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Start icosagon.

master
Stanislaw Adaszewski před 1 rokem
rodič
revize
3795545674
4 změnil soubory, kde provedl 180 přidání a 0 odebrání
  1. +3
    -0
      requirements.txt
  2. +1
    -0
      src/icosagon/__init__.py
  3. +127
    -0
      src/icosagon/data.py
  4. +49
    -0
      tests/icosagon/test_data.py

+ 3
- 0
requirements.txt Zobrazit soubor

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numpy
torch
dataclasses

+ 1
- 0
src/icosagon/__init__.py Zobrazit soubor

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from .data import Data

+ 127
- 0
src/icosagon/data.py Zobrazit soubor

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from collections import defaultdict
from dataclasses import dataclass
import torch
@dataclass
class NodeType(object):
name: str
count: int
@dataclass
class RelationType(object):
name: str
node_type_row: int
node_type_column: int
adjacency_matrix: torch.Tensor
is_autogenerated: bool
class Data(object):
def __init__(self) -> None:
self.node_types = []
self.relation_types = defaultdict(lambda: defaultdict(list))
def add_node_type(self, name: str, count: int) -> None:
name = str(name)
count = int(count)
if not name:
raise ValueError('You must provide a non-empty node type name')
if count <= 0:
raise ValueError('You must provide a positive node count')
self.node_types.append(NodeType(name, count))
def add_relation_type(self, name: str, node_type_row: int, node_type_column: int,
adjacency_matrix: torch.Tensor, adjacency_matrix_backward: torch.Tensor = None,
two_way: bool = True) -> None:
name = str(name)
node_type_row = int(node_type_row)
node_type_column = int(node_type_column)
if node_type_row < 0 or node_type_row > len(self.node_types):
raise ValueError('node_type_row outside of the valid range of node types')
if node_type_column < 0 or node_type_column > len(self.node_types):
raise ValueError('node_type_column outside of the valid range of node types')
if not isinstance(adjacency_matrix, torch.Tensor):
raise ValueError('adjacency_matrix must be a torch.Tensor')
if adjacency_matrix_backward and not isinstance(adjacency_matrix_backward, torch.Tensor):
raise ValueError('adjacency_matrix_backward must be a torch.Tensor')
if adjacency_matrix.shape != (self.node_types[node_type_row].count,
self.node_types[node_type_column].count):
raise ValueError('adjacency_matrix shape must be (num_row_nodes, num_column_nodes)')
if adjacency_matrix_backward is not None and \
adjacency_matrix_backward.shape != (self.node_types[node_type_column].count,
self.node_types[node_type_row].count):
raise ValueError('adjacency_matrix shape must be (num_column_nodes, num_row_nodes)')
two_way = bool(two_way)
if node_type_row == node_type_column and \
adjacency_matrix_backward is not None:
raise ValueError('Relation between nodes of the same type must be expressed using a single matrix')
self.relation_types[node_type_row][node_type_column].append(
RelationType(name, node_type_row, node_type_column,
adjacency_matrix, False))
if node_type_row != node_type_column and two_way:
if adjacency_matrix_backward is None:
adjacency_matrix_backward = adjacency_matrix.transpose(0, 1)
self.relation_types[node_type_column][node_type_row].append(
RelationType(name, node_type_column, node_type_row,
adjacency_matrix_backward, True))
def __repr__(self):
n = len(self.node_types)
if n == 0:
return 'Empty Icosagon Data'
s = ''
s += 'Icosagon Data with:\n'
s += '- ' + str(n) + ' node type(s):\n'
for nt in self.node_types:
s += ' - ' + nt.name + '\n'
if len(self.relation_types) == 0:
s += '- No relation types\n'
return s.strip()
s_1 = ''
count = 0
for i in range(n):
for j in range(n):
if i not in self.relation_types or \
j not in self.relation_types[i]:
continue
s_1 += ' - ' + self.node_types[i].name + ' -- ' + \
self.node_types[j].name + ':\n'
for r in self.relation_types[i][j]:
if r.is_autogenerated:
continue
s_1 += ' - ' + r.name + '\n'
count += 1
s += '- %d relation type(s):\n' % count
s += s_1
return s.strip()
# n = sum(map(len, self.relation_types))
#
# for i in range(n):
# for j in range(n):
# key = (i, j)
# if key not in self.relation_types:
# continue
# rels = self.relation_types[key]
#
# for r in rels:
#
# return s.strip()

+ 49
- 0
tests/icosagon/test_data.py Zobrazit soubor

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from icosagon import Data
import torch
import pytest
def test_data_01():
d = Data()
d.add_node_type('Gene', 1000)
d.add_node_type('Drug', 100)
dummy_0 = torch.zeros((100, 1000))
dummy_1 = torch.zeros((1000, 100))
dummy_2 = torch.zeros((100, 100))
dummy_3 = torch.zeros((1000, 1000))
d.add_relation_type('Target', 1, 0, dummy_0)
d.add_relation_type('Interaction', 0, 0, dummy_3)
d.add_relation_type('Side Effect: Nausea', 1, 1, dummy_2)
d.add_relation_type('Side Effect: Infertility', 1, 1, dummy_2)
d.add_relation_type('Side Effect: Death', 1, 1, dummy_2)
print(d)
def test_data_02():
d = Data()
d.add_node_type('Gene', 1000)
d.add_node_type('Drug', 100)
dummy_0 = torch.zeros((100, 1000))
dummy_1 = torch.zeros((1000, 100))
dummy_2 = torch.zeros((100, 100))
dummy_3 = torch.zeros((1000, 1000))
with pytest.raises(ValueError):
d.add_relation_type('Target', 1, 0, dummy_1)
with pytest.raises(ValueError):
d.add_relation_type('Interaction', 0, 0, dummy_2)
with pytest.raises(ValueError):
d.add_relation_type('Side Effect: Nausea', 1, 1, dummy_3)
with pytest.raises(ValueError):
d.add_relation_type('Side Effect: Infertility', 1, 1, dummy_3)
with pytest.raises(ValueError):
d.add_relation_type('Side Effect: Death', 1, 1, dummy_3)
print(d)
def test_data_03():
d = Data()
d.add_node_type('Gene', 1000)
d.add_node_type('Drug', 100)
with pytest.raises(ValueError):
d.add_relation_type('Target', 1, 0, None)
print(d)

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