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Main Authors:	Tang, Sophia, Zhu, Yuchen, Tao, Molei, Chatterjee, Pranam
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Biomolecules
Online Access:	https://arxiv.org/abs/2509.25171
Tags:	Add Tag No Tags, Be the first to tag this record!

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion
by: Tang, Sophia, et al.
Published: (2024)

Entangled Schrödinger Bridge Matching
by: Tang, Sophia, et al.
Published: (2025)

Minimal-Action Discrete Schrödinger Bridge Matching for Peptide Sequence Design
by: Goel, Shrey, et al.
Published: (2026)

TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation
by: Cao, Hanqun, et al.
Published: (2026)

Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation
by: Tang, Sophia, et al.
Published: (2025)

AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance
by: Chen, Tong, et al.
Published: (2025)

mRNAutilus: Multi-Objective-Guided Discrete Generation of mRNA with Optimized Therapeutic Properties
by: Patel, Sawan, et al.
Published: (2026)

Token-Level Guided Discrete Diffusion for Membrane Protein Design
by: Goel, Shrey, et al.
Published: (2024)

Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion
by: Xu, Dong, et al.
Published: (2025)

Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning
by: Ahmed, Salma J., et al.
Published: (2024)

Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
by: Shi, Liang, et al.
Published: (2026)

S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search
by: Zhou, Gengmo, et al.
Published: (2024)

Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
by: Klarner, Leo, et al.
Published: (2024)

Exploring Discrete Flow Matching for 3D De Novo Molecule Generation
by: Dunn, Ian, et al.
Published: (2024)

Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion
by: Gao, Bowen, et al.
Published: (2024)

3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation
by: Zhu, Huaisheng, et al.
Published: (2024)

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
by: Wang, Yan, et al.
Published: (2024)

Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
by: Qiu, Jiahao, et al.
Published: (2024)

Training-Free Guidance for Discrete Diffusion Models for Molecular Generation
by: Kerby, Thomas J., et al.
Published: (2024)

Generative Modeling of Molecular Dynamics Trajectories
by: Jing, Bowen, et al.
Published: (2024)

Protein Discovery with Discrete Walk-Jump Sampling
by: Frey, Nathan C., et al.
Published: (2023)

IBEX: Information-Bottleneck-EXplored Coarse-to-Fine Molecular Generation under Limited Data
by: Xu, Dong, et al.
Published: (2025)

Distributional Priors Guided Diffusion for Generating 3D Molecules in Low Data Regimes
by: Hong, Haokai, et al.
Published: (2024)

Generative Model for Small Molecules with Latent Space RL Fine-Tuning to Protein Targets
by: Sob, Ulrich A. Mbou, et al.
Published: (2024)

DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding
by: Lin, Haitao, et al.
Published: (2022)

Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization
by: Bergues, Noémie, et al.
Published: (2025)

SEISMO: Increasing Sample Efficiency in Molecular Optimization with a Trajectory-Aware LLM Agent
by: Krüger, Fabian P., et al.
Published: (2026)

MODA: A Unified 3D Diffusion Framework for Multi-Task Target-Aware Molecular Generation
by: Xu, Dong, et al.
Published: (2025)

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation
by: Yalabadi, Ali Khodabandeh, et al.
Published: (2025)

Structure-Aware Contrastive Learning with Fine-Grained Binding Representations for Drug Discovery
by: Lan, Jing, et al.
Published: (2025)

Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models
by: Zheng, Xinzhe, et al.
Published: (2025)

A Review on Fragment-based De Novo 2D Molecule Generation
by: Voloboev, Sergei
Published: (2024)

Guided Generation for Developable Antibodies
by: Zhao, Siqi, et al.
Published: (2025)

Improving Antibody Design with Force-Guided Sampling in Diffusion Models
by: Kulytė, Paulina, et al.
Published: (2024)

PepDoRA: A Unified Peptide Language Model via Weight-Decomposed Low-Rank Adaptation
by: Wang, Leyao, et al.
Published: (2024)

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
by: Peng, Xingang, et al.
Published: (2022)

DrugImproverGPT: A Large Language Model for Drug Optimization with Fine-Tuning via Structured Policy Optimization
by: Liu, Xuefeng, et al.
Published: (2025)

TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation
by: Zongying, Lin, et al.
Published: (2024)

Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization
by: Gu, Siyi, et al.
Published: (2024)

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