Search Results for author: Heng Li

Found 53 papers, 37 papers with code

RaffeSDG: Random Frequency Filtering enabled Single-source Domain Generalization for Medical Image Segmentation

1 code implementation2 May 2024 Heng Li, Haojin Li, Jianyu Chen, Zhongxi Qiu, Huazhu Fu, Lidai Wang, Yan Hu, Jiang Liu

To tackle domain shifts in data-scarce medical scenarios, we propose a Random frequency filtering enabled Single-source Domain Generalization algorithm (RaffeSDG), which promises robust out-of-domain inference with segmentation models trained on a single-source domain.

Data Augmentation Domain Generalization +4

Yi: Open Foundation Models by 01.AI

1 code implementation7 Mar 2024 01. AI, :, Alex Young, Bei Chen, Chao Li, Chengen Huang, Ge Zhang, Guanwei Zhang, Heng Li, Jiangcheng Zhu, Jianqun Chen, Jing Chang, Kaidong Yu, Peng Liu, Qiang Liu, Shawn Yue, Senbin Yang, Shiming Yang, Tao Yu, Wen Xie, Wenhao Huang, Xiaohui Hu, Xiaoyi Ren, Xinyao Niu, Pengcheng Nie, Yuchi Xu, Yudong Liu, Yue Wang, Yuxuan Cai, Zhenyu Gu, Zhiyuan Liu, Zonghong Dai

The Yi model family is based on 6B and 34B pretrained language models, then we extend them to chat models, 200K long context models, depth-upscaled models, and vision-language models.

Attribute Chatbot +2

Exploring gene content with pangenome gene graphs

1 code implementation25 Feb 2024 Heng Li, Maximillian Marin, Maha Reda Farhat

Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome.

Refining GPT-3 Embeddings with a Siamese Structure for Technical Post Duplicate Detection

1 code implementation22 Dec 2023 Xingfang Wu, Heng Li, Nobukazu Yoshioka, Hironori Washizaki, Foutse khomh

When applied to the dataset we constructed with a recent Stack Overflow dump, our approach attains a Top-1, Top-5, and Top-30 accuracy of 23. 1%, 43. 9%, and 68. 9%, respectively.

Characterizing and Classifying Developer Forum Posts with their Intentions

1 code implementation21 Dec 2023 Xingfang Wu, Eric Laufer, Heng Li, Foutse khomh, Santhosh Srinivasan, Jayden Luo

The modeling of the intentions of posts can provide an extra dimension to the current tag taxonomy.


AutoRepo: A general framework for multi-modal LLM-based automated construction reporting

no code implementations11 Oct 2023 Hongxu Pu, Xincong Yang, Jing Li, Runhao Guo, Heng Li

Ensuring the safety, quality, and timely completion of construction projects is paramount, with construction inspections serving as a vital instrument towards these goals.


ACT-Net: Anchor-context Action Detection in Surgery Videos

no code implementations5 Oct 2023 Luoying Hao, Yan Hu, Wenjun Lin, Qun Wang, Heng Li, Huazhu Fu, Jinming Duan, Jiang Liu

In this paper, to accurately detect fine-grained actions that happen at every moment, we propose an anchor-context action detection network (ACTNet), including an anchor-context detection (ACD) module and a class conditional diffusion (CCD) module, to answer the following questions: 1) where the actions happen; 2) what actions are; 3) how confidence predictions are.

Action Detection Denoising

A Generic Fundus Image Enhancement Network Boosted by Frequency Self-supervised Representation Learning

2 code implementations2 Sep 2023 Heng Li, Haofeng Liu, Huazhu Fu, Yanwu Xu, Hui Shu, Ke Niu, Yan Hu, Jiang Liu

Fundus photography is prone to suffer from image quality degradation that impacts clinical examination performed by ophthalmologists or intelligent systems.

Image Enhancement Representation Learning

Deploying Deep Reinforcement Learning Systems: A Taxonomy of Challenges

1 code implementation23 Aug 2023 Ahmed Haj Yahmed, Altaf Allah Abbassi, Amin Nikanjam, Heng Li, Foutse khomh

In this paper, we propose an empirical study on Stack Overflow (SO), the most popular Q&A forum for developers, to uncover and understand the challenges practitioners faced when deploying DRL systems.


On the Effectiveness of Log Representation for Log-based Anomaly Detection

1 code implementation17 Aug 2023 Xingfang Wu, Heng Li, Foutse khomh

We believe our comprehensive comparison of log representation techniques can help researchers and practitioners better understand the characteristics of different log representation techniques and provide them with guidance for selecting the most suitable ones for their ML-based log analysis workflow.

Anomaly Detection Log Parsing

Genome assembly in the telomere-to-telomere era

no code implementations15 Aug 2023 Heng Li, Richard Durbin

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads.

Optimal battery thermal management for electric vehicles with battery degradation minimization

no code implementations6 Aug 2023 Yue Wu, Zhiwu Huang, Dongjun Li, Heng Li, Jun Peng, Daniel Stroe, Ziyou Song

A control-oriented onboard BTMS model is proposed and verified under different speed profiles and temperatures.


Frequency-mixed Single-source Domain Generalization for Medical Image Segmentation

1 code implementation18 Jul 2023 Heng Li, Haojin Li, Wei Zhao, Huazhu Fu, Xiuyun Su, Yan Hu, Jiang Liu

Consequently, domain generalization (DG) is developed to boost the performance of segmentation models on unseen domains.

Domain Generalization Image Segmentation +3

Efficient Backdoor Attacks for Deep Neural Networks in Real-world Scenarios

1 code implementation14 Jun 2023 Ziqiang Li, Hong Sun, Pengfei Xia, Heng Li, Beihao Xia, Yi Wu, Bin Li

However, existing backdoor attack methods make unrealistic assumptions, assuming that all training data comes from a single source and that attackers have full access to the training data.

Backdoor Attack

Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph

1 code implementation6 Jun 2023 Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren, Heng Li

Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources.

Learnable Ophthalmology SAM

1 code implementation26 Apr 2023 Zhongxi Qiu, Yan Hu, Heng Li, Jiang Liu

Based on Segment Anything (SAM), we propose a simple but effective learnable prompt layer suitable for multiple target segmentation in ophthalmology multi-modal images, named Learnable Ophthalmology Segment Anything (SAM).


What Causes Exceptions in Machine Learning Applications? Mining Machine Learning-Related Stack Traces on Stack Overflow

no code implementations25 Apr 2023 Amin Ghadesi, Maxime Lamothe, Heng Li

Thus, studying the patterns in stack traces can help practitioners and researchers understand the causes of exceptions in ML applications and the challenges faced by ML developers.

De novo reconstruction of satellite repeat units from sequence data

1 code implementation19 Apr 2023 Yujie Zhang, Justin Chu, Haoyu Cheng, Heng Li

Existing algorithms for identifying satellite repeats either require the complete assembly of satellites or only work for simple repeat structures without HORs.

3D Former: Monocular Scene Reconstruction with 3D SDF Transformers

1 code implementation31 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.

Dense RGB SLAM with Neural Implicit Maps

no code implementations21 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.

Decoder Simultaneous Localization and Mapping

Foreground and Text-lines Aware Document Image Rectification

1 code implementation ICCV 2023 Heng Li, XiangPing Wu, Qingcai Chen, Qianjin Xiang

In this paper, we focus on the foreground and text-line regions of distorted paper and proposes a global and local fusion method to improve the rectification effect of distorted images and enhance the readability of document images.

RAGO: Recurrent Graph Optimizer For Multiple Rotation Averaging

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.

Degradation-invariant Enhancement of Fundus Images via Pyramid Constraint Network

1 code implementation18 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.

Image Enhancement

Protein-to-genome alignment with miniprot

1 code implementation14 Oct 2022 Heng Li

Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms.

Towards complete representation of bacterial contents in metagenomic samples

no code implementations30 Sep 2022 Xiaowen Feng, Heng Li

Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbiome communities.

Spacecraft Attitude Pointing Control under Pointing Forbidden Constraints with Guaranteed Accuracy

no code implementations13 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.

An Empirical Study on the Usage of Automated Machine Learning Tools

1 code implementation28 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.

Feature Engineering Hyperparameter Optimization +1

Fast sequence to graph alignment using the graph wavefront algorithm

1 code implementation27 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.

Structure-consistent Restoration Network for Cataract Fundus Image Enhancement

3 code implementations9 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.

Image Enhancement Medical Image Enhancement

Studying the Practices of Deploying Machine Learning Projects on Docker

no code implementations1 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.

BIG-bench Machine Learning Management

An Annotation-free Restoration Network for Cataractous Fundus Images

2 code implementations15 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.

A comparative study of non-deep learning, deep learning, and ensemble learning methods for sunspot number prediction

1 code implementation11 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.

Ensemble Learning

Metagenome assembly of high-fidelity long reads with hifiasm-meta

1 code implementation16 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.

Vocal Bursts Intensity Prediction

Integrating Attention Feedback into the Recurrent Neural Network

1 code implementation29 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.

text-classification Text Classification +1

Constructing Sub-scale Surrogate Model for Proppant Settling in Inclined Fractures from Simulation Data with Multi-fidelity Neural Network

no code implementations25 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.

New strategies to improve minimap2 alignment accuracy

1 code implementation7 Aug 2021 Heng Li

Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences.

End-to-End Rotation Averaging With Multi-Source Propagation

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.

Twelve years of SAMtools and BCFtools

2 code implementations18 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.

BGM: Building a Dynamic Guidance Map without Visual Images for Trajectory Prediction

no code implementations8 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.

Decoder Trajectory Prediction

Haplotype-resolved de novo assembly with phased assembly graphs

no code implementations3 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

The design and construction of reference pangenome graphs

1 code implementation13 Mar 2020 Heng Li, Xiaowen Feng, Chong Chu

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality.

Logram: Efficient Log Parsing Using n-Gram Dictionaries

2 code implementations7 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.

Software Engineering

Deep Learning of Subsurface Flow via Theory-guided Neural Network

no code implementations24 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.

Transfer Learning

Identifying centromeric satellites with dna-brnn

1 code implementation22 Jan 2019 Heng Li

Summary: Human alpha satellite and satellite 2/3 contribute to several percent of the human genome.

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

1 code implementation5 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.

Brain Tumor Segmentation Survival Prediction +1

Learning to Collaborate: Multi-Scenario Ranking via Multi-Agent Reinforcement Learning

no code implementations17 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

Minimap2: pairwise alignment for nucleotide sequences

3 code implementations4 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.

Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples

2 code implementations3 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.

Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

17 code implementations16 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.

3D Object Reconstruction From A Single Image Genomics

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