def call(self, input_tensor: tf.Tensor):
"""Takes a dense range image and projects it to a sparse 2d grid
Args:
input_tensor (tf.Tensor): Input range image. Expected shape is B x H x W x CK x 2,
where CK is each mixture model component for each class.
Innermost values should be relevant xy pair
training (bool, optional): [description]. Defaults to False.
Returns:
[type]: [description]
"""
# Input Size B x Hi x Wi x C x 2
# Reorder to B x C x Hi x Wi x 2
reordered_input = tf.transpose(input_tensor, perm=[0, 3, 1, 2, 4])
# Reshape to B*C*Hi*Wi x 2
flattened_xy = tf.reshape(reordered_input, [self.input_size, 2])
scaled_xy = tf.scalar_mul(self.scale_factor, flattened_xy) + self.xy_offset
quantized_xy = tf.cast(scaled_xy, tf.int64)
# [B, X, Y, C, Hi, Wi]
presence_indices = tf.concat([self.presence_b, quantized_xy, self.presence_chw], -1)
presence_tensor = sparse.SparseTensor(indices=presence_indices, values=self.presence_vals, dense_shape=self.presence_shape)\
position_vals = tf.reshape(scaled_xy, [self.input_size * 2])
position_indices = tf.concat([self.position_b, tf.repeat(quantized_xy, 2, 0), self.position_chwd], -1)
position_tensor = sparse.SparseTensor(indices=position_indices, values=position_vals, dense_shape=self.position_shape)
return position_tensor, position_tensor
def decode_libsvm(content, num_features, dtype=None, label_dtype=None):
"""Convert Libsvm records to a tensor of label and a tensor of feature.
Args:
content: A `Tensor` of type `string`. Each string is a record/row in
the Libsvm format.
num_features: The number of features.
dtype: The type of the output feature tensor. Default to tf.float32.
label_dtype: The type of the output label tensor. Default to tf.int64.
Returns:
features: A `SparseTensor` of the shape `[input_shape, num_features]`.
labels: A `Tensor` of the same shape as content.
"""
labels, indices, values, shape = core_ops.io_decode_libsvm(
content, num_features, dtype=dtype, label_dtype=label_dtype)
return sparse.SparseTensor(indices, values, shape), labels
def main():
DATA = path_arg(
"A script to parse the result of a searchhmm to a sparse tensor for use in the neural network",
"Path to the folder to be used for i/o").parse_args().path
# ------------------------------------------------------------------------------------------------------
# Read files
with open(DATA + "Pfam-A.hmm", encoding="utf-8") as pfamfile:
pfam = pfamfile.readlines()
with open(DATA + "uniprot_sprot.fasta") as fastafile:
fasta = fastafile.readlines()
with open(DATA + "hmmresult_full") as infile:
result = infile.readlines()
# ------------------------------------------------------------------------------------------------------
# Prepare empty sparse tensor
# Make a list of all Pfam accessions from the HMM file
pfam_Accessions = getaccessions(pfam, "ACC", r"\s", 3)
# Make a list of all protein accessions in swissprot from the fasta file
protein_Accessions = getaccessions(fasta, ">", "\|", 1)
# Create an empty, sparse tensor with the proportions of the lists that were made
hmmtensor = sparse.SparseTensor(
indices=[[0, 0]],
values=[float(0)],
dense_shape=[len(protein_Accessions),
len(pfam_Accessions)])
# ------------------------------------------------------------------------------------------------------
# Add scores to rows and columns denoted by protein and family respectively
for line in result:
if not line.startswith("#"):
# parse line for score
splitline = [col for col in re.split(r"\s", line) if col != ""]
protein_index = protein_Accessions.index(
splitline[0].split("|")[1])
pfam_index = pfam_Accessions.index(splitline[3])
hmmtensor = sparse.add(
hmmtensor,
sparse.SparseTensor(indices=[[protein_index, pfam_index]],
values=[float(splitline[5])],
dense_shape=[
len(protein_Accessions),
len(pfam_Accessions)
]))
# ------------------------------------------------------------------------------------------------------
# Write lists and sparse tensor to files
with open(DATA + "sparse_tensor",
"wb") as tensor, open(DATA + "proteins(r)",
"w") as rows, open(DATA + "families(c)",
"w") as columns:
pickle.dump(hmmtensor, tensor)
rows.write("\n".join(protein_Accessions))
columns.write("\n".join(pfam_Accessions))
def __init__(self,
deviceIdx,
KarrayA,
inputStoichio,
maskA,
maskComplementary,
derivLeak,
isSparse=False):
"""
Builds the neural network according to the provided masks.
We begin with a dense coding, but prepare to switch to the sparse case, which will probably appear.
In such case, tensorflow only enable product of at most 2D sparse matrix (rank==2 in tensorflow terms) against some dense matrix.
:param deviceIdx: the device on which the computation shall be done
:param KarrayA: A 2d-array, if sparse
:param inputStoichio:
:param maskA:
:param maskComplementary:
:param derivLeak:
"""
super(derivativeNetwork, self).__init__()
try:
assert len(KarrayA.shape) == 2
assert len(inputStoichio.shape) == 3
assert len(maskA.shape) == 3
assert len(maskComplementary.shape) == 3
except:
print("Wrong shape for masks")
raise
self.repeat = RepeatVector(maskA.shape[1])
self.maskIdxList = []
self.maskComplementaryList = []
self.stoichioList = []
self.deviceIdx = deviceIdx
self.isSparse = isSparse
if not isSparse:
for m in range(maskA.shape[0]):
self.maskIdxList += [tf.convert_to_tensor(maskA[m])]
self.maskComplementaryList += [
tf.convert_to_tensor(maskComplementary[m])
]
self.stoichioList += [tf.convert_to_tensor(inputStoichio[m])]
self.tfmask = tf.convert_to_tensor(maskA)
self.tfMaskComplementary = tf.convert_to_tensor(
maskComplementary)
self.tfStoichio = tf.convert_to_tensor(inputStoichio)
else:
"""
In tensorflow, the element-wise product is not defined for sparse matrix.
Therefore two possible solution is offered to us:
We can either compute a boolean mask for each row (of last axis) of the 3D masks, and compute on these masks and then aggregate.
We can also try to use the sparse_embedding_lookup function.
We implement the second solution.
"""
self.maskWeightList = []
## First we need to convert to the look-up made of two sparse matrix
## In the sparse matrix module, .coords is defined as a (ndim,nnz) shaped array.
for m in range(maskA.shape[0]):
coords = []
idxValues = []
weightValues = []
for idx, e in maskA.coords[0]:
if (e == m):
coords += [maskA.coords[1:, idx]]
idxValues += [maskA.coords[2, idx]]
weightValues += [inputStoichio.data[idx]]
if (len(coords) > 0):
self.maskIdxList += [
sparse.SparseTensor(indices=coords,
values=idxValues,
dense_shape=maskA.shape[1:])
]
self.maskWeightList += [
sparse.SparseTensor(indices=coords,
values=weightValues,
dense_shape=maskA.shape[1:])
]
self.Karray = tf.convert_to_tensor(KarrayA)
self.derivLeak = tf.convert_to_tensor(derivLeak,
dtype=self.Karray.dtype)
