Table 1 Ability of model to generalize on conformations and unseen molecules

test data splits (conformations, structures, scaffolds)

invDeepDFT

multiple

conformations

0.98

0.16

0.67

0.95

2.71

invDeepDFT

multiple

structures

1.18

0.26

0.73

1.13

8.31

invDeepDFT

multiple

scaffolds

1.20

0.23

0.72

1.17

3.78

invDeepDFT

single

conformations

1.03

0.23

0.65

0.98

3.53

invDeepDFT

single

structures

1.40

0.31

0.70

1.35

10.09

invDeepDFT

single

scaffolds

1.44

0.32

0.77

1.38

13.34

eqvDeepDFT

multiple

conformations

0.77

0.09

0.58

0.75

2.17

eqvDeepDFT

multiple

structures

0.90

0.13

0.59

0.88

3.07

eqvDeepDFT

multiple

scaffolds

0.92

0.13

0.60

0.90

3.43

eqvDeepDFT

single

conformations

1.18

0.90

0.79

1.13

47.47

eqvDeepDFT

single

structures

1.34

0.25

0.79

1.30

10.33

eqvDeepDFT

single

scaffolds

1.34

0.23

0.80

1.31

4.72

LAGNet

multiple

conformations

0.35

0.08

0.25

0.33

1.62

LAGNet

multiple

structures

0.46

0.11

0.27

0.44

2.20

LAGNet

multiple

scaffolds

0.46

0.11

0.25

0.44

2.24

LAGNet

single

conformations

0.56

0.14

0.36

0.53

2.39

LAGNet

single

structures

0.73

0.15

0.38

0.71

2.85

LAGNet

single

scaffolds

0.74

0.15

0.43

0.72

2.78

train data splits (single/multiple conformations per molecule)

invDeepDFT

multiple

multiple

0.97

0.15

0.67

0.95

2.23

invDeepDFT

multiple

single

0.97

0.15

0.67

0.94

1.81

invDeepDFT

single

multiple

1.06

0.23

0.63

1.00

3.79

invDeepDFT

single

single

0.98

0.18

0.63

0.94

2.29

eqvDeepDFT

multiple

multiple

0.77

0.08

0.58

0.76

1.53

eqvDeepDFT

multiple

single

0.76

0.08

0.60

0.74

1.21

eqvDeepDFT

single

multiple

1.18

0.21

0.78

1.14

7.59

eqvDeepDFT

single

single

1.08

0.12

0.78

1.06

1.60

LAGNet

multiple

multiple

0.35

0.06

0.25

0.34

1.26

LAGNet

multiple

single

0.35

0.07

0.26

0.33

0.84

LAGNet

single

multiple

0.58

0.14

0.34

0.55

2.43

LAGNet

single

single

0.52

0.09

0.36

0.50

1.03