diff --git a/docs/guide/signaling/carnival.ipynb b/docs/guide/signaling/carnival.ipynb index 7c6289f..f776c6b 100644 --- a/docs/guide/signaling/carnival.ipynb +++ b/docs/guide/signaling/carnival.ipynb @@ -30,7 +30,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 7, "id": "a1684e94", "metadata": {}, "outputs": [ @@ -83,7 +83,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 8, "id": "2a193cb0", "metadata": {}, "outputs": [ @@ -179,10 +179,10 @@ "\n" ], "text/plain": [ - "" + "" ] }, - "execution_count": 2, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } @@ -203,7 +203,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 9, "id": "176d8ced", "metadata": {}, "outputs": [ @@ -211,40 +211,38 @@ "name": "stdout", "output_type": "stream", "text": [ - "(CORNETO) May 11 10:48:17 PM - INFO : 2/2 inputs mapped to the graph\n", - "(CORNETO) May 11 10:48:17 PM - INFO : 2/2 outputs mapped to the graph\n", - "(CORNETO) May 11 10:48:17 PM - INFO : Pruning the graph with size: V x E = (6, 6)...\n", - "(CORNETO) May 11 10:48:17 PM - INFO : Finished. Final size: V x E = (6, 6).\n", - "(CORNETO) May 11 10:48:17 PM - INFO : 2/2 inputs after pruning.\n", - "(CORNETO) May 11 10:48:17 PM - INFO : 2/2 outputs after pruning.\n", - "(CORNETO) May 11 10:48:17 PM - INFO : Converting into a flow graph...\n", - "(CORNETO) May 11 10:48:17 PM - INFO : Creating a network flow problem...\n", - "(CORNETO) May 11 10:48:17 PM - INFO : Preprocess completed.\n", + "(CORNETO) May 12 11:21:35 AM - INFO : 2/2 inputs mapped to the graph\n", + "(CORNETO) May 12 11:21:35 AM - INFO : 2/2 outputs mapped to the graph\n", + "(CORNETO) May 12 11:21:35 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n", + "(CORNETO) May 12 11:21:35 AM - INFO : Finished. Final size: V x E = (6, 6).\n", + "(CORNETO) May 12 11:21:35 AM - INFO : 2/2 inputs after pruning.\n", + "(CORNETO) May 12 11:21:35 AM - INFO : 2/2 outputs after pruning.\n", + "(CORNETO) May 12 11:21:35 AM - INFO : Converting into a flow graph...\n", + "(CORNETO) May 12 11:21:35 AM - INFO : Creating a network flow problem...\n", + "(CORNETO) May 12 11:21:35 AM - INFO : Preprocess completed.\n", "===============================================================================\n", " CVXPY \n", " v1.5.1 \n", "===============================================================================\n", - "(CVXPY) May 11 10:48:17 PM: Your problem has 86 variables, 197 constraints, and 0 parameters.\n", - "(CVXPY) May 11 10:48:17 PM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) May 11 10:48:17 PM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) May 11 10:48:17 PM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) May 11 10:48:17 PM: Your problem is compiled with the CPP canonicalization backend.\n", + "(CVXPY) May 12 11:21:35 AM: Your problem has 86 variables, 197 constraints, and 0 parameters.\n", + "(CVXPY) May 12 11:21:35 AM: It is compliant with the following grammars: DCP, DQCP\n", + "(CVXPY) May 12 11:21:35 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", + "(CVXPY) May 12 11:21:35 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", + "(CVXPY) May 12 11:21:35 AM: Your problem is compiled with the CPP canonicalization backend.\n", "-------------------------------------------------------------------------------\n", " Compilation \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) May 11 10:48:17 PM: Compiling problem (target solver=GUROBI).\n", - "(CVXPY) May 11 10:48:17 PM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> GUROBI\n", - "(CVXPY) May 11 10:48:17 PM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) May 11 10:48:17 PM: Applying reduction Qp2SymbolicQp\n", - "(CVXPY) May 11 10:48:17 PM: Applying reduction QpMatrixStuffing\n", - "(CVXPY) May 11 10:48:17 PM: Applying reduction GUROBI\n", - "(CVXPY) May 11 10:48:17 PM: Finished problem compilation (took 3.959e-01 seconds).\n", + "(CVXPY) May 12 11:21:35 AM: Compiling problem (target solver=GUROBI).\n", + "(CVXPY) May 12 11:21:35 AM: Reduction chain: CvxAttr2Constr -> Qp2SymbolicQp -> QpMatrixStuffing -> GUROBI\n", + "(CVXPY) May 12 11:21:35 AM: Applying reduction CvxAttr2Constr\n", + "(CVXPY) May 12 11:21:35 AM: Applying reduction Qp2SymbolicQp\n", + "(CVXPY) May 12 11:21:35 AM: Applying reduction QpMatrixStuffing\n", + "(CVXPY) May 12 11:21:35 AM: Applying reduction GUROBI\n", + "(CVXPY) May 12 11:21:35 AM: Finished problem compilation (took 1.125e-01 seconds).\n", "-------------------------------------------------------------------------------\n", " Numerical solver \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) May 11 10:48:17 PM: Invoking solver GUROBI to obtain a solution.\n", - "Set parameter Username\n", - "Academic license - for non-commercial use only - expires 2024-12-23\n", + "(CVXPY) May 12 11:21:35 AM: Invoking solver GUROBI to obtain a solution.\n", "Set parameter QCPDual to value 1\n", "Gurobi Optimizer version 11.0.1 build v11.0.1rc0 (win64 - Windows 11.0 (22631.2))\n", "\n", @@ -252,7 +250,7 @@ "Thread count: 4 physical cores, 8 logical processors, using up to 8 threads\n", "\n", "Optimize a model with 197 rows, 86 columns and 397 nonzeros\n", - "Model fingerprint: 0xcd1a7f6f\n", + "Model fingerprint: 0x86a2333f\n", "Variable types: 24 continuous, 62 integer (62 binary)\n", "Coefficient statistics:\n", " Matrix range [1e-03, 1e+01]\n", @@ -261,12 +259,12 @@ " RHS range [1e-03, 1e+01]\n", "Found heuristic solution: objective 0.1000000\n", "Presolve removed 158 rows and 60 columns\n", - "Presolve time: 0.01s\n", + "Presolve time: 0.00s\n", "Presolved: 39 rows, 26 columns, 92 nonzeros\n", "Variable types: 7 continuous, 19 integer (19 binary)\n", "Found heuristic solution: objective -0.7000000\n", "\n", - "Root relaxation: objective -3.300000e+00, 23 iterations, 0.00 seconds (0.00 work units)\n", + "Root relaxation: objective -3.300000e+00, 20 iterations, 0.00 seconds (0.00 work units)\n", "\n", " Nodes | Current Node | Objective Bounds | Work\n", " Expl Unexpl | Obj Depth IntInf | Incumbent BestBd Gap | It/Node Time\n", @@ -274,7 +272,7 @@ "H 0 0 -3.3000000 -3.50000 6.06% - 0s\n", " 0 0 -3.30000 0 10 -3.30000 -3.30000 0.00% - 0s\n", "\n", - "Explored 1 nodes (23 simplex iterations) in 0.04 seconds (0.00 work units)\n", + "Explored 1 nodes (20 simplex iterations) in 0.04 seconds (0.00 work units)\n", "Thread count was 8 (of 8 available processors)\n", "\n", "Solution count 3: -3.3 -0.7 0.1 \n", @@ -285,11 +283,11 @@ "-------------------------------------------------------------------------------\n", " Summary \n", "-------------------------------------------------------------------------------\n", - "(CVXPY) May 11 10:48:18 PM: Problem status: optimal\n", - "(CVXPY) May 11 10:48:18 PM: Optimal value: 7.000e-01\n", - "(CVXPY) May 11 10:48:18 PM: Compilation took 3.959e-01 seconds\n", - "(CVXPY) May 11 10:48:18 PM: Solver (including time spent in interface) took 9.163e-02 seconds\n", - "(CORNETO) May 11 10:48:18 PM - INFO : Finished in 0.59 s.\n" + "(CVXPY) May 12 11:21:35 AM: Problem status: optimal\n", + "(CVXPY) May 12 11:21:35 AM: Optimal value: 7.000e-01\n", + "(CVXPY) May 12 11:21:35 AM: Compilation took 1.125e-01 seconds\n", + "(CVXPY) May 12 11:21:35 AM: Solver (including time spent in interface) took 8.493e-02 seconds\n", + "(CORNETO) May 12 11:21:35 AM - INFO : Finished in 0.32 s.\n" ] } ], @@ -323,7 +321,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 10, "id": "8b03e08d", "metadata": {}, "outputs": [ @@ -333,7 +331,7 @@ "array([0.])" ] }, - "execution_count": 4, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -346,26 +344,26 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 11, "id": "00d86874", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "{'_flow': Variable((14,), _flow),\n", - " 'species_inhibited_c0': Variable((10,), species_inhibited_c0, boolean=True),\n", - " 'reaction_sends_activation_c0': Variable((14,), reaction_sends_activation_c0, boolean=True),\n", + "{'reaction_sends_activation_c0': Variable((14,), reaction_sends_activation_c0, boolean=True),\n", + " '_flow': Variable((14,), _flow),\n", " '_flow_ipos': Variable((14,), _flow_ipos, boolean=True),\n", - " 'species_activated_c0': Variable((10,), species_activated_c0, boolean=True),\n", + " 'species_inhibited_c0': Variable((10,), species_inhibited_c0, boolean=True),\n", " 'reaction_sends_inhibition_c0': Variable((14,), reaction_sends_inhibition_c0, boolean=True),\n", + " 'species_activated_c0': Variable((10,), species_activated_c0, boolean=True),\n", " 'dag_layer_position_c0': Variable((10,), dag_layer_position_c0),\n", " 'flow': Variable((14,), _flow),\n", " 'edge_values_c0': Expression(AFFINE, UNKNOWN, (14,)),\n", " 'vertex_values_c0': Expression(AFFINE, UNKNOWN, (10,))}" ] }, - "execution_count": 5, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -377,7 +375,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 12, "id": "a1b0e7ec", "metadata": {}, "outputs": [ @@ -565,23 +563,21 @@ "\n" ], "text/plain": [ - "" + "" ] }, - "execution_count": 6, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "Gf.plot_problem(\n", - " vertex_values=P.expr.vertex_values_c0, edge_values=P.expr.edge_values_c0\n", - ")" + "Gf.plot_values(vertex_values=P.expr.vertex_values_c0, edge_values=P.expr.edge_values_c0)" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 13, "id": "c8be26ab", "metadata": {}, "outputs": [ @@ -677,10 +673,10 @@ "\n" ], "text/plain": [ - "" + "" ] }, - "execution_count": 7, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -694,7 +690,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 14, "id": "a7b0d803", "metadata": {}, "outputs": [ @@ -726,33 +722,33 @@ " \n", " \n", " 0\n", - " I1\n", - " 1.0\n", + " N2\n", + " -1.0\n", " \n", " \n", " 1\n", - " M1\n", + " M2\n", " 1.0\n", " \n", " \n", " 2\n", - " N2\n", - " -1.0\n", + " I1\n", + " 1.0\n", " \n", " \n", " 3\n", - " I2\n", - " 1.0\n", + " N1\n", + " 0.0\n", " \n", " \n", " 4\n", - " M2\n", + " M1\n", " 1.0\n", " \n", " \n", " 5\n", - " N1\n", - " 0.0\n", + " I2\n", + " 1.0\n", " \n", " \n", " 6\n", @@ -780,19 +776,19 @@ ], "text/plain": [ " V value\n", - "0 I1 1.0\n", - "1 M1 1.0\n", - "2 N2 -1.0\n", - "3 I2 1.0\n", - "4 M2 1.0\n", - "5 N1 0.0\n", + "0 N2 -1.0\n", + "1 M2 1.0\n", + "2 I1 1.0\n", + "3 N1 0.0\n", + "4 M1 1.0\n", + "5 I2 1.0\n", "6 _s 1.0\n", "7 _pert_c0 1.0\n", "8 _meas_c0 0.0\n", "9 _t 0.0" ] }, - "execution_count": 8, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -808,7 +804,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 15, "id": "7ff44c27", "metadata": {}, "outputs": [ @@ -930,7 +926,7 @@ "13 ((_t), ()) 0.0" ] }, - "execution_count": 9, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -941,7 +937,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 16, "id": "548f868d", "metadata": {}, "outputs": [ @@ -1007,10 +1003,10 @@ "\n" ], "text/plain": [ - "" + "" ] }, - "execution_count": 10, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -1032,7 +1028,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 17, "id": "ac0d1daa", "metadata": {}, "outputs": [ @@ -1042,7 +1038,7 @@ "(4931, 13157)" ] }, - "execution_count": 11, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -1057,7 +1053,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 18, "id": "0ae90239", "metadata": {}, "outputs": [ @@ -1092,7 +1088,7 @@ " 'ZBTB4': ('M', -1)}" ] }, - "execution_count": 12, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -1103,7 +1099,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 19, "id": "0ad5157f", "metadata": {}, "outputs": [], @@ -1114,7 +1110,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 20, "id": "437b70c6", "metadata": {}, "outputs": [ @@ -1124,17 +1120,11 @@ "text": [ "1/1 inputs mapped to the graph\n", "16/25 outputs mapped to the graph\n", - "Pruning the graph with size: V x E = (4931, 13157)...\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ + "Pruning the graph with size: V x E = (4931, 13157)...\n", "Finished. Final size: V x E = (1182, 5789).\n", - "HOXB7 (L4), ELK1 (L3), NFYB (L3), HIPK2 (L3), SIRT1 (L3), ZBTB4 (L4), NEUROD1 (L4), AEBP1 (L3), NFATC4 (L3), RUNX2 (L3)\n", + "HOXB7 (L4), ZBTB4 (L4), ELK1 (L3), NFYB (L3), RUNX2 (L3), HIPK2 (L3), SIRT1 (L3), NEUROD1 (L4), AEBP1 (L3), NFATC4 (L3)\n", "L1 : 1 iters, 0.00 s.\n", - "L2 : 41 iters, 0.02 s.\n", + "L2 : 41 iters, 0.01 s.\n", " > -EGFR -> +CRK -> +MAPK8 -> +SIRT1\n", " > -EGFR -> +CRK -> +MAPK8 -> -NFATC4\n", " > -EGFR -> -PTPN1 -> +ABL1 -> +HIPK2\n", @@ -1143,12 +1133,12 @@ " > -EGFR -> -MAP2K1 -> -MAPK1 -> -ELK1\n", " > -EGFR -> -MAP2K1 -> -MAPK1 -> -AEBP1\n", " > -EGFR -> -MAP2K1 -> -MAPK3 -> -RUNX2\n", - "L3 : 316 iters, 0.09 s.\n", + "L3 : 316 iters, 0.11 s.\n", " > -EGFR -> -STAT1 -> +CREBBP -> ... -> -NFYB\n", " > -EGFR -> -PIK3R1 -> -RAC1 -> ... -> -NEUROD1\n", " > -EGFR -> -PTPN1 -> +ABL1 -> ... -> -ZBTB4\n", " > -EGFR -> -ERBB2 -> +CDK1 -> ... -> -HOXB7\n", - "Finished (0.83 s)\n", + "Finished (0.61 s)\n", " > Number of selected edges: 26\n", " > Total iterations: 2287\n", " > Detected loops: 255\n", @@ -1166,7 +1156,7 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 21, "id": "5288e16b", "metadata": {}, "outputs": [], @@ -1184,14 +1174,14 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 22, "id": "88af4853", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "{'AEBP1': 1,\n", + "{'AEBP1': 0,\n", " 'CREB3': 1,\n", " 'EGR3': 1,\n", " 'ELK1': 0,\n", @@ -1200,25 +1190,25 @@ " 'FOXE1': 1,\n", " 'HIPK2': 0,\n", " 'HOXA2': 1,\n", - " 'HOXB7': 1,\n", + " 'HOXB7': 0,\n", " 'HOXD3': 1,\n", " 'KDM5C': 1,\n", " 'KDM5D': 1,\n", " 'KLF2': 1,\n", - " 'NEUROD1': 1,\n", + " 'NEUROD1': 0,\n", " 'NFATC4': 0,\n", - " 'NFYB': 1,\n", + " 'NFYB': 0,\n", " 'NHLH2': 1,\n", " 'PLAGL2': 1,\n", - " 'RUNX2': 1,\n", + " 'RUNX2': 0,\n", " 'SIRT1': 0,\n", " 'SUPT20H': 1,\n", " 'TBX20': 1,\n", " 'TET1': 1,\n", - " 'ZBTB4': 1}" + " 'ZBTB4': 0}" ] }, - "execution_count": 16, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } @@ -1229,7 +1219,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 24, "id": "8410ac74", "metadata": {}, "outputs": [ @@ -1624,594 +1614,16 @@ "\n" ], "text/plain": [ - "" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "G_sol.plot_values(vertices=vertex_values)" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "id": "57363f60", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'EGFR': -1,\n", - " 'CRK': 1,\n", - " 'MAPK8': 1,\n", - " 'SIRT1': 1,\n", - " 'NFATC4': -1,\n", - " 'PTPN1': -1,\n", - " 'ABL1': 1,\n", - " 'HIPK2': 1,\n", - " 'MAP2K1': -1,\n", - " 'MAPK1': -1,\n", - " 'ELK1': -1,\n", - " 'AEBP1': -1,\n", - " 'MAPK3': -1,\n", - " 'RUNX2': -1,\n", - " 'STAT1': -1,\n", - " 'CREBBP': 1,\n", - " 'TP53': 1,\n", - " 'NFYB': -1,\n", - " 'PIK3R1': -1,\n", - " 'RAC1': -1,\n", - " 'MAP3K10': -1,\n", - " 'NEUROD1': -1,\n", - " 'ZBTB4': -1,\n", - " 'ERBB2': -1,\n", - " 'CDK1': 1,\n", - " 'CSNK2A1': 1,\n", - " 'HOXB7': -1}" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [] - }, - { - "cell_type": "code", - "execution_count": 19, - "id": "68d444ae", - "metadata": { - "tags": [ - "skip-execution" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "(CORNETO) May 11 10:50:01 PM - INFO : 1/1 inputs mapped to the graph\n", - "(CORNETO) May 11 10:50:01 PM - INFO : 16/25 outputs mapped to the graph\n", - "(CORNETO) May 11 10:50:01 PM - INFO : Pruning the graph with size: V x E = (4931, 13157)...\n", - "(CORNETO) May 11 10:50:02 PM - INFO : Finished. Final size: V x E = (1182, 5789).\n", - "(CORNETO) May 11 10:50:02 PM - INFO : 1/1 inputs after pruning.\n", - "(CORNETO) May 11 10:50:02 PM - INFO : 10/16 outputs after pruning.\n", - "(CORNETO) May 11 10:50:02 PM - INFO : Converting into a flow graph...\n", - "(CORNETO) May 11 10:50:03 PM - INFO : Creating a network flow problem...\n", - "(CORNETO) May 11 10:50:04 PM - INFO : Preprocess completed.\n", - "===============================================================================\n", - " CVXPY \n", - " v1.5.1 \n", - "===============================================================================\n", - "(CVXPY) May 11 10:50:04 PM: Your problem has 26879 variables, 65446 constraints, and 0 parameters.\n", - "(CVXPY) May 11 10:50:04 PM: It is compliant with the following grammars: DCP, DQCP\n", - "(CVXPY) May 11 10:50:04 PM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n", - "(CVXPY) May 11 10:50:04 PM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n", - "(CVXPY) May 11 10:50:04 PM: Your problem is compiled with the CPP canonicalization backend.\n", - "-------------------------------------------------------------------------------\n", - " Compilation \n", - "-------------------------------------------------------------------------------\n", - "(CVXPY) May 11 10:50:04 PM: Compiling problem (target solver=SCIP).\n", - "(CVXPY) May 11 10:50:04 PM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n", - "(CVXPY) May 11 10:50:04 PM: Applying reduction Dcp2Cone\n", - "(CVXPY) May 11 10:50:04 PM: Applying reduction CvxAttr2Constr\n", - "(CVXPY) May 11 10:50:04 PM: Applying reduction ConeMatrixStuffing\n", - "(CVXPY) May 11 10:50:04 PM: Applying reduction SCIP\n", - "(CVXPY) May 11 10:50:04 PM: Finished problem compilation (took 5.129e-01 seconds).\n", - "-------------------------------------------------------------------------------\n", - " Numerical solver \n", - "-------------------------------------------------------------------------------\n", - "(CVXPY) May 11 10:50:04 PM: Invoking solver SCIP to obtain a solution.\n", - "presolving:\n", - "(round 1, fast) 1894 del vars, 21876 del conss, 0 add conss, 13735 chg bounds, 1 chg sides, 11603 chg coeffs, 0 upgd conss, 0 impls, 22761 clqs\n", - "(round 2, fast) 1918 del vars, 21892 del conss, 0 add conss, 13738 chg bounds, 2 chg sides, 11604 chg coeffs, 0 upgd conss, 0 impls, 22758 clqs\n", - "(round 3, exhaustive) 1921 del vars, 22693 del conss, 0 add conss, 13738 chg bounds, 2 chg sides, 11604 chg coeffs, 0 upgd conss, 0 impls, 22758 clqs\n", - "(round 4, exhaustive) 1921 del vars, 22705 del conss, 0 add conss, 13744 chg bounds, 2 chg sides, 11616 chg coeffs, 35916 upgd conss, 0 impls, 22758 clqs\n", - "(round 5, exhaustive) 1958 del vars, 22723 del conss, 0 add conss, 13744 chg bounds, 2 chg sides, 11616 chg coeffs, 35916 upgd conss, 11580 impls, 37680 clqs\n", - "(round 6, medium) 2132 del vars, 22792 del conss, 0 add conss, 13744 chg bounds, 2 chg sides, 11616 chg coeffs, 35916 upgd conss, 11580 impls, 37152 clqs\n", - "(round 7, fast) 2132 del vars, 22956 del conss, 0 add conss, 13744 chg bounds, 2 chg sides, 11616 chg coeffs, 35916 upgd conss, 11580 impls, 37152 clqs\n", - "(round 8, medium) 2132 del vars, 23288 del conss, 0 add conss, 13744 chg bounds, 2 chg sides, 11616 chg coeffs, 35916 upgd conss, 11580 impls, 37152 clqs\n", - " (10.0s) probing: 1000/18164 (5.5%) - 0 fixings, 33 aggregations, 22194 implications, 0 bound changes\n", - " (18.0s) probing: 2000/18164 (11.0%) - 0 fixings, 39 aggregations, 27901 implications, 0 bound changes\n", - " (22.0s) probing: 2521/18164 (13.9%) - 0 fixings, 39 aggregations, 28829 implications, 0 bound changes\n", - " (22.0s) probing aborted: 1000/1000 successive useless probings\n", - " (22.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)\n", - " (23.0s) symmetry computation finished: 49 generators found (max: 1500, log10 of symmetry group size: 15.4) (symcode time: 0.00)\n", - "dynamic symmetry handling statistics:\n", - " orbitopal reduction: 2 components: 13x3, 4x4\n", - " orbital reduction: no components\n", - " lexicographic reduction: 44 permutations with support sizes 26, 10, 38, 42, 26, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 8, 8, 10\n", - "handled 46 out of 46 symmetry components\n", - "presolving (9 rounds: 9 fast, 6 medium, 4 exhaustive):\n", - " 2146 deleted vars, 23302 deleted constraints, 0 added constraints, 13744 tightened bounds, 0 added holes, 2 changed sides, 11616 changed coefficients\n", - " 11900 implications, 50919 cliques\n", - "presolved problem has 24735 variables (17951 bin, 0 int, 0 impl, 6784 cont) and 42143 constraints\n", - " 11204 constraints of type \n", - " 22546 constraints of type \n", - " 6797 constraints of type \n", - " 1596 constraints of type \n", - "transformed objective value is always integral (scale: 0.2)\n", - "Presolving Time: 22.00\n", - "\n", - " time | node | left |LP iter|LP it/n|mem/heur|mdpt |vars |cons |rows |cuts |sepa|confs|strbr| dualbound | primalbound | gap | compl. \n", - " 24.0s| 1 | 0 | 901 | - | 437M | 0 | 24k| 42k| 42k| 0 | 0 | 23 | 0 |-6.760000e+00 | -- | Inf | unknown\n", - " 28.0s| 1 | 0 | 6957 | - | 445M | 0 | 24k| 42k| 42k| 2 | 1 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 30.0s| 1 | 0 | 7135 | - | 451M | 0 | 24k| 42k| 42k| 19 | 2 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 33.0s| 1 | 0 | 9865 | - | 459M | 0 | 24k| 42k| 42k| 27 | 3 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 35.0s| 1 | 0 | 12858 | - | 466M | 0 | 24k| 42k| 42k| 55 | 4 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 36.0s| 1 | 0 | 13897 | - | 472M | 0 | 24k| 42k| 42k| 100 | 5 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 38.0s| 1 | 0 | 14939 | - | 477M | 0 | 24k| 42k| 42k| 117 | 6 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 39.0s| 1 | 0 | 16396 | - | 483M | 0 | 24k| 42k| 42k| 148 | 7 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 41.0s| 1 | 0 | 18349 | - | 488M | 0 | 24k| 42k| 42k| 168 | 8 | 23 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 43.0s| 1 | 0 | 20035 | - | 494M | 0 | 24k| 42k| 42k| 188 | 9 | 24 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 45.0s| 1 | 0 | 21753 | - | 499M | 0 | 24k| 42k| 42k| 213 | 10 | 24 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 47.0s| 1 | 0 | 24498 | - | 503M | 0 | 24k| 42k| 42k| 231 | 11 | 24 | 0 |-6.600000e+00 | -- | Inf | unknown\n", - " 89.0s| 1 | 2 | 64560 | - | 508M | 0 | 24k| 42k| 42k| 231 | 11 | 39 | 25 |-6.600000e+00 | -- | Inf | unknown\n", - " 195s| 100 | 97 |243506 |2212.3 | 559M | 19 | 24k| 42k| 42k| 339 | 1 | 65 | 25 |-6.600000e+00 | -- | Inf | unknown\n", - "L 200s| 129 | 45 |252141 |1778.6 | alns| 20 | 24k| 42k| 42k| 369 | 1 | 67 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 10.50%\n", - " time | node | left |LP iter|LP it/n|mem/heur|mdpt |vars |cons |rows |cuts |sepa|confs|strbr| dualbound | primalbound | gap | compl. \n", - " 213s| 200 | 52 |257469 |1170.8 | 577M | 21 | 24k| 42k| 0 | 478 | 0 | 92 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 14.36%\n", - " 223s| 300 | 110 |267388 | 812.4 | 588M | 27 | 24k| 42k| 42k| 526 | 1 | 135 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 20.19%\n", - " 235s| 400 | 145 |279064 | 638.0 | 597M | 30 | 24k| 42k| 42k| 535 | 2 | 296 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 20.48%\n", - " 248s| 500 | 186 |291708 | 535.5 | 637M | 30 | 24k| 42k| 42k| 668 | 2 | 424 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 20.96%\n", - " 261s| 600 | 240 |308684 | 474.5 | 655M | 30 | 24k| 42k| 42k| 763 | 1 | 580 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 20.99%\n", - " 280s| 700 | 246 |334908 | 444.1 | 666M | 30 | 24k| 42k| 42k| 889 | 2 | 756 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 21.45%\n", - " 289s| 800 | 240 |341054 | 396.2 | 667M | 30 | 24k| 42k| 42k| 910 | 0 | 860 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 21.89%\n", - " 299s| 900 | 274 |351002 | 363.2 | 680M | 30 | 24k| 42k| 42k| 941 | 1 | 992 | 25 |-6.600000e+00 |-6.200000e+00 | 6.45%| 22.48%\n", - "\n", - "SCIP Status : solving was interrupted [time limit reached]\n", - "Solving Time (sec) : 300.00\n", - "Solving Nodes : 914\n", - "Primal Bound : -6.20000000000000e+00 (2 solutions)\n", - "Dual Bound : -6.59999999999992e+00\n", - "Gap : 6.45 %\n", - "-------------------------------------------------------------------------------\n", - " Summary \n", - "-------------------------------------------------------------------------------\n", - "(CVXPY) May 11 10:55:09 PM: Problem status: optimal_inaccurate\n", - "(CVXPY) May 11 10:55:09 PM: Optimal value: 1.980e+01\n", - "(CVXPY) May 11 10:55:09 PM: Compilation took 5.129e-01 seconds\n", - "(CVXPY) May 11 10:55:09 PM: Solver (including time spent in interface) took 3.049e+02 seconds\n", - "(CORNETO) May 11 10:55:09 PM - INFO : Finished in 308.46 s.\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "c:\\Users\\pablo\\AppData\\Local\\pypoetry\\Cache\\virtualenvs\\corneto-N5Qo8YGQ-py3.9\\lib\\site-packages\\cvxpy\\problems\\problem.py:1407: UserWarning: Solution may be inaccurate. Try another solver, adjusting the solver settings, or solve with verbose=True for more information.\n", - " warnings.warn(\n", - "Warning: node 'CSNK2A1', graph '%3' size too small for label\n", - "Warning: node 'MAPK1', graph '%3' size too small for label\n", - "Warning: node 'AEBP1', graph '%3' size too small for label\n", - "Warning: node 'EGFR', graph '%3' size too small for label\n", - "Warning: node 'PTPN1', graph '%3' size too small for label\n", - "Warning: node 'PPP2CA', graph '%3' size too small for label\n", - "Warning: node 'CASP6', graph '%3' size too small for label\n", - "Warning: node 'SIRT1', graph '%3' size too small for label\n", - "Warning: node 'HOXB7', graph '%3' size too small for label\n", - "Warning: node 'MAPK3', graph '%3' size too small for label\n", - "Warning: node 'RUNX2', graph '%3' size too small for label\n", - "Warning: node 'MAP3K10', graph '%3' size too small for label\n", - "Warning: node 'NEUROD1', graph '%3' size too small for label\n", - "Warning: node 'NFATC4', graph '%3' size too small for label\n", - "Warning: node 'HIPK2', graph '%3' size too small for label\n", - "Warning: node 'EP300', graph '%3' size too small for label\n", - "Warning: node 'NFYB', graph '%3' size too small for label\n", - "Warning: node 'ZBTB4', graph '%3' size too small for label\n", - "Warning: node 'CSNK2A1', graph '%3' size too small for label\n", - "Warning: node 'MAPK1', graph '%3' size too small for label\n", - "Warning: node 'AEBP1', graph '%3' size too small for label\n", - "Warning: node 'EGFR', graph '%3' size too small for label\n", - "Warning: node 'PTPN1', graph '%3' size too small for label\n", - "Warning: node 'PPP2CA', graph '%3' size too small for label\n", - "Warning: node 'CASP6', graph '%3' size too small for label\n", - "Warning: node 'SIRT1', graph '%3' size too small for label\n", - "Warning: node 'HOXB7', graph '%3' size too small for label\n", - "Warning: node 'MAPK3', graph '%3' size too small for label\n", - "Warning: node 'RUNX2', graph '%3' size too small for label\n", - "Warning: node 'MAP3K10', graph '%3' size too small for label\n", - "Warning: node 'NEUROD1', graph '%3' size too small for label\n", - "Warning: node 'NFATC4', graph '%3' size too small for label\n", - "Warning: node 'HIPK2', graph '%3' size too small for label\n", - "Warning: node 'EP300', graph '%3' size too small for label\n", - "Warning: node 'NFYB', graph '%3' size too small for label\n", - "Warning: node 'ZBTB4', graph '%3' size too small for label\n" - ] - }, - { - "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "SRC\n", - "\n", - "SRC\n", - "\n", - "\n", - "\n", - "RAC1\n", - "\n", - "RAC1\n", - "\n", - "\n", - "\n", - "SRC->RAC1\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "PPP2CA\n", - "\n", - "PPP2CA\n", - "\n", - "\n", - "\n", - "SRC->PPP2CA\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "MAP3K10\n", - "\n", - "MAP3K10\n", - "\n", - "\n", - 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backend_options={\"max_seconds\": 300},\n", - ")\n", - "V, E = get_result(P, Gf)\n", - "G_sol = Gf.edge_subgraph(get_selected_edges(P, Gf))\n", - "G_sol.plot()" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "id": "ea363108", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "(array([15.]), 24.0)" + "" ] }, - "execution_count": 20, + "execution_count": 24, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "P.objectives[0].value, P.objectives[1].value" + "G_sol.plot_values(vertex_values=vertex_values)" ] } ], diff --git a/poetry.lock b/poetry.lock index bac7d6f..33b650e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1919,46 +1919,46 @@ development = ["black", "isort", "tox"] [[package]] name = "osqp" -version = "0.6.4" +version = "0.6.5" description = "OSQP: The Operator Splitting QP Solver" optional = false python-versions = "*" files = [ - {file = "osqp-0.6.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = 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