Table 1 Summary of molecular representation methods developed in recent years

From: Recent advances in molecular representation methods and their applications in scaffold hopping

Type	Model	Year	Link	Ref.
Molecular Fingerprints & Descriptors	MolMapNet	2021	https://github.com/shenwanxiang/bidd-molmap	⁷³
	FP-ADMET	2021	https://gitlab.com/vishsoft/fpadmet	⁴⁶
	BoostSweet	2022	N.A.	⁵⁰
	FP-BERT	2022	https://github.com/fanganpai/fp2bert	⁵²
	MapLight	2023	https://github.com/maplightrx/MapLight-TDC	⁴⁵
	CrossFuse-XGBoost	2024	https://github.com/cqmu-lq/CrossFuse-XGBoost	⁵³
Language Model	Mol2vec	2018	https://github.com/samoturk/mol2vec	⁵⁵
	Mol-BERT	2021	https://github.com/cxfjiang/MolBERT	⁵⁷
	MOLFORMER	2022	https://github.com/daenuprobst/molsetrep	⁶⁷
	MTL-BERT	2022	https://github.com/zhang-xuan1314/MTL-BERT	⁵⁸
	DeepSA	2023	https://github.com/Shihang-Wang-58/DeepSA	⁶¹
	MolRoPE-BERT	2023	N.A.	⁵⁹
	t-SMILES	2024	https://github.com/juanniwu/t-SMILES	⁶⁸
	INTransformer	2024	https://github.com/Jiangjing0122/INTransformer	⁶⁹
Graph	GROVER	2020	https://github.com/tencent-ailab/grover	⁷²
	Attentive FP	2020	https://github.com/OpenDrugAI/AttentiveFP	⁷¹
	MolGNet	2021	https://github.com/pyli0628/MPG	⁷³
	ReLMole	2022	https://github.com/Meteor-han/ReLMole	⁷⁴
	GEM	2022	https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/pretrained_compound/ChemRL/GEM	⁷⁶
	GraphMVP	2022	https://github.com/chao1224/GraphMVP	⁷⁵
	FunQG	2023	https://github.com/hhaji/funqg	⁷⁷
	MolCAP	2023	https://github.com/wangyu-sd/MolCAP	⁷⁸
	SME	2023	https://doi.org/10.5281/zenodo.7707093	⁸⁵
	HiMol	2023	https://github.com/ZangXuan/HiMol	⁸⁰
	PharmHGT	2023	https://github.com/mindrank-ai/PharmHGT	⁸²
	IFGN	2023	http://graphadmet.cn/works/IFGN	⁸³
	KANO	2023	https://github.com/HICAI-ZJU/KANO	⁸⁷
	KPGT	2023	https://github.com/lihan97/KPGT	⁸⁸
	MMGX	2024	https://github.com/ohuelab/MMGX	⁸¹
	R-MAT	2024	https://github.com/gmum/huggingmolecules	⁸⁹
	SMPT	2024	https://github.com/liyishuilys/SMPT	⁷⁹
	TOML-BERT	2024	https://github.com/yanjing-duan/TOML-BERT	⁹⁰
	Gram matrix	2024	https://github.com/xiangwenkai/GRAM	⁸⁶
	GSL-MPP	2024	https://github.com/zby961104/GSL-MPP	⁸⁴
	MolFormer	2024	https://github.com/IBM/molformer	⁹¹
High-dimensional Features	UniMol	2023	https://github.com/deepmodeling/Uni-Mol/tree/main	²⁰
	GeminiMol	2024	https://github.com/Wang-Lin-boop/GeminiMol	²
	PhenoModel	2024	https://github.com/Shihang-Wang-58/PhenoScreen	⁹³
	Ouroboros	2025	https://github.com/Wang-Lin-boop/Ouroboros	⁹²
Multimodal	FP-GNN	2022	https://github.com/idrugLab/FP-GNN	⁹⁴
	ImageMol	2022	https://github.com/ChengF-Lab/ImageMol	¹⁰³
	CLAMP	2023	https://github.com/ml-jku/clamp	⁹⁷
	CGIP	2023	https://github.com/HongxinXiang/CGIP	⁹⁹
	UniMAP	2023	N.A.	¹⁰¹
	MoleSG	2024	https://github.com/ShenAoAO/MoleSG	⁹⁵
	MMFDL	2024	https://github.com/AIMedDrug/MMFDL.git	⁹⁶
	COATI	2024	https://github.com/terraytherapeutics/COATI/	⁹⁸
	DLF-MFF	2024	https://github.com/mamei1016/DLF-MFF	¹⁰⁰
	VideoMol	2024	https://github.com/HongxinXiang/VideoMol	¹⁰⁵
	MvMRL	2024	https://github.com/jedison-github/MvMRL	¹⁰⁶
	PremuNet	2024	https://github.com/A-Gentle-Cat/PremuNet	¹⁰²
	ISMol	2024	https://github.com/Mrzhang1999/ISMol	¹⁰⁴
Contractive Learning	GraphCL	2020	https://github.com/Shen-Lab/GraphCL	¹¹⁹
	MoCL	2021	https://github.com/illidanlab/MoCL-DK	¹⁰⁷
	iMolCLR	2022	https://github.com/yuyangw/iMolCLR	¹⁰⁹
	MolCLR	2022	https://github.com/yuyangw/MolCLR	¹⁰⁸
	ATMOL	2022	https://github.com/moen-hyb/ATMOL	¹¹⁴
	SMICLR	2022	https://github.com/CIDAG/SMICLR	¹¹⁶
	3DGCL	2023	https://github.com/moonkisung/3DGCL	¹¹²
	CasANGCL	2023	https://github.com/Sissizx/CASANGCL	¹¹⁵
	FraSICL	2023	https://github.com/ZiqiaoZhang/FraSICL	¹¹⁷
	MOCO	2024	N.A.	¹¹⁰
	MolFeSCue	2024	https://github.com/zhangruochi/MolFeSCue	¹¹¹
	3D-MOL	2024	https://github.com/AI-HPC-Research-Team/3D-Mol	¹¹³
	UniCorn	2024	N.A.	¹¹⁸

N.A. represents Not Available.

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Table 1 Summary of molecular representation methods developed in recent years

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