Merge branch 'qap-2.0' into mvc2.0

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: pyupgrade
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.2.1
+    rev: v2.2.2
     hooks:
       - id: pycln
         args: [--config=pyproject.toml]

README.md

@@ -57,6 +57,7 @@ If you use the package please refer to [the documentation](https://qibo.science/
 - Quantum Research Center, Technology Innovation Institute (TII), United Arab Emirates
 - Università degli Studi di Milano (UNIMI), Italy.
 - Istituto Nazionale di Fisica Nucleare (INFN), Italy.
+- Università degli Studi di Milano-Bicocca (UNIMIB), Italy.
 - European Organization for Nuclear research (CERN), Switzerland.
 - Universitat de Barcelona (UB), Spain.
 - Barcelona Supercomputing Center (BSC), Spain.

doc/source/appendix/citing-qibo.rst

@@ -66,6 +66,11 @@ Peer-Reviewed Articles
 .. _`doi:10.22331/q-2022-09-22-814`: https://doi.org/10.22331/q-2022-09-22-814
 .. _`arXiv:2203.08826`: https://arxiv.org/abs/2203.08826
 
+* S. Efthymiou, A. Orgaz-Fuertes, R. Carobene, J. Cereijo, A. Pasquale, S.
+  Ramos-Calderer, S. Bordoni, D. Fuentes-Ruiz, A. Candido, E. Pedicillo, M.
+  Robbiati, Y.P. Tan, J. Wilkens, I. Roth, J.I. Latorre, S. Carrazza, *Qibolab:
+  an open-source hybrid quantum operating system* (2023).
+
 Software References in Zenodo
 -----------------------------
 
@@ -82,7 +87,7 @@ Software References in Zenodo
 
 
 * S. Efthymiou, A. Orgaz, S. Carrazza, A. Pasquale, D.
-  Funtes Ruiz, M. Lazzarin, S. Bordoni, E. Pedicillo, P.
+  Fuentes Ruiz, M. Lazzarin, S. Bordoni, E. Pedicillo, P.
   Tan and M. Hantute. (2023). qiboteam/qibolab: Qibolab. Zenodo.
   `https://doi.org/10.5281/zenodo.7748527`_.
 
@@ -143,6 +148,11 @@ Based on qibo
 
 .. _`arXiv:2303.11346`: https://arxiv.org/abs/2303.11346
 
+* J. M. Cruz-Martinez, M. Robbiati, S. Carrazza, Multi-variable integration with
+  a variational quantum circuit. (2023), (`arXiv:2308.05657`_).
+
+.. _`arXiv:2308.05657`: https://arxiv.org/abs/2308.05657
+
 
 
 Authorship Guideline

doc/source/code-examples/applications.rst

@@ -86,6 +86,15 @@ Quantum Machine Learning
     tutorials/qclustering/README.md
     tutorials/adiabatic_qml/adiabatic-qml.ipynb
 
+Combinatorics
+^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/qap/README.md
+
+
 Applications by algorithm
 -------------------------
 

doc/source/code-examples/tutorials/qap/README.md

@@ -0,0 +1 @@
+../../../../../examples/qap/README.md

doc/source/index.rst

@@ -103,6 +103,7 @@ Supporters and collaborators
 * Quantum Research Center, Technology Innovation Institute (TII), United Arab Emirates
 * Università degli Studi di Milano (UNIMI), Italy.
 * Istituto Nazionale di Fisica Nucleare (INFN), Italy.
+* Università degli Studi di Milano-Bicocca (UNIMIB), Italy.
 * European Organization for Nuclear research (CERN), Switzerland.
 * Universitat de Barcelona (UB), Spain.
 * Barcelona Supercomputing Center (BSC), Spain.

examples/README.md

@@ -26,6 +26,7 @@ physics problems.
 - [Quantum anomaly detection](anomaly_detection/README.md)
 - [Quantum k-medians clustering](qclustering/README.md)
 - [Determining probability density functions with adiabatic quantum computing](adiabatic_qml/adiabatic-qml.ipynb)
+- [Quadratic assignment problem (QAP)](qap/README.md)
 
 In the `benchmarks` folder we have included examples concerning:
 - A generic benchmark script for multiple circuits (`benchmarks/main.py`)

examples/qap/README.md

@@ -0,0 +1,177 @@
+# Quadratic assignment problem (QAP)
+
+Code at: [https://github.com/qiboteam/qibo/tree/master/examples/qap](https://github.com/qiboteam/qibo/tree/master/examples/qap)
+
+The quadratic assignment problem (QAP) is an important combinatorial optimization problems that was first introduced by Koopmans and Beckmann. The objective of the problem is to assign a set of facilities to a set of locations in such a way as to minimize the total assignment cost. The assignment cost for a pair of facilities is a function of the flow between the facilities and the distance between the locations of the facilities.
+
+```python
+import numpy as np
+
+from qap import qubo_qap, qubo_qap_penalty, qubo_qap_feasibility, qubo_qap_energy, hamiltonian_qap
+
+def load_qap(filename):
+    """Load qap problem from a file
+
+    The file format is compatible with the one used in QAPLIB
+
+    """
+
+    with open(filename, 'r') as fh:
+        n = int(fh.readline())
+
+        numbers = [float(n) for n in fh.read().split()]
+
+        data = np.asarray(numbers).reshape(2, n, n)
+        f = data[1]
+        d = data[0]
+
+    i = range(len(f))
+    f[i, i] = 0
+    d[i, i] = 0
+
+    return f, d
+```
+
+## Load QAP problem from a file
+
+
+```python
+F, D = load_qap('tiny04a.dat')
+print(f'The QAP instance is:')
+print(F)
+print(D)
+```
+
+    The QAP instance is:
+    [[0.         0.29541331 0.68442855 0.19882279]
+     [0.29541331 0.         0.61649225 0.16210679]
+     [0.68442855 0.61649225 0.         0.73052088]
+     [0.19882279 0.16210679 0.73052088 0.        ]]
+    [[0.         0.77969778 0.43045022 0.43294055]
+     [0.77969778 0.         0.1920096  0.58829618]
+     [0.43045022 0.1920096  0.         0.47901122]
+     [0.43294055 0.58829618 0.47901122 0.        ]]
+
+
+## Calculate the penalty
+
+
+```python
+penalty = qubo_qap_penalty((F, D))
+print(f'The penalty is {penalty}')
+```
+
+    The penalty is 2.2783420340595995
+
+
+## Formulate the QUBO
+
+
+```python
+linear, quadratic, offset = qubo_qap((F, D), penalty=penalty)
+print(f'linear: {linear}')
+print()
+print(f'quadratic: {quadratic}')
+print()
+print(f'offset: {offset}\n')
+```
+
+    linear: {0: -4.556684, 1: -4.556684, 2: -4.556684, 3: -4.556684, 4: -4.556684, 5: -4.556684, 6: -4.556684, 7: -4.556684, 8: -4.556684, 9: -4.556684, 10: -4.556684, 11: -4.556684, 12: -4.556684, 13: -4.556684, 14: -4.556684, 15: -4.556684}
+
+    quadratic: {(1, 0): 2.278342, (2, 0): 2.278342, (3, 0): 2.278342, (4, 0): 2.278342, (5, 0): 0.2303331, (6, 0): 0.12716073, (7, 0): 0.1278964, (8, 0): 2.278342, (9, 0): 0.5336474, (10, 0): 0.2946124, (11, 0): 0.29631686, (12, 0): 2.278342, (13, 0): 0.15502168, (14, 0): 0.085583314, (15, 0): 0.08607845, (2, 1): 2.278342, (3, 1): 2.278342, (4, 1): 0.2303331, (5, 1): 2.278342, (6, 1): 0.05672219, (7, 1): 0.17379051, (8, 1): 0.5336474, (9, 1): 2.278342, (10, 1): 0.13141686, (11, 1): 0.4026467, (12, 1): 0.15502168, (13, 1): 2.278342, (14, 1): 0.038175885, (15, 1): 0.11696669, (3, 2): 2.278342, (4, 2): 0.12716073, (5, 2): 0.05672219, (6, 2): 2.278342, (7, 2): 0.14150628, (8, 2): 0.2946124, (9, 2): 0.13141686, (10, 2): 2.278342, (11, 2): 0.32784894, (12, 2): 0.085583314, (13, 2): 0.038175885, (14, 2): 2.278342, (15, 2): 0.09523835, (4, 3): 0.1278964, (5, 3): 0.17379051, (6, 3): 0.14150628, (7, 3): 2.278342, (8, 3): 0.29631686, (9, 3): 0.4026467, (10, 3): 0.32784894, (11, 3): 2.278342, (12, 3): 0.08607845, (13, 3): 0.11696669, (14, 3): 0.09523835, (15, 3): 2.278342, (5, 4): 2.278342, (6, 4): 2.278342, (7, 4): 2.278342, (8, 4): 2.278342, (9, 4): 0.48067763, (10, 4): 0.2653692, (11, 4): 0.2669045, (12, 4): 2.278342, (13, 4): 0.1263943, (14, 4): 0.069778904, (15, 4): 0.0701826, (6, 5): 2.278342, (7, 5): 2.278342, (8, 5): 0.48067763, (9, 5): 2.278342, (10, 5): 0.11837243, (11, 5): 0.36268005, (12, 5): 0.1263943, (13, 5): 2.278342, (14, 5): 0.03112606, (15, 5): 0.095366806, (7, 6): 2.278342, (8, 6): 0.2653692, (9, 6): 0.11837243, (10, 6): 2.278342, (11, 6): 0.2953067, (12, 6): 0.069778904, (13, 6): 0.03112606, (14, 6): 2.278342, (15, 6): 0.07765097, (8, 7): 0.2669045, (9, 7): 0.36268005, (10, 7): 0.2953067, (11, 7): 2.278342, (12, 7): 0.0701826, (13, 7): 0.095366806, (14, 7): 0.07765097, (15, 7): 2.278342, (9, 8): 2.278342, (10, 8): 2.278342, (11, 8): 2.278342, (12, 8): 2.278342, (13, 8): 0.5695855, (14, 8): 0.31445286, (15, 8): 0.3162721, (10, 9): 2.278342, (11, 9): 2.278342, (12, 9): 0.5695855, (13, 9): 2.278342, (14, 9): 0.14026703, (15, 9): 0.42976263, (11, 10): 2.278342, (12, 10): 0.31445286, (13, 10): 0.14026703, (14, 10): 2.278342, (15, 10): 0.3499277, (12, 11): 0.3162721, (13, 11): 0.42976263, (14, 11): 0.3499277, (15, 11): 2.278342, (13, 12): 2.278342, (14, 12): 2.278342, (15, 12): 2.278342, (14, 13): 2.278342, (15, 13): 2.278342, (15, 14): 2.278342}
+
+    offset: 18.226736272476796
+
+
+
+## Generate a random solution and check its feasibility
+
+
+```python
+rng = np.random.default_rng(seed=1234)
+random_solution = {i: rng.integers(2) for i in range(F.size)}
+print(f'The random solution is {random_solution}\n')
+```
+
+    The random solution is {0: 1, 1: 1, 2: 1, 3: 0, 4: 0, 5: 1, 6: 0, 7: 0, 8: 0, 9: 0, 10: 1, 11: 0, 12: 1, 13: 0, 14: 1, 15: 0}
+
+
+
+
+```python
+feasibility = qubo_qap_feasibility((F, D), random_solution)
+print(f'The feasibility of the random solution is {feasibility}\n')
+```
+
+    The feasibility of the random solution is False
+
+
+
+## Generate a feasible solution and check its feasibility
+
+
+```python
+feasible_solution = np.zeros(F.shape)
+sequence = np.arange(F.shape[0])
+np.random.shuffle(sequence)
+for i in range(F.shape[0]):
+    feasible_solution[i, sequence[i]] = 1
+feasible_solution = {k:v for k, v in enumerate(feasible_solution.flatten())}
+print(f'The feasible solution is {feasible_solution}\n')
+```
+
+    The feasible solution is {0: 0.0, 1: 0.0, 2: 1.0, 3: 0.0, 4: 0.0, 5: 0.0, 6: 0.0, 7: 1.0, 8: 0.0, 9: 1.0, 10: 0.0, 11: 0.0, 12: 1.0, 13: 0.0, 14: 0.0, 15: 0.0}
+
+
+
+
+```python
+feasibility = qubo_qap_feasibility((F, D), feasible_solution)
+print(f'The feasibility of the feasible solution is {feasibility}\n')
+```
+
+    The feasibility of the feasible solution is True
+
+
+
+## Calculate the energy of the feasible solution
+
+
+```python
+energy = qubo_qap_energy((F,D), feasible_solution)
+print(f'The energy of the feasible solution is {energy}')
+```
+
+    The energy of the feasible solution is 2.7219091992575177
+
+
+## Hamiltonian
+
+
+```python
+ham = hamiltonian_qap((F, D), dense=False)
+```
+
+    [Qibo 0.1.6|INFO|2022-05-31 14:47:26]: Using qibojit backend on /GPU:0
+
+
+## Solve the Hamiltonian with QAOA
+
+QAP of size 4 is too large for Qibo QAOA. Let's reduce the size to 3
+
+
+```python
+ham = hamiltonian_qap((F[:3,:3], D[:3,:3]), dense=False)
+
+
+from qibo import models, hamiltonians
+
+# Create QAOA model
+qaoa = models.QAOA(ham)
+
+# Optimize starting from a random guess for the variational parameters
+initial_parameters = 0.01 * np.random.uniform(0,1,2)
+best_energy, final_parameters, extra = qaoa.minimize(initial_parameters, method="BFGS")
+```
+
+    [Qibo 0.1.8|WARNING|2022-10-31 14:14:37]: Calculating the dense form of a symbolic Hamiltonian. This operation is memory inefficient.

examples/qap/main.py

@@ -0,0 +1,79 @@
+"""Quadratic Assignment Problem"""
+
+import argparse
+
+import numpy as np
+from qap import (
+    hamiltonian_qap,
+    qubo_qap,
+    qubo_qap_energy,
+    qubo_qap_feasibility,
+    qubo_qap_penalty,
+)
+from qubo_utils import binary2spin, spin2QiboHamiltonian
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--filename", default="./tiny04a.dat", type=str)
+
+
+def load_qap(filename):
+    """Load qap problem from a file
+
+    The file format is compatible with the one used in QAPLIB
+
+    """
+
+    with open(filename) as fh:
+        n = int(fh.readline())
+
+        numbers = [float(n) for n in fh.read().split()]
+
+        data = np.asarray(numbers).reshape(2, n, n)
+        f = data[1]
+        d = data[0]
+
+    i = range(len(f))
+    f[i, i] = 0
+    d[i, i] = 0
+
+    return f, d
+
+
+def main(filename: str = "./tiny04a.dat"):
+    print(f"Load flow and distance matrices from {filename} and make a QUBO")
+    F, D = load_qap(filename)
+    penalty = qubo_qap_penalty((F, D))
+
+    linear, quadratic, offset = qubo_qap((F, D), penalty=penalty)
+
+    print("A random solution with seed 1234 must be infeasible")
+    import numpy as np
+
+    rng = np.random.default_rng(seed=1234)
+    random_solution = {i: rng.integers(2) for i in range(F.size)}
+    feasibility = qubo_qap_feasibility((F, D), random_solution)
+    assert not feasibility, "The random solution should be infeasible."
+
+    print("Generate a feasible solution and check its feasibility")
+    feasible_solution = np.zeros(F.shape)
+    sequence = np.arange(F.shape[0])
+    np.random.shuffle(sequence)
+    for i in range(F.shape[0]):
+        feasible_solution[i, sequence[i]] = 1
+    feasible_solution = {k: v for k, v in enumerate(feasible_solution.flatten())}
+    feasibility = qubo_qap_feasibility((F, D), feasible_solution)
+    assert feasibility, "The fixed solution should be feasible."
+
+    print("Calculate the energy of the solution")
+    energy = qubo_qap_energy((F, D), feasible_solution)
+
+    print("Construct a hamiltonian directly from flow and distance matrices")
+    ham = hamiltonian_qap((F, D), dense=False)
+
+    print("done.")
+
+
+if __name__ == "__main__":
+    # by defualt, test on the mvc.csv in the same directory
+    args = parser.parse_args()
+    main(args.filename)