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Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…

Biomolecules · Quantitative Biology 2024-09-19 Junqi Liu , Shaoning Li , Chence Shi , Zhi Yang , Jian Tang

Enhancing the efficiency of high-quality image generation using Diffusion Models (DMs) is a significant challenge due to the iterative nature of the process. Flow Matching (FM) is emerging as a powerful generative modeling paradigm based on…

Computer Vision and Pattern Recognition · Computer Science 2025-05-28 Pascal Zwick , Nils Friederich , Maximilian Beichter , Lennart Hilbert , Ralf Mikut , Oliver Bringmann

The design of porous infill structures presents significant challenges due to their complex geometric configurations, such as the accurate representation of geometric boundaries and the control of localized maximum stress. In current…

Optimization and Control · Mathematics 2025-10-14 Shuzhi Xu , Hiroki Kawabe , Kentaro Yaji

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

Biomolecules · Quantitative Biology 2025-01-09 Bobin Yang , Jie Deng , Zhenghan Chen , Ruoxue Wu

Topology optimization(TO) is widely used in engineering because of its ability to save material and optimize structural performance. Although prior work has explored 2D human-centered design tool for TO, the results are often limited in…

Human-Computer Interaction · Computer Science 2026-04-24 Shuyue Feng , Cedric Caremel , Yoshihiro Kawahara

We introduce $\texttt{PairFlow}$, a lightweight preprocessing step for training Discrete Flow Models (DFMs) to achieve few-step sampling without requiring a pretrained teacher. DFMs have recently emerged as a new class of generative models…

Machine Learning · Computer Science 2026-05-26 Mingue Park , Jisung Hwang , Seungwoo Yoo , Kyeongmin Yeo , Minhyuk Sung

Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein…

Biomolecules · Quantitative Biology 2025-11-19 Xinzhe Zheng , Shiyu Jiang , Gustavo Seabra , Chenglong Li , Yanjun Li

Generative modeling has emerged as a powerful paradigm for representation learning, but its direct applicability to challenging fields like medical imaging remains limited: mere generation, without task alignment, fails to provide a robust…

Machine Learning · Computer Science 2025-10-28 Luca Caldera , Giacomo Bottacini , Lara Cavinato

Predictive models of the future are fundamental for an agent's ability to reason and plan. A common strategy learns a world model and unrolls it step-by-step at inference, where small errors can rapidly compound. Geometric Horizon Models…

Machine Learning · Computer Science 2025-03-14 Jesse Farebrother , Matteo Pirotta , Andrea Tirinzoni , Rémi Munos , Alessandro Lazaric , Ahmed Touati

Generative modelling of entire CT volumes conditioned on clinical reports has the potential to accelerate research through data augmentation, privacy-preserving synthesis and reducing regulator-constraints on patient data while preserving…

Computer Vision and Pattern Recognition · Computer Science 2025-08-19 Jiayi Wang , Hadrien Reynaud , Franciskus Xaverius Erick , Bernhard Kainz

Microtubules are cytoskeletal filaments that play essential roles in many cellular processes and are key therapeutic targets in several diseases. Accurate segmentation of microtubule networks is critical for studying their organization and…

Computer Vision and Pattern Recognition · Computer Science 2026-01-22 Sidi Mohamed Sid El Moctar , Achraf Ait Laydi , Yousef El Mourabit , Hélène Bouvrais

Bifurcation phenomena in nonlinear dynamical systems often lead to multiple coexisting stable solutions, particularly in the presence of symmetry breaking. Deterministic machine learning models are unable to capture this multiplicity,…

Machine Learning · Computer Science 2026-01-26 Fleur Hendriks , Ondřej Rokoš , Martin Doškář , Marc G. D. Geers , Vlado Menkovski

Recent advancements in diffusion techniques have propelled image and video generation to unprecedented levels of quality, significantly accelerating the deployment and application of generative AI. However, 3D shape generation technology…

Computer Vision and Pattern Recognition · Computer Science 2025-03-28 Yangguang Li , Zi-Xin Zou , Zexiang Liu , Dehu Wang , Yuan Liang , Zhipeng Yu , Xingchao Liu , Yuan-Chen Guo , Ding Liang , Wanli Ouyang , Yan-Pei Cao

We formulate a hierarchical rectified flow to model data distributions. It hierarchically couples multiple ordinary differential equations (ODEs) and defines a time-differentiable stochastic process that generates a data distribution from a…

Machine Learning · Computer Science 2025-03-04 Yichi Zhang , Yici Yan , Alex Schwing , Zhizhen Zhao

In recent years, generative models have shown remarkable capabilities across diverse fields, including images, videos, language, and decision-making. By applying powerful generative models such as flow-based models to reinforcement…

Machine Learning · Computer Science 2025-05-28 Jifeng Hu , Sili Huang , Siyuan Guo , Zhaogeng Liu , Li Shen , Lichao Sun , Hechang Chen , Yi Chang , Dacheng Tao

While diffusion models have shown impressive performance in 2D image/video generation, diffusion-based Text-to-Multi-view-Video (T2MVid) generation remains underexplored. The new challenges posed by T2MVid generation lie in the lack of…

Computer Vision and Pattern Recognition · Computer Science 2024-06-14 Bing Li , Cheng Zheng , Wenxuan Zhu , Jinjie Mai , Biao Zhang , Peter Wonka , Bernard Ghanem

Recent advances in cross-modal few-shot adaptation treat visual-semantic alignment as a continuous feature transport problem via Flow Matching (FM). However, we argue that Euclidean-based FM overlooks fundamental limitations of flat…

Computer Vision and Pattern Recognition · Computer Science 2026-02-25 Lin Li , Ziqi Jiang , Gefan Ye , Zhenqi He , Jiahui Li , Jun Xiao , Kwang-Ting Cheng , Long Chen

Deep generative models such as flow and diffusion models have proven to be effective in modeling high-dimensional and complex data types such as videos or proteins, and this has motivated their use in different data modalities, such as…

Machine Learning · Computer Science 2025-04-08 Ege Erdogan

Shape-based virtual screening is widely employed in ligand-based drug design to search chemical libraries for molecules with similar 3D shapes yet novel 2D chemical structures compared to known ligands. 3D deep generative models have the…

Chemical Physics · Physics 2022-10-12 Keir Adams , Connor W. Coley

Graphical forecasting models learn the structure of time series data via projecting onto a graph, with recent techniques capturing spatial-temporal associations between variables via edge weights. Hierarchical variants offer a distinct…

Machine Learning · Computer Science 2025-04-04 Thomas Bailie , Yun Sing Koh , S. Karthik Mukkavilli , Varvara Vetrova