Hongyi Xin

28 papers A* 2B 1C 1Journal 21Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Harmonizing qualitative and quantitative analyses in scRNA-seq via information geometry.
Briefings Bioinform.
Jinpu Cai, Yuxuan Wang, Yunhao Qiao, Cheng Wang, Ziqi Rong, Luting Zhou, Haoyang Liu, Jingyi Jessica Li, Hongyi Xin
2025 J jnl
Mutual exclusive gene expression reveals a stress-induced compensatory role of taurine uptake in dilated cardiomyopathy.
Briefings Bioinform.
Jinpu Cai, Xiaorui Liu, Cheng Wang, Yibo Zhang, Luqi Yang, Bingyi Li, Luting Zhou, Ziqi Rong, Haoyang Liu, Linkang He, Xinzhu Jiang, Hui Cheng, Yu Zhao, Bing He, Jianhua Yao, Hongbin Shen, Shyam Prabhakar, Qiuyu Lian, Liang Chen, Hongyi Xin
2025 J jnl
PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation.
CoRR
Jiabei Cheng, Changxi Chi, Jingbo Zhou, Hongyi Xin, Jun Xia
2024 J jnl
GAN-DIRNet: A Novel Deformable Image Registration Approach for Multimodal Histological Images.
Comput. Mater. Continua
Haiyue Li, Jing Xie, Jing Ke, Ye Yuan, Xiaoyong Pan, Hongyi Xin, Hongbin Shen
2024 — conf
L2 Normalization and Geodesic Distance for Enhanced Information Preservation in Visualizing High-dimensional Single-cell Sequencing Data.
BCB
Ziqi Rong, Jinpu Cai, Jiahao Qiu, Pengcheng Xu, Lana X. Garmire, Qiuyu Lian, Hongyi Xin
2024 J jnl
Semantic-Based Implicit Feature Transform for Few-Shot Classification.
Int. J. Comput. Vis.
Meihong Pan, Hongyi Xin, Hong-Bin Shen
2024 — conf
Team YXZ at BioLaySumm: Adapting Large Language Models for Biomedical Lay Summarization.
BioNLP@ACL
Jieli Zhou, Cheng Ye, Pengcheng Xu, Hongyi Xin
2023 J jnl
Few-shot classification with task-adaptive semantic feature learning.
Pattern Recognit.
Meihong Pan, Hongyi Xin, Chun-Qiu Xia, Hong-Bin Shen
2023 J jnl
MIRACLE: Multi-task Learning based Interpretable Regulation of Autoimmune Diseases through Common Latent Epigenetics.
CoRR
Pengcheng Xu, Jinpu Cai, Yulin Gao, Ziqi Rong, Hongyi Xin
2022 J jnl
SODA: Detecting COVID-19 in Chest X-Rays With Semi-Supervised Open Set Domain Adaptation.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jieli Zhou, Baoyu Jing, Zeya Wang, Hongyi Xin, Hanghang Tong
2022 J jnl
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics.
Genom. Proteom. Bioinform.
Yiran Shan, Qian Zhang, Wenbo Guo, Yanhong Wu, Yuxin Miao, Hongyi Xin, Qiuyu Lian, Jin Gu
2020 J jnl
Artificial-cell-type aware cell-type classification in CITE-seq.
Bioinform.
Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen
2020 J jnl
Context-aware seeds for read mapping.
Algorithms Mol. Biol.
Hongyi Xin, Mingfu Shao, Carl Kingsford
2020 J jnl
Deep-learning-based prediction of late age-related macular degeneration progression.
Nat. Mach. Intell.
Qi Yan, Daniel E. Weeks, Hongyi Xin, Anand Swaroop, Emily Y. Chew, Heng Huang, Ying Ding, Wei Chen
2019 — conf
Adaptively Accelerating Map-Reduce/Spark with GPUs: A Case Study.
ICAC
K. R. Jayaram, Anshul Gandhi, Hongyi Xin, Shu Tao
2019 C conf
Context-Aware Seeds for Read Mapping.
WABI
Hongyi Xin, Mingfu Shao, Carl Kingsford
2018 J jnl
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.
BMC Genom.
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2017 J jnl
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies.
CoRR
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2017 J jnl
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.
Bioinform.
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
2016 J jnl
GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture.
CoRR
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
2016 J jnl
Optimal seed solver: optimizing seed selection in read mapping.
Bioinform.
Hongyi Xin, Sunny Nahar, Richard L. Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2015 J jnl
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping.
CoRR
Hongyi Xin, Richard L. Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2015 J jnl
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.
Bioinform.
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2014 J jnl
Mitigating Prefetcher-Caused Pollution Using Informed Caching Policies for Prefetched Blocks.
ACM Trans. Archit. Code Optim.
Vivek Seshadri, Samihan Yedkar, Hongyi Xin, Onur Mutlu, Phillip B. Gibbons, Michael A. Kozuch, Todd C. Mowry
2013 J jnl
Accelerating read mapping with FastHASH.
BMC Genom.
Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, Can Alkan
2013 B conf
EMERALD: Characterization of emerging applications and algorithms for low-power devices.
ISPASS
Chuanjun Zhang, Glenn G. Ko, Jungwook Choi, Shang-nien Tsai, Minje Kim, Abner Guzmán-Rivera, Rob A. Rutenbar, Paris Smaragdis, Mi Sun Park, Vijaykrishnan Narayanan, Hongyi Xin, Onur Mutlu, Bin Li, Li Zhao, Mei Chen
2013 A* conf
Linearly compressed pages: a low-complexity, low-latency main memory compression framework.
MICRO
Gennady Pekhimenko, Vivek Seshadri, Yoongu Kim, Hongyi Xin, Onur Mutlu, Phillip B. Gibbons, Michael A. Kozuch, Todd C. Mowry
2012 A* conf
A case for unlimited watchpoints.
ASPLOS
Joseph L. Greathouse, Hongyi Xin, Yixin Luo, Todd M. Austin