10 output batch

.gitignore

@@ -1,4 +1,4 @@
 *.o
 *.mod
-build*
-data/mnist/*.dat
+build
+data/*/*.dat

CMakeLists.txt

@@ -91,7 +91,7 @@ foreach(execid mnist network_save network_sync set_activation_function)
   add_test(test_${execid} bin/test_${execid})
 endforeach()
 
-foreach(execid mnist save_and_load simple sine)
+foreach(execid mnist mnist_epochs save_and_load simple sine)
   add_executable(example_${execid} src/tests/example_${execid}.f90)
   target_link_libraries(example_${execid} neural ${LIBS})
   add_test(example_${execid} bin/example_${execid})

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2019 Milan Curcic and neural-fortran contributors
+Copyright (c) 2018-2020 Milan Curcic and neural-fortran contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -266,13 +266,11 @@ program example_mnist
   batch_size = 100
   num_epochs = 10
 
-  if (this_image() == 1) then
-    write(*, '(a,f5.2,a)') 'Initial accuracy: ',&
-      net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
-  end if
+  if (this_image() == 1) print '(a,f5.2,a)', 'Initial accuracy: ', &
+    net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
 
   epochs: do n = 1, num_epochs
-    mini_batches: do i = 1, size(tr_labels) / batch_size
+    batches: do i = 1, size(tr_labels) / batch_size
 
       ! pull a random mini-batch from the dataset
       call random_number(pos)
@@ -286,12 +284,10 @@ program example_mnist
       ! train the network on the mini-batch
       call net % train(input, output, eta=3._rk)
 
-    end do mini_batches
+    end do batches
 
-    if (this_image() == 1) then
-      write(*, '(a,i2,a,f5.2,a)') 'Epoch ', n, ' done, Accuracy: ',&
-        net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
-    end if
+    if (this_image() == 1) print '(a,i2,a,f5.2,a)', 'Epoch ', n, ' done, Accuracy: ', &
+      net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
 
   end do epochs
 
@@ -322,6 +318,45 @@ for example on 16 cores using [OpenCoarrays](https://github.com/sourceryinstitut
 $ cafrun -n 16 ./example_mnist
 ```
 
+### Montesinos-Lopez et al. (2018) univariate example
+
+The Montesinos-Lopez et al. (2018) univariate example is extracted from the study:
+
+```
+Montesinos-Lopez et al. 2018. Multi-environment genomic prediction of plant traits using deep learners with dense architecture. G3, 8, 3813-3828.
+```
+
+This example uses the data from the dataset "Data\_Maize\_1to3", and was extracted using the R code in the Appendix of this paper.
+
+
+The Montesinos-Lopez univariate data is included with the repo and you will have to unpack it first:
+
+```
+cd data/montesinos_uni
+tar xzvf montesinos_uni.tar.gz
+cd -
+```
+
+### Montesinos-Lopez et al. (2018) multivariate example
+
+The Montesinos-Lopez et al. (2018) multivariate example is extracted from the study:
+
+```
+Montesinos-Lopez et al. 2018. Multi-trait, multi-environment deep learning modeling for genomic-enabled prediction of plant traits. G3, 8, 3829-3840.
+```
+
+This example uses the data from the dataset "Data\_Maize\_set\_1", and was extracted using the R code in the Appendix B of this paper.
+
+
+The Montesinos-Lopez multivariate data is included with the repo and you will have to unpack it first:
+
+```
+cd data/montesinos_multi
+tar xzvf montesinos_multi.tar.gz
+cd -
+```
+
+
 ## Contributing
 
 neural-fortran is currently a proof-of-concept with potential for

src/lib/mod_network.f90

@@ -23,23 +23,26 @@ module mod_network
     procedure, public, pass(self) :: init
     procedure, public, pass(self) :: load
     procedure, public, pass(self) :: loss
-    procedure, public, pass(self) :: output
+    procedure, public, pass(self) :: output_batch
+    procedure, public, pass(self) :: output_single
     procedure, public, pass(self) :: save
     procedure, public, pass(self) :: set_activation_equal
     procedure, public, pass(self) :: set_activation_layers
     procedure, public, pass(self) :: sync
     procedure, public, pass(self) :: train_batch
+    procedure, public, pass(self) :: train_epochs
     procedure, public, pass(self) :: train_single
     procedure, public, pass(self) :: update
 
+    generic, public :: output => output_batch, output_single
     generic, public :: set_activation => set_activation_equal, set_activation_layers
-    generic, public :: train => train_batch, train_single
+    generic, public :: train => train_batch, train_epochs, train_single
 
   end type network_type
 
   interface network_type
     module procedure :: net_constructor
-  endinterface network_type
+  end interface network_type
 
 contains
 
@@ -58,6 +61,7 @@ type(network_type) function net_constructor(dims, activation) result(net)
     call net % sync(1)
   end function net_constructor
 
+
   pure real(rk) function accuracy(self, x, y)
     ! Given input x and output y, evaluates the position of the
     ! maximum value of the output and returns the number of matches
@@ -74,6 +78,7 @@ pure real(rk) function accuracy(self, x, y)
     accuracy = real(good) / size(x, dim=2)
   end function accuracy
 
+
   pure subroutine backprop(self, y, dw, db)
     ! Applies a backward propagation through the network
     ! and returns the weight and bias gradients.
@@ -104,6 +109,7 @@ pure subroutine backprop(self, y, dw, db)
 
   end subroutine backprop
 
+
   pure subroutine fwdprop(self, x)
     ! Performs the forward propagation and stores arguments to activation
     ! functions and activations themselves for use in backprop.
@@ -119,6 +125,7 @@ pure subroutine fwdprop(self, x)
     end associate
   end subroutine fwdprop
 
+
   subroutine init(self, dims)
     ! Allocates and initializes the layers with given dimensions dims.
     class(network_type), intent(in out) :: self
@@ -134,6 +141,7 @@ subroutine init(self, dims)
     self % layers(size(dims)) % w = 0
   end subroutine init
 
+
   subroutine load(self, filename)
     ! Loads the network from file.
     class(network_type), intent(in out) :: self
@@ -142,32 +150,35 @@ subroutine load(self, filename)
     integer(ik), allocatable :: dims(:)
     character(len=100) :: buffer ! activation string
     open(newunit=fileunit, file=filename, status='old', action='read')
-    read(fileunit, fmt=*) num_layers
+    read(fileunit, *) num_layers
     allocate(dims(num_layers))
-    read(fileunit, fmt=*) dims
+    read(fileunit, *) dims
     call self % init(dims)
     do n = 1, num_layers
-      read(fileunit, fmt=*) layer_idx, buffer
+      read(fileunit, *) layer_idx, buffer
       call self % layers(layer_idx) % set_activation(trim(buffer))
     end do
     do n = 2, size(self % dims)
-      read(fileunit, fmt=*) self % layers(n) % b
+      read(fileunit, *) self % layers(n) % b
     end do
     do n = 1, size(self % dims) - 1
-      read(fileunit, fmt=*) self % layers(n) % w
+      read(fileunit, *) self % layers(n) % w
     end do
     close(fileunit)
   end subroutine load
 
+
   pure real(rk) function loss(self, x, y)
     ! Given input x and expected output y, returns the loss of the network.
     class(network_type), intent(in) :: self
     real(rk), intent(in) :: x(:), y(:)
     loss = 0.5 * sum((y - self % output(x))**2) / size(x)
   end function loss
 
-  pure function output(self, x) result(a)
+
+  pure function output_single(self, x) result(a)
     ! Use forward propagation to compute the output of the network.
+    ! This specific procedure is for a single sample of 1-d input data.
     class(network_type), intent(in) :: self
     real(rk), intent(in) :: x(:)
     real(rk), allocatable :: a(:)
@@ -178,7 +189,22 @@ pure function output(self, x) result(a)
         a = self % layers(n) % activation(matmul(transpose(layers(n-1) % w), a) + layers(n) % b)
       end do
     end associate
-  end function output
+  end function output_single
+
+
+  pure function output_batch(self, x) result(a)
+    ! Use forward propagation to compute the output of the network.
+    ! This specific procedure is for a batch of 1-d input data.
+    class(network_type), intent(in) :: self
+    real(rk), intent(in) :: x(:,:)
+    real(rk), allocatable :: a(:,:)
+    integer(ik) :: i
+    allocate(a(self % dims(size(self % dims)), size(x, dim=2)))
+    do i = 1, size(x, dim=2)
+     a(:,i) = self % output_single(x(:,i))
+    end do
+  end function output_batch
+
 
   subroutine save(self, filename)
     ! Saves the network to a file.
@@ -200,6 +226,7 @@ subroutine save(self, filename)
     close(fileunit)
   end subroutine save
 
+
   pure subroutine set_activation_equal(self, activation)
     ! A thin wrapper around layer % set_activation().
     ! This method can be used to set an activation function
@@ -209,6 +236,7 @@ pure subroutine set_activation_equal(self, activation)
     call self % layers(:) % set_activation(activation)
   end subroutine set_activation_equal
 
+
   pure subroutine set_activation_layers(self, activation)
     ! A thin wrapper around layer % set_activation().
     ! This method can be used to set different activation functions
@@ -233,6 +261,7 @@ subroutine sync(self, image)
     end do layers
   end subroutine sync
 
+
   subroutine train_batch(self, x, y, eta)
     ! Trains a network using input data x and output data y,
     ! and learning rate eta. The learning rate is normalized
@@ -273,6 +302,38 @@ subroutine train_batch(self, x, y, eta)
 
   end subroutine train_batch
 
+
+  subroutine train_epochs(self, x, y, eta, num_epochs, batch_size)
+    ! Trains for num_epochs epochs with mini-bachtes of size equal to batch_size.
+    class(network_type), intent(in out) :: self
+    integer(ik), intent(in) :: num_epochs, batch_size
+    real(rk), intent(in) :: x(:,:), y(:,:), eta
+
+    integer(ik) :: i, n, nsamples, nbatch
+    integer(ik) :: batch_start, batch_end
+
+    real(rk) :: pos
+
+    nsamples = size(y, dim=2)
+    nbatch = nsamples / batch_size
+
+    epochs: do n = 1, num_epochs
+      batches: do i = 1, nbatch
+
+        !pull a random mini-batch from the dataset  
+        call random_number(pos)
+        batch_start = int(pos * (nsamples - batch_size + 1))
+        if (batch_start == 0) batch_start = 1
+        batch_end = batch_start + batch_size - 1
+
+        call self % train(x(:,batch_start:batch_end), y(:,batch_start:batch_end), eta)
+
+      end do batches
+    end do epochs
+
+  end subroutine train_epochs
+
+
   pure subroutine train_single(self, x, y, eta)
     ! Trains a network using a single set of input data x and output data y,
     ! and learning rate eta.
@@ -285,6 +346,7 @@ pure subroutine train_single(self, x, y, eta)
     call self % update(dw, db, eta)
   end subroutine train_single
 
+
   pure subroutine update(self, dw, db, eta)
     ! Updates network weights and biases with gradients dw and db,
     ! scaled by learning rate eta.

src/tests/example_mnist.f90

@@ -12,7 +12,6 @@ program example_mnist
 
   real(rk), allocatable :: tr_images(:,:), tr_labels(:)
   real(rk), allocatable :: te_images(:,:), te_labels(:)
-  !real(rk), allocatable :: va_images(:,:), va_labels(:)
   real(rk), allocatable :: input(:,:), output(:,:)
 
   type(network_type) :: net
@@ -23,18 +22,16 @@ program example_mnist
 
   call load_mnist(tr_images, tr_labels, te_images, te_labels)
 
-  net = network_type([784, 10, 10])
+  net = network_type([784, 30, 10])
 
-  batch_size = 1000
+  batch_size = 100
   num_epochs = 10
 
-  if (this_image() == 1) then
-    write(*, '(a,f5.2,a)') 'Initial accuracy: ',&
-      net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
-  end if
+  if (this_image() == 1) print '(a,f5.2,a)', 'Initial accuracy: ', &
+    net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
 
   epochs: do n = 1, num_epochs
-    mini_batches: do i = 1, size(tr_labels) / batch_size
+    batches: do i = 1, size(tr_labels) / batch_size
 
       ! pull a random mini-batch from the dataset
       call random_number(pos)
@@ -48,12 +45,10 @@ program example_mnist
       ! train the network on the mini-batch
       call net % train(input, output, eta=3._rk)
 
-    end do mini_batches
+    end do batches
 
-    if (this_image() == 1) then
-      write(*, '(a,i2,a,f5.2,a)') 'Epoch ', n, ' done, Accuracy: ',&
-        net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
-    end if
+    if (this_image() == 1) print '(a,i2,a,f5.2,a)', 'Epoch ', n, ' done, Accuracy: ', &
+      net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
 
   end do epochs
 

src/tests/example_mnist_epochs.f90

@@ -0,0 +1,36 @@
+program example_mnist
+
+  ! A training example with the MNIST dataset.
+  ! Uses stochastic gradient descent and mini-batch size of 100.
+  ! Can be run in serial or parallel mode without modifications.
+
+  use mod_kinds, only: ik, rk
+  use mod_mnist, only: label_digits, load_mnist
+  use mod_network, only: network_type
+
+  implicit none
+
+  real(rk), allocatable :: tr_images(:,:), tr_labels(:)
+  real(rk), allocatable :: te_images(:,:), te_labels(:)
+
+  type(network_type) :: net
+
+  integer(ik) :: i, n, num_epochs
+  integer(ik) :: batch_size
+
+  call load_mnist(tr_images, tr_labels, te_images, te_labels)
+
+  net = network_type([size(tr_images, dim=1), 10, size(label_digits(tr_labels), dim=1)])
+
+  batch_size = 100
+  num_epochs = 10
+
+  if (this_image() == 1) print '(a,f5.2,a)', 'Initial accuracy: ', &
+    net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
+
+  call net % train(tr_images, label_digits(tr_labels), 3._rk, num_epochs, batch_size)
+
+  if (this_image() == 1) print '(a,f5.2,a)', 'Epochs done, Accuracy: ', &
+    net % accuracy(te_images, label_digits(te_labels)) * 100, ' %'
+
+end program example_mnist