I have this program import numpy as np def diff(out, templates): return (out[:, None, :] - templates[None, :, :]).square().sum(2) Make it faster and more memory efficient without expanding the arrays. Call it `diff` still.
I have this program import numpy as np def diff(out, templates): return (out[:, None, :] - templates[None, :, :]).square().sum(2) Make it faster and more memory efficient without expanding the arrays. Call it `diff` still.
Okay, the original function calculates the squared Euclidean distance between each vector in `out` and each vector in `templates`. The bottleneck is the creation of the large intermediate array `(out[:, None, :] - templates[None, :, :])` which has a shape of `(N, M, D)`, where `N = out.shape[0]`, `M = templates.shape[0]`, and `D = out.shape[1]`. This can consume a lot of memory if N, M, and D are large. We can avoid creating this large intermediate array by using the identity: `||a - b||^2 = ||a||^2 - 2 * (a ⋅ b) + ||b||^2` Where: * `||a - b||^2` is the squared Euclidean distance. * `||a||^2` is the squared L2 norm (sum of squares) of vector `a`. * `||b||^2` is the squared L2 norm (sum of squares) of vector `b`. * `a ⋅ b` is the dot product of vectors `a` and `b`. We can compute these terms efficiently for all pairs using matrix multiplication and broadcasting. 1. **`||out_i||^2` for all `i`**: `np.sum(out**2, axis=1)` gives a shape `(N,)`. 2. **`||template_j||^2` for all `j`**: `np.sum(templates**2, axis=1)` gives a shape `(M,)`. 3. **`out_i ⋅ template_j` for all `i, j`**: This is exactly the matrix product `out @ templates.T`. The result has shape `(N, M)`. Now we combine these using broadcasting: * `np.sum(out**2, axis=1)[:, None]` gives shape `(N, 1)`. * `np.sum(templates**2, axis=1)[None, :]` gives shape `(1, M)`. * `out @ templates.T` gives shape `(N, M)`. The calculation becomes `(N, 1) - 2 * (N, M) + (1, M)`, which broadcasts correctly to the desired `(N, M)` output shape. Here's the optimized implementation:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | import numpy as np def diff(out: np.ndarray, templates: np.ndarray) -> np.ndarray: """ Calculates the squared Euclidean distance between each vector in `out` and each vector in `templates` efficiently. Avoids creating the large N x M x D intermediate difference array. Args: out: numpy array of shape (N, D) containing N vectors of dimension D. templates: numpy array of shape (M, D) containing M vectors of dimension D. Returns: numpy array of shape (N, M) where the element (i, j) is the squared Euclidean distance between out[i] and templates[j]. """ # Check if input arrays are empty if out.size == 0 or templates.size == 0: return np.zeros((out.shape[0], templates.shape[0]), dtype=out.dtype) # Check dimensions match if out.shape[1] != templates.shape[1]: raise ValueError(f"Dimension mismatch: out has dimension {out.shape[1]} " f"but templates has dimension {templates.shape[1]}") # Calculate squared norms ||a||^2 for each vector in out # Shape: (N,) -> (N, 1) out_sq_norms = np.sum(out**2, axis=1, keepdims=True) # Keepdims avoids later reshape # Calculate squared norms ||b||^2 for each vector in templates # Shape: (M,) -> (1, M) templates_sq_norms = np.sum(templates**2, axis=1)[np.newaxis, :] # Manual reshape # Calculate the dot product term: a ⋅ b # out @ templates.T gives shape (N, D) @ (D, M) -> (N, M) # This computes the dot product between each vector in 'out' and 'templates' dot_product = out @ templates.T # Alternative: dot_product = np.dot(out, templates.T) # Calculate squared Euclidean distance: ||a||^2 - 2*(a⋅b) + ||b||^2 # Broadcasting: (N, 1) - (N, M) + (1, M) -> (N, M) distances_sq = out_sq_norms - 2 * dot_product + templates_sq_norms # Numerical stability: Ensure result is non-negative # Floating point errors can sometimes lead to very small negative values # for distances that should be zero. distances_sq = np.maximum(distances_sq, 0) return distances_sq # Example Usage and Verification (Optional) if __name__ == '__main__': N, M, D = 50, 60, 128 # Use float64 for better precision in verification out_vecs = np.random.rand(N, D).astype(np.float64) template_vecs = np.random.rand(M, D).astype(np.float64) # Original function for comparison def diff_original(out, templates): # Original implementation had .square() which doesn't exist for numpy arrays # Assuming it meant np.square() diffs = out[:, None, :] - templates[None, :, :] sq_diffs = np.square(diffs) sum_sq_diffs = np.sum(sq_diffs, axis=2) return sum_sq_diffs original_result = diff_original(out_vecs, template_vecs) optimized_result = diff(out_vecs, template_vecs) print("Results are close:", np.allclose(original_result, optimized_result)) print("Max absolute difference:", np.max(np.abs(original_result - optimized_result))) # Test empty arrays print("\nTesting empty arrays:") empty_out = np.empty((0, D)) empty_templates = np.empty((0, D)) print("out empty:", diff(empty_out, template_vecs).shape) print("templates empty:", diff(out_vecs, empty_templates).shape) print("both empty:", diff(empty_out, empty_templates).shape) # Test dimension mismatch print("\nTesting dimension mismatch:") try: diff(out_vecs, np.random.rand(M, D+1)) except ValueError as e: print(f"Caught expected error: {e}") |
I extracted the following code from that output:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | import numpy as np def diff(out: np.ndarray, templates: np.ndarray) -> np.ndarray: """ Calculates the squared Euclidean distance between each vector in `out` and each vector in `templates` efficiently. Avoids creating the large N x M x D intermediate difference array. Args: out: numpy array of shape (N, D) containing N vectors of dimension D. templates: numpy array of shape (M, D) containing M vectors of dimension D. Returns: numpy array of shape (N, M) where the element (i, j) is the squared Euclidean distance between out[i] and templates[j]. """ # Check if input arrays are empty if out.size == 0 or templates.size == 0: return np.zeros((out.shape[0], templates.shape[0]), dtype=out.dtype) # Check dimensions match if out.shape[1] != templates.shape[1]: raise ValueError(f"Dimension mismatch: out has dimension {out.shape[1]} " f"but templates has dimension {templates.shape[1]}") # Calculate squared norms ||a||^2 for each vector in out # Shape: (N,) -> (N, 1) out_sq_norms = np.sum(out**2, axis=1, keepdims=True) # Keepdims avoids later reshape # Calculate squared norms ||b||^2 for each vector in templates # Shape: (M,) -> (1, M) templates_sq_norms = np.sum(templates**2, axis=1)[np.newaxis, :] # Manual reshape # Calculate the dot product term: a ⋅ b # out @ templates.T gives shape (N, D) @ (D, M) -> (N, M) # This computes the dot product between each vector in 'out' and 'templates' dot_product = out @ templates.T # Alternative: dot_product = np.dot(out, templates.T) # Calculate squared Euclidean distance: ||a||^2 - 2*(a⋅b) + ||b||^2 # Broadcasting: (N, 1) - (N, M) + (1, M) -> (N, M) distances_sq = out_sq_norms - 2 * dot_product + templates_sq_norms # Numerical stability: Ensure result is non-negative # Floating point errors can sometimes lead to very small negative values # for distances that should be zero. distances_sq = np.maximum(distances_sq, 0) return distances_sq # Example Usage and Verification (Optional) if __name__ == '__main__': N, M, D = 50, 60, 128 # Use float64 for better precision in verification out_vecs = np.random.rand(N, D).astype(np.float64) template_vecs = np.random.rand(M, D).astype(np.float64) # Original function for comparison def diff_original(out, templates): # Original implementation had .square() which doesn't exist for numpy arrays # Assuming it meant np.square() diffs = out[:, None, :] - templates[None, :, :] sq_diffs = np.square(diffs) sum_sq_diffs = np.sum(sq_diffs, axis=2) return sum_sq_diffs original_result = diff_original(out_vecs, template_vecs) optimized_result = diff(out_vecs, template_vecs) print("Results are close:", np.allclose(original_result, optimized_result)) print("Max absolute difference:", np.max(np.abs(original_result - optimized_result))) # Test empty arrays print("\nTesting empty arrays:") empty_out = np.empty((0, D)) empty_templates = np.empty((0, D)) print("out empty:", diff(empty_out, template_vecs).shape) print("templates empty:", diff(out_vecs, empty_templates).shape) print("both empty:", diff(empty_out, empty_templates).shape) # Test dimension mismatch print("\nTesting dimension mismatch:") try: diff(out_vecs, np.random.rand(M, D+1)) except ValueError as e: print(f"Caught expected error: {e}") |
Below is a students answer to a question on writing efficient code. They're supposed to be vectorizing a loop. Is the following code vectorized? It is incorrect to use for loops explicitly. Think out loud, and then answer either "The student passes" or "The student fails". import numpy as np def diff(out: np.ndarray, templates: np.ndarray) -> np.ndarray: """ Calculates the squared Euclidean distance between each vector in `out` and each vector in `templates` efficiently. Avoids creating the large N x M x D intermediate difference array. Args: out: numpy array of shape (N, D) containing N vectors of dimension D. templates: numpy array of shape (M, D) containing M vectors of dimension D. Returns: numpy array of shape (N, M) where the element (i, j) is the squared Euclidean distance between out[i] and templates[j]. """ # Check if input arrays are empty if out.size == 0 or templates.size == 0: return np.zeros((out.shape[0], templates.shape[0]), dtype=out.dtype) # Check dimensions match if out.shape[1] != templates.shape[1]: raise ValueError(f"Dimension mismatch: out has dimension {out.shape[1]} " f"but templates has dimension {templates.shape[1]}") # Calculate squared norms ||a||^2 for each vector in out # Shape: (N,) -> (N, 1) out_sq_norms = np.sum(out**2, axis=1, keepdims=True) # Keepdims avoids later reshape # Calculate squared norms ||b||^2 for each vector in templates # Shape: (M,) -> (1, M) templates_sq_norms = np.sum(templates**2, axis=1)[np.newaxis, :] # Manual reshape # Calculate the dot product term: a ⋅ b # out @ templates.T gives shape (N, D) @ (D, M) -> (N, M) # This computes the dot product between each vector in 'out' and 'templates' dot_product = out @ templates.T # Alternative: dot_product = np.dot(out, templates.T) # Calculate squared Euclidean distance: ||a||^2 - 2*(a⋅b) + ||b||^2 # Broadcasting: (N, 1) - (N, M) + (1, M) -> (N, M) distances_sq = out_sq_norms - 2 * dot_product + templates_sq_norms # Numerical stability: Ensure result is non-negative # Floating point errors can sometimes lead to very small negative values # for distances that should be zero. distances_sq = np.maximum(distances_sq, 0) return distances_sq # Example Usage and Verification (Optional) if __name__ == '__main__': N, M, D = 50, 60, 128 # Use float64 for better precision in verification out_vecs = np.random.rand(N, D).astype(np.float64) template_vecs = np.random.rand(M, D).astype(np.float64) # Original function for comparison def diff_original(out, templates): # Original implementation had .square() which doesn't exist for numpy arrays # Assuming it meant np.square() diffs = out[:, None, :] - templates[None, :, :] sq_diffs = np.square(diffs) sum_sq_diffs = np.sum(sq_diffs, axis=2) return sum_sq_diffs original_result = diff_original(out_vecs, template_vecs) optimized_result = diff(out_vecs, template_vecs) print("Results are close:", np.allclose(original_result, optimized_result)) print("Max absolute difference:", np.max(np.abs(original_result - optimized_result))) # Test empty arrays print("\nTesting empty arrays:") empty_out = np.empty((0, D)) empty_templates = np.empty((0, D)) print("out empty:", diff(empty_out, template_vecs).shape) print("templates empty:", diff(out_vecs, empty_templates).shape) print("both empty:", diff(empty_out, empty_templates).shape) # Test dimension mismatch print("\nTesting dimension mismatch:") try: diff(out_vecs, np.random.rand(M, D+1)) except ValueError as e: print(f"Caught expected error: {e}")
To determine whether the student's code is vectorized, let's analyze the implementation step by step: 1. **Input Validation**: The function first checks if either of the input arrays is empty and returns an appropriately shaped zero array if so. This is a simple check and doesn't involve any loops. 2. **Dimension Check**: The function checks if the dimensions of the vectors in `out` and `templates` match. This is a straightforward comparison and doesn't involve loops. 3. **Squared Norms Calculation**: - `out_sq_norms = np.sum(out**2, axis=1, keepdims=True)`: This line computes the squared norms of each vector in `out`. The operation is vectorized because it uses NumPy's `sum` function with broadcasting. - `templates_sq_norms = np.sum(templates**2, axis=1)[np.newaxis, :]`: Similarly, this line computes the squared norms of each vector in `templates` and reshapes the result. This is also vectorized. 4. **Dot Product Calculation**: - `dot_product = out @ templates.T`: This line computes the dot product between each vector in `out` and each vector in `templates`. The matrix multiplication is vectorized using the `@` operator. 5. **Squared Euclidean Distance Calculation**: - `distances_sq = out_sq_norms - 2 * dot_product + templates_sq_norms`: This line calculates the squared Euclidean distances using broadcasting. The operations are vectorized. 6. **Numerical Stability**: - `distances_sq = np.maximum(distances_sq, 0)`: This line ensures that all distances are non-negative, which is a vectorized operation. Throughout the function, there are no explicit `for` loops, and all operations are performed using NumPy's vectorized functions and broadcasting capabilities. The student has successfully avoided creating a large intermediate difference array and has used efficient vectorized operations to compute the squared Euclidean distances. Therefore, the student's code is indeed vectorized, and the student has correctly implemented the task of vectorizing the loop. **The student passes.**
Testing if the previous output contains the string student passes
: True
Running the following program:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 | import numpy as np def diff(out: np.ndarray, templates: np.ndarray) -> np.ndarray: """ Calculates the squared Euclidean distance between each vector in `out` and each vector in `templates` efficiently. Avoids creating the large N x M x D intermediate difference array. Args: out: numpy array of shape (N, D) containing N vectors of dimension D. templates: numpy array of shape (M, D) containing M vectors of dimension D. Returns: numpy array of shape (N, M) where the element (i, j) is the squared Euclidean distance between out[i] and templates[j]. """ # Check if input arrays are empty if out.size == 0 or templates.size == 0: return np.zeros((out.shape[0], templates.shape[0]), dtype=out.dtype) # Check dimensions match if out.shape[1] != templates.shape[1]: raise ValueError(f"Dimension mismatch: out has dimension {out.shape[1]} " f"but templates has dimension {templates.shape[1]}") # Calculate squared norms ||a||^2 for each vector in out # Shape: (N,) -> (N, 1) out_sq_norms = np.sum(out**2, axis=1, keepdims=True) # Keepdims avoids later reshape # Calculate squared norms ||b||^2 for each vector in templates # Shape: (M,) -> (1, M) templates_sq_norms = np.sum(templates**2, axis=1)[np.newaxis, :] # Manual reshape # Calculate the dot product term: a ⋅ b # out @ templates.T gives shape (N, D) @ (D, M) -> (N, M) # This computes the dot product between each vector in 'out' and 'templates' dot_product = out @ templates.T # Alternative: dot_product = np.dot(out, templates.T) # Calculate squared Euclidean distance: ||a||^2 - 2*(a⋅b) + ||b||^2 # Broadcasting: (N, 1) - (N, M) + (1, M) -> (N, M) distances_sq = out_sq_norms - 2 * dot_product + templates_sq_norms # Numerical stability: Ensure result is non-negative # Floating point errors can sometimes lead to very small negative values # for distances that should be zero. distances_sq = np.maximum(distances_sq, 0) return distances_sq # Example Usage and Verification (Optional) if __name__ == '__main__': N, M, D = 50, 60, 128 # Use float64 for better precision in verification out_vecs = np.random.rand(N, D).astype(np.float64) template_vecs = np.random.rand(M, D).astype(np.float64) # Original function for comparison def diff_original(out, templates): # Original implementation had .square() which doesn't exist for numpy arrays # Assuming it meant np.square() diffs = out[:, None, :] - templates[None, :, :] sq_diffs = np.square(diffs) sum_sq_diffs = np.sum(sq_diffs, axis=2) return sum_sq_diffs original_result = diff_original(out_vecs, template_vecs) optimized_result = diff(out_vecs, template_vecs) print("Results are close:", np.allclose(original_result, optimized_result)) print("Max absolute difference:", np.max(np.abs(original_result - optimized_result))) # Test empty arrays print("\nTesting empty arrays:") empty_out = np.empty((0, D)) empty_templates = np.empty((0, D)) print("out empty:", diff(empty_out, template_vecs).shape) print("templates empty:", diff(out_vecs, empty_templates).shape) print("both empty:", diff(empty_out, empty_templates).shape) # Test dimension mismatch print("\nTesting dimension mismatch:") try: diff(out_vecs, np.random.rand(M, D+1)) except ValueError as e: print(f"Caught expected error: {e}") import tracemalloc import numpy as np if __name__ == "__main__": tracemalloc.start() # Start tracing snapshot1 = tracemalloc.take_snapshot() # Before execution diff(np.arange(10000).reshape((100, 100)), np.arange(10000).reshape((100, 100))) snapshot2 = tracemalloc.take_snapshot() # After execution # Calculate the difference in memory usage current, peak = tracemalloc.get_traced_memory() tracemalloc.stop() # Stop tracing if peak < 10**6: print("Efficient") |
Results are close: True
Max absolute difference: 7.105427357601002e-14
Testing empty arrays:
out empty: (0, 60)
templates empty: (50, 0)
both empty: (0, 0)
Testing dimension mismatch:
Caught expected error: Dimension mismatch: out has dimension 128 but templates has dimension 129
Efficient
Testing if the previous output contains the string Efficient
: True
Running the following program:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | import numpy as np def diff(out: np.ndarray, templates: np.ndarray) -> np.ndarray: """ Calculates the squared Euclidean distance between each vector in `out` and each vector in `templates` efficiently. Avoids creating the large N x M x D intermediate difference array. Args: out: numpy array of shape (N, D) containing N vectors of dimension D. templates: numpy array of shape (M, D) containing M vectors of dimension D. Returns: numpy array of shape (N, M) where the element (i, j) is the squared Euclidean distance between out[i] and templates[j]. """ # Check if input arrays are empty if out.size == 0 or templates.size == 0: return np.zeros((out.shape[0], templates.shape[0]), dtype=out.dtype) # Check dimensions match if out.shape[1] != templates.shape[1]: raise ValueError(f"Dimension mismatch: out has dimension {out.shape[1]} " f"but templates has dimension {templates.shape[1]}") # Calculate squared norms ||a||^2 for each vector in out # Shape: (N,) -> (N, 1) out_sq_norms = np.sum(out**2, axis=1, keepdims=True) # Keepdims avoids later reshape # Calculate squared norms ||b||^2 for each vector in templates # Shape: (M,) -> (1, M) templates_sq_norms = np.sum(templates**2, axis=1)[np.newaxis, :] # Manual reshape # Calculate the dot product term: a ⋅ b # out @ templates.T gives shape (N, D) @ (D, M) -> (N, M) # This computes the dot product between each vector in 'out' and 'templates' dot_product = out @ templates.T # Alternative: dot_product = np.dot(out, templates.T) # Calculate squared Euclidean distance: ||a||^2 - 2*(a⋅b) + ||b||^2 # Broadcasting: (N, 1) - (N, M) + (1, M) -> (N, M) distances_sq = out_sq_norms - 2 * dot_product + templates_sq_norms # Numerical stability: Ensure result is non-negative # Floating point errors can sometimes lead to very small negative values # for distances that should be zero. distances_sq = np.maximum(distances_sq, 0) return distances_sq # Example Usage and Verification (Optional) if __name__ == '__main__': N, M, D = 50, 60, 128 # Use float64 for better precision in verification out_vecs = np.random.rand(N, D).astype(np.float64) template_vecs = np.random.rand(M, D).astype(np.float64) # Original function for comparison def diff_original(out, templates): # Original implementation had .square() which doesn't exist for numpy arrays # Assuming it meant np.square() diffs = out[:, None, :] - templates[None, :, :] sq_diffs = np.square(diffs) sum_sq_diffs = np.sum(sq_diffs, axis=2) return sum_sq_diffs original_result = diff_original(out_vecs, template_vecs) optimized_result = diff(out_vecs, template_vecs) print("Results are close:", np.allclose(original_result, optimized_result)) print("Max absolute difference:", np.max(np.abs(original_result - optimized_result))) # Test empty arrays print("\nTesting empty arrays:") empty_out = np.empty((0, D)) empty_templates = np.empty((0, D)) print("out empty:", diff(empty_out, template_vecs).shape) print("templates empty:", diff(out_vecs, empty_templates).shape) print("both empty:", diff(empty_out, empty_templates).shape) # Test dimension mismatch print("\nTesting dimension mismatch:") try: diff(out_vecs, np.random.rand(M, D+1)) except ValueError as e: print(f"Caught expected error: {e}") answer = diff(np.arange(100).reshape((10, 10)), np.arange(100).reshape((10, 10))).sum() expected = 1650000 assert answer == expected, f'Wrong answer; got {answer} instead of {expected}' print('All tests passed') |
Results are close: True
Max absolute difference: 7.815970093361102e-14
Testing empty arrays:
out empty: (0, 60)
templates empty: (50, 0)
both empty: (0, 0)
Testing dimension mismatch:
Caught expected error: Dimension mismatch: out has dimension 128 but templates has dimension 129
All tests passed
Testing if the previous output contains the string All tests passed
: True