DrugBank-Descrition \multirow{3}{*}{SMILES} & Random & 24.59 $\pm$ 1.14 & 10.12 $\pm$ 1.38 & 4.97 $\pm$ 0.42 & 24.54 $\pm$ 0.97 & 9.97 $\pm$ 0.81 & 5.09 $\pm$ 0.37\\ & Frozen & 25.07 $\pm$ 1.24 & 10.22 $\pm$ 1.19 & 5.12 $\pm$ 0.65 & 24.69 $\pm$ 1.87 & 10.20 $\pm$ 1.38 & 5.37 $\pm$ 1.15\\ & Similarity & 36.35 $\pm$ 0.59 & 23.22 $\pm$ 0.58 & 16.40 $\pm$ 0.59 & 22.74 $\pm$ 0.24 & 10.31 $\pm$ 0.24 & 5.34 $\pm$ 0.24\\ & KV-PLM & 73.80 $\pm$ 0.00 & 53.96 $\pm$ 0.29 & 40.07 $\pm$ 0.38 & 72.86 $\pm$ 0.00 & 52.55 $\pm$ 0.29 & 40.33 $\pm$ 0.00\\ & \model\, & 97.50 $\pm$ 0.46 & 94.18 $\pm$ 0.46 & 91.12 $\pm$ 0.46 & 98.21 $\pm$ 0.00 & 94.54 $\pm$ 0.37 & 91.97 $\pm$ 0.46\\ \multirow{3}{*}{Graph} & Random & 25.78 $\pm$ 1.43 & 10.71 $\pm$ 0.97 & 4.83 $\pm$ 1.00 & 24.98 $\pm$ 0.32 & 10.20 $\pm$ 0.40 & 4.80 $\pm$ 0.21\\ & Frozen & 24.01 $\pm$ 1.34 & 9.39 $\pm$ 0.92 & 4.85 $\pm$ 0.52 & 24.00 $\pm$ 1.66 & 9.91 $\pm$ 0.71 & 5.07 $\pm$ 0.75\\ & Similarity & 30.03 $\pm$ 0.38 & 13.63 $\pm$ 0.27 & 7.07 $\pm$ 0.10 & 24.81 $\pm$ 0.27 & 10.22 $\pm$ 0.24 & 4.74 $\pm$ 0.24\\ & \model\, & 99.15 $\pm$ 0.00 & 97.19 $\pm$ 0.00 & 95.66 $\pm$ 0.00 & 99.05 $\pm$ 0.37 & 97.50 $\pm$ 0.46 & 95.71 $\pm$ 0.46\\ DrugBank-Pharmacodynamics \multirow{4}{*}{SMILES} & Random & 24.49 $\pm$ 0.68 & 9.73 $\pm$ 0.34 & 5.14 $\pm$ 0.57 & 25.61 $\pm$ 0.62 & 10.10 $\pm$ 0.91 & 5.07 $\pm$ 0.69\\ & Frozen & 25.47 $\pm$ 1.12 & 10.55 $\pm$ 0.75 & 5.48 $\pm$ 0.70 & 25.34 $\pm$ 0.41 & 9.86 $\pm$ 0.44 & 4.84 $\pm$ 0.26\\ & Similarity & 27.85 $\pm$ 0.03 & 10.75 $\pm$ 0.02 & 5.67 $\pm$ 0.01 & 24.58 $\pm$ 0.03 & 11.25 $\pm$ 0.03 & 5.29 $\pm$ 0.02\\ & KV-PLM & 68.38 $\pm$ 0.03 & 47.59 $\pm$ 0.03 & 36.54 $\pm$ 0.03 & 67.68 $\pm$ 0.03 & 48.00 $\pm$ 0.02 & 34.66 $\pm$ 0.02\\ & \model\, & 88.07 $\pm$ 0.01 & 81.70 $\pm$ 0.02 & 75.94 $\pm$ 0.02 & 88.46 $\pm$ 0.01 & 81.01 $\pm$ 0.02 & 74.64 $\pm$ 0.03\\ \multirow{3}{*}{Graph} & Random & 26.00 $\pm$ 0.37 & 9.65 $\pm$ 0.88 & 4.95 $\pm$ 0.36 & 25.11 $\pm$ 0.63 & 9.99 $\pm$ 0.62 & 4.82 $\pm$ 0.54\\ & Frozen & 25.49 $\pm$ 1.82 & 10.19 $\pm$ 1.47 & 4.74 $\pm$ 0.56 & 25.55 $\pm$ 0.45 & 10.15 $\pm$ 0.77 & 4.88 $\pm$ 0.55\\ & Similarity & 25.33 $\pm$ 0.27 & 9.89 $\pm$ 0.52 & 4.61 $\pm$ 0.08 & 25.28 $\pm$ 0.03 & 10.64 $\pm$ 0.02 & 5.47 $\pm$ 0.02\\ & \model\, & 92.14 $\pm$ 0.02 & 86.27 $\pm$ 0.02 & 81.08 $\pm$ 0.05 & 91.44 $\pm$ 0.02 & 86.76 $\pm$ 0.03 & 81.68 $\pm$ 0.03\\ DrugBank-ATC \multirow{4}{*}{SMILES} & Random & 25.03 $\pm$ 0.33 & 9.83 $\pm$ 0.19 & 4.80 $\pm$ 0.22 & 25.44 $\pm$ 1.21 & 10.03 $\pm$ 0.94 & 5.11 $\pm$ 0.79\\ & Frozen & 25.05 $\pm$ 0.94 & 10.17 $\pm$ 0.63 & 4.99 $\pm$ 0.54 & 25.35 $\pm$ 0.78 & 10.32 $\pm$ 0.44 & 5.22 $\pm$ 0.34\\ & Similarity & 30.03 $\pm$ 0.00 & 13.35 $\pm$ 0.02 & 7.53 $\pm$ 0.02 & 26.74 $\pm$ 0.03 & 11.01 $\pm$ 0.00 & 5.62 $\pm$ 0.00\\ & KV-PLM & 60.94 $\pm$ 0.00 & 42.35 $\pm$ 0.00 & 30.32 $\pm$ 0.00 & 60.67 $\pm$ 0.00 & 40.19 $\pm$ 0.00 & 29.02 $\pm$ 0.00\\ & \model\,& 70.84 $\pm$ 0.07 & 56.75 $\pm$ 0.05 & 46.12 $\pm$ 0.07 & 73.07 $\pm$ 0.03 & 58.19 $\pm$ 0.03 & 48.97 $\pm$ 0.06\\ \multirow{3}{*}{Graph} & Random & 24.48 $\pm$ 0.66 & 9.97 $\pm$ 0.25 & 4.81 $\pm$ 0.34 & 25.48 $\pm$ 0.59 & 10.40 $\pm$ 0.37 & 5.38 $\pm$ 0.30\\ & Frozen & 24.19 $\pm$ 0.77 & 10.24 $\pm$ 0.71 & 4.87 $\pm$ 0.47 & 24.95 $\pm$ 1.52 & 10.07 $\pm$ 0.80 & 5.06 $\pm$ 0.36\\ & Similarity & 29.46 $\pm$ 0.00 & 12.34 $\pm$ 0.00 & 6.52 $\pm$ 0.00 & 25.78 $\pm$ 1.53 & 10.23 $\pm$ 0.70 & 5.06 $\pm$ 0.67\\ & \model\, & 69.33 $\pm$ 0.03 & 54.83 $\pm$ 0.04 & 44.13 $\pm$ 0.05 & 71.81 $\pm$ 0.05 & 58.34 $\pm$ 0.07 & 47.58 $\pm$ 0.05\\ Four case studies in DrugBank-ATC ===== CC1(C)S[C@@H]2[C@H](NC(=O)Cc3ccccc3)C(=O)N2[C@H]1C(=O)O ===== ground_truth_index_list [1455, 1456, 1457] 164 (ground-truth) & 0 & This molecule is for combinations of penicillins, incl beta-lactamase inhibitors & 0.88546\\ 264 (ground-truth) & 1 & This molecule is for beta-lactamase sensitive penicillins & 0.88080\\ 177 & 2 & This molecule is for penicillins with extended spectrum & 0.88012\\ 165 & 3 & This molecule is for beta-lactamase resistant penicillins & 0.87402\\ 284 & 4 & This molecule is for first-generation cephalosporins & 0.78288\\ 101 & 5 & This molecule is for second-generation cephalosporins & 0.76969\\ 166 & 6 & This molecule is for carbapenems & 0.75941\\ 137 & 7 & This molecule is for third-generation cephalosporins & 0.75750\\ 490 & 8 & This molecule is for fourth-generation cephalosporins & 0.75560\\ 539 & 9 & This molecule is for other cephalosporins and penems & 0.74622\\ 497 & 10 & This molecule is for beta-lactamase inhibitors & 0.61334\\ 409 & 11 & This molecule is for penicillamine and similar agents & 0.58855\\ 391 & 12 & This molecule is for thiazides, combinations with psycholeptics and/or analgesics & 0.55448\\ 441 & 13 & This molecule is for thiazides, combinations with other drugs & 0.52038\\ 229 & 14 & This molecule is for hypnotics and sedatives in combination, excl barbiturates & 0.51279\\ ===== COC(=O)C1=C(C)NC(C)=C(C(=O)OC)C1c1ccccc1[N+](=O)[O-] ===== ground_truth_index_list [1550, 1551, 1552] 138 (ground-truth) & 0 & This molecule is for dihydropyridine derivatives & 0.75934\\ 236 (ground-truth) & 1 & This molecule is for calcium channel blockers and diuretics & 0.69904\\ 451 & 2 & This molecule is for other non-selective calcium channel blockers & 0.68354\\ 65 & 3 & This molecule is for antivirals & 0.61045\\ 60 & 4 & This molecule is for other hypnotics and sedatives & 0.58330\\ 136 & 5 & This molecule is for vitamin k antagonists & 0.58269\\ 519 & 6 & This molecule is for contact laxatives & 0.56338\\ 372 & 7 & This molecule is for other antiallergics & 0.55953\\ 396 & 8 & This molecule is for antiinflammatory products for vaginal administration & 0.53786\\ 193 & 9 & This molecule is for antiinflammatory preparations, non-steroids for topical use & 0.53353\\ 459 & 10 & This molecule is for sulfonium derivatives & 0.53035\\ 374 & 11 & This molecule is for esters of aminobenzoic acid & 0.52889\\ 21 & 12 & This molecule is for other antipsoriatics for topical use & 0.52805\\ 376 & 13 & This molecule is for organic nitrates & 0.52797\\ 384 & 14 & This molecule is for mucolytics & 0.52201\\ ===== OC(Cn1cncn1)(Cn1cncn1)c1ccc(F)cc1F ===== ground_truth_index_list [84, 85, 86] 68 (ground-truth) & 0 & This molecule is for triazole derivatives & 0.84318\\ 69 (ground-truth) & 1 & This molecule is for imidazole and triazole derivatives & 0.82524\\ 221 & 2 & This molecule is for aromatase inhibitors & 0.72836\\ 412 & 3 & This molecule is for other cough suppressants & 0.65468\\ 42 & 4 & This molecule is for angiotensin ii receptor blockers (arbs), other combinations & 0.58697\\ 444 & 5 & This molecule is for other systemic drugs for obstructive airway diseases & 0.58359\\ 390 & 6 & This molecule is for tyrosine hydroxylase inhibitors & 0.57834\\ 44 & 7 & This molecule is for angiotensin ii receptor blockers (arbs), plain & 0.55402\\ 403 & 8 & This molecule is for butylpyrazolidines & 0.54885\\ 598 & 9 & This molecule is for pyrazolone derivatives & 0.54669\\ 594 & 10 & This molecule is for dichloroacetamide derivatives & 0.53727\\ 491 & 11 & This molecule is for pyrazolones & 0.53277\\ 199 & 12 & This molecule is for diphenylpropylamine derivatives & 0.53106\\ 298 & 13 & This molecule is for coxibs & 0.52894\\ 220 & 14 & This molecule is for oxazol, thiazine, and triazine derivatives & 0.52620\\ ===== CCCc1nc(C(C)(C)O)c(C(=O)O)n1Cc1ccc(-c2ccccc2-c2nnn[nH]2)cc1 ===== ground_truth_index_list [197, 198, 199, 200] 44 (ground-truth) & 0 & This molecule is for angiotensin ii receptor blockers (arbs), plain & 0.91829\\ 42 (ground-truth) & 1 & This molecule is for angiotensin ii receptor blockers (arbs), other combinations & 0.89567\\ 45 (ground-truth) & 2 & This molecule is for angiotensin ii receptor blockers (arbs) and calcium channel blockers & 0.86173\\ 43 (ground-truth) & 3 & This molecule is for angiotensin ii receptor blockers (arbs) and diuretics & 0.83438\\ 221 & 4 & This molecule is for aromatase inhibitors & 0.68312\\ 69 & 5 & This molecule is for imidazole and triazole derivatives & 0.66734\\ 216 & 6 & This molecule is for pyrimidine derivatives & 0.65323\\ 598 & 7 & This molecule is for pyrazolone derivatives & 0.61263\\ 298 & 8 & This molecule is for coxibs & 0.61227\\ 40 & 9 & This molecule is for hmg coa reductase inhibitors, other combinations & 0.60269\\ 401 & 10 & This molecule is for purine derivatives & 0.59775\\ 68 & 11 & This molecule is for triazole derivatives & 0.59397\\ 180 & 12 & This molecule is for pyrimidine analogues & 0.57502\\ 491 & 13 & This molecule is for pyrazolones & 0.57500\\ 113 & 14 & This molecule is for purine analogues & 0.56304\\