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Published at November 25

Exploring Discrete Flow Matching for 3D De Novo Molecule Generation

q-bio.BM

Released Date: November 25, 2024

Authors: Ian Dunn¹, David R. Koes

Aff.: ¹Dept. of Computational & Systems Biology, University of Pittsburgh

Arxiv: http://arxiv.org/abs/2411.16644v1

Refer to caption

Model	Mols Stable (%) ( $\uparrow$ )	Mols Valid (%) ( $\uparrow$ )	JS(E) ( $\downarrow$ )	Structural Alerts (per mol) ( $\downarrow$ )	OOD Rings (per mol) ( $\downarrow$ )	Parameters ( $10^{6}$ ) ( $\downarrow$ )
(Training Data)	$100$	$100$	$0$	$0.69$	$0.04$	-
MiDi	$85.1{\scriptstyle\pm 0.9}$	$71.6{\scriptstyle\pm 0.9}$	$0.23{\scriptstyle\pm 0.00}$	$1.01{\scriptstyle\pm 0.01}$	$0.33{\scriptstyle\pm 0.00}$	$24.1$
JODO	$90.7{\scriptstyle\pm 0.5}$	$76.5{\scriptstyle\pm 0.8}$	$0.17{\scriptstyle\pm 0.01}$	$\mathbf{0.84{\scriptstyle\pm 0.02}}$	$\mathbf{0.21{\scriptstyle\pm 0.00}}$	$5.7$
EQGAT-Diff	$93.4{\scriptstyle\pm 0.2}$	$86.1{\scriptstyle\pm 0.3}$	$\mathbf{0.11{\scriptstyle\pm 0.00}}$	$1.06{\scriptstyle\pm 0.01}$	$0.27{\scriptstyle\pm 0.00}$	$12.3$
FlowMol-CTMC	$\mathbf{96.2{\scriptstyle\pm 0.1}}$	$\mathbf{91.6{\scriptstyle\pm 0.1}}$	$0.14{\scriptstyle\pm 0.00}$	$1.23{\scriptstyle\pm 0.01}$	$0.28{\scriptstyle\pm 0.00}$	$\mathbf{4.3}$