Convolutional LSTM for spatial forecasting

This post is the first in a loose series exploring forecasting
of spatially-determined data over time. By spatially-determined I
mean that whatever the quantities we’re trying to predict – be
they univariate or multivariate time series, of spatial
dimensionality or not – the input data are given on a spatial

For example, the input could be atmospheric measurements, such
as sea surface temperature or pressure, given at some set of
latitudes and longitudes. The target to be predicted could then
span that same (or another) grid. Alternatively, it could be a
univariate time series, like a meteorological index.

But wait a second, you may be thinking. For time-series
prediction, we have that time-honored set of recurrent
architectures (e.g., LSTM, GRU), right? Right. We do; but, once we
feed spatial data to an RNN, treating different locations as
different input features, we lose an essential structural
relationship. Importantly, we need to operate in both space and
time. We want both: recurrence relations and convolutional filters.
Enter convolutional RNNs.

What to expect from this post

Today, we won’t jump into real-world applications just yet.
Instead, we’ll take our time to build a convolutional LSTM
(henceforth: convLSTM) in torch. For one, we have to – there is
no official PyTorch implementation.

Keras, on the other hand, has one. If you’re interested in
quickly playing around with a Keras convLSTM, check out this
nice example

What’s more, this post can serve as an introduction to
building your own modules. This is something you may be familiar
with from Keras or not – depending on whether you’ve used
custom models or rather, preferred the declarative define ->
compile -> fit style. (Yes, I’m implying there’s some
transfer going on if one comes to torch from Keras custom training.
Syntactic and semantic details may be different, but both share the
object-oriented style that allows for great flexibility and

Last but not least, we’ll also use this as a hands-on
experience with RNN architectures (the LSTM, specifically). While
the general concept of recurrence may be easy to grasp, it is not
necessarily self-evident how those architectures should, or could,
be coded. Personally, I find that independent of the framework
used, RNN-related documentation leaves me confused. What exactly is
being returned from calling an LSTM, or a GRU? (In Keras this
depends on how you’ve defined the layer in question.) I suspect
that once we’ve decided what we want to return, the actual code
won’t be that complicated. Consequently, we’ll take a detour
clarifying what it is that torch and Keras are giving us.
Implementing our convLSTM will be a lot more straightforward

A torch convLSTM

The code discussed here may be found on GitHub. (Depending on
when you’re reading this, the code in that repository may have
evolved though.)

My starting point was one of the PyTorch implementations found
on the net, namely,
this one
. If you search for “PyTorch convGRU” or “PyTorch
convLSTM”, you will find stunning discrepancies in how these are
realized – discrepancies not just in syntax and/or engineering
ambition, but on the semantic level, right at the center of what
the architectures may be expected to do. As they say, let the buyer
beware. (Regarding the implementation I ended up porting, I am
confident that while numerous optimizations will be possible, the
basic mechanism matches my expectations.)

What do I expect? Let’s approach this task in a top-down

Input and output

The convLSTM’s input will be a time series of spatial data,
each observation being of size (time steps, channels, height,

Compare this with the usual RNN input format, be it in torch or
Keras. In both frameworks, RNNs expect tensors of size (timesteps,
input_dim)1. input_dim is
(1) for univariate time series and greater than (1) for
multivariate ones. Conceptually, we may match this to convLSTM’s
channels dimension: There could be a single channel, for
temperature, say – or there could be several, such as for
pressure, temperature, and humidity. The two additional dimensions
found in convLSTM, height and width, are spatial indexes into the

In sum, we want to be able to pass data that:

  • consist of one or more features,

  • evolve in time, and

  • are indexed in two spatial dimensions.

How about the output? We want to be able to return forecasts for
as many time steps as we have in the input sequence. This is
something that torch RNNs do by default, while Keras equivalents do
not. (You have to pass return_sequences = TRUE to obtain that
effect.) If we’re interested in predictions for just a single
point in time, we can always pick the last time step in the output

However, with RNNs, it is not all about outputs. RNN
architectures also carry through hidden states.

What are hidden states? I carefully phrased that sentence to be
as general as possible – deliberately circling around the
confusion that, in my view, often arises at this point. We’ll
attempt to clear up some of that confusion in a second, but let’s
first finish our high-level requirements specification.

We want our convLSTM to be usable in different contexts and
applications. Various architectures exist that make use of hidden
states, most prominently perhaps, encoder-decoder architectures.
Thus, we want our convLSTM to return those as well. Again, this is
something a torch LSTM does by default, while in Keras it is
achieved using return_state = TRUE.

Now though, it really is time for that interlude. We’ll sort
out the ways things are called by both torch and Keras, and inspect
what you get back from their respective GRUs and LSTMs.

Interlude: Outputs, states, hidden values … what’s what?

For this to remain an interlude, I summarize findings on a high
level. The code snippets in the appendix show how to arrive at
these results. Heavily commented, they probe return values from
both Keras and torch GRUs and LSTMs. Running these will make the
upcoming summaries seem a lot less abstract.

First, let’s look at the ways you create an LSTM in both
frameworks. (I will generally use LSTM as the “prototypical RNN
example”, and just mention GRUs when there are differences
significant in the context in question.)

In Keras, to create an LSTM you may write something like

lstm <- layer_lstm(units = 1)

The torch equivalent would be:

lstm <- nn_lstm( input_size = 2, # number of input features hidden_size = 1 # number of hidden (and output!) features )

Don’t focus on torch‘s input_size parameter for this
discussion. (It’s the number of features in the input tensor.)
The parallel occurs between Keras’ units and torch’s
hidden_size. If you’ve been using Keras, you’re probably
thinking of units as the thing that determines output size
(equivalently, the number of features in the output). So when torch
lets us arrive at the same result using hidden_size, what does that
mean? It means that somehow we’re specifying the same thing,
using different terminology. And it does make sense, since at every
time step current input and previous hidden state are added2:

[ mathbf{h}_t = mathbf{W}_{x}mathbf{x}_t +
mathbf{W}_{h}mathbf{h}_{t-1} ]

Now, about those hidden states.

When a Keras LSTM is defined with return_state = TRUE, its
return value is a structure of three entities called output, memory
state, and carry state. In torch, the same entities are referred to
as output, hidden state, and cell state. (In torch, we always get
all of them.)

So are we dealing with three different types of entities? We are

The cell, or carry state is that special thing that sets apart
LSTMs from GRUs deemed responsible for the “long” in “long
short-term memory”. Technically, it could be reported to the user
at all points in time; as we’ll see shortly though, it is

What about outputs and hidden, or memory states? Confusingly,
these really are the same thing. Recall that for each input item in
the input sequence, we’re combining it with the previous state,
resulting in a new state, to be made used of in the next

[ mathbf{h}_t = mathbf{W}_{x}mathbf{x}_t +
mathbf{W}_{h}mathbf{h}_{t-1} ]

Now, say that we’re interested in looking at just the final
time step – that is, the default output of a Keras LSTM. From
that point of view, we can consider those intermediate computations
as “hidden”. Seen like that, output and hidden states feel

However, we can also request to see the outputs for every time
step. If we do so, there is no difference – the
outputs (plural) equal the hidden states. This can
be verified using the code in the appendix.

Thus, of the three things returned by an LSTM, two are really
the same. How about the GRU, then? As there is no “cell state”,
we really have just one type of thing left over – call it outputs
or hidden states.

Let’s summarize this in a table.

Table 1: RNN terminology. Comparing torch-speak and
Keras-speak. In row 1, the terms are parameter names. In rows 2 and
3, they are pulled from current documentation.

Referring to this entity: torch says: Keras says:

Number of features in the output

This determines both how many output features there are and the
dimensionality of the hidden states.

hidden_size units

Per-time-step output; latent state; intermediate state …

This could be named “public state” in the sense that we, the
users, are able to obtain all values.

hidden state memory state

Cell state; inner state … (LSTM only)

This could be named “private state” in that we are able to
obtain a value only for the last time step. More on that in a

cell state carry state

Now, about that public vs.private distinction. In both
frameworks, we can obtain outputs (hidden states) for every time
step. The cell state, however, we can access only for the very last
time step. This is purely an implementation decision. As we’ll
see when building our own recurrent module, there are no obstacles
inherent in keeping track of cell states and passing them back to
the user.

If you dislike the pragmatism of this distinction, you can
always go with the math. When a new cell state has been computed
(based on prior cell state, input, forget, and cell gates – the
specifics of which we are not going to get into here), it is
transformed to the hidden (a.k.a. output) state making use of yet
another, namely, the output gate:

[ h_t = o_t odot tanh(c_t) ]

Definitely, then, hidden state (output, resp.) builds on cell
state, adding additional modeling power.

Now it is time to get back to our original goal and build that
convLSTM. First though, let’s summarize the return values
obtainable from torch and Keras.

Table 2: Contrasting ways of obtaining various return values
in torch vs. Keras. Cf. the appendix for complete examples.

To achieve this goal: in torch do: in Keras do:
access all intermediate outputs ( = per-time-step outputs) ret[[1]] return_sequences = TRUE
access both “hidden state” (output) and “cell state”
from final time step (only!)
ret[[2]] return_state = TRUE
access all intermediate outputs and the final “cell
both of the above return_sequences = TRUE, return_state = TRUE
access all intermediate outputs and “cell states” from all
time steps
no way no way

convLSTM, the plan

In both torch and Keras RNN architectures, single time steps are
processed by corresponding Cell classes: There is an LSTM Cell
matching the LSTM, a GRU Cell matching the GRU, and so on. We do
the same for ConvLSTM. In convlstm_cell(), we first define what
should happen to a single observation; then in convlstm(), we build
up the recurrence logic.

Once we’re done, we create a dummy dataset, as
reduced-to-the-essentials as can be. With more complex datasets,
even artificial ones, chances are that if we don’t see any
training progress, there are hundreds of possible explanations. We
want a sanity check that, if failed, leaves no excuses. Realistic
applications are left to future posts.

A single step: convlstm_cell

Our convlstm_cell’s constructor takes arguments input_dim ,
hidden_dim, and bias, just like a torch LSTM Cell.

But we’re processing two-dimensional input data. Instead of
the usual affine combination of new input and previous state, we
use a convolution of kernel size kernel_size. Inside convlstm_cell,
it is self$conv that takes care of this.

Note how the channels dimension, which in the original input
data would correspond to different variables, is creatively used to
consolidate four convolutions into one: Each channel output will be
passed to just one of the four cell gates. Once in possession of
the convolution output, forward() applies the gate logic, resulting
in the two types of states it needs to send back to the caller.

library(torch) library(zeallot) convlstm_cell <- nn_module( initialize = function(input_dim, hidden_dim, kernel_size, bias) { self$hidden_dim <- hidden_dim padding <- kernel_size %/% 2 self$conv <- nn_conv2d( in_channels = input_dim + self$hidden_dim, # for each of input, forget, output, and cell gates out_channels = 4 * self$hidden_dim, kernel_size = kernel_size, padding = padding, bias = bias ) }, forward = function(x, prev_states) { c(h_prev, c_prev) %<-% prev_states combined <- torch_cat(list(x, h_prev), dim = 2) # concatenate along channel axis combined_conv <- self$conv(combined) c(cc_i, cc_f, cc_o, cc_g) %<-% torch_split(combined_conv, self$hidden_dim, dim = 2) # input, forget, output, and cell gates (corresponding to torch's LSTM) i <- torch_sigmoid(cc_i) f <- torch_sigmoid(cc_f) o <- torch_sigmoid(cc_o) g <- torch_tanh(cc_g) # cell state c_next <- f * c_prev + i * g # hidden state h_next <- o * torch_tanh(c_next) list(h_next, c_next) }, init_hidden = function(batch_size, height, width) { list( torch_zeros(batch_size, self$hidden_dim, height, width, device = self$conv$weight$device), torch_zeros(batch_size, self$hidden_dim, height, width, device = self$conv$weight$device)) } )

Now convlstm_cell has to be called for every time step. This is
done by convlstm.

Iteration over time steps: convlstm

A convlstm may consist of several layers, just like a torch
LSTM. For each layer, we are able to specify hidden and kernel
sizes individually.

During initialization, each layer gets its own convlstm_cell. On
call, convlstm executes two loops. The outer one iterates over
layers. At the end of each iteration, we store the final pair
(hidden state, cell state) for later reporting. The inner loop runs
over input sequences, calling convlstm_cell at each time step.

We also keep track of intermediate outputs, so we’ll be able
to return the complete list of hidden_states seen during the
process. Unlike a torch LSTM, we do this for every layer.

convlstm <- nn_module( # hidden_dims and kernel_sizes are vectors, with one element for each layer in n_layers initialize = function(input_dim, hidden_dims, kernel_sizes, n_layers, bias = TRUE) { self$n_layers <- n_layers self$cell_list <- nn_module_list() for (i in 1:n_layers) { cur_input_dim <- if (i == 1) input_dim else hidden_dims[i - 1] self$cell_list$append(convlstm_cell(cur_input_dim, hidden_dims[i], kernel_sizes[i], bias)) } }, # we always assume batch-first forward = function(x) { c(batch_size, seq_len, num_channels, height, width) %<-% x$size() # initialize hidden states init_hidden <- vector(mode = "list", length = self$n_layers) for (i in 1:self$n_layers) { init_hidden[[i]] <- self$cell_list[[i]]$init_hidden(batch_size, height, width) } # list containing the outputs, of length seq_len, for each layer # this is the same as h, at each step in the sequence layer_output_list <- vector(mode = "list", length = self$n_layers) # list containing the last states (h, c) for each layer layer_state_list <- vector(mode = "list", length = self$n_layers) cur_layer_input <- x hidden_states <- init_hidden # loop over layers for (i in 1:self$n_layers) { # every layer's hidden state starts from 0 (non-stateful) c(h, c) %<-% hidden_states[[i]] # outputs, of length seq_len, for this layer # equivalently, list of h states for each time step output_sequence <- vector(mode = "list", length = seq_len) # loop over time steps for (t in 1:seq_len) { c(h, c) %<-% self$cell_list[[i]](cur_layer_input[ , t, , , ], list(h, c)) # keep track of output (h) for every time step # h has dim (batch_size, hidden_size, height, width) output_sequence[[t]] <- h } # stack hs for all time steps over seq_len dimension # stacked_outputs has dim (batch_size, seq_len, hidden_size, height, width) # same as input to forward (x) stacked_outputs <- torch_stack(output_sequence, dim = 2) # pass the list of outputs (hs) to next layer cur_layer_input <- stacked_outputs # keep track of list of outputs or this layer layer_output_list[[i]] <- stacked_outputs # keep track of last state for this layer layer_state_list[[i]] <- list(h, c) } list(layer_output_list, layer_state_list) } )

Calling the convlstm

Let’s see the input format expected by convlstm, and how to
access its different outputs.

Here is a suitable input tensor.

# batch_size, seq_len, channels, height, width x <- torch_rand(c(2, 4, 3, 16, 16))

First we make use of a single layer.

model <- convlstm(input_dim = 3, hidden_dims = 5, kernel_sizes = 3, n_layers = 1) c(layer_outputs, layer_last_states) %<-% model(x)

We get back a list of length two, which we immediately split up
into the two types of output returned: intermediate outputs from
all layers, and final states (of both types) for the last

With just a single layer, layer_outputs[[1]]holds all of the
layer’s intermediate outputs, stacked on dimension two.

dim(layer_outputs[[1]]) # [1] 2 4 5 16 16

layer_last_states[[1]]is a list of tensors, the first of which
holds the single layer’s final hidden state, and the second, its
final cell state.

dim(layer_last_states[[1]][[1]]) # [1] 2 5 16 16 dim(layer_last_states[[1]][[2]]) # [1] 2 5 16 16

For comparison, this is how return values look for a multi-layer

model <- convlstm(input_dim = 3, hidden_dims = c(5, 5, 1), kernel_sizes = rep(3, 3), n_layers = 3) c(layer_outputs, layer_last_states) %<-% model(x) # for each layer, tensor of size (batch_size, seq_len, hidden_size, height, width) dim(layer_outputs[[1]]) # 2 4 5 16 16 dim(layer_outputs[[3]]) # 2 4 1 16 16 # list of 2 tensors for each layer str(layer_last_states) # List of 3 # $ :List of 2 # ..$ :Float [1:2, 1:5, 1:16, 1:16] # ..$ :Float [1:2, 1:5, 1:16, 1:16] # $ :List of 2 # ..$ :Float [1:2, 1:5, 1:16, 1:16] # ..$ :Float [1:2, 1:5, 1:16, 1:16] # $ :List of 2 # ..$ :Float [1:2, 1:1, 1:16, 1:16] # ..$ :Float [1:2, 1:1, 1:16, 1:16] # h, of size (batch_size, hidden_size, height, width) dim(layer_last_states[[3]][[1]]) # 2 1 16 16 # c, of size (batch_size, hidden_size, height, width) dim(layer_last_states[[3]][[2]]) # 2 1 16 16

Now we want to sanity-check this module with the
simplest-possible dummy data.

Sanity-checking the convlstm

We generate black-and-white “movies” of diagonal beams
successively translated in space.

Each sequence consists of six time steps, and each beam of six
pixels. Just a single sequence is created manually. To create that
one sequence, we start from a single beam:

library(torchvision) beams <- vector(mode = "list", length = 6) beam <- torch_eye(6) %>% nnf_pad(c(6, 12, 12, 6)) # left, right, top, bottom beams[[1]] <- beam

Using torch_roll() , we create a pattern where this beam moves
up diagonally, and stack the individual tensors along the timesteps

for (i in 2:6) { beams[[i]] <- torch_roll(beam, c(-(i-1),i-1), c(1, 2)) } init_sequence <- torch_stack(beams, dim = 1)

That’s a single sequence. Thanks to
torchvision::transform_random_affine(), we almost effortlessly
produce a dataset of a hundred sequences. Moving beams start at
random points in the spatial frame, but they all share that
upward-diagonal motion.

sequences <- vector(mode = "list", length = 100) sequences[[1]] <- init_sequence for (i in 2:100) { sequences[[i]] <- transform_random_affine(init_sequence, degrees = 0, translate = c(0.5, 0.5)) } input <- torch_stack(sequences, dim = 1) # add channels dimension input <- input$unsqueeze(3) dim(input) # [1] 100 6 1 24 24

That’s it for the raw data. Now we still need a dataset and a
dataloader. Of the six time steps, we use the first five as input
and try to predict the last one.

dummy_ds <- dataset( initialize = function(data) { self$data <- data }, .getitem = function(i) { list(x = self$data[i, 1:5, ..], y = self$data[i, 6, ..]) }, .length = function() { nrow(self$data) } ) ds <- dummy_ds(input) dl <- dataloader(ds, batch_size = 100)

Here is a tiny-ish convLSTM, trained for motion prediction:

model <- convlstm(input_dim = 1, hidden_dims = c(64, 1), kernel_sizes = c(3, 3), n_layers = 2) optimizer <- optim_adam(model$parameters) num_epochs <- 100 for (epoch in 1:num_epochs) { model$train() batch_losses <- c() for (b in enumerate(dl)) { optimizer$zero_grad() # last-time-step output from last layer preds <- model(b$x)[[2]][[2]][[1]] loss <- nnf_mse_loss(preds, b$y) batch_losses <- c(batch_losses, loss$item()) loss$backward() optimizer$step() } if (epoch %% 10 == 0) cat(sprintf("nEpoch %d, training loss:%3fn", epoch, mean(batch_losses))) }
Epoch 10, training loss:0.008522 Epoch 20, training loss:0.008079 Epoch 30, training loss:0.006187 Epoch 40, training loss:0.003828 Epoch 50, training loss:0.002322 Epoch 60, training loss:0.001594 Epoch 70, training loss:0.001376 Epoch 80, training loss:0.001258 Epoch 90, training loss:0.001218 Epoch 100, training loss:0.001171

Loss decreases, but that in itself is not a guarantee the model
has learned anything. Has it? Let’s inspect its forecast for the
very first sequence and see.

For printing, I’m zooming in on the relevant region in the
24×24-pixel frame. Here is the ground truth for time step six:

b$y[1, 1, 6:15, 10:19]
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

And here is the forecast. This does not look bad at all, given
there was neither experimentation nor tuning involved.

round(as.matrix(preds[1, 1, 6:15, 10:19]), 2)
 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0 [2,] -0.02 0.36 0.01 0.06 0.00 0.00 0.00 0.00 0.00 0 [3,] 0.00 -0.01 0.71 0.01 0.06 0.00 0.00 0.00 0.00 0 [4,] -0.01 0.04 0.00 0.75 0.01 0.06 0.00 0.00 0.00 0 [5,] 0.00 -0.01 -0.01 -0.01 0.75 0.01 0.06 0.00 0.00 0 [6,] 0.00 0.01 0.00 -0.07 -0.01 0.75 0.01 0.06 0.00 0 [7,] 0.00 0.01 -0.01 -0.01 -0.07 -0.01 0.75 0.01 0.06 0 [8,] 0.00 0.00 0.01 0.00 0.00 -0.01 0.00 0.71 0.00 0 [9,] 0.00 0.00 0.00 0.01 0.01 0.00 0.03 -0.01 0.37 0 [10,] 0.00 0.00 0.00 0.00 0.00 0.00 -0.01 -0.01 -0.01 0

This should suffice for a sanity check. If you made it till the
end, thanks for your patience! In the best case, you’ll be able
to apply this architecture (or a..

Leave a Reply

Your email address will not be published. Required fields are marked *