├── .gitignore ├── LICENSE ├── README.md ├── dataset ├── expr_matrix_pearsonresidual_7.txt ├── expr_matrix_raw_7.txt └── expr_matrix_sctransform_7.txt ├── matlab ├── i_fullcirc.m ├── i_fullcirc_asym.m ├── i_fullcirc_symm.m ├── i_fullcirc_workaround.m ├── i_kldiverg.m ├── i_normvlpi.m ├── i_qrstates.m ├── i_randpmpi.m ├── nmultichoosek.m ├── permn.m ├── real_data │ ├── s1_readdataset.m │ ├── s4_symmetricnt.m │ ├── s5_asymmetri.m │ ├── xs2_randomparas.m │ ├── xs3_optimzparas.m │ ├── xs3_optimzparas_workaround.m │ └── y1_diffnet.m └── simulated_data │ ├── SERGIO │ ├── gene.py │ ├── old_sergio.py │ └── sergio.py │ ├── coalescent_embedding-master - Shortcut.lnk │ ├── demo_code.m │ ├── example_grn.mat │ ├── i_show_problem.m │ ├── input.mat │ ├── officialpkg - Shortcut.lnk │ ├── output.mat │ ├── pkg_e_qgrn_1.m │ ├── pkg_e_qgrn_2.m │ ├── pkg_e_qgrn_3.m │ ├── pkg_e_writesergiogrn.m │ ├── regs.txt │ ├── require.py │ ├── script.py │ ├── targets.txt │ └── usage_example │ ├── Isomap.m │ ├── PSO_network.mat │ ├── RUN_EXAMPLE.m │ ├── angular_alignment.m │ ├── coalescent_embedding.m │ ├── compare_embedding.m │ ├── greedy_routing.m │ ├── opsahl_11.mat │ ├── plot_embedding.m │ ├── test_01.m │ ├── test_02_smallnet.m │ ├── test_03_angle2qubits.m │ ├── test_04_entanglebits.m │ ├── test_05_optim.m │ ├── test_06_optim_complete.m │ ├── test_a1_simulate_small_networks.m │ └── test_a2_embeding_to_pol.m ├── qscgrn ├── __init__.py ├── optimizer.py ├── qcircuit │ ├── __init__.py │ ├── gates.py │ ├── quantum_circuit.py │ └── utils.py ├── run │ ├── __init__.py │ └── run_qiskit.py ├── utils.py └── visualization │ ├── __init__.py │ ├── qsc_grn.py │ └── qsc_hist.py ├── requirements.txt ├── setup.py ├── test ├── 01_comparison.svg ├── 01_evo_theta.csv ├── 01_example.py ├── 01_p_obs.svg ├── 01_qgrn_network.svg ├── 02_comparison_obs_out.svg ├── 02_comparison_obs_qiskit.svg ├── 02_example.py ├── 02_p_obs.svg ├── 02_qgrn_circuit.svg ├── 02_qgrn_network.svg └── Figure_4_heatmaps_cRY_boundaryeffect.m 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