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An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…

Soft Condensed Matter · Physics 2018-10-03 Angus McMullen , Miranda Holmes-Cerfon , Francesco Sciortino , Alexander Y. Grosberg , Jasna Brujic

Diffusion models have emerged as a powerful class of generative models for molecular design, capable of capturing complex structural distributions and achieving high fidelity in 3D molecule generation. However, their widespread use remains…

Machine Learning · Computer Science 2026-01-15 Adrita Das , Peiran Jiang , Dantong Zhu , Barnabas Poczos , Jose Lugo-Martinez

The ability to generate virtual environments is crucial for applications ranging from gaming to physical AI domains such as robotics, autonomous driving, and industrial AI. Current learning-based 3D reconstruction methods rely on the…

Computer Vision and Pattern Recognition · Computer Science 2025-09-24 Sherwin Bahmani , Tianchang Shen , Jiawei Ren , Jiahui Huang , Yifeng Jiang , Haithem Turki , Andrea Tagliasacchi , David B. Lindell , Zan Gojcic , Sanja Fidler , Huan Ling , Jun Gao , Xuanchi Ren

We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…

Statistical Mechanics · Physics 2015-11-04 Ziya Kalay

Goal-directed molecular generation requires satisfying heterogeneous constraints such as protein--ligand compatibility and multi-objective drug-like properties, yet existing methods often optimize these constraints in isolation, failing to…

Machine Learning · Computer Science 2026-04-14 Yanting Li , Zhuoyang Jiang , Enyan Dai , Lei Wang , Wen-Cai Ye , Li Liu

Generating physically realistic 3D molecular structures remains a core challenge in molecular generative modeling. While diffusion models equipped with equivariant neural networks have made progress in capturing molecular geometries, they…

Machine Learning · Computer Science 2025-08-25 Zhijian Zhou , Junyi An , Zongkai Liu , Yunfei Shi , Xuan Zhang , Fenglei Cao , Chao Qu , Yuan Qi

We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…

Biomolecules · Quantitative Biology 2022-11-15 Shitong Luo , Jiaqi Guan , Jianzhu Ma , Jian Peng

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled…

Biomolecules · Quantitative Biology 2026-02-05 Nayoung Kim , Seongsu Kim , Sungsoo Ahn

The formation of microstructures in metallic alloys during hot metal forming involves simultaneous metallurgical complex phenomena. Traditional high-fidelity numerical frameworks used on the polycrystalline scale tend to focus on…

Materials Science · Physics 2024-05-24 Nitish Chandrappa , Marc Bernacki

In layout-to-image (L2I) synthesis, controlled complex scenes are generated from coarse information like bounding boxes. Such a task is exciting to many downstream applications because the input layouts offer strong guidance to the…

Computer Vision and Pattern Recognition · Computer Science 2025-03-18 Ruyu Wang , Xuefeng Hou , Sabrina Schmedding , Marco F. Huber

Models that accurately predict properties based on chemical structure are valuable tools in drug discovery. However, for many properties, public and private training sets are typically small, and it is difficult for the models to generalize…

Quantitative Methods · Quantitative Biology 2022-11-08 Oscar Méndez-Lucio , Christos Nicolaou , Berton Earnshaw

Due to the vast design space of molecules, generating molecules conditioned on a specific sub-structure relevant to a particular function or therapeutic target is a crucial task in computer-aided drug design. Existing works mainly focus on…

Biomolecules · Quantitative Biology 2024-12-24 Qi Zhengyang , Liu Zijing , Zhang Jiying , Cao He , Li Yu

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing…

Machine Learning · Computer Science 2024-06-21 He Cao , Yanjun Shao , Zhiyuan Liu , Zijing Liu , Xiangru Tang , Yuan Yao , Yu Li

In the past decade, Artificial Intelligence driven drug design and discovery has been a hot research topic, where an important branch is molecule generation by generative models, from GAN-based models and VAE-based models to the latest…

Biomolecules · Quantitative Biology 2023-10-10 Siyuan Guo , Jihong Guan , Shuigeng Zhou

Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…

Computational Engineering, Finance, and Science · Computer Science 2025-06-12 Ayush Jain , Rampi Ramprasad

Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…

Machine Learning · Statistics 2020-11-02 Marco Podda , Davide Bacciu , Alessio Micheli

Controllable generation is a fundamental task in NLP with many applications, providing a basis for function calling to agentic communication. However, even state-of-the-art autoregressive Large Language Models (LLMs) today exhibit…

Computation and Language · Computer Science 2025-09-29 Zhen Xiong , Yujun Cai , Zhecheng Li , Yiwei Wang

Machine learning has recently emerged as a powerful tool for generating new molecular and material structures. The success of state-of-the-art models stems from their ability to incorporate physical symmetries, such as translation,…

Machine Learning · Computer Science 2024-05-16 Bingqing Cheng

Recent advancements in deep learning-based modeling of molecules promise to accelerate in silico drug discovery. A plethora of generative models is available, building molecules either atom-by-atom and bond-by-bond or fragment-by-fragment.…

Anatomy shape modeling is a fundamental problem in medical data analysis. However, the geometric complexity and topological variability of anatomical structures pose significant challenges to accurate anatomical shape generation. In this…

Computer Vision and Pattern Recognition · Computer Science 2026-03-13 Guoqing Zhang , Jingyun Yang , Siqi Chen , Anping Zhang , Yang Li