Xinghua Lu

33 papers Misc 1Journal 25Unranked 7
YearRankTypeTitle / Venue / Authors
2025 J jnl
IBI-DT: a novel approach combining individualized Bayesian inference and decision tree for identifying cancer drivers and their interactions.
Briefings Bioinform.
Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu
2025 J jnl
Knowledge-guided Contextual Gene Set Analysis Using Large Language Models.
CoRR
Zhizheng Wang, Chi-Ping Day, Chih-Hsuan Wei, Qiao Jin, Robert Leaman, Yifan Yang, Shubo Tian, Aodong Qiu, Yin Fang, Qingqing Zhu, Xinghua Lu, Zhiyong Lu
2024 J jnl
An interpretable deep learning framework for genome-informed precision oncology.
Nat. Mac. Intell.
Shuangxia Ren, Gregory F. Cooper, Lujia Chen, Xinghua Lu
2022 J jnl
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
PLoS Comput. Biol.
Xueer Chen, Lujia Chen, Cornelius H. L. Kürten, Fattaneh Jabbari, Lazar Vujanovic, Ying Ding, Binfeng Lu, Kevin Lu, Aditi Kulkarni, Tracy Tabib, Robert Lafyatis, Gregory F. Cooper, Robert Ferris, Xinghua Lu
2022 J jnl
Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution.
Bioinform.
Manqi Cai, Molin Yue, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan C. Celedón, Chris McKennan, Wei Chen, Jiebiao Wang
2020 J jnl
Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks.
BMC Bioinform.
Jinling Liu, Xiaojun Ma, Gregory F. Cooper, Xinghua Lu
2020 Misc conf
From Genome to Phenome: Predicting Multiple Cancer Phenotypes Based on Somatic GenomicAlterations via the Genomic Impact Transformer.
PSB
Yifeng Tao, Chunhui Cai, William W. Cohen, Xinghua Lu
2020 — conf
Learning Latent Causal Structures with a Redundant Input Neural Network.
CD@KDD
Jonathan D. Young, Bryan Andrews, Gregory F. Cooper, Xinghua Lu
2020 J jnl
Learning Latent Causal Structures with a Redundant Input Neural Network.
CoRR
Jonathan D. Young, Bryan Andrews, Gregory F. Cooper, Xinghua Lu
2020 — conf
Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative Filtering with Contextual Attention.
MLHC
Yifeng Tao, Shuangxia Ren, Michael Q. Ding, Russell Schwartz, Xinghua Lu
2019 — conf
Deep Contextualized Biomedical Abbreviation Expansion.
BioNLP@ACL
Qiao Jin, Jinling Liu, Xinghua Lu
2019 J jnl
Deep Contextualized Biomedical Abbreviation Expansion.
CoRR
Qiao Jin, Jinling Liu, Xinghua Lu
2019 J jnl
Integrating data and knowledge to identify functional modules of genes: a multilayer approach.
BMC Bioinform.
Lifan Liang, Vicky Chen, Kunju Zhu, Xiaonan Fan, Xinghua Lu, Songjian Lu
2019 J jnl
Probing Biomedical Embeddings from Language Models.
CoRR
Qiao Jin, Bhuwan Dhingra, William W. Cohen, Xinghua Lu
2019 — conf
PubMedQA: A Dataset for Biomedical Research Question Answering.
EMNLP/IJCNLP (1)
Qiao Jin, Bhuwan Dhingra, Zhengping Liu, William W. Cohen, Xinghua Lu
2019 J jnl
PubMedQA: A Dataset for Biomedical Research Question Answering.
CoRR
Qiao Jin, Bhuwan Dhingra, Zhengping Liu, William W. Cohen, Xinghua Lu
2019 J jnl
Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference.
PLoS Comput. Biol.
Chunhui Cai, Gregory F. Cooper, Kevin N. Lu, Xiaojun Ma, Shuping Xu, Zhenlong Zhao, Xueer Chen, Yifan Xue, Adrian V. Lee, Nathan Clark, Vicky Chen, Songjian Lu, Lujia Chen, Liyue Yu, Harry Hochheiser, Xia Jiang, Q. Jane Wang, Xinghua Lu
2017 J jnl
Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma.
BMC Bioinform.
Jonathan D. Young, Chunhui Cai, Xinghua Lu
2016 J jnl
An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem.
Algorithms Mol. Biol.
Songjian Lu, Gunasheil Mandava, Gaibo Yan, Xinghua Lu
2016 J jnl
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.
BMC Bioinform.
Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu
2015 J jnl
Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets.
PLoS Comput. Biol.
Songjian Lu, Kevin N. Lu, Shi-Yuan Cheng, Bo Hu, Xiaojun Ma, Nicholas Nystrom, Xinghua Lu
2015 — conf
Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets.
BIBM
Songjian Lu, Kevin N. Lu, Shi-Yuan Cheng, Bo Hu, Xiaojun Ma, Nicholas Nystrom, Xinghua Lu
2015 J jnl
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data.
BMC Bioinform.
Henry Ogoe, Shyam Visweswaran, Xinghua Lu, Vanathi Gopalakrishnan
2015 J jnl
The center for causal discovery of biomedical knowledge from big data.
J. Am. Medical Informatics Assoc.
Gregory F. Cooper, Ivet Bahar, Michael J. Becich, Panayiotis V. Benos, Jeremy M. Berg, Jeremy U. Espino, Clark Glymour, Rebecca Crowley Jacobson, Michelle Kienholz, Adrian V. Lee, Xinghua Lu, Richard Scheines
2015 J jnl
Trans-species learning of cellular signaling systems with bimodal deep belief networks.
Bioinform.
Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu
2014 J jnl
An exact algorithm for the weighed mutually exclusive maximum set cover problem.
CoRR
Songjian Lu, Xinghua Lu
2013 J jnl
An exact algorithm with the time complexity of $O^*(1.299^m)$ for the weighed mutually exclusive set cover problem
CoRR
Songjian Lu, Xinghua Lu
2013 J jnl
Using graph model to find transcription factor modules: the hitting set problem and an exact algorithm.
Algorithms Mol. Biol.
Songjian Lu, Xinghua Lu
2011 — conf
A graph model and an exact algorithm for finding transcription factor modules.
BCB
Songjian Lu, Xinghua Lu
2008 J jnl
Multi-label literature classification based on the Gene Ontology graph.
BMC Bioinform.
Bo Jin, Brian Muller, ChengXiang Zhai, Xinghua Lu
2006 J jnl
Research Paper: Enhancing Text Categorization with Semantic-enriched Representation and Training Data Augmentation.
J. Am. Medical Informatics Assoc.
Xinghua Lu, Bin Zheng, Atulya Velivelli, ChengXiang Zhai
2005 — conf
UIUC/MUSC at TREC 2005 Genomics Track.
TREC
ChengXiang Zhai, Xu Ling, Xin He, Atulya Velivelli, Xuanhui Wang, Hui Fang, Azadeh Shakery, Xinghua Lu
2004 J jnl
Automatic annotation of protein motif function with Gene Ontology terms.
BMC Bioinform.
Xinghua Lu, ChengXiang Zhai, Vanathi Gopalakrishnan, Bruce G. Buchanan