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Discrete diffusion models offer a flexible, controllable approach to structured sequence generation, yet they still lag behind causal language models in expressive power. A key limitation lies in their reliance on the Markovian assumption,…

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a…

Computation and Language · Computer Science 2024-10-11 Peng Zhou , Jianmin Wang , Chunyan Li , Zixu Wang , Yiping Liu , Siqi Sun , Jianxin Lin , Leyi Wei , Xibao Cai , Houtim Lai , Wei Liu , Longyue Wang , Yuansheng Liu , Xiangxiang Zeng

Large Language Models (LLMs) have significantly advanced molecular discovery, but existing multimodal molecular architectures fundamentally rely on autoregressive (AR) backbones. This strict left-to-right inductive bias is sub-optimal for…

Artificial Intelligence · Computer Science 2026-04-08 Seohyeon Shin , HanJun Choi , Jun-Hyung Park , Hong Kook Kim , Mansu Kim

Molecular optimization (MO) is a crucial stage in drug discovery in which task-oriented generated molecules are optimized to meet practical industrial requirements. Existing mainstream MO approaches primarily utilize external property…

Machine Learning · Computer Science 2025-12-17 Yida Xiong , Kun Li , Jiameng Chen , Hongzhi Zhang , Di Lin , Yan Che , Wenbin Hu

Billions of organic molecules are known, but only a tiny fraction of the functional inorganic materials have been discovered, a particularly relevant problem to the community searching for new quantum materials. Recent advancements in…

Accurate protein structures are essential for understanding biological function, yet incorporating experimental data into protein generative models remains a major challenge. Most predictors of experimental observables are…

Machine Learning · Computer Science 2025-11-18 Nadav Bojan Sellam , Meital Bojan , Paul Schanda , Alex Bronstein

While Diffusion Language Models (DLMs) are theoretically well-suited for iterative refinement due to their non-causal structure, they often fail to reliably revise incorrect tokens in practice. The key challenge lies in the model's…

Machine Learning · Computer Science 2026-01-30 Shuibai Zhang , Fred Zhangzhi Peng , Yiheng Zhang , Jin Pan , Grigorios G. Chrysos

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…

Machine Learning · Computer Science 2025-10-21 Yingxu Wang , Kunyu Zhang , Jiaxin Huang , Nan Yin , Siwei Liu , Eran Segal

Developing bioactive molecules remains a central, time- and cost-heavy challenge in drug discovery, particularly for novel targets lacking structural or functional data. Pharmacophore modeling presents an alternative for capturing the key…

Machine Learning · Computer Science 2025-05-16 Amira Alakhdar , Barnabas Poczos , Newell Washburn

Robotic learning for navigation in unfamiliar environments needs to provide policies for both task-oriented navigation (i.e., reaching a goal that the robot has located), and task-agnostic exploration (i.e., searching for a goal in a novel…

Robotics · Computer Science 2023-10-13 Ajay Sridhar , Dhruv Shah , Catherine Glossop , Sergey Levine

Efficient exploration of the vast chemical space is a fundamental challenge in materials design and discovery, particularly for designing functional inorganic crystalline materials with targeted properties. Diffusion-based generative models…

Materials Science · Physics 2026-03-20 Sourav Mal , Nehad Ahmed , Junaid Jami , Subhankar Mishra , Prasenjit Sen

Despite the remarkable generative capabilities of diffusion models, their integration into safety-critical or scientifically rigorous applications remains hindered by the need to ensure compliance with stringent physical, structural, and…

Machine Learning · Computer Science 2025-06-03 Jacob K. Christopher , Michael Cardei , Jinhao Liang , Ferdinando Fioretto

The objective for establishing dense correspondence between paired images consists of two terms: a data term and a prior term. While conventional techniques focused on defining hand-designed prior terms, which are difficult to formulate,…

Computer Vision and Pattern Recognition · Computer Science 2024-01-26 Jisu Nam , Gyuseong Lee , Sunwoo Kim , Hyeonsu Kim , Hyoungwon Cho , Seyeon Kim , Seungryong Kim

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…

Machine Learning · Computer Science 2025-05-27 Raul Ortega-Ochoa , Tejs Vegge , Jes Frellsen

Given an unconditional generative model and a predictor for a target property (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. As a highly…

Machine Learning · Computer Science 2025-03-19 Haowei Lin , Shanda Li , Haotian Ye , Yiming Yang , Stefano Ermon , Yitao Liang , Jianzhu Ma

Diffusion models have demonstrated remarkable performance in generating unimodal data across various tasks, including image, video, and text generation. On the contrary, the joint generation of multimodal data through diffusion models is…

Machine Learning · Computer Science 2025-06-16 Kevin Rojas , Yuchen Zhu , Sichen Zhu , Felix X. -F. Ye , Molei Tao

Diffusion models (DMs) are a type of generative model that has a huge impact on image synthesis and beyond. They achieve state-of-the-art generation results in various generative tasks. A great diversity of conditioning inputs, such as text…

Machine Learning · Computer Science 2024-02-02 Weiguo Lu , Xuan Wu , Deng Ding , Jinqiao Duan , Jirong Zhuang , Gangnan Yuan

Understanding and designing biomolecules, such as proteins and small molecules, is central to advancing drug discovery, synthetic biology and enzyme engineering. Recent breakthroughs in artificial intelligence have revolutionized…

Computation and Language · Computer Science 2025-07-28 Xiang Zhuang , Keyan Ding , Tianwen Lyu , Yinuo Jiang , Xiaotong Li , Zhuoyi Xiang , Zeyuan Wang , Ming Qin , Kehua Feng , Jike Wang , Qiang Zhang , Huajun Chen

Disordered metamaterials are promising for programming physical properties across diverse applications, yet their inverse design remains challenging due to the non-intuitive structure-property relationships and large design spaces. Recent…

Computational Engineering, Finance, and Science · Computer Science 2026-03-18 Ziyuan Xie , Weipeng Xu , Dazhi Zhao , Wenchang Zhang , Daoyang Dong , Bingbing Xu , Ning Liu , Sheng Mao , Tianju Xue

Diffusion-based generative modeling has been achieving state-of-the-art results on various generation tasks. Most diffusion models, however, are limited to a single-generation modeling. Can we generalize diffusion models with the ability of…

Computer Vision and Pattern Recognition · Computer Science 2024-09-26 Changyou Chen , Han Ding , Bunyamin Sisman , Yi Xu , Ouye Xie , Benjamin Z. Yao , Son Dinh Tran , Belinda Zeng