

• Support for PES implementation changes in Nengo core (see #1627 and #1640). (#181)

Fixed

• Global default Keras dtype will now be reset correctly when an exception occurs in a Simulator method outside the with Simulator context. (#173)

• Support new LinearFilter step type introduced in Nengo core (see #1629). (#173)

• Fixed a bug when slicing multi-dimensional Signals (e.g. Ensemble encoders). (#181)

• Fixed a bug when loading weights saved in a different Python version. (#187)

3.3.0 (August 14, 2020)

Compatible with Nengo 3.0.0

Compatible with TensorFlow 2.2.0 - 2.3.0

Added

• Added support for new Nengo core NeuronType state implementation. (#159)

• Compatible with TensorFlow 2.3.0. (#159)

• Added support for nengo.Tanh, nengo.RegularSpiking, nengo.StochasticSpiking, and nengo.PoissonSpiking neuron types. (#159)

• Added nengo_dl.configure_settings(learning_phase=True/False) configuration option. This mimics the previous behaviour of tf.keras.backend.learning_phase_scope (which was deprecated by TensorFlow). That is, if you would like to override the default behaviour so that, e.g., sim.predict runs in training mode, set nengo_dl.configure_settings(learning_phase=True). (#163)

Changed

• Simulator.evaluate no longer prints any information to stdout in TensorFlow 2.2 in graph mode (due to a TensorFlow issue, see https://github.com/tensorflow/tensorflow/issues/39456). Loss/metric values will still be returned from the function as normal. (#153)

• A warning will now be raised if activation types are passed to Converter.swap_activations that aren’t actually in the model. (#168)

• Updated TensorFlow installation instruction in documentation. (#170)

• NengoDL will now use TensorFlow’s eager mode by default. The previous graph-mode behaviour can be restored by calling tf.compat.v1.disable_eager_execution(), but we cannot guarantee that that behaviour will be supported in the future. (#163)

• NengoDL will now use TensorFlow’s “control flow v2” by default. The previous behaviour can be restored by calling tf.compat.v1.disable_control_flow_v2(), but we cannot guarantee that that behaviour will be supported in the future. (#163)

• NengoDL will now default to allowing TensorFlow’s “soft placement” logic, meaning that even if you specify an explicit device like "/gpu:0", TensorFlow may not allocate an op to that device if there isn’t a compatible implementation available. The previous behaviour can be restored by calling tf.config.set_soft_device_placement(False). (#163)

• Internal NengoDL OpBuilder classes now separate the “pre build” stage from OpBuilder.__init__ (so that the same OpBuilder class can be re-used across multiple calls, rather than instantiating a new OpBuilder each time). Note that this has no impact on front-end users, this is only relevant to anyone that has implemented a custom build class. The logic that would previously have gone in OpBuilder.__init__ should now go in OpBuilder.build_pre. In addition, the ops argument has been removed from OpBuilder.build_pre; that will be passed to OpBuilder.__init__ ( and will be available in build_pre as self.ops). Similarly, the ops and config argument have been removed from build_post, and can instead be accessed through self.ops/config. (#163)

• Minimum TensorFlow version is now 2.2.0. (#163)

Fixed

• Support Sparse transforms in Simulator.get_nengo_params. (#149)

• Fixed bug in TensorGraph log message when logging was enabled. (#151)

• Updated the KerasWrapper class in the tensorflow-models example to fix a compatibility issue in TensorFlow 2.2. (#153)

• Handle Nodes that are not connected to anything else, but are probed (this only occurs in Nengo>=3.1.0). (#159)

• More robust support for converting nested Keras models in TensorFlow 2.3. (#161)

• Fix bug when probing slices of certain probeable attributes (those that are directly targeting a Signal in the model). (#164)

Removed

• Removed nengo_dl.utils.print_op (use tf.print instead). (#163)

3.2.0 (April 2, 2020)

Compatible with Nengo 3.0.0

Compatible with TensorFlow 2.0.0 - 2.2.0

Added

• Added nengo_dl.LeakyReLU and nengo_dl.SpikingLeakyReLU neuron models. (#126)

• Added support for leaky ReLU Keras layers to nengo_dl.Converter. (#126)

• Added a new remove_reset_incs graph simplification step. (#129)

• Added support for UpSampling layers to nengo_dl.Converter. (#130)

• Added tolerance parameters to nengo_dl.Converter.verify. (#130)

• Added scale_firing_rates option to nengo_dl.Converter. (#134)

• Added Converter.layers attribute which will map Keras layers/tensors to the converted Nengo objects, to make it easier to access converted components. (#134)

• Compatible with TensorFlow 2.2.0. (#140)

• Added a new synapse argument to the Converter, which can be used to automatically add synaptic filters on the output of neural layers during the conversion process. (#141)

• Added a new example demonstrating how to use the NengoDL Converter to convert a Keras model to a spiking Nengo network. (#141)

Changed

• Re-enabled the remove_constant_copies graph simplification by default. (#129)

• Reduced the amount of state that needs to be stored in the simulation. (#129)

• Added more information to the error message when loading saved parameters that don’t match the current model. (#129)

• More efficient implementation of convolutional biases in the Converter. (#130)

• Saved simulator state will no longer be included in Simulator.keras_model.weights. This means that Simulator.keras_model.save/load_weights will not include the saved simulator state, making it easier to reuse weights between models (as long as the models have the same weights, they do not need to have the same state variables). Simulator.save/load_params(..., include_state=True) can be used to explicitly save the simulator state, if desired. (#140)

• Model parameters (e.g., connection weights) that are not trainable (because they’ve been marked non-trainable by user or targeted by an online learning rule) will now be treated separately from simulator state. For example, Simulator.save_params(..., include_state=False) will still include those parameters, and the results of any online learning will persist between calls even with stateful=False. (#140)

• Added include_probes, include_trainable, and include_processes arguments to Simulator.reset to provide more fine-grained control over Simulator resetting. This replicates the previous functionality in Simulator.soft_reset. (#139)

• More informative error messages when accessing invalid Simulator functionality after the Simulator has been closed. (#139)

• A warning is now raised when the number of input data items passed to the simulator does not match the number of input nodes, to help avoid unintentionally passing data to the wrong input node. This warning can be avoided by passing data for all nodes, or using the dictionary input style if you want to only pass data for a specific node. (#139)

• Dictionaries returned by sim.predict/evaluate will now be ordered. (#141)

Fixed

• Fixed bug in error message when passing data with batch size less than Simulator minibatch size. (#139)

• More informative error message when validation_split does not result in batch sizes evenly divisible by minibatch size. (#139)

• Added tensorflow-cpu distributions to installation checks (so Nengo DL will not attempt to reinstall TensorFlow if tensorflow-cpu is already installed). (#142)

• Fixed bug when applying the Converter to Keras models that re-use intermediate layers as output layers. (#137)

• Fixed bug in conversion of Keras Dense layers with non-native activation functions. (#144)

Deprecated

• Renamed Simulator.save/load_params include_non_trainable parameter to include_state. (#140)

• Simulator.soft_reset has been deprecated. Use Simulator.reset(include_probes=False, include_trainable=False, include_processes=False) instead. (#139)

3.1.0 (March 4, 2020)

Compatible with Nengo 3.0.0

Compatible with TensorFlow 2.0.0 - 2.1.0

Added

• Added inference_only=True option to the Converter, which will allow some Layers/parameters that cannot be fully converted to native Nengo objects to be converted in a way that only matches the inference behaviour of the source Keras model (not the training behaviour). (#119)

Changed

• Improved build time of networks containing lots of TensorNodes. (#119)

• Improved memory usage of build process. (#119)

• Saved simulation state may now be placed on GPU (this should improve the speed of state updates, but may slightly increase GPU memory usage). (#119)

• Changed Converter freeze_batchnorm=True option to inference_only=True (effect of the parameter is the same on BatchNormalization layers, but also has broader effects). (#119)

• The precision of the Nengo core build process will now be set based on the nengo_dl.configure_settings(dtype=...) config option. Note that this will override the default precision set in nengo.rc. (#119)

• Minimum Numpy version is now 1.16.0 (required by TensorFlow). (#119)

• Added support for the new transform=None default in Nengo connections (see Nengo#1591). Note that this may change the number of trainable parameters in a network as the scalar default transform=1 weights on non-Ensemble connections will no longer be present. (#128)

Fixed

• Provide a more informative error message if Layer shape_in/shape_out contains undefined (None) elements. (#119)

• Fixed bug in Converter when source model contains duplicate nodes. (#119)

• Fixed bug in Converter for Concatenate layers with axis != 1. (#119)

• Fixed bug in Converter for models containing passthrough Input layers inside submodels. (#119)

• Keras Layers inside TensorNodes will be called with the training argument set correctly (previously it was always set to the default value). (#119)

• Fixed compatibility with progressbar2 version 3.50.0. (#136)

3.0.0 (December 17, 2019)

Compatible with Nengo 3.0.0

Compatible with TensorFlow 2.0.0

There are a lot of breaking changes in NengoDL 3.0. See the migration guide for all the details.

Added

• Keras Layer classes can now be used with nengo_dl.Layer/tensor_layer.

• TensorGraph can now be used as a Keras Layer.

• Added Simulator.predict/evaluate/fit functions, which implement the Keras Model API.

• Added a warning that changing the TensorFlow seed (e.g. on Simulator.reset) will not affect any existing TensorFlow operations (this was always true in TensorFlow, the warning is just to help avoid confusion).

• Added TensorGraph.build_inputs, which will return a set of Keras Input layers that can be used as input to the TensorGraph layer itself.

• Added nengo_dl.callbacks.TensorBoard. This is identical to tf.keras.callbacks.TensorBoard, except it will also perform profiling during inference (rather than only during training).

• Added stateful option to Simulator.run which can be set to False to avoid updating the saved simulation state at the end of a run.

• Added nengo_dl.configure_settings(stateful=False) option to avoid building the parts of the model responsible for preserving state between executions (this will override any stateful=True arguments in individual functions).

• Added nengo_dl.configure_settings(use_loop=False) option to avoid building the simulation inside a symbolic TensorFlow loop. This may improve simulation speed, but the simulation can only run for exactly unroll_simulation timesteps.

• NengoDL now requires jinja2 (used to template some of the docstrings).

• Added an inputs argument to Simulator.check_gradients, which can be used to control the initial value of input Nodes during the gradient calculations.

• Added nengo_dl.Converter for automatically converting Keras models to native Nengo networks. See the documentation for more details.

• Added Legendre Memory Unit RNN example.

Changed

• Minimum TensorFlow version is now 2.0.0.

• Simulator.save/load_params now uses a single include_non_trainable=True/False (equivalent to the previous include_local). Trainable parameters will always be saved, so the include_global argument is removed.

• Standardized all signals/operations in a simulation to be batch-first.

• The dtype option is now specified as a string (e.g. "float32" rather than tf.float32).

• If the requested number of simulation steps is not evenly divisible by Simulator.unroll_simulation then probe values and sim.time/n_steps will be updated based on the number of steps actually run (rather than the requested number of steps). Note that these extra steps were also run previously, but their results were hidden from the user.

• Renamed TensorGraph.input_ph to TensorGraph.node_inputs.

• Simulator.time/n_steps are now read-only.

• Simulator.n_steps/time are now managed as part of the op graph, rather than manually in the Simulator.

• Renamed nengo_dl.objectives to nengo_dl.losses (to align with tf.losses).

• nengo_dl.objectives.Regularize now takes two arguments (y_true and y_pred) in order to be compatible with the tf.losses.Loss API (y_true is ignored).

• The remove_constant_copies simplification step is now disabled by default. In certain situations this could be an unsafe manipulation (specifically, when using Simulator.save/load_params it could change which parameters are saved). It can be manually re-enabled through the simplifications configuration option.

• Simulator.check_gradients now only accepts an optional list of Probes (no longer accepts arbitrary Tensors).

• Eager execution is no longer disabled on import (it is still disabled within the Simulator context, for performance reasons; see https://github.com/tensorflow/tensorflow/issues/33052).

• nengo_dl.tensor_layer(x, func, ...) now passes any extra kwargs to the nengo_dl.TensorNode constructor (rather than to func). If you need to pass information to func consider using partial functions (e.g. tensor_layer(functools.partial(x, func, arg=5), ...) or a callable class (e.g., tensor_layer(x, MyFunc(arg=5), ...)). When using Keras Layers with nengo_dl.tensor_layer, a fully instantiated Layer object should be passed rather than a Layer class (e.g., use tensor_layer(x, tf.keras.layers.Dense(units=10), ...) instead of tensor_layer(x, tf.keras.layers.Dense, units=10)).

• benchmarks.run_profile now uses the TensorBoard format when profiling, see the documentation for instructions on how to view this information (the information is the same, it is just accessed through TensorBoard rather than requiring that it be loaded directly in a Chrome browser).

• nengo_dl.TensorNode now takes shape_in and shape_out arguments (which specify a possibly multidimensional shape), rather than the scalar size_in and size_out.

• TensorNode functions no longer use the pre_build/post_build functionality. If you need to implement more complex behaviour in a TensorNode, use a custom Keras Layer subclass instead. For example, TensorNodes Layers can create new parameter Variables inside the Layer build method.

• TensorNode now has an optional pass_time parameter which can be set to False to disable passing the current simulation time to the TensorNode function.

• Added nengo_dl.Layer. Similar to the old nengo_dl.tensor_layer, this is a wrapper for constructing TensorNodes, but it mimics the new tf.keras.layers.Layer API rather than the old tf.layers.

• TensorFlow’s “control flow v2” is disabled on import, for performance reasons; see https://github.com/tensorflow/tensorflow/issues/33052.

• Renamed nengo_dl.objectives.mse to nengo_dl.losses.nan_mse (to emphasize the special logic it provides for nan targets).

• Connections created by nengo_dl.Layer/tensor_layer will be marked as non-trainable by default.

• Updated all documentation and examples for the new syntax (in particular, see the updated Coming from TensorFlow tutorial and TensorFlow/Keras integration example, and the new Tips and tricks page).

• The training/inference build logic (e.g., swapping spiking neurons with rate implementations) can be overridden by setting the global Keras learning phase (tf.keras.backend.set_learning_phase) before the Simulator is constructed.

• Increased minimum Nengo core version to 3.0.0.

• Reduced size of TensorFlow constants created by Reset ops.

• DotInc operators with different signal sizes will no longer be merged (these merged operators had to use a less efficient sparse matrix multiplication, and in general this cost outweighed the benefit of merging).

• Trainability can now be configured in the config of subnetworks. This replaces the ability to mark Networks as (non)trainable. See the updated documentation for details.

• Training/evaluation target data can now have a different number of timesteps than input data (as long as it aligns with the number of timesteps expected by the loss function).

• Whether or not to display progress bars in Simulator.run and Simulator.run_steps now defaults to the value of Simulator(..., progress_bar=x).

Fixed

• Fixed bug due to non-determinism of Process state ordering in Python 3.5.

• Nested Keras layers passed to TensorNode will be rebuilt correctly if necessary.

Deprecated

• nengo_dl.tensor_layer has been deprecated. Use nengo_dl.Layer instead; tensor_layer(x, func, **kwargs) is equivalent to Layer(func)(x, **kwargs).

Removed

• Removed the session_config configuration option. Use the updated TensorFlow config system instead.

• Removed the deprecated nengo_dl.Simulator(..., dtype=...) argument. Use nengo_dl.configure_settings(dtype=...) instead.

• Removed the deprecated Simulator.run(..., input_feeds=...) argument. Use Simulator.run(..., data=...) instead.

• Removed the Simulator.sess attribute (Sessions are no longer used in TensorFlow 2.0). The underlying Keras model (Simulator.keras_model) should be used as the entrypoint into the engine underlying a Simulator instead.

• Removed the Simulator.loss function (use Simulator.compile and Simulator.evaluate to compute loss values instead).

• Removed the Simulator.train function (use Simulator.compile and Simulator.fit to optimize a network instead).

• Removed the nengo_dl.objectives.Regularize(weight=x, ...) argument. Use the Simulator.compile(loss_weights=...) functionality instead.

• Removed the Simulator.run(..., extra_feeds=...) argument. TensorFlow 2.0 no longer uses the Session/feed execution model.

• Removed Simulator.run_batch. This functionality is now managed by the underlying Simulator.keras_model.

• Removed TensorGraph.training_step. The training step is now managed by Keras.

• Removed TensorGraph.build_outputs and TensorGraph.build_optimizer_func. Building loss functions/optimizers is now managed by Keras.

• Removed nengo_dl.utils.find_non_differentiable (this no longer works in TF2.0’s eager mode).

• Removed Simulator(..., tensorboard=...) argument. Use the Keras TensorBoard callback approach for TensorBoard logging instead (see tf.keras.callbacks.TensorBoard or nengo_dl.callbacks.NengoSummaries).

• NengoDL will no longer monkeypatch fix the tf.dynamic_stitch gradients on import. The gradients are still incorrect (see https://github.com/tensorflow/tensorflow/issues/7397), but we no longer use this operation within NengoDL so we leave it up to the user to fix it in their own code if needed.

• Removed benchmarks.matmul_vs_reduce. We use matmul for everything now, so this comparison is no longer necessary.

• Removed utils.minibatch_generator (training/inference loops are now managed by Keras).

2.2.2 (November 20, 2019)

Compatible with Nengo 2.8.0 - 3.0.0

Compatible with TensorFlow 1.4.0 - 2.0.0

Fixed

• Compatibility with Nengo 3.0 release

2.2.1 (October 2, 2019)

Compatible with Nengo 2.8.0

Compatible with TensorFlow 1.4.0 - 2.0.0

Changed

• Update testing framework to use new nengo pytest ecosystem (pytest-rng, pytest-allclose, and pytest-nengo)

• Disable TensorFlow 2.0 behaviour (e.g. control flow v2) by default. This will be re-enabled when full TensorFlow 2.0 support is added.

Fixed

• Fixed tensorflow-gpu installation check in pep517-style isolated build environments.

2.2.0 (July 24, 2019)

Compatible with Nengo 2.8.0

Compatible with TensorFlow 1.4.0 - 2.0.0

Added

• Added a new example demonstrating how to integrate a Keras model with NengoDL (thanks to new contributor @NickleDave).

• Added support for TensorFlow 2.0 (pre-release).

• Added support for sparse transforms (see https://github.com/nengo/nengo/pull/1532).

• Added support for stateful Processes (see https://github.com/nengo/nengo/pull/1387).

Changed

• The default session will now be set to the NengoDL session before calling TensorNodes’ post_build function.

• Renamed the pytest unroll_simulation argument to unroll-simulation.

• Switched to nengo-bones templating system for TravisCI config/scripts.

• NengoDL will disable eager execution on import (and will probably not work properly if it is manually re-enabled).

• Increased minimum numpy version to 1.14.5 (required by TensorFlow 1.14).

• Minimum Nengo version is now 2.8.0.

• Update LinearFilter synapse implementation to match recent changes in Nengo core (see https://github.com/nengo/nengo/pull/1535).

Fixed

• Fixed TensorFlow seeding so that randomness can be reliably controlled by setting the Simulator seed.

• Improved robustness of tensorflow-gpu installation check (in particular, it will now correctly detect GPU dists installed through conda).

• Fixed inspection of TensorNode.tensor_func arguments for partial functions.

• Simulator seed will now be deterministic for a given top-level Network seed.

• Raise a more informative error if user attempts to pickle a Simulator (this is not possible to do with TensorFlow sessions; see the documentation for other methods of saving/loading a NengoDL model).

Removed

• NengoDL no longer supports Python 3.4 (official support for 3.4 ended in March 2019).

2.1.1 (January 11, 2019)

Added

• Added nengo_dl.obj as a shortcut alias for nengo_dl.objectives.

• Added tutorial for Nengo users coming to NengoDL

• Added tutorial for TensorFlow users coming to NengoDL

Changed

• Increased minimum progressbar2 version to 3.39.0.

• We now only provide sdist releases, not bdist_wheel. Due to the way the TensorFlow packages are organized, bdist_wheel forces any existing TensorFlow installations (e.g. tensorflow-gpu or tf-nightly) to be overwritten by tensorflow, which we don’t want to do.

Removed

• Removed the nef-init tutorial (replaced by the new from-nengo tutorial).

2.1.0 (December 5, 2018)

Added

• Added a built-in objective to assist in applying regularization during training.

• Added keep_history config option, which can be set to False on Probes if only the data from the most recent simulation step is desired (as opposed to the default behaviour of keeping the data from all steps).

Changed

• Moved utils.mse to objectives.mse.

• sim.loss will now apply nengo_dl.objectives.mse to all probes in data if no explicit objective is given (mirroring the default behaviour in sim.train).

• The Spaun benchmark network will now be installed through pip rather than manually cloning and importing the repo.

Fixed

• Fixed objective argument parsing if objective is a callable class or method.

• Fixed bug in sim.train 1-step synapse warning when explicitly specifying n_steps (rather than passing in data).

Deprecated

• Passing "mse" as the objective in sim.train/sim.loss is no longer supported. Use the function nengo_dl.objectives.mse instead.

2.0.0 (November 23, 2018)

Breaking API changes

• sim.train and sim.loss now accept a single data argument, which combines the previous inputs and targets arguments. For example,

  sim.train({my_node: x}, {my_probe: y}, ...)

  is now equivalent to

  sim.train({my_node: x, my_probe: y}, ...)

  The motivation for this change is that not all objective functions require target values. Switching to the more generic data argument simplifies the API and makes it more flexible, allowing users to specify whatever training/loss data is actually required.

• The objective argument in sim.train/sim.loss is now always specified as a dictionary mapping probes to objective functions. Note that this was available but optional previously; it was also possible to pass a single value for the objective function, which would be applied to all probes in targets. The latter is no longer supported. For example,

  sim.train(..., objective="mse")

  must now be explicitly specified as

  sim.train(..., objective={my_probe: "mse"})

  The motivation for this change is that, especially with the other new features introduced in the 2.0 update, there were a lot of different ways to specify the objective argument. This made it somewhat unclear how exactly this argument worked, and the automatic “broadcasting” was also ambiguous (e.g., should the single objective be applied to each probe individually, or to all of them together?). Making the argument explicit helps clarify the mental model.

Added

• An integer number of steps can now be passed for the sim.loss/sim.train data argument, if no input/target data is required.

• The objective dict in sim.train/sim.loss can now contain tuples of probes as the keys, in which case the objective function will be called with a corresponding tuple of probe/target values as each argument.

• Added the sim.run_batch function. This exposes all the functionality that the sim.run/sim.train/sim.loss functions are based on, allowing advanced users full control over how to run a NengoDL simulation.

• Added option to disable progress bar in sim.train and sim.loss.

• Added training argument to sim.loss to control whether the loss is evaluated in training or inference mode.

• Added support for the new Nengo Transform API (see https://github.com/nengo/nengo/pull/1481).

Changed

• Custom objective functions passed to sim.train/sim.loss can now accept a single argument (my_objective(outputs): ... instead of my_objective(outputs, targets): ...) if no target values are required.

• utils.minibatch_generator now accepts a single data argument rather than inputs and targets (see discussion in “Breaking API changes”).

• sim.training_step is now the same as tf.train.get_or_create_global_step().

• Switched documentation to new nengo-sphinx-theme.

• Reorganized documentation into “User guide” and “API reference” sections.

• Improve build speed of models with large constants (#69)

• Moved op-specific merge logic into the OpBuilder classes.

Fixed

• Ensure that training step is always updated before TensorBoard events are added (previously it could update before or after depending on the platform).

Deprecated

• The sim.run input_feeds argument has been renamed to data (for consistency with other simulator functions).

Removed

• NengoDL no longer supports Python 2 (see https://python3statement.org/ for more information)

1.2.1 (November 2, 2018)

Added

• Added a warning if users run one-timestep training with a network containing synaptic filters.

Changed

• Test Simulator parameters are now controlled through pytest arguments, rather than environment variables.

• Disable INFO-level TensorFlow logging (from C side) on import. Added a NengoDL log message indicating the device the simulation will run on, as a more concise replacement.

• Boolean signals are now supported (#61)

Fixed

• Avoid backpropagating NaN gradients from spiking neurons.

• Fixed an error that was thrown when calling get_tensor on a Signal that was first initialized inside the Simulation while loop (#56)

• Allow TensorNodes to run in Nengo GUI.

• Avoid bug in TensorFlow 1.11.0 that prevents certain models from running (see https://github.com/tensorflow/tensorflow/issues/23383). Note that this doesn’t prevent this from occurring in user models, as we cannot control the model structure there. If your model hangs indefinitely when you call sim.train, try downgrading to TensorFlow 1.10.0.

• Ensure that sim.training_step is always updated after the optimization step (in certain race conditions it would sometimes update part-way through the optimization step).

1.2.0 (September 5, 2018)

Added

• NengoDL will now automatically use a rate-based approximation to compute the gradient for spiking neuron types, if one is known (no more need to manually swap neuron types for training and inference).

• Added nengo_dl.configure_settings(inference_only=True) option, which will build the network in inference-only mode. This will slightly improve the inference speed of the simulation, but the network will not be trainable.

• Added nengo_dl.configure_settings(lif_smoothing=x) option, which will control how much smoothing is applied to the LIF function during gradient calculations (if any).

• Added documentation on the various NengoDL config options.

• Added better validation for TensorNode output when size_out != None (#51)

Changed

• More informative error message if the user tries to pass target values for a probe that isn’t used in the objective function.

• Switched to ADD_N gradient accumulation (from TREE); this will increase the memory usage during training, but improve performance.

• Revert to Timeline profiling method. tf.profiler can produce incorrect output, and isn’t maintained any more (https://github.com/tensorflow/tensorflow/issues/15214#issuecomment-382442357)

• Reduce memory usage during training by caching temporary variables used when computing ScatterUpdate gradient.

• Increase minimum TensorFlow version to 1.4.0.

• Increased minimum NumPy version to 1.12.1 (required by TensorFlow)

• Sort write signals as well as reads during graph optimization (encourages tighter partitioning, which can improve training/inference speed).

• Moved configure_settings from utils.py to config.py.

Fixed

• Fixed a bug where nengo_dl.dists.VarianceScaling(..., distribution="normal") did not respect the seed if one was given.

Deprecated

• The Simulator(dtype=...) argument has been deprecated; use nengo_dl.configure_settings(dtype=...) instead. Will be removed in 1.3.0.

1.1.0 (July 24, 2018)

Added

• The default TensorFlow Session is now set to the underlying Simulator session within the Simulator context.

• Added CLI for benchmarks.py

• Added sim.freeze_params tool, to more easily extract model parameters for reuse in different Simulators.

• Added documentation on saving and loading model parameters.

• Added Spaun example in benchmarks.py

Changed

• Move tensorflow-gpu installation check to Simulator init, and only apply if device=None.

• Switched to pylint for style checks.

• TensorFlow INFO-level log messages are now disabled by default on import

• All previous releases now tracked in documentation

• Updated spiking MNIST example to simplify and improve performance.

• Passing unknown configuration options to nengo_dl.configure_settings will now give a more explicit error message.

• Improved speed of parameter fetching though get_nengo_params

• Raise a warning if user tries to train a network with non-differentiable elements (requires tensorflow>=1.9.0)

• Improved accuracy of SoftLIFRate implementation for small values (#45)

• Simplified how TensorSignals are loaded into the TensorFlow graph

Fixed

• Better handling of Simulator errors not associated with a specific op (fixes #41)

• Fixed node outputs changing after simulator is built (fixes #4)

• Fixed some broken cross references in the documentation

• Fixed several edge cases for get_nengo_params; don’t use trained gains for direct neuron connections, error raised if get_nengo_params applied to an Ensemble with Direct neurons

• Compatible with tensorflow==1.9.0 release

• Fixed bug in nengo_dl.configure_settings(session_config=...) when passing a pre-build model to the Simulator instead of a Network

• Fixed TensorFlow version comparisons for 1.10.0

Deprecated

• Simulator.trange argument dt has been deprecated (replaced with sample_every, see https://github.com/nengo/nengo/pull/1384)

Removed

• Removed nengo_dl.DATA_DIR constant

• Removed benchmarks.compare_backends (use whitepaper2018_plots.py:compare_backends instead)

• Removed ghp-import dependency

1.0.0 (May 30, 2018)

Added

• User can now directly specify the output error gradient, rather than using targets/objective (useful for when you have some external process for computing error that is not easy to implement as an objective function). See the documentation for details.

• Added NengoDL white paper

Changed

• Extra requirements for documentation/testing are now stored in setup.py’s extra_requires instead of requirements-*.txt. For example, instead of doing pip install -r requirements-test.txt, instead use pip install nengo-dl[tests] (or pip install -e .[tests] for a developer installation).

• Improved efficiency of PES implementation

Removed

• Removed sphinxcontrib-versioning dependency for building documentation

0.6.2 (May 4, 2018)

Added

• Added sim.get_nengo_params function to more easily extract model parameters for reuse when building different models.

• Added Simulator(..., progress_bar=False) option to disable the progress information printed to console when the network is building.

• TensorFlow session config options can now be set using nengo_dl.configure_settings (e.g., nengo_dl.configure_settings(session_config={"gpu_options.allow_growth": True}))

• The signal sorting/graph simplificaton functions can now be configured through nengo_dl.configure_settings

• Added extra_feeds parameter to sim.run/train/loss, which can be used to feed Tensor values directly into the TensorFlow session

Changed

• Improved speed of PES implementation by adding a custom operator.

• Renamed project from nengo_dl to nengo-dl (to be more consistent with standard conventions). This only affects the display name of the project on PyPI/GitHub, and the documentation now resides at https://www.nengo.ai/nengo-dl/; there are no functional changes to user code.

• Minor efficiency improvements to graph planner

• Avoid using tf.constant, to get around TensorFlow’s 2GB limit on graph size when building large models

Fixed

• Checking nengo_dl version without nengo installed will no longer result in an error.

• Updated progress bar to work with progressbar2>=3.37.0

• Updated PES implementation to work with generic synapse types (see https://github.com/nengo/nengo/pull/1095)

• Fixed installation to work with pip>=10.0

• Fixed bug when using a TensorNode with a pre_build function and size_in==0

0.6.1 (March 7, 2018)

Added

• Added TensorFlow implementation for nengo.SpikingRectifiedLinear neuron type.

Changed

• Optimizer variables (e.g., momentum values) will only be initialized the first time that optimizer is passed to sim.train. Subsequent calls to sim.train will resume with the values from the previous call.

• Low-level simulation input/output formats have been reworked to make them slightly easier to use (for users who want to bypass sim.run or sim.train and access the TensorFlow session directly).

• Batch dimension will always be first (if present) when checking model parameters via sim.data.

• TensorFlow ops created within the Simulator context will now default to the same device as the Simulator.

• Update minimum Nengo version to 2.7.0

Fixed

• Better error message if training data has incorrect rank

• Avoid reinstalling TensorFlow if one of the nightly build packages is already installed

• Lowpass synapse can now be applied to multidimensional inputs

• TensorNodes will no longer be built into the default graph when checking their output dimensionality.

Removed

• Removed utils.cast_dtype function

0.6.0 (December 13, 2017)

Added

• The SoftLIFRate neuron type now has an amplitude parameter, which scales the output in the same way as the new amplitude parameter in LIF/LIFRate (see Nengo PR #1325).

• Added progress_bar=False option to sim.run, which will disable the information about the simulation status printed to standard output (#17).

• Added progress bars for the build/simulation process.

• Added truncated backpropagation option to sim.train (useful for reducing memory usage during training). See the documentation for details.

Changed

• Changed the default tensorboard argument in Simulator from False to None

• Use the new tf.profiler tool to collect profiling data in sim.run_steps and sim.train when profile=True.

• Minor improvements to efficiency of build process.

• Minor improvements to simulation efficiency targeting small ops (tf.reshape/identity/constant).

• Process inputs are now reseeded for each input when batch processing (if seed is not manually set).

• Users can pass a dict of config options for the profile argument in run_steps/train, which will be passed on to the TensorFlow profiler; see the tf.profiler documentation for the available options.

Removed

• Removed backports.print_function dependency

Fixed

• Fixed a bug where input nodes that were only read as a view were not feedable

• Updated tensorflow-gpu installation check

• Improved numerical stability of LIFRate gradients (#26)

• Added more informative error message when data is provided with fewer items than sim.minibatch_size (#30)

0.5.2 (October 11, 2017)

Added

• TensorNode outputs can now define a post_build function that will be executed after the simulation is initialized (see the TensorNode documentation for details).

• Added functionality for outputting summary data during the training process that can be viewed in TensorBoard (see the sim.train documentation).

• Added some examples demonstrating how to use Nengo DL in a more complicated task using semantic pointers to encode/retrieve information

• Added sim.training_step variable which will track the current training iteration (can be used, e.g., for TensorFlow’s variable learning rate operations).

• Users can manually create tf.summary ops and pass them to sim.train summaries

• The Simulator context will now also set the default TensorFlow graph to the one associated with the Simulator (so any TensorFlow ops created within the Simulator context will automatically be added to the correct graph)

• Users can now specify a different objective for each output probe during training/loss calculation (see the sim.train documentation).

Changed

• Resetting the simulator now only rebuilds the necessary components in the graph (as opposed to rebuilding the whole graph)

• The default "mse" loss implementation will now automatically convert np.nan values in the target to zero error

• If there are multiple target probes given to sim.train/sim.loss the total error will now be summed across probes (instead of averaged)

Fixed

• sim.data now implements the full collections.Mapping interface

• Fixed bug where signal order was non-deterministic for Networks containing objects with duplicate names (#9)

• Fixed bug where non-slot optimizer variables were not initialized (#11)

• Implemented a modified PES builder in order to avoid slicing encoders on non-decoded PES connections

• TensorBoard output directory will be automatically created if it doesn’t exist

0.5.1 (August 28, 2017)

Changed

• sim.data[obj] will now return live parameter values from the simulation, rather than initial values from the build process. That means that it can be used to get the values of object parameters after training, e.g. sim.data[my_conn].weights.

• Increased minimum Nengo version to 2.5.0.

• Increased minimum TensorFlow version to 1.3.0.

0.5.0 (July 11, 2017)

Added

• Added nengo_dl.tensor_layer to help with the construction of layer-style TensorNodes (see the TensorNode documentation)

• Added an example demonstrating how to train a neural network that can run in spiking neurons

• Added some distributions for weight initialization to nengo_dl.dists

• Added sim.train(..., profile=True) option to collect profiling information during training

• Added new methods to simplify the Nengo operation graph, resulting in faster simulation/training speed

• The default graph planner can now be modified by setting the planner attribute on the top-level Network config

• Added TensorFlow implementation for general linear synapses

• Added backports.tempfile and backports.print_function requirement for Python 2.7 systems

Changed

• Increased minimum TensorFlow version to 1.2.0

• Improved error checking for input/target data

• Improved efficiency of stateful gradient operations, resulting in faster training speed

• The functionality for nengo_dl.configure_trainable has been subsumed into the more general nengo_dl.configure_settings(trainable=x). This has resulted in some small changes to how trainability is controlled within subnetworks; see the updated documentation for details.

• Calling Simulator.train/Simulator.loss no longer resets the internal state of the simulation (so they can be safely intermixed with calls to Simulator.run)

Deprecated

• The old step_blocks/unroll_simulation syntax has been fully deprecated, and will result in errors if used

Fixed

• Fixed bug related to changing the output of a Node after the model is constructed (#4)

• Order of variable creation is now deterministic (helps make saving/loading parameters more reliable)

• Configuring whether or not a model element is trainable does not affect whether or not that element is minibatched

• Correctly reuse variables created inside a TensorNode when unroll_simulation > 1

• Correctly handle probes that aren’t connected to any ops

• Swapped fan_in/fan_out in dists.VarianceScaling to align with the standard definitions

• Temporary patch to fix memory leak in TensorFlow (see #11273)

• Fixed bug related to nodes that had matching output functions but different size_out

• Fixed bug related to probes that do not contain any data yet

0.4.0 (June 8, 2017)

Added

• Added ability to manually specify which parts of a model are trainable (see the sim.train documentation)

• Added some code examples (see the docs/examples directory, or the pre-built examples in the documentation)

• Added the SoftLIFRate neuron type for training LIF networks (based on this paper)

Changed

• Updated TensorFuncParam to new Nengo Param syntax

• The interface for Simulator step_blocks/unroll_simulation has been changed. Now unroll_simulation takes an integer as argument which is equivalent to the old step_blocks value, and unroll_simulation=1 is equivalent to the old unroll_simulation=False. For example, Simulator(..., unroll_simulation=True, step_blocks=10) is now equivalent to Simulator(..., unroll_simulation=10).

• Simulator.train/Simulator.loss no longer require step_blocks (or the new unroll_simulation) to be specified; the number of steps to train across will now be inferred from the input data.

0.3.1 (May 12, 2017)

Added

• Added more documentation on Simulator arguments

Changed

• Improved efficiency of tree_planner, made it the new default planner

Fixed

• Correctly handle input feeds when n_steps > step_blocks

• Detect cycles in transitive planner

• Fix bug in uneven step_blocks rounding

• Fix bug in Simulator.print_params

• Fix bug related to merging of learning rule with different dimensionality

• Use tf.Session instead of tf.InteractiveSession, to avoid strange side effects if the simulator isn’t closed properly

0.3.0 (April 25, 2017)

Added

• Use logger for debug/builder output

• Implemented TensorFlow gradients for sparse Variable update Ops, to allow models with those elements to be trained

• Added tutorial/examples on using Simulator.train

• Added support for training models when unroll_simulation=False

• Compatibility changes for Nengo 2.4.0

• Added a new graph planner algorithm, which can improve simulation speed at the cost of build time

Changed

• Significant improvements to simulation speed

  • Use sparse Variable updates for signals.scatter/gather

  • Improved graph optimizer memory organization

  • Implemented sparse matrix multiplication op, to allow more aggressive merging of DotInc operators

• Significant improvements to build speed

  • Added early termination to graph optimization

  • Algorithmic improvements to graph optimization functions

• Reorganized documentation to more clearly direct new users to relevant material

Fixed

• Fix bug where passing a built model to the Simulator more than once would result in an error

• Cache result of calls to tensor_graph.build_loss/build_optimizer, so that we don’t unnecessarily create duplicate elements in the graph on repeated calls

• Fix support for Variables on GPU when unroll_simulation=False

• SimPyFunc operators will always be assigned to CPU, even when device="/gpu:0", since there is no GPU kernel

• Fix bug where Simulator.loss was not being computed correctly for models with internal state

• Data/targets passed to Simulator.train will be truncated if not evenly divisible by the specified minibatch size

• Fixed bug where in some cases Nodes with side effects would not be run if their output was not used in the simulation

• Fixed bug where strided reads that cover a full array would be interpreted as non-strided reads of the full array

0.2.0 (March 13, 2017)

Initial release of TensorFlow-based NengoDL

0.1.0 (June 12, 2016)

Initial release of Lasagne-based NengoDL