no code implementations • 20 Apr 2024 • Chenru Duan, Guan-Horng Liu, Yuanqi Du, Tianrong Chen, Qiyuan Zhao, Haojun Jia, Carla P. Gomes, Evangelos A. Theodorou, Heather J. Kulik
The RMSD and barrier height error is further improved by roughly 25% through pretraining React-OT on a large reaction dataset obtained with a lower level of theory, GFN2-xTB.
no code implementations • 28 Feb 2024 • Lingkai Kong, Yuanqi Du, Wenhao Mu, Kirill Neklyudov, Valentin De Bortol, Haorui Wang, Dongxia Wu, Aaron Ferber, Yi-An Ma, Carla P. Gomes, Chao Zhang
To constrain the optimization process to the data manifold, we reformulate the original optimization problem as a sampling problem from the product of the Boltzmann distribution defined by the objective function and the data distribution learned by the diffusion model.
1 code implementation • 29 Sep 2023 • Yanqiao Zhu, Jeehyun Hwang, Keir Adams, Zhen Liu, Bozhao Nan, Brock Stenfors, Yuanqi Du, Jatin Chauhan, Olaf Wiest, Olexandr Isayev, Connor W. Coley, Yizhou Sun, Wei Wang
Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design.
1 code implementation • NeurIPS 2023 • Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Li-Ping Liu
Self-supervised training methods for transformers have demonstrated remarkable performance across various domains.
1 code implementation • 17 Jul 2023 • Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Haiyang Yu, Yuqing Xie, Xiang Fu, Alex Strasser, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik Bekkers, Michael Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess Smidt, Shuiwang Ji
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences.
2 code implementations • 14 Jun 2023 • Yinghao Li, Lingkai Kong, Yuanqi Du, Yue Yu, Yuchen Zhuang, Wenhao Mu, Chao Zhang
While some studies have included UQ to improve molecular pre-trained models, the process of selecting suitable backbone and UQ methods for reliable molecular uncertainty estimation remains underexplored.
1 code implementation • 12 Apr 2023 • Chenru Duan, Yuanqi Du, Haojun Jia, Heather J. Kulik
Provided reactant and product, this model generates a TS structure in seconds instead of hours required when performing quantum chemistry-based optimizations.
1 code implementation • NeurIPS 2023 • Weitao Du, Yuanqi Du, Limei Wang, Dieqiao Feng, Guifeng Wang, Shuiwang Ji, Carla Gomes, Zhi-Ming Ma
Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects.
no code implementations • 3 Feb 2023 • Junwen Bai, Yuanqi Du, Yingheng Wang, Shufeng Kong, John Gregoire, Carla Gomes
Modern machine learning techniques have been extensively applied to materials science, especially for property prediction tasks.
1 code implementation • NeurIPS 2023 • Ryan-Rhys Griffiths, Leo Klarner, Henry B. Moss, Aditya Ravuri, Sang Truong, Samuel Stanton, Gary Tom, Bojana Rankovic, Yuanqi Du, Arian Jamasb, Aryan Deshwal, Julius Schwartz, Austin Tripp, Gregory Kell, Simon Frieder, Anthony Bourached, Alex Chan, Jacob Moss, Chengzhi Guo, Johannes Durholt, Saudamini Chaurasia, Felix Strieth-Kalthoff, Alpha A. Lee, Bingqing Cheng, Alán Aspuru-Guzik, Philippe Schwaller, Jian Tang
By defining such kernels in GAUCHE, we seek to open the door to powerful tools for uncertainty quantification and Bayesian optimisation in chemistry.
no code implementations • 5 Dec 2022 • Xian Liu, Qianyi Wu, Hang Zhou, Yuanqi Du, Wayne Wu, Dahua Lin, Ziwei Liu
Our key insight is that the co-speech gestures can be decomposed into common motion patterns and subtle rhythmic dynamics.
2 code implementations • 29 Oct 2022 • Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design.
2 code implementations • 24 Oct 2022 • Arne Schneuing, Yuanqi Du, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla Gomes, Max Welling, Michael Bronstein, Bruno Correia
Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets.
no code implementations • 1 Oct 2022 • Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William Wuest, Amarda Shehu, Liang Zhao
Developing deep generative models has been an emerging field due to the ability to model and generate complex data for various purposes, such as image synthesis and molecular design.
1 code implementation • 29 Sep 2022 • Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu
Molecular pretraining, which learns molecular representations over massive unlabeled data, has become a prominent paradigm to solve a variety of tasks in computational chemistry and drug discovery.
no code implementations • 19 Jul 2022 • Shiyu Wang, Yuanqi Du, Xiaojie Guo, Bo Pan, Zhaohui Qin, Liang Zhao
This article is a systematic review that explains this promising research area, commonly known as controllable deep data generation.
1 code implementation • NeurIPS 2023 • Lars Holdijk, Yuanqi Du, Ferry Hooft, Priyank Jaini, Bernd Ensing, Max Welling
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e. g. a folded and unfolded protein or products and reactants of a chemical reaction.
no code implementations • 17 Jun 2022 • Weitao Du, Tao Yang, He Zhang, Yuanqi Du
Despite the empirical success of the hand-crafted fixed forward SDEs, a great quantity of proper forward SDEs remain unexplored.
1 code implementation • 4 May 2022 • Runsheng Xu, Zhengzhong Tu, Yuanqi Du, Xiaoyu Dong, Jinlong Li, Zibo Meng, Jiaqi Ma, Alan Bovik, Hongkai Yu
Our proposed framework consists of three modules: a restoration sub-network that conducts restoration from degradations, a similarity network that performs color histogram matching and color transfer, and a colorization subnet that learns to predict the chroma elements of images conditioned on chromatic reference signals.
no code implementations • 28 Mar 2022 • Yuanqi Du, Tianfan Fu, Jimeng Sun, Shengchao Liu
Recently, with the rapid development of machine learning methods, especially generative methods, molecule design has achieved great progress by leveraging machine learning models to generate candidate molecules.
no code implementations • 13 Mar 2022 • Yanqiao Zhu, Yuanqi Du, Yinkai Wang, Yichen Xu, Jieyu Zhang, Qiang Liu, Shu Wu
In this paper, we conduct a comprehensive review on the existing literature of deep graph generation from a variety of emerging methods to its wide application areas.
no code implementations • 10 Mar 2022 • Quan Quan, Qiyuan Wang, Yuanqi Du, Liu Li, S. Kevin Zhou
While medical images such as computed tomography (CT) are stored in DICOM format in hospital PACS, it is still quite routine in many countries to print a film as a transferable medium for the purposes of self-storage and secondary consultation.
no code implementations • 28 Feb 2022 • Yuanqi Du, Xiaojie Guo, Hengning Cao, Yanfang Ye, Liang Zhao
Spatiotemporal graph represents a crucial data structure where the nodes and edges are embedded in a geometric space and can evolve dynamically over time.
no code implementations • 28 Feb 2022 • Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
Recent advances in deep graph generative models treat molecule design as graph generation problems which provide new opportunities toward the breakthrough of this long-lasting problem.
3 code implementations • 16 Feb 2022 • Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
Pretrained Language Models (PLMs) such as BERT have revolutionized the landscape of Natural Language Processing (NLP).
no code implementations • 5 Feb 2022 • Runsheng Xu, Zhengzhong Tu, Yuanqi Du, Xiaoyu Dong, Jinlong Li, Zibo Meng, Jiaqi Ma, Hongkai Yu
Renovating the memories in old photos is an intriguing research topic in computer vision fields.
no code implementations • 15 Dec 2021 • Yinkai Wang, Aowei Ding, Kaiyi Guan, Shixi Wu, Yuanqi Du
Student performance prediction is a critical research problem to understand the students' needs, present proper learning opportunities/resources, and develop the teaching quality.
1 code implementation • 26 Oct 2021 • Weitao Du, He Zhang, Yuanqi Du, Qi Meng, Wei Chen, Bin Shao, Tie-Yan Liu
In this paper, we propose a framework to construct SE(3) equivariant graph neural networks that can approximate the geometric quantities efficiently.
no code implementations • 29 Sep 2021 • Yuanqi Du, Xian Liu, Shengchao Liu, Bolei Zhou
In this work, we develop a simple yet effective method to interpret the latent space of the learned generative models with various molecular properties for more interactive molecule generation and discovery.
no code implementations • NeurIPS Workshop AI4Scien 2021 • Ziming Liu, Yunyue Chen, Yuanqi Du, Max Tegmark
Integrating physical inductive biases into machine learning can improve model generalizability.
1 code implementation • NeurIPS Workshop AI4Scien 2021 • Yuanqi Du, Shiyu Wang, Xiaojie Guo, Hengning Cao, Shujie Hu, Junji Jiang, Aishwarya Varala, Abhinav Angirekula, Liang Zhao
Graph generation, which learns from known graphs and discovers novel graphs, has great potential in numerous research topics like drug design and mobility synthesis and is one of the fastest-growing domains recently due to its promise for discovering new knowledge.
no code implementations • 24 Jun 2021 • Yuanqi Du, Quan Quan, Hu Han, S. Kevin Zhou
Pseudo-normality synthesis, which computationally generates a pseudo-normal image from an abnormal one (e. g., with lesions), is critical in many perspectives, from lesion detection, data augmentation to clinical surgery suggestion.
no code implementations • 4 Mar 2021 • Yanqiao Zhu, Weizhi Xu, Jinghao Zhang, Yuanqi Du, Jieyu Zhang, Qiang Liu, Carl Yang, Shu Wu
Specifically, we first formulate a general pipeline of GSL and review state-of-the-art methods classified by the way of modeling graph structures, followed by applications of GSL across domains.
1 code implementation • ICLR 2021 • Xiaojie Guo, Yuanqi Du, Liang Zhao
Deep generative models have made important progress towards modeling complex, high dimensional data via learning latent representations.
no code implementations • 17 Dec 2020 • Quan Quan, Qiyuan Wang, Liu Li, Yuanqi Du, S. Kevin Zhou
We also record all accompanying information related to the geometric deformation (such as 3D coordinate, depth, normal, and UV maps) and illumination variation (such as albedo map).
1 code implementation • 16 Dec 2020 • Pengbo Liu, Hu Han, Yuanqi Du, Heqin Zhu, Yinhao Li, Feng Gu, Honghu Xiao, Jun Li, Chunpeng Zhao, Li Xiao, Xinbao Wu, S. Kevin Zhou
Due to the lack of a large-scale pelvic CT dataset with annotations, deep learning methods are not fully explored.
1 code implementation • 8 Apr 2020 • Xiaojie Guo, Yuanqi Du, Sivani Tadepalli, Liang Zhao, Amarda Shehu
Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function.