Faster method of computing confusion matrix?

Question

I am computing my confusion matrix as shown below for image semantic segmentation which is a pretty verbose approach:

def confusion_matrix(preds, labels, con         


        

Answer 1

Thanks to Grigory Feldman for the answer! I had to change a few things to work with my implementation.

For future lookers, here is my final function that sums up the percentages of each confusion matrix over a batch of inputs (to be used in training or testing loops)

def confusion_matrix_2(y_true, y_pred, sample_sz, conf_m):
    y_pred = normalize(y_pred,0.9)
    obj = y_true[y_true==1]
    no_obj = y_true[y_true==0]
    N = torch.tensor(torch.max(torch.max(y_true), torch.max(y_pred)) + 1,dtype=torch.int)
    y_true = torch.tensor(y_true, dtype=torch.long)
    y_pred = torch.tensor(y_pred, dtype=torch.long)
    y = N * y_true + y_pred
    y = torch.bincount(y.flatten())
    if len(y) < N * N:
        y = torch.cat((y, torch.zeros(N * N - len(y), dtype=torch.long)))
    y = y.reshape(N.item(), N.item())
    y = y.float()
    conf_m[0,:] += y[0,:]/(len(no_obj)*sample_sz)
    conf_m[1,:] += y[1,:]/(len(obj)*sample_sz)
    return conf_m

...
conf_m = torch.zeros((2, 2),dtype=torch.float) # two classes (object or no-object)
for _, data in enumerate(dataloader):
    for img,label in enumerate(data):
        ...
        out = Net(img)
        conf_m = confusion_matrix(out, label, len(data))
        ...
    ...

Answer 2

I use these 2 functions to calc confusion matrix (as it defined in sklearn):

# rewrite sklearn method to torch
def confusion_matrix_1(y_true, y_pred):
    N = max(max(y_true), max(y_pred)) + 1
    y_true = torch.tensor(y_true, dtype=torch.long)
    y_pred = torch.tensor(y_pred, dtype=torch.long)
    return torch.sparse.LongTensor(
        torch.stack([y_true, y_pred]), 
        torch.ones_like(y_true, dtype=torch.long),
        torch.Size([N, N])).to_dense()

# weird trick with bincount
def confusion_matrix_2(y_true, y_pred):
    N = max(max(y_true), max(y_pred)) + 1
    y_true = torch.tensor(y_true, dtype=torch.long)
    y_pred = torch.tensor(y_pred, dtype=torch.long)
    y = N * y_true + y_pred
    y = torch.bincount(y)
    if len(y) < N * N:
        y = torch.cat(y, torch.zeros(N * N - len(y), dtype=torch.long))
    y = y.reshape(N, N)
    return y

y_true = [2, 0, 2, 2, 0, 1]
y_pred = [0, 0, 2, 2, 0, 2]

confusion_matrix_1(y_true, y_pred)
# tensor([[2, 0, 0],
#         [0, 0, 1],
#         [1, 0, 2]])

Second function is faster in case of small number of classes.

%%timeit
confusion_matrix_1(y_true, y_pred)
# 102 µs ± 30.7 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

%%timeit
confusion_matrix_2(y_true, y_pred)
# 25 µs ± 149 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)