NetworkRecurrentLayer.py

import numpy
from theano import tensor as T
import theano
from NetworkHiddenLayer import HiddenLayer, CAlignmentLayer
from NetworkBaseLayer import Container, Layer
from ActivationFunctions import strtoact
from math import sqrt
from OpLSTM import LSTMOpInstance
from OpLSTM import LSTMSOpInstance
from OpBLSTM import BLSTMOpInstance
import RecurrentTransform
import json
from TheanoUtil import print_to_file

class Unit(Container):
  """
  Abstract descriptor class for all kinds of recurrent units.
  """
  def __init__(self, n_units, n_in, n_out, n_re, n_act):
    """
    :param n_units: number of cells
    :param n_in: cell fan in
    :param n_out: cell fan out
    :param n_re: recurrent fan in
    :param n_act: number of outputs
    """
    self.n_units, self.n_in, self.n_out, self.n_re, self.n_act = n_units, n_in, n_out, n_re, n_act
    self.slice = T.constant(self.n_units, dtype='int32')
    self.params = {}

  def set_parent(self, parent):
    """
    :type parent: RecurrentUnitLayer
    """
    self.parent = parent

  def scan(self, x, z, non_sequences, i, outputs_info, W_re, W_in, b, go_backwards=False, truncate_gradient=-1):
    """
    Executes the iteration over the time axis (usually with theano.scan)
    :param step: python function to be executed
    :param x: unmapped input tensor in (time,batch,dim) shape
    :param z: same as x but already transformed to self.n_in
    :param non_sequences: see theano.scan
    :param i: index vector in (time, batch) shape
    :param outputs_info: see theano.scan
    :param W_re: recurrent weight matrix
    :param W_in: input weight matrix
    :param b: input bias
    :param go_backwards: whether to scan the sequence from 0 to T or from T to 0
    :param truncate_gradient: see theano.scan
    :return:
    """
    self.outputs_info = outputs_info
    self.non_sequences = non_sequences
    self.W_re = W_re
    self.W_in = W_in
    self.b = b
    self.go_backwards = go_backwards
    self.truncate_gradient = truncate_gradient
    try:
      self.xc = z if not x else T.concatenate([s.output for s in x], axis = -1)
    except Exception:
      self.xc = z if not x else T.concatenate(x, axis = -1)

    outputs, _ = theano.scan(self.step,
                             #strict = True,
                             truncate_gradient = truncate_gradient,
                             go_backwards = go_backwards,
                             sequences = [i,self.xc,z],
                             non_sequences = non_sequences,
                             outputs_info = outputs_info)
    return outputs

  def scan_seg(self, x, z, att, non_sequences, i, outputs_info, W_re, W_in, b, go_backwards=False, truncate_gradient=-1):
    """
    Executes the iteration over the time axis (usually with theano.scan)
    :param step: python function to be executed
    :param x: unmapped input tensor in (time,batch,dim) shape
    :param z: same as x but already transformed to self.n_in
    :param non_sequences: see theano.scan
    :param i: index vector in (time, batch) shape
    :param outputs_info: see theano.scan
    :param W_re: recurrent weight matrix
    :param W_in: input weight matrix
    :param b: input bias
    :param go_backwards: whether to scan the sequence from 0 to T or from T to 0
    :param truncate_gradient: see theano.scan
    :return:
    """
    self.outputs_info = outputs_info
    self.non_sequences = non_sequences
    self.W_re = W_re
    self.W_in = W_in
    self.b = b
    self.go_backwards = go_backwards
    self.truncate_gradient = truncate_gradient
    try:
      self.xc = z if not x else T.concatenate([s.output for s in x], axis = -1)
    except Exception:
      self.xc = z if not x else T.concatenate(x, axis = -1)

    outputs, _ = theano.scan(self.step,
                             #strict = True,
                             truncate_gradient = truncate_gradient,
                             go_backwards = go_backwards,
                             sequences = [i,self.xc,z,att],
                             non_sequences = non_sequences,
                             outputs_info = outputs_info)
    return outputs


class VANILLA(Unit):
  """
  A simple tanh unit
  """
  def __init__(self, n_units,  **kwargs):
    super(VANILLA, self).__init__(n_units, n_units, n_units, n_units, 1)

  def step(self, i_t, x_t, z_t, z_p, h_p):
    """
    performs one iteration of the recursion
    :param i_t: index at time step t
    :param x_t: raw input at time step t
    :param z_t: mapped input at time step t
    :param z_p: previous input from time step t-1
    :param h_p: previous hidden activation from time step t-1
    :return:
    """
    return [ T.tanh(z_t + z_p) ]


class LSTME(Unit):
  """
  A theano based LSTM implementation
  """
  def __init__(self, n_units, **kwargs):
    super(LSTME, self).__init__(
      n_units=n_units,
      n_in=n_units * 4,  # input gate, forget gate, output gate, net input
      n_out=n_units,
      n_re=n_units * 4,
      n_act=2  # output, cell state
    )
    self.o_output = T.as_tensor(numpy.ones((n_units,), dtype='float32'))
    self.o_h = T.as_tensor(numpy.ones((n_units,), dtype='float32'))

  def step(self, i_t, x_t, z_t, y_p, c_p, *other_args):
    # See Unit.scan() for seqs.
    # args: seqs (x_t = unit.xc, z_t, i_t), outputs (# unit.n_act, y_p, c_p, ...), non_seqs (none)
    other_outputs = []
    if self.recurrent_transform:
      state_vars = other_args[:len(self.recurrent_transform.state_vars)]
      self.recurrent_transform.set_sorted_state_vars(state_vars)
      z_r, r_updates = self.recurrent_transform.step(y_p)
      z_t += z_r
      for v in self.recurrent_transform.get_sorted_state_vars():
        other_outputs += [r_updates[v]]
    z_t += T.dot(y_p, self.W_re)
    partition = z_t.shape[1] // 4
    ingate = T.nnet.sigmoid(z_t[:,:partition])
    forgetgate = T.nnet.sigmoid(z_t[:,partition:2*partition])
    outgate = T.nnet.sigmoid(z_t[:,2*partition:3*partition])
    input = T.tanh(z_t[:,3*partition:4*partition])
    c_t = forgetgate * c_p + ingate * input
    y_t = outgate * T.tanh(c_t)
    i_output = T.outer(i_t, self.o_output)
    i_h = T.outer(i_t, self.o_h)
    # return: next outputs (# unit.n_act, y_t, c_t, ...)
    return (y_t * i_output, c_t * i_h + c_p * (1 - i_h)) + tuple(other_outputs)

class LSTMS(Unit):
  """
  A theano based LSTM implementation
  """
  def __init__(self, n_units, **kwargs):
    super(LSTMS, self).__init__(
      n_units=n_units,
      n_in=n_units * 4,  # input gate, forget gate, output gate, net input
      n_out=n_units,
      n_re=n_units * 4,
      n_act=2  # output, cell state
    )
    self.o_output = T.as_tensor(numpy.ones((n_units,), dtype='float32'))
    self.o_h = T.as_tensor(numpy.ones((n_units,), dtype='float32'))

  def step(self, i_t, x_t, z_t, att_p, y_p, c_p, *other_args):
    # See Unit.scan() for seqs.
    # args: seqs (x_t = unit.xc, z_t, i_t), outputs (# unit.n_act, y_p, c_p, ...), non_seqs (none)
    other_outputs = []
    #att_p = theano.printing.Print('att in lstms', attrs=['__str__'])(att_p)
    if self.recurrent_transform:
      state_vars = other_args[:len(self.recurrent_transform.state_vars)]
      self.recurrent_transform.set_sorted_state_vars(state_vars)
      z_r, r_updates = self.recurrent_transform.step(y_p)
      z_t += z_r
      for v in self.recurrent_transform.get_sorted_state_vars():
        other_outputs += [r_updates[v]]
    maxatt = att_p.repeat(z_t.shape[1]).reshape((z_t.shape[0],z_t.shape[1]))#.dimshuffle(1,0)
    #maxatt = theano.printing.Print('maxatt',attrs=['__str__','shape'])(maxatt)
    z_t = T.switch(maxatt>0,z_t,z_t + T.dot(y_p, self.W_re))
    #z_t += T.dot(y_p, self.W_re)
    #z_t = theano.printing.Print('z_t lstms',attrs=['shape'])(z_t)

    partition = z_t.shape[1] // 4
    ingate = T.nnet.sigmoid(z_t[:,:partition])
    forgetgate = ((T.nnet.sigmoid(z_t[:,partition:2*partition])).T * (1.-att_p)).T
    outgate = T.nnet.sigmoid(z_t[:,2*partition:3*partition])
    input = T.tanh(z_t[:,3*partition:4*partition])
    #c_t = ((forgetgate * c_p + ingate * input).T * (1.-T.max(att_p,axis=-1))).T
    c_t = forgetgate * c_p + ingate * input
    y_t = outgate * T.tanh(c_t)
    i_output = T.outer(i_t, self.o_output)
    i_h = T.outer(i_t, self.o_h)
    # return: next outputs (# unit.n_act, y_t, c_t, ...)
    return (y_t * i_output, c_t * i_h + c_p * (1 - i_h)) + tuple(other_outputs)

class LEAKYLSTM(Unit):
  """
  A 1D cell proposed in http://jmlr.org/papers/volume17/14-203/14-203.pdf
  The simplified equations can be seen in Table 7, page 36.
  Type A with gamma_3==0.
  This cell has 3 units instead of 4 like LSTM
  """
  def __init__(self, n_units, **kwargs):
    super(LEAKYLSTM, self).__init__(
      n_units=n_units,
      n_in=n_units * 3,  # forget gate (FG), output gate (OG), net input (IN)
      n_out=n_units,
      n_re=n_units * 3,
      n_act=2  # output, cell state
    )
    self.o_output = T.as_tensor(numpy.ones((n_units,), dtype='float32'))
    self.o_h = T.as_tensor(numpy.ones((n_units,), dtype='float32'))

  def step(self, i_t, x_t, z_t, y_p, c_p, *other_args):
    # See Unit.scan() for seqs.
    # args: seqs (x_t = unit.xc, z_t, i_t), outputs (# unit.n_act, y_p, c_p, ...), non_seqs (none)
    other_outputs = []
    if self.recurrent_transform:
      state_vars = other_args[:len(self.recurrent_transform.state_vars)]
      self.recurrent_transform.set_sorted_state_vars(state_vars)
      z_r, r_updates = self.recurrent_transform.step(y_p)
      z_t += z_r
      for v in self.recurrent_transform.get_sorted_state_vars():
        other_outputs += [r_updates[v]]
    z_t += T.dot(y_p, self.W_re)
    partition = z_t.shape[1] // 3 #number of units
    forgetgate = T.nnet.sigmoid(z_t[:,:partition])
    outgate = T.nnet.sigmoid(z_t[:,partition:2*partition])
    input = T.tanh(z_t[:,2*partition:3*partition])
    # c(t) = (1 - FG(t)) * IN(t) + FG(t) * c(t-1)
    c_t = (1-forgetgate) * input + forgetgate * c_p
    # y(t) = OG(t) * c(t) HINT: There can be added an additional nonlinearity (substitute c_t:=T.tanh(x_t))
    y_t = outgate * c_t
    i_output = T.outer(i_t, self.o_output)
    i_h = T.outer(i_t, self.o_h)
    # return: next outputs (# unit.n_act, y_t, c_t, ...)
    return (y_t * i_output, c_t * i_h + c_p * (1 - i_h)) + tuple(other_outputs)


class LEAKYLPLSTM(Unit):
  """
  A 1D cell proposed in http://jmlr.org/papers/volume17/14-203/14-203.pdf
  The simplified equations can be seen in Table 7, page 36.
  Type A.
  This cell has 4 units like the LSTM
  """
  def __init__(self, n_units, **kwargs):
    super(LEAKYLPLSTM, self).__init__(
      n_units=n_units,
      n_in=n_units * 4,  # forget gate (FG), output gate 1 (OG1), output gate 2 (OG2), net input (IN)
      n_out=n_units,
      n_re=n_units * 4,
      n_act=2  # output, cell state
    )
    self.o_output = T.as_tensor(numpy.ones((n_units,), dtype='float32'))
    self.o_h = T.as_tensor(numpy.ones((n_units,), dtype='float32'))

  def step(self, i_t, x_t, z_t, y_p, c_p, *other_args):
    # See Unit.scan() for seqs.
    # args: seqs (x_t = unit.xc, z_t, i_t), outputs (# unit.n_act, y_p, c_p, ...), non_seqs (none)
    other_outputs = []
    if self.recurrent_transform:
      state_vars = other_args[:len(self.recurrent_transform.state_vars)]
      self.recurrent_transform.set_sorted_state_vars(state_vars)
      z_r, r_updates = self.recurrent_transform.step(y_p)
      z_t += z_r
      for v in self.recurrent_transform.get_sorted_state_vars():
        other_outputs += [r_updates[v]]
    z_t += T.dot(y_p, self.W_re)
    partition = z_t.shape[1] // 4 #number of units
    forgetgate = T.nnet.sigmoid(z_t[:,:partition])
    outgate1 = T.nnet.sigmoid(z_t[:,partition:2*partition])
    outgate2 = T.nnet.sigmoid(z_t[:,2*partition:3*partition])
    input = T.tanh(z_t[:,3*partition:4*partition])
    # c(t) = (1 - FG(t)) * IN(t) + FG(t) * c(t-1)
    c_t = (1-forgetgate) * input + forgetgate * c_p
    # y(t) = tanh( OG1(t) * c(t) + OG2(t) * c(t-1) ) HINT: The additional nonlinearity maybe has not a significant effect
    y_t = T.tanh(outgate1 * c_t + outgate2 * c_p)
    i_output = T.outer(i_t, self.o_output)
    i_h = T.outer(i_t, self.o_h)
    # return: next outputs (# unit.n_act, y_t, c_t, ...)
    return (y_t * i_output, c_t * i_h + c_p * (1 - i_h)) + tuple(other_outputs)


class PIDLSTM(Unit):
  """
  A 1D cell proposed in http://jmlr.org/papers/volume17/14-203/14-203.pdf
  The simplified equations can be seen in Table 7, page 36.
  Type E. This cell works as a dynamic PID filter of the input. The forget gate
  determines if it has PD od PI characteristic, the Proportional gate gates the P/I part,
  the Difference gate the D/P part. It can have advantages if there is no subsampling in
  the layer.
  This cell has 4 units like the LSTM
  """
  def __init__(self, n_units, **kwargs):
    super(PIDLSTM, self).__init__(
      n_units=n_units,
      n_in=n_units * 4,  # forget gate (FG), Proportinal gate (PG), Difference gate (DG), net input (IN)
      n_out=n_units,
      n_re=n_units * 4,
      n_act=2  # output, cell state
    )
    self.o_output = T.as_tensor(numpy.ones((n_units,), dtype='float32'))
    self.o_h = T.as_tensor(numpy.ones((n_units,), dtype='float32'))

  def step(self, i_t, x_t, z_t, y_p, c_p, *other_args):
    # See Unit.scan() for seqs.
    # args: seqs (x_t = unit.xc, z_t, i_t), outputs (# unit.n_act, y_p, c_p, ...), non_seqs (none)
    other_outputs = []
    if self.recurrent_transform:
      state_vars = other_args[:len(self.recurrent_transform.state_vars)]
      self.recurrent_transform.set_sorted_state_vars(state_vars)
      z_r, r_updates = self.recurrent_transform.step(y_p)
      z_t += z_r
      for v in self.recurrent_transform.get_sorted_state_vars():
        other_outputs += [r_updates[v]]
    z_t += T.dot(y_p, self.W_re)
    partition = z_t.shape[1] // 4 #number of units
    forgetgate = T.nnet.sigmoid(z_t[:,:partition])
    propgate = T.nnet.sigmoid(z_t[:,partition:2*partition])
    diffgate = T.nnet.sigmoid(z_t[:,2*partition:3*partition])
    input = T.tanh(z_t[:,3*partition:4*partition])
    # c(t) = (1 - FG(t)) * IN(t) + FG(t) * c(t-1)
    c_t = (1-forgetgate) * input + forgetgate * c_p
    # y(t) = tanh( PG(t) * c(t) + DG(t) * ( c(t) - c(t-1)) ) HINT: The additional nonlinearity maybe has not a significant effect
    y_t = T.tanh(propgate * c_t + diffgate * ( c_t - c_p))
    i_output = T.outer(i_t, self.o_output)
    i_h = T.outer(i_t, self.o_h)
    # return: next outputs (# unit.n_act, y_t, c_t, ...)
    return (y_t * i_output, c_t * i_h + c_p * (1 - i_h)) + tuple(other_outputs)


class LSTMP(Unit):
  """
  Very fast custom LSTM implementation
  """
  def __init__(self, n_units, **kwargs):
    super(LSTMP, self).__init__(n_units, n_units * 4, n_units, n_units * 4, 2)

  def scan(self, x, z, non_sequences, i, outputs_info, W_re, W_in, b, go_backwards = False, truncate_gradient = -1):
    z = T.inc_subtensor(z[-1 if go_backwards else 0], T.dot(outputs_info[0],W_re))
    result = LSTMOpInstance(z[::-(2 * go_backwards - 1)], W_re, outputs_info[1], i[::-(2 * go_backwards - 1)])
    return [ result[0], result[2].dimshuffle('x',0,1) ]

class LSTMPS(Unit):
  """
  Very fast custom LSTM implementation for segment encoding
  """
  def __init__(self, n_units, **kwargs):
    super(LSTMPS, self).__init__(n_units, n_units * 4, n_units, n_units * 4, 2)

  def scan_seg(self, x, z, non_sequences, i, att, outputs_info, W_re, W_in, b, go_backwards = False, truncate_gradient = -1):
    z = T.inc_subtensor(z[-1 if go_backwards else 0], T.dot(outputs_info[0],W_re))
    result = LSTMSOpInstance(z[::-(2 * go_backwards - 1)], W_re, outputs_info[1], i[::-(2 * go_backwards - 1)], att)
    return [ result[0], result[2].dimshuffle('x',0,1) ]

class LSTMB(Unit):
  """
  Very fast custom BLSTM implementation
  """
  def __init__(self, n_units, **kwargs):
    super(LSTMB, self).__init__(n_units, n_units * 8, n_units * 2, n_units * 4, 2)

  def scan(self, x, z, non_sequences, i, outputs_info, W_re, W_in, b, go_backwards = False, truncate_gradient = -1):
    W_re_b = self.parent.add_param(
      self.parent.create_recurrent_weights(self.n_units, self.n_re, name="W_re_b_%s" % self.parent.name))
    z_f = z[:,:,:z.shape[2]/2]
    z_b = z[::-1,:,z.shape[2]/2:]
    z_f = T.inc_subtensor(z_f[0], T.dot(outputs_info[0], W_re))
    z_b = T.inc_subtensor(z_b[0], T.dot(outputs_info[0], W_re_b))
    result = BLSTMOpInstance(z_f,z_b, W_re, W_re_b, outputs_info[1], T.zeros_like(outputs_info[1]), i, i[::-1])
    return [ T.concatenate([result[0],result[1][::-1]],axis=2), T.concatenate([result[4],result[5][::-1]],axis=1).dimshuffle('x',0,1) ]
BLSTM = LSTMB # alternative name


class LSTMC(Unit):
  """
  The same implementation as above, but it executes a theano function (recurrent transform)
  in each iteration. This allows for additional dependencies in the recursion of the LSTM.
  """
  def __init__(self, n_units, **kwargs):
    super(LSTMC, self).__init__(n_units, n_units * 4, n_units, n_units * 4, 2)

  def scan(self, x, z, non_sequences, i, outputs_info, W_re, W_in, b, go_backwards = False, truncate_gradient = -1):
    assert self.parent.recurrent_transform
    import OpLSTMCustom
    op = OpLSTMCustom.register_func(self.parent.recurrent_transform)
    custom_vars = self.parent.recurrent_transform.get_sorted_custom_vars()
    initial_state_vars = self.parent.recurrent_transform.get_sorted_state_vars_initial()
    # See OpLSTMCustom.LSTMCustomOp.
    # Inputs args are: Z, c, y0, i, W_re, custom input vars, initial state vars
    # Results: (output) Y, (gates and cell state) H, (final cell state) d, state vars sequences
    op_res = op(z[::-(2 * go_backwards - 1)],
                outputs_info[1], outputs_info[0], i[::-(2 * go_backwards - 1)], T.ones((i.shape[1],),'float32'), W_re, *(custom_vars + initial_state_vars))
    result = [ op_res[0], op_res[2].dimshuffle('x',0,1) ] + op_res[3:]
    assert len(result) == len(outputs_info)
    return result


class LSTMR(Unit):
  """
  Same as LSTMC but without recurrent matrix multiplication
  """
  def __init__(self, n_units, **kwargs):
    super(LSTMR, self).__init__(n_units, n_units * 4, n_units, n_units * 4, 2)
    self.n_re = 0

  def scan(self, x, z, non_sequences, i, outputs_info, W_re, W_in, b, go_backwards = False, truncate_gradient = -1):
    assert self.parent.recurrent_transform
    import OpLSTMRec
    op = OpLSTMRec.register_func(self.parent.recurrent_transform)
    custom_vars = self.parent.recurrent_transform.get_sorted_custom_vars()
    initial_state_vars = self.parent.recurrent_transform.get_sorted_state_vars_initial()
    # See OpLSTMRec.LSTMRecOp.
    # Inputs args are: Z, c, y0, i, custom input vars, initial state vars
    # Results: (output) Y, (gates and cell state) H, (final cell state) d, state vars sequences
    op_res = op(z[::-(2 * go_backwards - 1)],
                outputs_info[1], outputs_info[0], i[::-(2 * go_backwards - 1)], *(custom_vars + initial_state_vars))
    result = [ op_res[0], op_res[2].dimshuffle('x',0,1) ] + op_res[3:]
    assert len(result) == len(outputs_info)
    return result


class GRU(Unit):
  """
  Gated recurrent unit as described in http://arxiv.org/abs/1502.02367
  """
  def __init__(self, n_units, **kwargs):
    super(GRU, self).__init__(n_units, n_units * 3, n_units, n_units * 2, 2)
    l = sqrt(6.) / sqrt(n_units * 3)
    rng = numpy.random.RandomState(1234)
    values = numpy.asarray(rng.uniform(low=-l, high=l, size=(n_units, n_units)), dtype=theano.config.floatX)
    self.W_reset = theano.shared(value=values, borrow=True, name = "W_reset")
    self.params['W_reset'] = self.W_reset

  def step(self, i_t, x_t, z_t, z_p, h_p):
    CI, GR, GU = [T.tanh, T.nnet.sigmoid, T.nnet.sigmoid]
    u_t = GU(z_t[:,:self.slice] + z_p[:,:self.slice])
    r_t = GR(z_t[:,self.slice:2*self.slice] + z_p[:,self.slice:2*self.slice])
    h_c = CI(z_t[:,2*self.slice:] + T.dot(r_t * h_p, self.W_reset))
    return z_t, u_t * h_p + (1 - u_t) * h_c


class SRU(Unit):
  """
  Same as GRU but without reset weights, which allows for a faster computation on GPUs
  """
  def __init__(self, n_units, **kwargs):
    super(SRU, self).__init__(n_units, n_units * 3, n_units, n_units * 3, 1)

  def step(self, i_t, x_t, z_t, z_p, h_p):
    CI, GR, GU = [T.tanh, T.nnet.sigmoid, T.nnet.sigmoid]
    u_t = GU(z_t[:,:self.slice] + z_p[:,:self.slice])
    r_t = GR(z_t[:,self.slice:2*self.slice] + z_p[:,self.slice:2*self.slice])
    h_c = CI(z_t[:,2*self.slice:3*self.slice] + r_t * z_p[:,2*self.slice:3*self.slice])
    return  u_t * h_p + (1 - u_t) * h_c


class RecurrentUnitLayer(Layer):
  """
  Layer class to execute recurrent units
  """
  recurrent = True
  layer_class = "rec"

  def __init__(self,
               n_out = None,
               n_units = None,
               direction = 1,
               truncation = -1,
               sampling = 1,
               encoder = None,
               unit = 'lstm',
               n_dec = 0,
               attention = "none",
               recurrent_transform = "none",
               recurrent_transform_attribs = "{}",
               attention_template = 128,
               attention_distance = 'l2',
               attention_step = "linear",
               attention_beam = 0,
               attention_norm = "exp",
               attention_momentum = "none",
               attention_sharpening = 1.0,
               attention_nbest = 0,
               attention_store = False,
               attention_smooth = False,
               attention_glimpse = 1,
               attention_filters = 1,
               attention_accumulator = 'sum',
               attention_loss = 0,
               attention_bn = 0,
               attention_lm = 'none',
               attention_ndec = 1,
               attention_memory = 0,
               attention_alnpts = 0,
               attention_epoch  = 1,
               attention_segstep=0.01,
               attention_offset=0.95,
               attention_method="epoch",
               attention_scale=10,
               context=-1,
               base = None,
               aligner = None,
               lm = False,
               force_lm = False,
               droplm = 1.0,
               forward_weights_init=None,
               bias_random_init_forget_shift=0.0,
               copy_weights_from_base=False,
               segment_input=False,
               join_states=False,
               state_memory=False,
               sample_segment=None,
               **kwargs):
    """
    :param n_out: number of cells
    :param n_units: used when initialized via Network.from_hdf_model_topology
    :param direction: process sequence in forward (1) or backward (-1) direction
    :param truncation: gradient truncation
    :param sampling: scan every nth frame only
    :param encoder: list of encoder layers used as initalization for the hidden state
    :param unit: cell type (one of 'lstm', 'vanilla', 'gru', 'sru')
    :param n_dec: absolute number of steps to unfold the network if integer, else relative number of steps from encoder
    :param recurrent_transform: name of recurrent transform
    :param recurrent_transform_attribs: dictionary containing parameters for a recurrent transform
    :param attention_template:
    :param attention_distance:
    :param attention_step:
    :param attention_beam:
    :param attention_norm:
    :param attention_sharpening:
    :param attention_nbest:
    :param attention_store:
    :param attention_align:
    :param attention_glimpse:
    :param attention_lm:
    :param base: list of layers which outputs are considered as based during attention mechanisms
    :param lm: activate RNNLM
    :param force_lm: expect previous labels to be given during testing
    :param droplm: probability to take the expected output as predecessor instead of the real one when LM=true
    :param bias_random_init_forget_shift: initialize forget gate bias of lstm networks with this value
    """
    source_index = None
    if len(kwargs['sources']) == 1 and (kwargs['sources'][0].layer_class.endswith('length') or kwargs['sources'][0].layer_class.startswith('length')):
      kwargs['sources'] = []
      source_index = kwargs['index']
    unit_given = unit
    from Device import is_using_gpu
    if unit == 'lstm':  # auto selection
      if not is_using_gpu():
        unit = 'lstme'
      elif recurrent_transform == 'none' and (not lm or droplm == 0.0):
        unit = 'lstmp'
      else:
        unit = 'lstmc'
    elif unit in ("lstmc", "lstmp") and not is_using_gpu():
      unit = "lstme"
    if segment_input:
      if is_using_gpu():
        unit = "lstmps"
      else:
        unit = "lstms"
    if n_out is None:
      assert encoder
      n_out = sum([enc.attrs['n_out'] for enc in encoder])
    kwargs.setdefault("n_out", n_out)
    if n_units is not None:
      assert n_units == n_out
    self.attention_weight = T.constant(1.,'float32')
    if len(kwargs['sources']) == 1 and kwargs['sources'][0].layer_class.startswith('length'):
      kwargs['sources'] = []
    elif len(kwargs['sources']) == 1 and kwargs['sources'][0].layer_class.startswith('signal'):
      kwargs['sources'] = []
    super(RecurrentUnitLayer, self).__init__(**kwargs)
    self.set_attr('from', ",".join([s.name for s in self.sources]) if self.sources else "null")
    self.set_attr('n_out', n_out)
    self.set_attr('unit', unit_given.encode("utf8"))
    self.set_attr('truncation', truncation)
    self.set_attr('sampling', sampling)
    self.set_attr('direction', direction)
    self.set_attr('lm', lm)
    self.set_attr('force_lm', force_lm)
    self.set_attr('droplm', droplm)
    if bias_random_init_forget_shift:
      self.set_attr("bias_random_init_forget_shift", bias_random_init_forget_shift)
    self.set_attr('attention_beam', attention_beam)
    self.set_attr('recurrent_transform', recurrent_transform.encode("utf8"))
    if isinstance(recurrent_transform_attribs, str):
      recurrent_transform_attribs = json.loads(recurrent_transform_attribs)
    if attention_template is not None:
      self.set_attr('attention_template', attention_template)
    self.set_attr('recurrent_transform_attribs', recurrent_transform_attribs)
    self.set_attr('attention_distance', attention_distance.encode("utf8"))
    self.set_attr('attention_step', attention_step.encode("utf8"))
    self.set_attr('attention_norm', attention_norm.encode("utf8"))
    self.set_attr('attention_sharpening', attention_sharpening)
    self.set_attr('attention_nbest', attention_nbest)
    attention_store = attention_store or attention_smooth or attention_momentum != 'none'
    self.set_attr('attention_store', attention_store)
    self.set_attr('attention_smooth', attention_smooth)
    self.set_attr('attention_momentum', attention_momentum.encode('utf8'))
    self.set_attr('attention_glimpse', attention_glimpse)
    self.set_attr('attention_filters', attention_filters)
    self.set_attr('attention_lm', attention_lm)
    self.set_attr('attention_bn', attention_bn)
    self.set_attr('attention_accumulator', attention_accumulator)
    self.set_attr('attention_ndec', attention_ndec)
    self.set_attr('attention_memory', attention_memory)
    self.set_attr('attention_loss', attention_loss)
    self.set_attr('n_dec', n_dec)
    self.set_attr('segment_input', segment_input)
    self.set_attr('attention_alnpts', attention_alnpts)
    self.set_attr('attention_epoch', attention_epoch)
    self.set_attr('attention_segstep', attention_segstep)
    self.set_attr('attention_offset', attention_offset)
    self.set_attr('attention_method', attention_method)
    self.set_attr('attention_scale', attention_scale)
    if segment_input:
      if not self.eval_flag:
      #if self.eval_flag:
        if isinstance(self.sources[0],RecurrentUnitLayer):
          self.inv_att = self.sources[0].inv_att #NBT
        else:
          if not join_states:
            self.inv_att = self.sources[0].attention #NBT
          else:
            assert hasattr(self.sources[0], "nstates"), "source does not have number of states!"
            ns = self.sources[0].nstates
            self.inv_att = self.sources[0].attention[(ns-1)::ns]
        inv_att = T.roll(self.inv_att.dimshuffle(2, 1, 0),1,axis=0)#TBN
        inv_att = T.set_subtensor(inv_att[0],T.zeros((inv_att.shape[1],inv_att.shape[2])))
        inv_att = T.max(inv_att,axis=-1)
      else:
        inv_att = T.zeros((self.sources[0].output.shape[0],self.sources[0].output.shape[1]))
    if encoder and hasattr(encoder[0],'act'):
      self.set_attr('encoder', ",".join([e.name for e in encoder]))
    if base:
      self.set_attr('base', ",".join([b.name for b in base]))
    else:
      base = encoder
    self.base = base
    self.encoder = encoder
    if aligner:
      self.aligner = aligner
    self.set_attr('n_units', n_out)
    unit = eval(unit.upper())(**self.attrs)
    assert isinstance(unit, Unit)
    self.unit = unit
    kwargs.setdefault("n_out", unit.n_out)
    n_out = unit.n_out
    self.set_attr('n_out', unit.n_out)
    if n_dec < 0:
      source_index = self.index
      n_dec *= -1
    if n_dec != 0:
      self.target_index = self.index
      if isinstance(n_dec,float):
        if not source_index:
          source_index = encoder[0].index if encoder else base[0].index
        lengths = T.cast(T.ceil(T.sum(T.cast(source_index,'float32'),axis=0) * n_dec), 'int32')
        idx, _ = theano.map(lambda l_i, l_m:T.concatenate([T.ones((l_i,),'int8'),T.zeros((l_m-l_i,),'int8')]),
                            [lengths], [T.max(lengths)+1])
        self.index = idx.dimshuffle(1,0)[:-1]
        n_dec = T.cast(T.ceil(T.cast(source_index.shape[0],'float32') * numpy.float32(n_dec)),'int32')
      else:
        if encoder:
          self.index = encoder[0].index
        self.index = T.ones((n_dec,self.index.shape[1]),'int8')
    else:
      n_dec = self.index.shape[0]
    # initialize recurrent weights
    self.W_re = None
    if unit.n_re > 0:
      self.W_re = self.add_param(self.create_recurrent_weights(unit.n_units, unit.n_re, name="W_re_%s" % self.name))
    # initialize forward weights
    bias_init_value = self.create_bias(unit.n_in).get_value()
    if bias_random_init_forget_shift:
      assert unit.n_units * 4 == unit.n_in  # (input gate, forget gate, output gate, net input)
      bias_init_value[unit.n_units:2 * unit.n_units] += bias_random_init_forget_shift
    self.b.set_value(bias_init_value)
    if not forward_weights_init:
      forward_weights_init = "random_uniform(p_add=%i)" % unit.n_re
    else:
      self.set_attr('forward_weights_init', forward_weights_init)
    self.forward_weights_init = forward_weights_init
    self.W_in = []
    sample_mean, gamma = None, None
    if copy_weights_from_base:
      self.params = {}
      #self.W_re = self.add_param(base[0].W_re)
      #self.W_in = [ self.add_param(W) for W in base[0].W_in ]
      #self.b = self.add_param(base[0].b)
      self.W_re = base[0].W_re
      self.W_in = base[0].W_in
      self.b = base[0].b
      if self.attrs.get('batch_norm', False):
        sample_mean = base[0].sample_mean
        gamma = base[0].gamma
      #self.masks = base[0].masks
      #self.mass = base[0].mass
    else:
      for s in self.sources:
        W = self.create_forward_weights(s.attrs['n_out'], unit.n_in, name="W_in_%s_%s" % (s.name, self.name))
        self.W_in.append(self.add_param(W))
    # make input
    z = self.b
    for x_t, m, W in zip(self.sources, self.masks, self.W_in):
      if x_t.attrs['sparse']:
        if x_t.output.ndim == 3: out_dim = x_t.output.shape[2]
        elif x_t.output.ndim == 2: out_dim = 1
        else: assert False, x_t.output.ndim
        if x_t.output.ndim == 3:
          z += W[T.cast(x_t.output[:,:,0], 'int32')]
        elif x_t.output.ndim == 2:
          z += W[T.cast(x_t.output, 'int32')]
        else:
          assert False, x_t.output.ndim
      elif m is None:
        z += T.dot(x_t.output, W)
      else:
        z += self.dot(self.mass * m * x_t.output, W)
    #if self.attrs['batch_norm']:
    #  z = self.batch_norm(z, unit.n_in)
    num_batches = self.index.shape[1]
    self.num_batches = num_batches
    non_sequences = []
    if self.attrs['lm'] or attention_lm != 'none':
      if not 'target' in self.attrs:
        self.attrs['target'] = 'classes'
      if self.attrs['droplm'] > 0.0 or not (self.train_flag or force_lm):
        if copy_weights_from_base:
          self.W_lm_in = base[0].W_lm_in
          self.b_lm_in = base[0].b_lm_in
        else:
          l = sqrt(6.) / sqrt(unit.n_out + self.y_in[self.attrs['target']].n_out)
          values = numpy.asarray(self.rng.uniform(low=-l, high=l, size=(unit.n_out, self.y_in[self.attrs['target']].n_out)), dtype=theano.config.floatX)
          self.W_lm_in = self.add_param(self.shared(value=values, borrow=True, name = "W_lm_in_"+self.name))
          self.b_lm_in = self.create_bias(self.y_in[self.attrs['target']].n_out, 'b_lm_in')
      l = sqrt(6.) / sqrt(unit.n_in + self.y_in[self.attrs['target']].n_out)
      values = numpy.asarray(self.rng.uniform(low=-l, high=l, size=(self.y_in[self.attrs['target']].n_out, unit.n_in)), dtype=theano.config.floatX)
      if copy_weights_from_base:
        self.W_lm_out = base[0].W_lm_out
      else:
        self.W_lm_out = self.add_param(self.shared(value=values, borrow=True, name = "W_lm_out_"+self.name))
      if self.attrs['droplm'] == 0.0 and (self.train_flag or force_lm):
        self.lmmask = 1
        #if recurrent_transform != 'none':
        #  recurrent_transform = recurrent_transform[:-3]
      elif self.attrs['droplm'] < 1.0 and (self.train_flag or force_lm):
        from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
        srng = RandomStreams(self.rng.randint(1234) + 1)
        self.lmmask = T.cast(srng.binomial(n=1, p=1.0 - self.attrs['droplm'], size=self.index.shape), theano.config.floatX).dimshuffle(0,1,'x').repeat(unit.n_in,axis=2)
      else:
        self.lmmask = T.zeros_like(self.index, dtype='float32').dimshuffle(0,1,'x').repeat(unit.n_in,axis=2)

    if recurrent_transform == 'input': # attention is just a sequence dependent bias (lstmp compatible)
      src = []
      src_names = []
      n_in = 0
      for e in base:
        #src_base = [ s for s in e.sources if s.name not in src_names ]
        #src_names += [ s.name for s in e.sources ]
        src_base = [ e ]
        src_names += [e.name]
        src += [s.output for s in src_base]
        n_in += sum([s.attrs['n_out'] for s in src_base])
      self.xc = T.concatenate(src, axis=2)
      l = sqrt(6.) / sqrt(self.attrs['n_out'] + n_in)
      values = numpy.asarray(self.rng.uniform(low=-l, high=l, size=(n_in, 1)), dtype=theano.config.floatX)
      self.W_att_xc = self.add_param(self.shared(value=values, borrow=True, name = "W_att_xc"))
      values = numpy.asarray(self.rng.uniform(low=-l, high=l, size=(n_in, self.attrs['n_out'] * 4)), dtype=theano.config.floatX)
      self.W_att_in = self.add_param(self.shared(value=values, borrow=True, name = "W_att_in"))
      zz = T.exp(T.tanh(T.dot(self.xc, self.W_att_xc))) # TB1
      self.zc = T.dot(T.sum(self.xc * (zz / T.sum(zz, axis=0, keepdims=True)).repeat(self.xc.shape[2],axis=2), axis=0, keepdims=True), self.W_att_in)
      recurrent_transform = 'none'
    elif recurrent_transform == 'attention_align':
      max_skip = base[0].attrs['max_skip']
      values = numpy.zeros((max_skip,), dtype=theano.config.floatX)
      self.T_b = self.add_param(self.shared(value=values, borrow=True, name="T_b"), name="T_b")
      l = sqrt(6.) / sqrt(self.attrs['n_out'] + max_skip)
      values = numpy.asarray(self.rng.uniform(
        low=-l, high=l, size=(self.attrs['n_out'], max_skip)), dtype=theano.config.floatX)
      self.T_W = self.add_param(self.shared(value=values, borrow=True, name="T_W"), name="T_W")
      y_t = T.dot(self.base[0].attention, T.arange(self.base[0].output.shape[0], dtype='float32'))  # NB
      y_t = T.concatenate([T.zeros_like(y_t[:1]), y_t], axis=0)  # (N+1)B
      y_t = y_t[1:] - y_t[:-1]  # NB
      self.y_t = y_t # T.clip(y_t,numpy.float32(0),numpy.float32(max_skip - 1))

      self.y_t = T.cast(self.base[0].backtrace,'float32')
    elif recurrent_transform == 'attention_segment':
      assert aligner.attention, "Segment-wise attention requires attention points!"

    recurrent_transform_inst = RecurrentTransform.transform_classes[recurrent_transform](layer=self)
    assert isinstance(recurrent_transform_inst, RecurrentTransform.RecurrentTransformBase)
    unit.recurrent_transform = recurrent_transform_inst
    self.recurrent_transform = recurrent_transform_inst
    state_memory *= self.train_flag
    # scan over sequence
    for s in range(self.attrs['sampling']):
      index = self.index[s::self.attrs['sampling']]

      if context > 0:
        from TheanoUtil import context_batched
        n_batches = z.shape[1]
        time, batch, dim = z.shape[0], z.shape[1], z.shape[2]
        #z = context_batched(z[::direction or 1], window=context)[::direction or 1] # TB(CD)

        from theano.ifelse import ifelse
        def context_window(idx, x_in, i_in):
          x_out = x_in[idx:idx + context]
          x_out = x_out.dimshuffle('x',1,0,2).reshape((1, batch, dim * context))
          i_out = i_in[idx:idx+1].repeat(context, axis=0)
          i_out = ifelse(T.lt(idx,context),T.set_subtensor(i_out[:context - idx],numpy.int8(0)),i_out).reshape((1, batch * context))
          return x_out, i_out

        z = z[::direction or 1]
        i = index[::direction or 1]
        out, _ = theano.map(context_window, sequences = [T.arange(z.shape[0])], non_sequences = [T.concatenate([T.zeros((context - 1,z.shape[1],z.shape[2]),dtype='float32'),z],axis=0), i])
        z = out[0][::direction or 1]
        i = out[1][::direction or 1]  # T(BC)
        direction = 1
        z = z.reshape((time * batch, context * dim))  # (TB)(CD)
        z = z.reshape((time * batch, context, dim)).dimshuffle(1,0,2)  # C(TB)D
        i = i.reshape((time * batch, context)).dimshuffle(1,0)  # C(TB)

        index = i
        num_batches = time * batch

      sequences = z
      sources = self.sources
      if state_memory:
        self.init_state = [
          self.add_param(self.shared(numpy.zeros((state_memory or 1, unit.n_units), dtype='float32'), name='init_%d_%s' % (a, self.name)))
          for a in range(unit.n_act)]  # has to be initialized for train and test
      if encoder:
        if recurrent_transform == "attention_segment":
          if hasattr(encoder[0],'act'):
            outputs_info = [T.concatenate([e.act[i][-1] for e in encoder], axis=1) for i in range(unit.n_act)]
          else:
           # outputs_info = [ T.concatenate([e[i] for e in encoder], axis=1) for i in range(unit.n_act) ]
            outputs_info[0] = self.aligner.output[-1]
        elif hasattr(encoder[0],'act'):
          outputs_info = [ T.concatenate([e.act[i][-1] for e in encoder], axis=1) for i in range(unit.n_act) ]
        else:
          outputs_info = [ T.concatenate([e[i] for e in encoder], axis=1) for i in range(unit.n_act) ]
        sequences += T.alloc(numpy.cast[theano.config.floatX](0), n_dec, num_batches, unit.n_in) + (self.zc if self.attrs['recurrent_transform'] == 'input' else numpy.float32(0))
      elif state_memory:
        outputs_info = self.init_state
      else:
        outputs_info = [ T.alloc(numpy.cast[theano.config.floatX](0), num_batches, unit.n_units) for a in range(unit.n_act) ]

      if self.attrs['lm'] and self.attrs['droplm'] == 0.0 and (self.train_flag or force_lm):
        if self.network.y[self.attrs['target']].ndim == 3:
          sequences += T.dot(self.network.y[self.attrs['target']],self.W_lm_out)
        else:
          y = self.y_in[self.attrs['target']].flatten()
          sequences += self.W_lm_out[y].reshape((index.shape[0],index.shape[1],unit.n_in))

      if sequences == self.b:
        sequences += T.alloc(numpy.cast[theano.config.floatX](0), n_dec, num_batches, unit.n_in) + (self.zc if self.attrs['recurrent_transform'] == 'input' else numpy.float32(0))

      if unit.recurrent_transform:
        outputs_info += unit.recurrent_transform.get_sorted_state_vars_initial()

      index_f = T.cast(index, theano.config.floatX)
      unit.set_parent(self)

      if segment_input:
        outputs = unit.scan_seg(x=sources,
                                z=sequences[s::self.attrs['sampling']],
                                att = inv_att,
                                non_sequences=non_sequences,
                                i=index_f,
                                outputs_info=outputs_info,
                                W_re=self.W_re,
                                W_in=self.W_in,
                                b=self.b,
                                go_backwards=direction == -1,
                                truncate_gradient=self.attrs['truncation'])
      else:
        outputs = unit.scan(x=sources,
                            z=sequences[s::self.attrs['sampling']],
                            non_sequences=non_sequences,
                            i=index_f,
                            outputs_info=outputs_info,
                            W_re=self.W_re,
                            W_in=self.W_in,
                            b=self.b,
                            go_backwards=direction == -1,
                            truncate_gradient=self.attrs['truncation'])

      if not isinstance(outputs, list):
        outputs = [outputs]
      if outputs:
        outputs[0].name = "%s.act[0]" % self.name
        if context > 0:
          for i in range(len(outputs)):
            outputs[i] = outputs[i][-1].reshape((outputs[i].shape[1]//n_batches,n_batches,outputs[i].shape[2]))

      if unit.recurrent_transform:
        unit.recurrent_transform_state_var_seqs = outputs[-len(unit.recurrent_transform.state_vars):]

      if self.attrs['sampling'] > 1:
        if s == 0:
          self.act = [ T.alloc(numpy.cast['float32'](0), self.index.shape[0], self.index.shape[1], n_out) for act in outputs ]
        self.act = [ T.set_subtensor(tot[s::self.attrs['sampling']], act) for tot,act in zip(self.act, outputs) ]
      else:
        self.act = outputs[:unit.n_act]
        if len(outputs) > unit.n_act:
          self.aux = outputs[unit.n_act:]
        if state_memory:
          for i in range(len(self.act)):
            self.init_state[i].live_update = self.act[i][-1]
    if self.attrs['attention_store']:
      self.attention = [ self.aux[i].dimshuffle(0,2,1) for i,v in enumerate(sorted(unit.recurrent_transform.state_vars.keys())) if v.startswith('att_') ] # NBT
      for i in range(len(self.attention)):
        vec = T.eye(self.attention[i].shape[2], 1, -direction * (self.attention[i].shape[2] - 1))
        last = vec.dimshuffle(1, 'x', 0).repeat(self.index.shape[1], axis=1)
        self.attention[i] = T.concatenate([self.attention[i][1:],last],axis=0)[::direction]

    self.cost_val = numpy.float32(0)
    if recurrent_transform == 'attention_align':
      back = T.ceil(self.aux[sorted(unit.recurrent_transform.state_vars.keys()).index('t')])
      def make_output(base, yout, trace, length):
        length = T.cast(length, 'int32')
        idx = T.cast(trace[:length][::-1],'int32')
        x_out = T.concatenate([base[idx],T.zeros((self.index.shape[0] + 1 - length, base.shape[1]), 'float32')],axis=0)
        y_out = T.concatenate([yout[idx,T.arange(length)],T.zeros((self.index.shape[0] + 1 - length, ), 'float32')],axis=0)
        return x_out, y_out

      output, _ = theano.map(make_output,
                             sequences = [base[0].output.dimshuffle(1,0,2),
                                          self.y_t.dimshuffle(1,2,0),
                                          back.dimshuffle(1,0),
                                          T.sum(self.index,axis=0,dtype='float32')])
      self.attrs['n_out'] = base[0].attrs['n_out']
      self.params.update(unit.params)
      self.output = output[0].dimshuffle(1,0,2)[:-1]

      z = T.dot(self.act[0], self.T_W)[:-1] + self.T_b
      z = z.reshape((z.shape[0] * z.shape[1], z.shape[2]))
      idx = (self.index[1:].flatten() > 0).nonzero()
      idy = (self.index[1:][::-1].flatten() > 0).nonzero()
      y_out = T.cast(output[1],'int32').dimshuffle(1, 0)[:-1].flatten()
      nll, _ = T.nnet.crossentropy_softmax_1hot(x=z[idx], y_idx=y_out[idy])
      self.cost_val = T.sum(nll)
      recog = T.argmax(z[idx], axis=1)
      real = y_out[idy]
      self.errors = lambda: T.sum(T.neq(recog, real))

      return

      back += T.arange(self.index.shape[1], dtype='float32') * T.cast(self.base[0].index.shape[0], 'float32')
      idx = (self.index[:-1].flatten() > 0).nonzero()
      idx = T.cast(back[::-1].flatten()[idx],'int32')
      x_out = base[0].output
      #x_out = x_out.dimshuffle(1,0,2).reshape((x_out.shape[0] * x_out.shape[1], x_out.shape[2]))[idx]
      #x_out = x_out.reshape((self.index.shape[1], self.index.shape[0] - 1, x_out.shape[1])).dimshuffle(1,0,2)
      x_out = x_out.reshape((x_out.shape[0] * x_out.shape[1], x_out.shape[2]))[idx]
      x_out = x_out.reshape((self.index.shape[0] - 1, self.index.shape[1], x_out.shape[1]))
      self.output = T.concatenate([x_out, base[0].output[1:]],axis=0)
      self.attrs['n_out'] = base[0].attrs['n_out']
      self.params.update(unit.params)
      return


      skips = T.dot(T.nnet.softmax(z), T.arange(z.shape[1], dtype='float32')).reshape(self.index[1:].shape)
      shift = T.arange(self.index.shape[1], dtype='float32') * T.cast(self.base[0].index.shape[0], 'float32')
      skips = T.concatenate([T.zeros_like(self.y_t[:1]),self.y_t[:-1]],axis=0)
      idx = shift + T.cumsum(skips, axis=0)
      idx = T.cast(idx[:-1].flatten(),'int32')
      #idx = (idx.flatten() > 0).nonzero()
      #idx = base[0].attention.flatten()
      x_out = base[0].output[::-1]
      x_out = x_out.reshape((x_out.shape[0] * x_out.shape[1], x_out.shape[2]))[idx]
      x_out = x_out.reshape((self.index.shape[0], self.index.shape[1], x_out.shape[1]))
      self.output = T.concatenate([base[0].output[-1:], x_out], axis=0)[::-1]
      self.attrs['n_out'] = base[0].attrs['n_out']
      self.params.update(unit.params)
      return

    if recurrent_transform == 'batch_norm':
      self.params['sample_mean_batch_norm'].custom_update = T.dot(T.mean(self.act[0],axis=[0,1]),self.W_re)
      self.params['sample_mean_batch_norm'].custom_update_normalized = True

    self.make_output(self.act[0][::direction or 1], sample_mean=sample_mean, gamma=gamma)
    self.params.update(unit.params)

  def cost(self):
    """
    :rtype: (theano.Variable | None, dict[theano.Variable,theano.Variable] | None)
    :returns: cost, known_grads
    """
    cost_val = self.cost_val
    if self.unit.recurrent_transform:
      transform_cost = self.unit.recurrent_transform.cost()
      if transform_cost is not None:
        cost_val += transform_cost
    return cost_val, {}

  def create_seg_wise_encoder_output(self, att, aligner=None):
    assert aligner,"please provide an inverted aligner!"
    t = self.base[0].output.shape[0]
    b = self.base[0].output.shape[1]
    att_with_first_index = T.concatenate([T.zeros((1,att.shape[1]))-numpy.float32(1),att],axis=0) #(N+1)B
    max_diff = T.cast(T.extra_ops.diff(att_with_first_index,axis=0).flatten().sort()[-1],'int32')
    reduced_index = aligner.reduced_index.repeat(max_diff).reshape((aligner.reduced_index.shape[0], aligner.reduced_index.shape[1],max_diff)) #NB(max_diff)
    att_wo_last_ind = att_with_first_index[:-1] #NB
    att_wo_last_ind +=numpy.int32(1)
    att_rep = att_wo_last_ind.repeat(max_diff).reshape((att_wo_last_ind.shape[0],att_wo_last_ind.shape[1],max_diff))#NB(max_diff)
    att_rep = T.switch(reduced_index>0, att_rep + T.arange(max_diff),T.zeros((1,),'float32')-numpy.float32(1))
    att_rep = att_rep.dimshuffle(0,2,1) #N(max_diff)B
    reduced_index = reduced_index.dimshuffle(0,2,1) #N(max_diff)B
    att_rep = T.switch(reduced_index > 0,att_rep + (T.arange(b) * t),T.zeros((1,),'float32')-numpy.float32(1))
    att_rep = att_rep.clip(0,(t*b-1))
    diff_arr = att_with_first_index[1:]-att_with_first_index[:-1]
    diff_arr = diff_arr.clip(0,max_diff) - numpy.float32(1)#NB
    mask = diff_arr.dimshuffle(0,'x',1).repeat(max_diff,axis=1) - T.arange(max_diff).dimshuffle('x',0,'x')
    ind = T.cast(T.where(T.lt(mask,numpy.float32(0)),T.zeros((1,),'float32'),numpy.float32(1)),'int8')
    self.rec_transform_enc = att_rep
    self.rec_transform_index = ind

  def get_params_vars(self):
    return [ p for p in super(RecurrentUnitLayer, self).get_params_vars() if p.live_update is None ]

class RecurrentUpsampleLayer(RecurrentUnitLayer):
  layer_class = 'recurrent_upsample'

  def __init__(self, factor, **kwargs):
    h = T.concatenate([s.act[0] for s in kwargs['sources']],axis=2)
    time = h.shape[0]
    batch = h.shape[1]
    src = Layer([],sum([s.attrs['n_out'] for s in kwargs['sources']]),kwargs['index'])
    src.output = h.reshape((1,h.shape[0] * h.shape[1], h.shape[2])).repeat(factor,axis=0)
    src.index = kwargs['sources'][0].index
    src.layer_class = ''
    kwargs['sources'] = [ src ]
    kwargs['index'] = kwargs['index'].flatten().dimshuffle('x',0).repeat(factor,axis=0)
    kwargs['n_dec'] = factor
    super(RecurrentUpsampleLayer, self).__init__(**kwargs)
    self.index = self.index.reshape((self.index.shape[0]*time,batch))
    self.output = self.output.reshape((self.output.shape[0]*time,batch,self.output.shape[2]))


class LinearRecurrentLayer(HiddenLayer):
  """
  Inspired from: http://arxiv.org/abs/1510.02693
  Basically a very simple LSTM.
  """
  recurrent = True
  layer_class = "linear_recurrent"

  def __init__(self, n_out, direction=1, **kwargs):
    super(LinearRecurrentLayer, self).__init__(n_out=n_out, **kwargs)
    self.set_attr('direction', direction)
    a = T.nnet.sigmoid(self.add_param(self.create_bias(n_out, "a")))
    x = self.get_linear_forward_output()  # time,batch,n_out
    i = T.cast(self.index, dtype="float32")  # so that it can run on gpu. (time,batch)
    def step(x_t, i_t, h_p):
      i_t_bc = i_t.dimshuffle(0, 'x')  # batch,n_out
      return (a * h_p + x_t) * i_t_bc + h_p * (numpy.float32(1) - i_t_bc)
    n_batch = x.shape[1]
    h_initial = T.zeros((n_batch, n_out), dtype="float32")
    go_backwards = {1:False, -1:True}[direction]
    h, _ = theano.scan(step, sequences=[x, i], outputs_info=[h_initial], go_backwards=go_backwards)
    h = h[::direction]
    self.output = self.activation(h)