no code implementations • 31 Jan 2023 • Weihao Yuan, Xiaodong Gu, Heng Li, Zilong Dong, Siyu Zhu
In this work, we propose an SDF transformer network, which replaces the role of 3D CNN for better 3D feature aggregation.
no code implementations • 21 Jan 2023 • Heng Li, Xiaodong Gu, Weihao Yuan, Luwei Yang, Zilong Dong, Ping Tan
To reach this challenging goal without depth input, we introduce a hierarchical feature volume to facilitate the implicit map decoder.
1 code implementation • CVPR 2022 • Heng Li, Zhaopeng Cui, Shuaicheng Liu, Ping Tan
Our graph optimizer iteratively refines the global camera rotations by minimizing each node's single rotation objective function.
1 code implementation • 18 Oct 2022 • Haofeng Liu, Heng Li, Huazhu Fu, Ruoxiu Xiao, Yunshu Gao, Yan Hu, Jiang Liu
For boosting the clinical deployment of fundus image enhancement, this paper proposes the pyramid constraint to develop a degradation-invariant enhancement network (PCE-Net), which mitigates the demand for clinical data and stably enhances unknown data.
1 code implementation • 14 Oct 2022 • Heng Li
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms.
no code implementations • 30 Sep 2022 • Xiaowen Feng, Heng Li
Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbiome communities.
no code implementations • 13 Sep 2022 • Jiakun Lei, Tao Meng, Weijia Wang, Shujian Sun, Heng Li, Zhonghe Jin
To resolve this problem, a switching controller structure is proposed in this paper based on the reduced-attitude representation, fusing the artificial potential field (APF) methodology and the Prescribed Performance Control (PPC) scheme together.
1 code implementation • 28 Aug 2022 • Forough Majidi, Moses Openja, Foutse khomh, Heng Li
Machine learning (ML) practitioners use AutoML tools to automate and optimize the process of feature engineering, model training, and hyperparameter optimization and so on.
1 code implementation • 27 Jun 2022 • Haowen Zhang, Shiqi Wu, Srinivas Aluru, Heng Li
Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them.
1 code implementation • 9 Jun 2022 • Heng Li, Haofeng Liu, Huazhu Fu, Hai Shu, Yitian Zhao, Xiaoling Luo, Yan Hu, Jiang Liu
In this paper, to circumvent the strict deployment requirement, a structure-consistent restoration network (SCR-Net) for cataract fundus images is developed from synthesized data that shares an identical structure.
no code implementations • 1 Jun 2022 • Moses Openja, Forough Majidi, Foutse khomh, Bhagya Chembakottu, Heng Li
Studies have recently explored the use of Docker for deploying general software projects with no specific focus on how Docker is used to deploy ML-based projects.
1 code implementation • 15 Mar 2022 • Heng Li, Haofeng Liu, Yan Hu, Huazhu Fu, Yitian Zhao, Hanpei Miao, Jiang Liu
The restoration model is learned from the synthesized images and adapted to real cataract images.
no code implementations • 15 Mar 2022 • Zehua Zhang, Lu Zhang, Xuyi Zhuang, Yukun Qian, Heng Li, Mingjiang Wang
In recent years, deep learning-based approaches have significantly improved the performance of single-channel speech enhancement.
1 code implementation • 11 Mar 2022 • Yuchen Dang, Ziqi Chen, Heng Li, Hai Shu
An open-source Python package of our XGBoost-DL for the sunspot number prediction is available at https://github. com/yd1008/ts_ensemble_sunspot.
1 code implementation • 16 Oct 2021 • Xiaowen Feng, Haoyu Cheng, Daniel Portik, Heng Li
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads.
1 code implementation • 29 Sep 2021 • Heng Li
The HA-LSTM structure is different from the standard LSTM structure because a scaled dot-product attention-based sliding controller is introduced to the LSTM structure.
no code implementations • 25 Sep 2021 • Pengfei Tang, Junsheng Zeng, Dongxiao Zhang, Heng Li
The results demonstrate that constructing the settling surrogate with the MFNN can reduce the need for high-fidelity data and thus computational cost by 80%, while the accuracy lost is less than 5% compared to a high-fidelity surrogate.
1 code implementation • 10 Sep 2021 • Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo, Klaus-Peter Koepfli, Lara Urban, Neil J. Gemmell, Heng Li
Routine single-sample haplotype-resolved assembly remains an unresolved problem.
1 code implementation • 7 Aug 2021 • Heng Li
Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences.
1 code implementation • CVPR 2021 • Luwei Yang, Heng Li, Jamal Ahmed Rahim, Zhaopeng Cui, Ping Tan
These methods can suffer from bad initializations due to the noisy spanning tree or outliers in input relative rotations.
2 code implementations • 18 Dec 2020 • Petr Danecek, James K. Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A. McCarthy, Robert M. Davies, Heng Li
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data.
no code implementations • 8 Oct 2020 • Beihao Xia, Conghao Wong, Heng Li, Shiming Chen, Qinmu Peng, Xinge You
Visual images usually contain the informative context of the environment, thereby helping to predict agents' behaviors.
no code implementations • 3 Aug 2020 • Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng, Haowen Zhang, Heng Li
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome.
Genomics Quantitative Methods
1 code implementation • 13 Mar 2020 • Heng Li, Xiaowen Feng, Chong Chu
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality.
1 code implementation • 7 Jan 2020 • Hetong Dai, Heng Li, Weiyi Shang, Tse-Hsun Chen, Che-Shao Chen
As logs are usually very large in size, automated log analysis is needed to assist practitioners in their software operation and maintenance efforts.
no code implementations • 24 Oct 2019 • Nanzhe Wang, Dongxiao Zhang, Haibin Chang, Heng Li
The TgNN can achieve higher accuracy than the ordinary Artificial Neural Network (ANN) because the former provides physically feasible predictions and can be more readily generalized beyond the regimes covered with the training data.
1 code implementation • 22 Jan 2019 • Heng Li
Summary: Human alpha satellite and satellite 2/3 contribute to several percent of the human genome.
1 code implementation • 5 Nov 2018 • Spyridon Bakas, Mauricio Reyes, Andras Jakab, Stefan Bauer, Markus Rempfler, Alessandro Crimi, Russell Takeshi Shinohara, Christoph Berger, Sung Min Ha, Martin Rozycki, Marcel Prastawa, Esther Alberts, Jana Lipkova, John Freymann, Justin Kirby, Michel Bilello, Hassan Fathallah-Shaykh, Roland Wiest, Jan Kirschke, Benedikt Wiestler, Rivka Colen, Aikaterini Kotrotsou, Pamela Lamontagne, Daniel Marcus, Mikhail Milchenko, Arash Nazeri, Marc-Andre Weber, Abhishek Mahajan, Ujjwal Baid, Elizabeth Gerstner, Dongjin Kwon, Gagan Acharya, Manu Agarwal, Mahbubul Alam, Alberto Albiol, Antonio Albiol, Francisco J. Albiol, Varghese Alex, Nigel Allinson, Pedro H. A. Amorim, Abhijit Amrutkar, Ganesh Anand, Simon Andermatt, Tal Arbel, Pablo Arbelaez, Aaron Avery, Muneeza Azmat, Pranjal B., W Bai, Subhashis Banerjee, Bill Barth, Thomas Batchelder, Kayhan Batmanghelich, Enzo Battistella, Andrew Beers, Mikhail Belyaev, Martin Bendszus, Eze Benson, Jose Bernal, Halandur Nagaraja Bharath, George Biros, Sotirios Bisdas, James Brown, Mariano Cabezas, Shilei Cao, Jorge M. Cardoso, Eric N Carver, Adrià Casamitjana, Laura Silvana Castillo, Marcel Catà, Philippe Cattin, Albert Cerigues, Vinicius S. Chagas, Siddhartha Chandra, Yi-Ju Chang, Shiyu Chang, Ken Chang, Joseph Chazalon, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Chen, Kun Cheng, Ahana Roy Choudhury, Roger Chylla, Albert Clérigues, Steven Colleman, Ramiro German Rodriguez Colmeiro, Marc Combalia, Anthony Costa, Xiaomeng Cui, Zhenzhen Dai, Lutao Dai, Laura Alexandra Daza, Eric Deutsch, Changxing Ding, Chao Dong, Shidu Dong, Wojciech Dudzik, Zach Eaton-Rosen, Gary Egan, Guilherme Escudero, Théo Estienne, Richard Everson, Jonathan Fabrizio, Yong Fan, Longwei Fang, Xue Feng, Enzo Ferrante, Lucas Fidon, Martin Fischer, Andrew P. French, Naomi Fridman, Huan Fu, David Fuentes, Yaozong Gao, Evan Gates, David Gering, Amir Gholami, Willi Gierke, Ben Glocker, Mingming Gong, Sandra González-Villá, T. Grosges, Yuanfang Guan, Sheng Guo, Sudeep Gupta, Woo-Sup Han, Il Song Han, Konstantin Harmuth, Huiguang He, Aura Hernández-Sabaté, Evelyn Herrmann, Naveen Himthani, Winston Hsu, Cheyu Hsu, Xiaojun Hu, Xiaobin Hu, Yan Hu, Yifan Hu, Rui Hua, Teng-Yi Huang, Weilin Huang, Sabine Van Huffel, Quan Huo, Vivek HV, Khan M. Iftekharuddin, Fabian Isensee, Mobarakol Islam, Aaron S. Jackson, Sachin R. Jambawalikar, Andrew Jesson, Weijian Jian, Peter Jin, V Jeya Maria Jose, Alain Jungo, B Kainz, Konstantinos Kamnitsas, Po-Yu Kao, Ayush Karnawat, Thomas Kellermeier, Adel Kermi, Kurt Keutzer, Mohamed Tarek Khadir, Mahendra Khened, Philipp Kickingereder, Geena Kim, Nik King, Haley Knapp, Urspeter Knecht, Lisa Kohli, Deren Kong, Xiangmao Kong, Simon Koppers, Avinash Kori, Ganapathy Krishnamurthi, Egor Krivov, Piyush Kumar, Kaisar Kushibar, Dmitrii Lachinov, Tryphon Lambrou, Joon Lee, Chengen Lee, Yuehchou Lee, M Lee, Szidonia Lefkovits, Laszlo Lefkovits, James Levitt, Tengfei Li, Hongwei Li, Hongyang Li, Xiaochuan Li, Yuexiang Li, Heng Li, Zhenye Li, Xiaoyu Li, Zeju Li, Xiaogang Li, Wenqi Li, Zheng-Shen Lin, Fengming Lin, Pietro Lio, Chang Liu, Boqiang Liu, Xiang Liu, Mingyuan Liu, Ju Liu, Luyan Liu, Xavier Llado, Marc Moreno Lopez, Pablo Ribalta Lorenzo, Zhentai Lu, Lin Luo, Zhigang Luo, Jun Ma, Kai Ma, Thomas Mackie, Anant Madabushi, Issam Mahmoudi, Klaus H. Maier-Hein, Pradipta Maji, CP Mammen, Andreas Mang, B. S. Manjunath, Michal Marcinkiewicz, S McDonagh, Stephen McKenna, Richard McKinley, Miriam Mehl, Sachin Mehta, Raghav Mehta, Raphael Meier, Christoph Meinel, Dorit Merhof, Craig Meyer, Robert Miller, Sushmita Mitra, Aliasgar Moiyadi, David Molina-Garcia, Miguel A. B. Monteiro, Grzegorz Mrukwa, Andriy Myronenko, Jakub Nalepa, Thuyen Ngo, Dong Nie, Holly Ning, Chen Niu, Nicholas K Nuechterlein, Eric Oermann, Arlindo Oliveira, Diego D. C. Oliveira, Arnau Oliver, Alexander F. I. Osman, Yu-Nian Ou, Sebastien Ourselin, Nikos Paragios, Moo Sung Park, Brad Paschke, J. Gregory Pauloski, Kamlesh Pawar, Nick Pawlowski, Linmin Pei, Suting Peng, Silvio M. Pereira, Julian Perez-Beteta, Victor M. Perez-Garcia, Simon Pezold, Bao Pham, Ashish Phophalia, Gemma Piella, G. N. Pillai, Marie Piraud, Maxim Pisov, Anmol Popli, Michael P. Pound, Reza Pourreza, Prateek Prasanna, Vesna Prkovska, Tony P. Pridmore, Santi Puch, Élodie Puybareau, Buyue Qian, Xu Qiao, Martin Rajchl, Swapnil Rane, Michael Rebsamen, Hongliang Ren, Xuhua Ren, Karthik Revanuru, Mina Rezaei, Oliver Rippel, Luis Carlos Rivera, Charlotte Robert, Bruce Rosen, Daniel Rueckert, Mohammed Safwan, Mostafa Salem, Joaquim Salvi, Irina Sanchez, Irina Sánchez, Heitor M. Santos, Emmett Sartor, Dawid Schellingerhout, Klaudius Scheufele, Matthew R. Scott, Artur A. Scussel, Sara Sedlar, Juan Pablo Serrano-Rubio, N. Jon Shah, Nameetha Shah, Mazhar Shaikh, B. Uma Shankar, Zeina Shboul, Haipeng Shen, Dinggang Shen, Linlin Shen, Haocheng Shen, Varun Shenoy, Feng Shi, Hyung Eun Shin, Hai Shu, Diana Sima, M Sinclair, Orjan Smedby, James M. Snyder, Mohammadreza Soltaninejad, Guidong Song, Mehul Soni, Jean Stawiaski, Shashank Subramanian, Li Sun, Roger Sun, Jiawei Sun, Kay Sun, Yu Sun, Guoxia Sun, Shuang Sun, Yannick R Suter, Laszlo Szilagyi, Sanjay Talbar, DaCheng Tao, Zhongzhao Teng, Siddhesh Thakur, Meenakshi H Thakur, Sameer Tharakan, Pallavi Tiwari, Guillaume Tochon, Tuan Tran, Yuhsiang M. Tsai, Kuan-Lun Tseng, Tran Anh Tuan, Vadim Turlapov, Nicholas Tustison, Maria Vakalopoulou, Sergi Valverde, Rami Vanguri, Evgeny Vasiliev, Jonathan Ventura, Luis Vera, Tom Vercauteren, C. A. Verrastro, Lasitha Vidyaratne, Veronica Vilaplana, Ajeet Vivekanandan, Qian Wang, Chiatse J. Wang, Wei-Chung Wang, Duo Wang, Ruixuan Wang, Yuanyuan Wang, Chunliang Wang, Guotai Wang, Ning Wen, Xin Wen, Leon Weninger, Wolfgang Wick, Shaocheng Wu, Qiang Wu, Yihong Wu, Yong Xia, Yanwu Xu, Xiaowen Xu, Peiyuan Xu, Tsai-Ling Yang, Xiaoping Yang, Hao-Yu Yang, Junlin Yang, Haojin Yang, Guang Yang, Hongdou Yao, Xujiong Ye, Changchang Yin, Brett Young-Moxon, Jinhua Yu, Xiangyu Yue, Songtao Zhang, Angela Zhang, Kun Zhang, Xue-jie Zhang, Lichi Zhang, Xiaoyue Zhang, Yazhuo Zhang, Lei Zhang, Jian-Guo Zhang, Xiang Zhang, Tianhao Zhang, Sicheng Zhao, Yu Zhao, Xiaomei Zhao, Liang Zhao, Yefeng Zheng, Liming Zhong, Chenhong Zhou, Xiaobing Zhou, Fan Zhou, Hongtu Zhu, Jin Zhu, Ying Zhuge, Weiwei Zong, Jayashree Kalpathy-Cramer, Keyvan Farahani, Christos Davatzikos, Koen van Leemput, Bjoern Menze
This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i. e., 2012-2018.
no code implementations • 17 Sep 2018 • Jun Feng, Heng Li, Minlie Huang, Shichen Liu, Wenwu Ou, Zhirong Wang, Xiaoyan Zhu
The first one is lack of collaboration between scenarios meaning that each strategy maximizes its own objective but ignores the goals of other strategies, leading to a sub-optimal overall performance.
Multi-agent Reinforcement Learning reinforcement-learning +1
3 code implementations • 4 Aug 2017 • Heng Li
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length.
2 code implementations • 3 Apr 2014 • Heng Li
By investigating false heterozygous calls in the haploid genome, we identified the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample as the two major sources of errors, which press for continued improvements in these two areas.
17 code implementations • 16 Mar 2013 • Heng Li
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human.