Chun-Nan Hsu

Title(s)Project Scientist, Neurosciences
SchoolVc-health Sciences-schools
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    Collapse Biography 
    Collapse Education and Training
    University of Southern California, Los Angeles, CAPhDComputer Science
    Collapse Awards and Honors
    Association for Computing Machinery2011ACM Senior Member
    The International Business Machines Corp.2012IBM Faculty Award
    Automated Knowledge Base Construction (AKBC) Conference2019Best Application Paper Award

    Collapse Research 
    Collapse Research Activities and Funding
    Deep Learning for Imaging Report Generation to Support Diagnosis of Military-Relevant Injury in a Deployed or Operational Environment
    DoD W81XWH2010693Jul 15, 2020 - Jan 14, 2023
    Role: PI
    Accelerating Curation of GWAS Catalog by Automatic Text Mining
    NIH U01HG006894Sep 24, 2012 - Sep 30, 2016
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. RadBERT: Adapting Transformer-based Language Models to Radiology. Radiol Artif Intell. 2022 Jul; 4(4):e210258. Yan A, McAuley J, Lu X, Du J, Chang EY, Gentili A, Hsu CN. PMID: 35923376; PMCID: PMC9344353.
      View in: PubMed   Mentions: 15  
    2. Federated learning for predicting clinical outcomes in patients with COVID-19. Nat Med. 2021 10; 27(10):1735-1743. Dayan I, Roth HR, Zhong A, Harouni A, Gentili A, Abidin AZ, Liu A, Costa AB, Wood BJ, Tsai CS, Wang CH, Hsu CN, Lee CK, Ruan P, Xu D, Wu D, Huang E, Kitamura FC, Lacey G, de Antônio Corradi GC, Nino G, Shin HH, Obinata H, Ren H, Crane JC, Tetreault J, Guan J, Garrett JW, Kaggie JD, Park JG, Dreyer K, Juluru K, Kersten K, Rockenbach MABC, Linguraru MG, Haider MA, AbdelMaseeh M, Rieke N, Damasceno PF, E Silva PMC, Wang P, Xu S, Kawano S, Sriswasdi S, Park SY, Grist TM, Buch V, Jantarabenjakul W, Wang W, Tak WY, Li X, Lin X, Kwon YJ, Quraini A, Feng A, Priest AN, Turkbey B, Glicksberg B, Bizzo B, Kim BS, Tor-Díez C, Lee CC, Hsu CJ, Lin C, Lai CL, Hess CP, Compas C, Bhatia D, Oermann EK, Leibovitz E, Sasaki H, Mori H, Yang I, Sohn JH, Murthy KNK, Fu LC, de Mendonça MRF, Fralick M, Kang MK, Adil M, Gangai N, Vateekul P, Elnajjar P, Hickman S, Majumdar S, McLeod SL, Reed S, Gräf S, Harmon S, Kodama T, Puthanakit T, Mazzulli T, de Lavor VL, Rakvongthai Y, Lee YR, Wen Y, Gilbert FJ, Flores MG, Li Q. PMID: 34526699; PMCID: PMC9157510.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansCells
    3. Antibody Watch: Text mining antibody specificity from the literature. PLoS Comput Biol. 2021 05; 17(5):e1008967. Hsu CN, Chang CH, Poopradubsil T, Lo A, William KA, Lin KW, Bandrowski A, Ozyurt IB, Grethe JS, Martone ME. PMID: 34043624; PMCID: PMC8189493.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    4. Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. Database (Oxford). 2021 04 29; 2021. Klie A, Tsui BY, Mollah S, Skola D, Dow M, Hsu CN, Carter H. PMID: 33914028; PMCID: PMC8083811.
      View in: PubMed   Mentions: 6     Fields:    
    5. Federated Learning used for predicting outcomes in SARS-COV-2 patients. Res Sq. 2021 Jan 08. Flores M, Dayan I, Roth H, Zhong A, Harouni A, Gentili A, Abidin A, Liu A, Costa A, Wood B, Tsai CS, Wang CH, Hsu CN, Lee CK, Ruan C, Xu D, Wu D, Huang E, Kitamura F, Lacey G, César de Antônio Corradi G, Shin HH, Obinata H, Ren H, Crane J, Tetreault J, Guan J, Garrett J, Park JG, Dreyer K, Juluru K, Kersten K, Bezerra Cavalcanti Rockenbach MA, Linguraru M, Haider M, AbdelMaseeh M, Rieke N, Damasceno P, Cruz E Silva PM, Wang P, Xu S, Kawano S, Sriswasdi S, Park SY, Grist T, Buch V, Jantarabenjakul W, Wang W, Tak WY, Li X, Lin X, Kwon F, Gilbert F, Kaggie J, Li Q, Quraini A, Feng A, Priest A, Turkbey B, Glicksberg B, Bizzo B, Kim BS, Tor-Diez C, Lee CC, Hsu CJ, Lin C, Lai CL, Hess C, Compas C, Bhatia D, Oermann E, Leibovitz E, Sasaki H, Mori H, Yang I, Sohn JH, Keshava Murthy KN, Fu LC, Furtado de Mendonça MR, Fralick M, Kang MK, Adil M, Gangai N, Vateekul P, Elnajjar P, Hickman S, Majumdar S, McLeod S, Reed S, Graf S, Harmon S, Kodama T, Puthanakit T, Mazzulli T, de Lima Lavor V, Rakvongthai Y, Lee YR, Wen Y. PMID: 33442676; PMCID: PMC7805458.
      View in: PubMed   Mentions:
    6. Learning Visual-Semantic Embeddings for Reporting Abnormal Findings on Chest X-rays. Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: Findings. 2020; 1954--1960. Ni, Jianmo and Hsu, Chun-nan and Gentili, Amilcare and McAuley, Julian. View Publication.
    7. A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS One. 2019; 14(12):e0226771. Pendergrass SA, Buyske S, Jeff JM, Frase A, Dudek S, Bradford Y, Ambite JL, Avery CL, Buzkova P, Deelman E, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Lin Y, Le Marchand L, Matise TC, Monroe KR, Moreland L, North KE, Park SL, Reiner A, Wallace R, Wilkens LR, Kooperberg C, Ritchie MD, Crawford DC. PMID: 31891604; PMCID: PMC6938343.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    8. Challenges in the construction of knowledge bases for human microbiome-disease associations. Microbiome. 2019 09 05; 7(1):129. Badal VD, Wright D, Katsis Y, Kim HC, Swafford AD, Knight R, Hsu CN. PMID: 31488215; PMCID: PMC6728997.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    9. NormCo: Deep Disease Normalization for Biomedical Knowledge Base Construction. Automated Knowledge Base Construction Conference. 2019. Dustin Wright, Yannis Katsis, Raghav Mehta, Chun-Nan Hsu. . View Publication.
    10. Evaluation and accurate diagnoses of pediatric diseases using artificial intelligence. Nat Med. 2019 03; 25(3):433-438. Liang H, Tsui BY, Ni H, Valentim CCS, Baxter SL, Liu G, Cai W, Kermany DS, Sun X, Chen J, He L, Zhu J, Tian P, Shao H, Zheng L, Hou R, Hewett S, Li G, Liang P, Zang X, Zhang Z, Pan L, Cai H, Ling R, Li S, Cui Y, Tang S, Ye H, Huang X, He W, Liang W, Zhang Q, Jiang J, Yu W, Gao J, Ou W, Deng Y, Hou Q, Wang B, Yao C, Liang Y, Zhang S, Duan Y, Zhang R, Gibson S, Zhang CL, Li O, Zhang ED, Karin G, Nguyen N, Wu X, Wen C, Xu J, Xu W, Wang B, Wang W, Li J, Pizzato B, Bao C, Xiang D, He W, He S, Zhou Y, Haw W, Goldbaum M, Tremoulet A, Hsu CN, Carter H, Zhu L, Zhang K, Xia H. PMID: 30742121.
      View in: PubMed   Mentions: 163     Fields:    Translation:Humans
    11. Identifying and characterizing highly similar notes in big clinical note datasets. J Biomed Inform. 2018 06; 82:63-69. Gabriel RA, Kuo TT, McAuley J, Hsu CN. PMID: 29679685.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    12. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. AMIA Annu Symp Proc. 2016; 2016:1880-1889. Kuo TT, Rao P, Maehara C, Doan S, Chaparro JD, Day ME, Farcas C, Ohno-Machado L, Hsu CN. PMID: 28269947; PMCID: PMC5333200.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    13. Building a Natural Language Processing Tool to Identify Patients With High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes. Acad Emerg Med. 2016 05; 23(5):628-36. Doan S, Maehara CK, Chaparro JD, Lu S, Liu R, Graham A, Berry E, Hsu CN, Kanegaye JT, Lloyd DD, Ohno-Machado L, Burns JC, Tremoulet AH, Pediatric Emergency Medicine Kawasaki Disease Research Group. PMID: 26826020; PMCID: PMC5031359.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    14. Weakly supervised learning of biomedical information extraction from curated data. BMC Bioinformatics. 2016 Jan 11; 17 Suppl 1:1. Jain S, Tumkur KR, Kuo TT, Bhargava S, Lin G, Hsu CN. PMID: 26817711; PMCID: PMC4847485.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    15. Citing a Data Repository: A Case Study of the Protein Data Bank. PLoS One. 2015; 10(8):e0136631. Huang YH, Rose PW, Hsu CN. PMID: 26317409; PMCID: PMC4552849.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    16. Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study. Circ Cardiovasc Genet. 2014 Aug; 7(4):505-13. Carty CL, Bhattacharjee S, Haessler J, Cheng I, Hindorff LA, Aroda V, Carlson CS, Hsu CN, Wilkens L, Liu S, Selvin E, Jackson R, North KE, Peters U, Pankow JS, Chatterjee N, Kooperberg C. PMID: 25023634; PMCID: PMC4142758.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    17. PombeX: robust cell segmentation for fission yeast transillumination images. PLoS One. 2013; 8(12):e81434. Peng JY, Chen YJ, Green MD, Sabatinos SA, Forsburg SL, Hsu CN. PMID: 24353754; PMCID: PMC3865994.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    18. Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing. Oncogene. 2014 Sep 25; 33(39):4786-94. Lin KT, Shann YJ, Chau GY, Hsu CN, Huang CY. PMID: 24141781.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    19. Analysis of protein-protein interactions in cross-talk pathways reveals CRKL protein as a novel prognostic marker in hepatocellular carcinoma. Mol Cell Proteomics. 2013 May; 12(5):1335-49. Liu CH, Chen TC, Chau GY, Jan YH, Chen CH, Hsu CN, Lin KT, Juang YL, Lu PJ, Cheng HC, Chen MH, Chang CF, Ting YS, Kao CY, Hsiao M, Huang CY. PMID: 23397142; PMCID: PMC3650343.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    20. Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet. 2013; 9(1):e1003087. Pendergrass SA, Brown-Gentry K, Dudek S, Frase A, Torstenson ES, Goodloe R, Ambite JL, Avery CL, Buyske S, Bužková P, Deelman E, Fesinmeyer MD, Haiman CA, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Monroe KR, Moreland L, Park SL, Reiner A, Wallace R, Wilkens LR, Crawford DC, Ritchie MD. PMID: 23382687; PMCID: PMC3561060.
      View in: PubMed   Mentions: 104     Fields:    Translation:Humans
    21. A ν-support vector regression based approach for predicting imputation quality. BMC Proc. 2012 Nov 13; 6 Suppl 7:S3. Huang YH, Rice JP, Saccone SF, Ambite JL, Arens Y, Tischfield JA, Hsu CN. PMID: 23173775; PMCID: PMC3504919.
      View in: PubMed   Mentions: 1  
    22. MetaMirClust: discovery of miRNA cluster patterns using a data-mining approach. Genomics. 2012 Sep; 100(3):141-8. Chan WC, Ho MR, Li SC, Tsai KW, Lai CH, Hsu CN, Lin WC. PMID: 22735742.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    23. Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores. Bioinformatics. 2012 Jun 15; 28(12):i106-14. Hochbaum DS, Hsu CN, Yang YT. PMID: 22689749; PMCID: PMC3371864.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    24. Automatic morphological subtyping reveals new roles of caspases in mitochondrial dynamics. PLoS Comput Biol. 2011 Oct; 7(10):e1002212. Peng JY, Lin CC, Chen YJ, Kao LS, Liu YC, Chou CC, Huang YH, Chang FR, Wu YC, Tsai YS, Hsu CN. PMID: 21998575; PMCID: PMC3188504.
      View in: PubMed   Mentions: 73     Fields:    Translation:AnimalsCells
    25. Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S6. Kuo CJ, Ling MH, Hsu CN. PMID: 22152021; PMCID: PMC3269941.
      View in: PubMed   Mentions: 2     Fields:    
    26. The gene normalization task in BioCreative III. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S2. Lu Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai RT, Dai HJ, Okazaki N, Cho HC, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston KM, Wilbur WJ. PMID: 22151901; PMCID: PMC3269937.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimals
    27. UMARS: Un-MAppable Reads Solution. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S9. Li SC, Chan WC, Lai CH, Tsai KW, Hsu CN, Jou YS, Chen HC, Chen CH, Lin WC. PMID: 21342592; PMCID: PMC3044317.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    28. Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics. 2010 Dec 02; 11 Suppl 4:S8. Li SC, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Hwang PP, Lin WC. PMID: 21143817; PMCID: PMC3005926.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    29. From NPC therapeutic target identification to potential treatment strategy. Mol Cancer Ther. 2010 Sep; 9(9):2511-23. Lan MY, Chen CL, Lin KT, Lee SA, Yang WL, Hsu CN, Wu JC, Ho CY, Lin JC, Huang CY. PMID: 20716640.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    30. A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images. Bioinformatics. 2010 Jun 15; 26(12):i29-37. Lin YS, Lin CC, Tsai YS, Ku TC, Huang YH, Hsu CN. PMID: 20529919; PMCID: PMC2881379.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    31. Sequence features involved in the mechanism of 3' splice junction wobbling. BMC Mol Biol. 2010 May 07; 11:34. Tsai KW, Chan WC, Hsu CN, Lin WC. PMID: 20459675; PMCID: PMC2875228.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    32. Identification of homologous microRNAs in 56 animal genomes. Genomics. 2010 Jul; 96(1):1-9. Li SC, Chan WC, Hu LY, Lai CH, Hsu CN, Lin WC. PMID: 20347954.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansAnimalsCells
    33. NIPS 2009. Periodic Step Size Adaptation for Single Pass On-line Learning. 2009; 22:763-771. Hsu CN, Chang YM, Huang HS, Lee YJ. View Publication.
    34. Integrating high dimensional bi-directional parsing models for gene mention tagging. Bioinformatics. 2008 Jul 01; 24(13):i286-94. Hsu CN, Chang YM, Kuo CJ, Lin YS, Huang HS, Chung IF. PMID: 18586726; PMCID: PMC2718659.
      View in: PubMed   Mentions: 39     Fields:    
    35. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W635-41. Yuan HY, Chiou JJ, Tseng WH, Liu CH, Liu CK, Lin YJ, Wang HH, Yao A, Chen YT, Hsu CN. PMID: 16845089; PMCID: PMC1538865.
      View in: PubMed   Mentions: 254     Fields:    
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