decagon-pytorch/tests/icosagon/test_fastconv.py

from icosagon.fastconv import _sparse_diag_cat, \
    _cat, \
    FastGraphConv, \
    FastConvLayer
from icosagon.data import _equal
import torch
import pdb
import time
from icosagon.data import Data
from icosagon.input import OneHotInputLayer
from icosagon.convlayer import DecagonLayer


def _make_symmetric(x: torch.Tensor):
    x = (x + x.transpose(0, 1)) / 2
    return x


def _symmetric_random(n_rows, n_columns):
    return _make_symmetric(torch.rand((n_rows, n_columns),
        dtype=torch.float32).round())


def _some_data_with_interactions():
    d = Data()
    d.add_node_type('Gene', 1000)
    d.add_node_type('Drug', 100)

    fam = d.add_relation_family('Drug-Gene', 1, 0, True)
    fam.add_relation_type('Target',
        torch.rand((100, 1000), dtype=torch.float32).round())

    fam = d.add_relation_family('Gene-Gene', 0, 0, True)
    fam.add_relation_type('Interaction',
        _symmetric_random(1000, 1000))

    fam = d.add_relation_family('Drug-Drug', 1, 1, True)
    fam.add_relation_type('Side Effect: Nausea',
        _symmetric_random(100, 100))
    fam.add_relation_type('Side Effect: Infertility',
        _symmetric_random(100, 100))
    fam.add_relation_type('Side Effect: Death',
        _symmetric_random(100, 100))
    return d


def test_sparse_diag_cat_01():
    matrices = [ torch.rand(5, 10).round() for _ in range(7) ]
    ground_truth = torch.zeros(35, 70)
    ground_truth[0:5, 0:10] = matrices[0]
    ground_truth[5:10, 10:20] = matrices[1]
    ground_truth[10:15, 20:30] = matrices[2]
    ground_truth[15:20, 30:40] = matrices[3]
    ground_truth[20:25, 40:50] = matrices[4]
    ground_truth[25:30, 50:60] = matrices[5]
    ground_truth[30:35, 60:70] = matrices[6]
    res = _sparse_diag_cat([ m.to_sparse() for m in matrices ])
    res = res.to_dense()
    assert torch.all(res == ground_truth)


def test_sparse_diag_cat_02():
    x = [ torch.rand(5, 10).round() for _ in range(7) ]
    a = [ m.to_sparse() for m in x ]
    a = _sparse_diag_cat(a)
    b = torch.rand(70, 64)
    res = torch.sparse.mm(a, b)

    ground_truth = torch.zeros(35, 64)
    ground_truth[0:5, :] = torch.mm(x[0], b[0:10])
    ground_truth[5:10, :] = torch.mm(x[1], b[10:20])
    ground_truth[10:15, :] = torch.mm(x[2], b[20:30])
    ground_truth[15:20, :] = torch.mm(x[3], b[30:40])
    ground_truth[20:25, :] = torch.mm(x[4], b[40:50])
    ground_truth[25:30, :] = torch.mm(x[5], b[50:60])
    ground_truth[30:35, :] = torch.mm(x[6], b[60:70])

    assert torch.all(res == ground_truth)


def test_cat_01():
    matrices = [ torch.rand(5, 10) for _ in range(7) ]
    res = _cat(matrices)
    assert res.shape == (35, 10)
    assert not res.is_sparse
    ground_truth = torch.zeros(35, 10)
    for i in range(7):
        ground_truth[i*5:(i+1)*5, :] = matrices[i]
    assert torch.all(res == ground_truth)


def test_cat_02():
    matrices = [ torch.rand(5, 10) for _ in range(7) ]
    ground_truth = torch.zeros(35, 10)
    for i in range(7):
        ground_truth[i*5:(i+1)*5, :] = matrices[i]
    res = _cat([ m.to_sparse() for m in matrices ])
    assert res.shape == (35, 10)
    assert res.is_sparse
    assert torch.all(res.to_dense() == ground_truth)


def test_fast_graph_conv_01():
    # pdb.set_trace()
    adj_mats = [ torch.rand(10, 15).round().to_sparse() \
        for _ in range(23) ]
    fgc = FastGraphConv(32, 64, adj_mats)
    in_repr = torch.rand(15, 32)
    _ = fgc(in_repr)


def test_fast_graph_conv_02():
    t = time.time()
    m = (torch.rand(2000, 2000) < .001).to(torch.float32).to_sparse()
    adj_mats = [ m for _ in range(1300) ]
    print('Generating adj_mats took:', time.time() - t)
    t = time.time()
    fgc = FastGraphConv(32, 64, adj_mats)
    print('FGC constructor took:', time.time() - t)
    in_repr = torch.rand(2000, 32)

    for _ in range(3):
        t = time.time()
        _ = fgc(in_repr)
        print('FGC forward pass took:', time.time() - t)


def test_fast_graph_conv_03():
    adj_mat = [
        [ 0, 0, 1, 0, 1 ],
        [ 0, 1, 0, 1, 0 ],
        [ 1, 0, 1, 0, 0 ]
    ]
    in_repr = torch.rand(5, 32)
    adj_mat = torch.tensor(adj_mat, dtype=torch.float32)
    fgc = FastGraphConv(32, 64, [ adj_mat.to_sparse() ])
    out_repr = fgc(in_repr)
    assert out_repr.shape == (1, 3, 64)
    assert (torch.mm(adj_mat, torch.mm(in_repr, fgc.weights)).view(1, 3, 64) == out_repr).all()


def test_fast_graph_conv_04():
    adj_mat = [
        [ 0, 0, 1, 0, 1 ],
        [ 0, 1, 0, 1, 0 ],
        [ 1, 0, 1, 0, 0 ]
    ]
    in_repr = torch.rand(5, 32)
    adj_mat = torch.tensor(adj_mat, dtype=torch.float32)
    fgc = FastGraphConv(32, 64, [ adj_mat.to_sparse(), adj_mat.to_sparse() ])
    out_repr = fgc(in_repr)
    assert out_repr.shape == (2, 3, 64)
    adj_mat_1 = torch.zeros(adj_mat.shape[0] * 2, adj_mat.shape[1] * 2)
    adj_mat_1[0:3, 0:5] = adj_mat
    adj_mat_1[3:6, 5:10] = adj_mat
    res = torch.mm(in_repr, fgc.weights)
    res = torch.split(res, res.shape[1] // 2, dim=1)
    res = torch.cat(res)
    res = torch.mm(adj_mat_1, res)
    assert (res.view(2, 3, 64) == out_repr).all()


def test_fast_conv_layer_01():
    d = _some_data_with_interactions()
    in_layer = OneHotInputLayer(d)

    d_layer = DecagonLayer(in_layer.output_dim, [32, 32], d)
    seq_1 = torch.nn.Sequential(in_layer, d_layer)
    out_repr_1 = seq_1(None)

    conv_layer = FastConvLayer(in_layer.output_dim, [32, 32], d)
    seq_2 = torch.nn.Sequential(in_layer, conv_layer)
    out_repr_2 = seq_2(None)