pytorch-dnc/README.md

# Differentiable Neural Computers and family, for Pytorch

Includes:
1. Differentiable Neural Computers (DNC)
2. Sparse Access Memory (SAM)
3. Sparse Differentiable Neural Computers (SDNC)

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- [Install](#install)
  - [From source](#from-source)
- [Architecure](#architecure)
- [Usage](#usage)
  - [DNC](#dnc)
    - [Example usage](#example-usage)
    - [Debugging](#debugging)
  - [SDNC](#sdnc)
    - [Example usage](#example-usage-1)
    - [Debugging](#debugging-1)
  - [SAM](#sam)
    - [Example usage](#example-usage-2)
    - [Debugging](#debugging-2)
- [Tasks](#tasks)
  - [Copy task (with curriculum and generalization)](#copy-task-with-curriculum-and-generalization)
  - [Generalizing Addition task](#generalizing-addition-task)
  - [Generalizing Argmax task](#generalizing-argmax-task)
- [Code Structure](#code-structure)
- [General noteworthy stuff](#general-noteworthy-stuff)

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[![Build Status](https://travis-ci.org/ixaxaar/pytorch-dnc.svg?branch=master)](https://travis-ci.org/ixaxaar/pytorch-dnc) [![PyPI version](https://badge.fury.io/py/dnc.svg)](https://badge.fury.io/py/dnc)

This is an implementation of [Differentiable Neural Computers](http://people.idsia.ch/~rupesh/rnnsymposium2016/slides/graves.pdf), described in the paper [Hybrid computing using a neural network with dynamic external memory, Graves et al.](https://www.nature.com/articles/nature20101)
and Sparse DNCs (SDNCs) and Sparse Access Memory (SAM) described in [Scaling Memory-Augmented Neural Networks with Sparse Reads and Writes](http://papers.nips.cc/paper/6298-scaling-memory-augmented-neural-networks-with-sparse-reads-and-writes.pdf).

## Install

```bash
pip install dnc
```

### From source

```
git clone https://github.com/ixaxaar/pytorch-dnc
cd pytorch-dnc
pip install -r ./requirements.txt
pip install -e .
```

For using fully GPU based SDNCs or SAMs, install FAISS:

```bash
conda install faiss-gpu -c pytorch
```

`pytest` is required to run the test

## Architecure

<img src="./docs/dnc.png" height="600" />

## Usage

### DNC

**Constructor Parameters**:

Following are the constructor parameters:

Following are the constructor parameters:

| Argument | Default | Description |
| --- | --- | --- |
| input_size | `None` | Size of the input vectors |
| hidden_size | `None` | Size of hidden units |
| rnn_type | `'lstm'` | Type of recurrent cells used in the controller |
| num_layers | `1` | Number of layers of recurrent units in the controller |
| num_hidden_layers | `2` | Number of hidden layers per layer of the controller |
| bias | `True` | Bias |
| batch_first | `True` | Whether data is fed batch first |
| dropout | `0` | Dropout between layers in the controller |
| bidirectional | `False` | If the controller is bidirectional (Not yet implemented |
| nr_cells | `5` | Number of memory cells |
| read_heads | `2` | Number of read heads |
| cell_size | `10` | Size of each memory cell |
| nonlinearity | `'tanh'` | If using 'rnn' as `rnn_type`, non-linearity of the RNNs |
| gpu_id | `-1` | ID of the GPU, -1 for CPU |
| independent_linears | `False` | Whether to use independent linear units to derive interface vector |
| share_memory | `True` | Whether to share memory between controller layers |

Following are the forward pass parameters:

| Argument | Default | Description |
| --- | --- | --- |
| input | - | The input vector `(B*T*X)` or `(T*B*X)` |
| hidden | `(None,None,None)` | Hidden states `(controller hidden, memory hidden, read vectors)` |
| reset_experience | `False` | Whether to reset memory |
| pass_through_memory | `True` | Whether to pass through memory |


#### Example usage

```python
from dnc import DNC

rnn = DNC(
  input_size=64,
  hidden_size=128,
  rnn_type='lstm',
  num_layers=4,
  nr_cells=100,
  cell_size=32,
  read_heads=4,
  batch_first=True,
  gpu_id=0
)

(controller_hidden, memory, read_vectors) = (None, None, None)

output, (controller_hidden, memory, read_vectors) = \
  rnn(torch.randn(10, 4, 64), (controller_hidden, memory, read_vectors), reset_experience=True)
```


#### Debugging

The `debug` option causes the network to return its memory hidden vectors (numpy `ndarray`s) for the first batch each forward step.
These vectors can be analyzed or visualized, using visdom for example.

```python
from dnc import DNC

rnn = DNC(
  input_size=64,
  hidden_size=128,
  rnn_type='lstm',
  num_layers=4,
  nr_cells=100,
  cell_size=32,
  read_heads=4,
  batch_first=True,
  gpu_id=0,
  debug=True
)

(controller_hidden, memory, read_vectors) = (None, None, None)

output, (controller_hidden, memory, read_vectors), debug_memory = \
  rnn(torch.randn(10, 4, 64), (controller_hidden, memory, read_vectors), reset_experience=True)
```

Memory vectors returned by forward pass (`np.ndarray`):

| Key | Y axis (dimensions) | X axis (dimensions) |
| --- | --- | --- |
| `debug_memory['memory']` | layer * time | nr_cells * cell_size
| `debug_memory['link_matrix']` | layer * time | nr_cells * nr_cells
| `debug_memory['precedence']` | layer * time | nr_cells
| `debug_memory['read_weights']` | layer * time | read_heads * nr_cells
| `debug_memory['write_weights']` | layer * time | nr_cells
| `debug_memory['usage_vector']` | layer * time | nr_cells


### SDNC

**Constructor Parameters**:

Following are the constructor parameters:

| Argument | Default | Description |
| --- | --- | --- |
| input_size | `None` | Size of the input vectors |
| hidden_size | `None` | Size of hidden units |
| rnn_type | `'lstm'` | Type of recurrent cells used in the controller |
| num_layers | `1` | Number of layers of recurrent units in the controller |
| num_hidden_layers | `2` | Number of hidden layers per layer of the controller |
| bias | `True` | Bias |
| batch_first | `True` | Whether data is fed batch first |
| dropout | `0` | Dropout between layers in the controller |
| bidirectional | `False` | If the controller is bidirectional (Not yet implemented |
| nr_cells | `5000` | Number of memory cells |
| read_heads | `4` | Number of read heads |
| sparse_reads | `4` | Number of sparse memory reads per read head |
| temporal_reads | `4` | Number of temporal reads |
| cell_size | `10` | Size of each memory cell |
| nonlinearity | `'tanh'` | If using 'rnn' as `rnn_type`, non-linearity of the RNNs |
| gpu_id | `-1` | ID of the GPU, -1 for CPU |
| independent_linears | `False` | Whether to use independent linear units to derive interface vector |
| share_memory | `True` | Whether to share memory between controller layers |

Following are the forward pass parameters:

| Argument | Default | Description |
| --- | --- | --- |
| input | - | The input vector `(B*T*X)` or `(T*B*X)` |
| hidden | `(None,None,None)` | Hidden states `(controller hidden, memory hidden, read vectors)` |
| reset_experience | `False` | Whether to reset memory |
| pass_through_memory | `True` | Whether to pass through memory |


#### Example usage

```python
from dnc import SDNC

rnn = SDNC(
  input_size=64,
  hidden_size=128,
  rnn_type='lstm',
  num_layers=4,
  nr_cells=100,
  cell_size=32,
  read_heads=4,
  sparse_reads=4,
  batch_first=True,
  gpu_id=0
)

(controller_hidden, memory, read_vectors) = (None, None, None)

output, (controller_hidden, memory, read_vectors) = \
  rnn(torch.randn(10, 4, 64), (controller_hidden, memory, read_vectors), reset_experience=True)
```


#### Debugging

The `debug` option causes the network to return its memory hidden vectors (numpy `ndarray`s) for the first batch each forward step.
These vectors can be analyzed or visualized, using visdom for example.

```python
from dnc import SDNC

rnn = SDNC(
  input_size=64,
  hidden_size=128,
  rnn_type='lstm',
  num_layers=4,
  nr_cells=100,
  cell_size=32,
  read_heads=4,
  batch_first=True,
  sparse_reads=4,
  temporal_reads=4,
  gpu_id=0,
  debug=True
)

(controller_hidden, memory, read_vectors) = (None, None, None)

output, (controller_hidden, memory, read_vectors), debug_memory = \
  rnn(torch.randn(10, 4, 64), (controller_hidden, memory, read_vectors), reset_experience=True)
```

Memory vectors returned by forward pass (`np.ndarray`):

| Key | Y axis (dimensions) | X axis (dimensions) |
| --- | --- | --- |
| `debug_memory['memory']` | layer * time | nr_cells * cell_size
| `debug_memory['visible_memory']` | layer * time | sparse_reads+2*temporal_reads+1 * nr_cells
| `debug_memory['read_positions']` | layer * time | sparse_reads+2*temporal_reads+1
| `debug_memory['link_matrix']` | layer * time | sparse_reads+2*temporal_reads+1 * sparse_reads+2*temporal_reads+1
| `debug_memory['rev_link_matrix']` | layer * time | sparse_reads+2*temporal_reads+1 * sparse_reads+2*temporal_reads+1
| `debug_memory['precedence']` | layer * time | nr_cells
| `debug_memory['read_weights']` | layer * time | read_heads * nr_cells
| `debug_memory['write_weights']` | layer * time | nr_cells
| `debug_memory['usage']` | layer * time | nr_cells

### SAM

**Constructor Parameters**:

Following are the constructor parameters:

| Argument | Default | Description |
| --- | --- | --- |
| input_size | `None` | Size of the input vectors |
| hidden_size | `None` | Size of hidden units |
| rnn_type | `'lstm'` | Type of recurrent cells used in the controller |
| num_layers | `1` | Number of layers of recurrent units in the controller |
| num_hidden_layers | `2` | Number of hidden layers per layer of the controller |
| bias | `True` | Bias |
| batch_first | `True` | Whether data is fed batch first |
| dropout | `0` | Dropout between layers in the controller |
| bidirectional | `False` | If the controller is bidirectional (Not yet implemented |
| nr_cells | `5000` | Number of memory cells |
| read_heads | `4` | Number of read heads |
| sparse_reads | `4` | Number of sparse memory reads per read head |
| cell_size | `10` | Size of each memory cell |
| nonlinearity | `'tanh'` | If using 'rnn' as `rnn_type`, non-linearity of the RNNs |
| gpu_id | `-1` | ID of the GPU, -1 for CPU |
| independent_linears | `False` | Whether to use independent linear units to derive interface vector |
| share_memory | `True` | Whether to share memory between controller layers |

Following are the forward pass parameters:

| Argument | Default | Description |
| --- | --- | --- |
| input | - | The input vector `(B*T*X)` or `(T*B*X)` |
| hidden | `(None,None,None)` | Hidden states `(controller hidden, memory hidden, read vectors)` |
| reset_experience | `False` | Whether to reset memory |
| pass_through_memory | `True` | Whether to pass through memory |


#### Example usage

```python
from dnc import SAM

rnn = SAM(
  input_size=64,
  hidden_size=128,
  rnn_type='lstm',
  num_layers=4,
  nr_cells=100,
  cell_size=32,
  read_heads=4,
  sparse_reads=4,
  batch_first=True,
  gpu_id=0
)

(controller_hidden, memory, read_vectors) = (None, None, None)

output, (controller_hidden, memory, read_vectors) = \
  rnn(torch.randn(10, 4, 64), (controller_hidden, memory, read_vectors), reset_experience=True)
```


#### Debugging

The `debug` option causes the network to return its memory hidden vectors (numpy `ndarray`s) for the first batch each forward step.
These vectors can be analyzed or visualized, using visdom for example.

```python
from dnc import SAM

rnn = SAM(
  input_size=64,
  hidden_size=128,
  rnn_type='lstm',
  num_layers=4,
  nr_cells=100,
  cell_size=32,
  read_heads=4,
  batch_first=True,
  sparse_reads=4,
  gpu_id=0,
  debug=True
)

(controller_hidden, memory, read_vectors) = (None, None, None)

output, (controller_hidden, memory, read_vectors), debug_memory = \
  rnn(torch.randn(10, 4, 64), (controller_hidden, memory, read_vectors), reset_experience=True)
```

Memory vectors returned by forward pass (`np.ndarray`):

| Key | Y axis (dimensions) | X axis (dimensions) |
| --- | --- | --- |
| `debug_memory['memory']` | layer * time | nr_cells * cell_size
| `debug_memory['visible_memory']` | layer * time | sparse_reads+2*temporal_reads+1 * nr_cells
| `debug_memory['read_positions']` | layer * time | sparse_reads+2*temporal_reads+1
| `debug_memory['read_weights']` | layer * time | read_heads * nr_cells
| `debug_memory['write_weights']` | layer * time | nr_cells
| `debug_memory['usage']` | layer * time | nr_cells


## Tasks

### Copy task (with curriculum and generalization)

The copy task, as descibed in the original paper, is included in the repo.

From the project root:
```bash
python ./tasks/copy_task.py -cuda 0 -optim rmsprop -batch_size 32 -mem_slot 64 # (like original implementation)

python ./tasks/copy_task.py -cuda 0 -lr 0.001 -rnn_type lstm -nlayer 1 -nhlayer 2 -dropout 0 -mem_slot 32 -batch_size 1000 -optim adam -sequence_max_length 8 # (faster convergence)

For SDNCs:
python ./tasks/copy_task.py -cuda 0 -lr 0.001 -rnn_type lstm -memory_type sdnc -nlayer 1 -nhlayer 2 -dropout 0 -mem_slot 100 -mem_size 10  -read_heads 1 -sparse_reads 10 -batch_size 20 -optim adam -sequence_max_length 10

and for curriculum learning for SDNCs:
python ./tasks/copy_task.py -cuda 0 -lr 0.001 -rnn_type lstm -memory_type sdnc -nlayer 1 -nhlayer 2 -dropout 0 -mem_slot 100 -mem_size 10  -read_heads 1 -sparse_reads 4 -temporal_reads 4 -batch_size 20 -optim adam -sequence_max_length 4 -curriculum_increment 2 -curriculum_freq 10000
```

For the full set of options, see:
```
python ./tasks/copy_task.py --help
```

The copy task can be used to debug memory using [Visdom](https://github.com/facebookresearch/visdom).

Additional step required:

```bash
pip install visdom
python -m visdom.server
```

Open http://localhost:8097/ on your browser, and execute the copy task:

```bash
python ./tasks/copy_task.py -cuda 0
```

The visdom dashboard shows memory as a heatmap for batch 0 every `-summarize_freq` iteration:

![Visdom dashboard](./docs/dnc-mem-debug.png)

### Generalizing Addition task

The adding task is as described in [this github pull request](https://github.com/Mostafa-Samir/DNC-tensorflow/pull/4#issue-199369192).
This task
- creates one-hot vectors of size `input_size`, each representing a number
- feeds a sentence of them to a network
- the output of which is added to get the sum of the decoded outputs

The task first trains the network for sentences of size ~100, and then tests if the network genetalizes for lengths ~1000.

```bash
python ./tasks/adding_task.py -cuda 0 -lr 0.0001 -rnn_type lstm -memory_type sam -nlayer 1 -nhlayer 1 -nhid 100 -dropout 0 -mem_slot 1000 -mem_size 32 -read_heads 1 -sparse_reads 4 -batch_size 20 -optim rmsprop -input_size 3 -sequence_max_length 100
```

### Generalizing Argmax task

The second adding task is similar to the first one, except that the network's output at the last time step is expected to be the argmax of the input.

```bash
python ./tasks/argmax_task.py -cuda 0 -lr 0.0001 -rnn_type lstm -memory_type dnc -nlayer 1 -nhlayer 1 -nhid 100 -dropout 0 -mem_slot 100 -mem_size 10 -read_heads 2 -batch_size 1 -optim rmsprop -sequence_max_length 15 -input_size 10 -iterations 10000
```



## Code Structure

1. DNCs:
  - [dnc/dnc.py](dnc/dnc.py) - Controller code.
  - [dnc/memory.py](dnc/memory.py) - Memory module.
2. SDNCs:
  - [dnc/sdnc.py](dnc/sdnc.py) - Controller code, inherits [dnc.py](dnc/dnc.py).
  - [dnc/sparse_temporal_memory.py](dnc/sparse_temporal_memory.py) - Memory module.
  - [dnc/flann_index.py](dnc/flann_index.py) - Memory index using kNN.
3. SAMs:
  - [dnc/sam.py](dnc/sam.py) - Controller code, inherits [dnc.py](dnc/dnc.py).
  - [dnc/sparse_memory.py](dnc/sparse_memory.py) - Memory module.
  - [dnc/flann_index.py](dnc/flann_index.py) - Memory index using kNN.
4. Tests:
  - All tests are in [./tests](./tests) folder.

## General noteworthy stuff

1. SDNCs use the [FLANN approximate nearest neigbhour library](https://github.com/mariusmuja/flann), with its python binding [pyflann3](https://github.com/primetang/pyflann) and [FAISS](https://github.com/facebookresearch/faiss).

FLANN can be installed either from pip (automatically as a dependency), or from source (e.g. for multithreading via OpenMP):

```bash
# install openmp first: e.g. `sudo pacman -S openmp` for Arch.
git clone git://github.com/mariusmuja/flann.git
cd flann
mkdir build
cd build
cmake ..
make -j 4
sudo make install
```

FAISS can be installed using:

```bash
conda install faiss-gpu -c pytorch
```

FAISS is much faster, has a GPU implementation and is interoperable with pytorch tensors.
We try to use FAISS by default, in absence of which we fall back to FLANN.

2. `nan`s in the gradients are common, try with different batch sizes

Repos referred to for creation of this repo:

- [deepmind/dnc](https://github.com/deepmind/dnc)
- [ypxie/pytorch-NeuCom](https://github.com/ypxie/pytorch-NeuCom)
- [jingweiz/pytorch-dnc](https://github.com/jingweiz/pytorch-dnc)