You are here

Home > By Date > Abstract > Journal > Mobile App > Text Processing > Software > API
  • Sarrouti M, Quatik EL, Alaoui S. SemBioNLQA: A semantic biomedical question answering system for retrieving exact and ideal answers to natural language questions. Artif Intell Med. 2020 Jan;102:101767. doi: 10.1016/j.artmed.2019.101767. Epub 2019 Nov 28.
    Abstract | PMID:  31980104
    Abstract
  • Zou J, Antani SK, Thoma G. Unified Deep Neural Network for Segmentation and Labeling of Multi-Panel Biomedical Figures Journal of the Association for Information Science and Technology (JASIST), 2019
    Abstract
    Abstract
  • Zou J. Unified Deep Neural Network for Segmentation and Labeling of Multi-Panel Biomedical Figures Journal of the Association for Information Science and Technology (JASIST), 2019
    Abstract
    Abstract
  • Rosemblat G, Fiszman, M, Shin D, Kilicoglu H. Towards a characterization of apparent contradictions in the biomedical literature using context analysis. Journal of Biomedical Informatics. 2019. In Press. https://doi.org/10.1016/j.jbi.2019.103275.
    Abstract
    Abstract
  • Kim I, Rajaraman S, Antani SK. Visual Interpretation of Convolutional Neural Network Predictions in Classifying Medical Image Modalities. Diagnostics (Basel). 2019 Apr 3;9(2). pii: E38. doi: 10.3390/diagnostics9020038.
    Abstract | PMID:  30987172 | URL:  https://www.mdpi.com/2075-4418/9/2/38/htm
    AbstractExternal link
  • Candemir S, Antani SK. A review on lung boundary detection in chest X-rays. Int J Comput Assist Radiol Surg. 2019 Feb 7. doi: 10.1007/s11548-019-01917-1.
    Abstract | PMID:  30730032
    Abstract
  • Hu L, Bell D, Antani SK, Xue Z, Yu K, Horning MP, Gachuhi N, Wilson B, Jaiswal MS, Befano B, Long LR, Herrero R, Einstein MH, Burk RD, Demarco M, Gage JC, Wentzensen N, Schiffman M. An Observational Study of Deep Learning and Automated Evaluation of Cervical Images for Cancer Screening. J Natl Cancer Inst. 2019 Jan 10. doi: 10.1093/jnci/djy225
    Abstract | PMID:  30629194
    Abstract
  • Jaeger S, Juarez-Espinosa OH, Candemir S, Poostchi M, Yang F, Kim L, Ding M, Folio LR, Antani SK, Gabrielian A, Hurt D, Rosenthal A, Thoma GR. Detecting drug-resistant tuberculosis in chest radiographs. Int J Comput Assist Radiol Surg. 2018 Dec;13(12):1915-1925. doi: 10.1007/s11548-018-1857-9. Epub 2018 Oct 3.
    Abstract | PMID:  30284153 | PMCID:  PMC6223762
    Abstract
  • Dhoot R, Humphrey JM, O'Meara P, Gardner A, McDonald CJ, Ogot K, Antani SK, Abuya J, Kohli M. Implementing a mobile diagnostic unit to increase access to imaging and laboratory services in western Kenya. BMJ Glob Health. 2018 Oct 8;3(5):e000947. doi: 10.1136/bmjgh-2018-000947. eCollection 2018.
    Abstract | PMID:  30364326 | PMCID:  PMC6195141
    Abstract
  • Poostchi M, Ilker E, McMenamin K, Gordon E, Palaniappan N, Pierce S, Maude RJ, Bansal A, Srinivasan P, Miller L, Palaniappan K, Thoma GR, Jaeger S. Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy. J Med Imaging (Bellingham). 2018 Oct;5(4):044506. doi: 10.1117/1.JMI.5.4.044506. Epub 2018 Dec 12.
    Abstract | PMID:  30840746 | PMCID:  PMC6290955
    Abstract
  • Vajda S, Karargyris A, Jaeger S, Santosh KC, Candemir S, Xue Z, Antani SK, Thoma GR. Feature Selection for Automatic Tuberculosis Screening in Frontal Chest Radiographs. J Med Syst. 2018 Jun 29;42(8):146. doi: 10.1007/s10916-018-0991-9.
    Abstract | PMID:  29959539
    Abstract
  • Rajaraman S, Silamut K, Hossain MA, Ersoy I, Maude RJ, Jaeger S, Thoma GR, Antani SK. Understanding the learned behavior of customized convolutional neural networks toward malaria parasite detection in thin blood smear images. J Med Imaging (Bellingham). 2018 Jul;5(3):034501. doi: 10.1117/1.JMI.5.3.034501. Epub 2018 Jul 18.
    Abstract | pub9809.pdf | PMID:  30035153 | PMCID:  PMC6050500
    AbstractDownload
  • Thamizhvani TR, Lakshmanan S, Rajaraman S. Mobile application-based computer-aided diagnosis of skin tumours from dermal images. The Imaging Science Journal, 66:6, 382-391, 2018, DOI: 10.1080/13682199.2018.1492682
    Abstract | pub9811.pdf
    AbstractDownload
  • Kilicoglu H, Rosemblat G, Malicki M, Ter Riet G. Automatic recognition of self-acknowledged limitations in clinical research literature. J Am Med Inform Assoc. 2018 Jul 1;25(7):855-861. doi: 10.1093/jamia/ocy038.
    Abstract | PMID:  29718377 | PMCID:  PMC6016608
    Abstract
  • Yaniv Z, Lowekamp B, Johnson HJ, Beare R. SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research. J Digit Imaging. 2018 Jun;31(3):290-303. doi: 10.1007/s10278-017-0037-8.
    Abstract | PMID:  29181613 | PMCID:  PMC5959828
    Abstract
  • Sornapudi S, Stanley RJ, Stoecker WV, Almubarak H, Long LR, Antani SK, Thoma GR, Zuna R, Frazier SR. Deep Learning Nuclei Detection in Digitized Histology Images by Superpixels. J Pathol Inform. 2018 Mar 5;9:5. doi: 10.4103/jpi.jpi_74_17. eCollection 2018.
    Abstract | PMID:  29619277 | PMCID:  PMC5869967
    Abstract
  • Santosh KC, Antani SK. Automated chest x-ray screening: Can lung region symmetry help detect pulmonary abnormalities? doi: 10.1109/TMI.2017.2775636 vol. 37, no. 5, 1168-1177.
    Abstract
    Abstract
  • Rajaraman S, Antani SK, Poostchi Mohammadabadi M, Silamut K, Hossain MA, Maude RJ, Jaeger S, Thoma GR. Pre-trained convolutional neural networks as feature extractors toward improved malaria parasite detection in thin blood smear images. PeerJ. 2018 Apr 16;6:e4568. doi: 10.7717/peerj.4568. eCollection 2018.
    Abstract | pub9752.pdf | PMID:  29682411 | PMCID:  PMC5907772
    AbstractDownload
  • Demner-Fushman D. A dataset of 200 structured product labels annotated for adverse drug reactions. Sci Data. 2018 Jan 30;5:180001. doi: 10.1038/sdata.2018.1.
    Abstract | PMID:  29381145 | PMCID:  PMC5789866
    Abstract
  • Poostchi M, Silamut K, Maude RJ, Jaeger S, Thoma GR. Image analysis and machine learning for detecting malaria. Transl Res. 2018 Apr;194:36-55. doi: 10.1016/j.trsl.2017.12.004. Epub 2018 Jan 12.
    Abstract | pub9624.pdf | PMID:  29360430 | PMCID:  PMC5840030
    AbstractDownload
  • Kayaalp M. Patient Privacy in the Era of Big Data. Balkan Med J. 2018 Jan 20;35(1):8-17. doi: 10.4274/balkanmedj.2017.0966. Epub 2017 Sep 13.
    Abstract | PMID:  28903886 | PMCID:  PMC5820452
    Abstract
  • Chatain GP, Patronas N, Smirniotopoulos J, James G, Piazza M, Benzo S, Ray-Chaudrury A, Sharma S, Lodish M, Nieman L, Stratakis CA, Chittiboina P. Potential utility of FLAIR in MRI-negative Cushing's disease. J Neurosurg. 2017 Oct 13:1-9. doi: 10.3171/2017.4.JNS17234.
    Abstract | PMID:  29027863
    Abstract
  • Coakley M, Hurt D, Weder N, Mtingwa M, Fincher EC, Alekseyev V, Chen D, Yun A, Gizaw M, Swan J, Yoo TS, Huyen Y. The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints 3D Print Additive Manufacturing, Sep. 1, 2014, 1(3):137-140.
    Abstract
    Abstract
  • Blake C, Rindflesch TC. Leveraging syntax to better capture the semantics of elliptical coordinated compound noun phrases. J Biomed Inform. 2017 Aug;72:120-131. doi: 10.1016/j.jbi.2017.07.001. Epub 2017 Jul 4.
    Abstract | PMID:  28687199
    Abstract
  • Kilicoglu H, Rosemblat G, Rindflesch TC. Assigning factuality values to semantic relations extracted from biomedical research literature. PLoS One. 2017 Jul 5;12(7):e0179926. doi: 10.1371/journal.pone.0179926. eCollection 2017.
    Abstract | PMID:  28678823 | PMCID:  PMC5497973
    Abstract
  • Rindflesch TC, Blake CL, Fiszman M, Kilicoglu H, Rosemblat G, Schneider J, Zeiss CJ. Informatics Support for Basic Research in Biomedicine. ILAR J. 2017 Jul 1;58(1):80-89. doi: 10.1093/ilar/ilx004.
    Abstract | PMID:  28838071 | PMCID:  PMC5886329
    Abstract
  • Zhang, K, Demner-Fushman D. Automated classification of eligibility criteria in clinical trials to facilitate patient-trial matching for specific patient populations. J Am Med Inform Assoc. 2017 Jul 1;24(4):781-787. doi: 10.1093/jamia/ocw176.
    Abstract | PMID:  28339690 | PMCID:  PMC6080677
    Abstract
  • Kilicoglu H. Biomedical text mining for research rigor and integrity: tasks, challenges, directions. Brief Bioinform. 2017 Jun 13. doi: 10.1093/bib/bbx057.
    Abstract | PMID:  28633401
    Abstract
  • Candemir S. Chest X-ray Screening System: Segmentation Module – v3
    Abstract
    Abstract
  • Mork JG, Aronson A, Demner-Fushman D. 12 years on - Is the NLM medical text indexer still useful and relevant? J Biomed Semantics. 2017 Feb 23;8(1):8. doi: 10.1186/s13326-017-0113-5.
    Abstract | PMID:  28231809 | PMCID:  PMC5324252
    Abstract
  • Lure F, Jaeger S, Antani SK. Automated Systems for microscopic and radiographic tuberculosis screening. Electronic Journal of Emerging Infectious Diseases, Vol. 2, No. 1, pp. 5-9, February 2017. [In Chinese]
    Abstract | pub9528.pdf
    AbstractDownload
  • Demner-Fushman D, Rogers W, Aronson A. MetaMap Lite: an evaluation of a new Java implementation of MetaMap. J Am Med Inform Assoc. 2017 Jul 1;24(4):841-844. doi: 10.1093/jamia/ocw177.
    Abstract | PMID:  28130331
    Abstract
  • KC S, Antani SK. Automated chest X-ray screening: Can lung region symmetry help detect pulmonary abnormalities? IEEE Transactions on Medical Imaging. doi: https://doi.org/10.1109/TMI.2017.2775636.
    Abstract
    Abstract
  • KC S, Aafaque A, Antani SK, Thoma GR. Line Segment-Based Stitched Multipanel Figure Separation for Effective Biomedical CBIR. Int. J. Patt. Recogn. Artif. Intelligence 31, 1757003 (2017) https://doi.org/10.1142/S0218001417570038.
    Abstract
    Abstract
  • Lu C, Tormey D, McCreedy L, Browne AC. Enhanced LexSynonym Acquisition for Effective UMLS Concept Mapping. Stud Health Technol Inform. 2017;245:501-505.
    Abstract | pub9776.pdf | PMID:  29295145
    AbstractDownload
  • Guo P, Almubarak H, Banerjee K, Stanley RJ, Long LR, Antani SK, Thoma GR, Zuna R, Frazier S, Moss R, Stoecker W. Enhancements in localized classification for uterine cervical cancer digital histology image assessment. J Pathol Inform. 2016 Dec 30;7:51. doi: 10.4103/2153-3539.197193. eCollection 2016.
    Abstract | pub9466.pdf | PMID:  28163974 | PMCID:  PMC5248401
    AbstractDownload
  • Guo P, Stanley RJ, De S, Long LR, Antani SK, Thoma GR, Demner-Fushman D, Sornapudia S. Features Advances to Automatically Find Images for Application to Clinical Decision Support. Medical Research Archives. 4(7) 2016. DOI: 10.18103/mra.v4i7.761
    Abstract | pub9467.pdf
    AbstractDownload
  • Linte CA, Yaniv Z. Image-Guided Interventions: We've come a long way, but are we there? IEEE Pulse. 2016 Nov-Dec;7(6):46-50.
    Abstract | PMID:  27875119
    Abstract
  • Kastrin A, Rindflesch TC, Hristovski D. Link prediction on a network of co-occurring MeSH terms: Towards literature-based discovery. Methods of Information in Medicine 55(4):340-6.
    Abstract
    Abstract
  • KC S, Vajda S, Antani S, Thoma GR. Edge map analysis in chest X-rays for automatic pulmonary abnormality screening. Int J Comput Assist Radiol Surg. 2016 Sep;11(9):1637-46. doi: 10.1007/s11548-016-1359-6. Epub 2016 Mar 19.
    Abstract | PMID:  26995600
    Abstract
  • Xu T, Zhang H, Xin C, Kim E, Long LR, Xue Z, Antani SK, Huang Z. Multi-feature based Benchmark for Cervical Dysplasia Classification Evaluation. Pattern Recognition. ISSN 0031-3203, DOI: 10.1016/j.patcog.2016.09.027.
    Abstract | pub9468.pdf | PMID:  28603299 | PMCID:  PMC5464748
    AbstractDownload
  • Hristovski D, Kastrin A, Dinevski D, Burgun A, Ziberna L, Rindflesch TC. Using Literature-Based Discovery to Explain Adverse Drug Effects. J Med Syst. 2016 Aug;40(8):185. doi: 10.1007/s10916-016-0544-z. Epub 2016 Jun 18.
    Abstract | PMID:  27318993
    Abstract
  • Wei W, Marmor R, Singh S, Wang S, Demner-Fushman D, Kuo TT, Hsu CN, Ohno-Machado L. Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:225-34. eCollection 2016.
    Abstract | PMID:  27570676 | PMCID:  PMC5001748
    Abstract
  • Ben Abacha A, Demner-Fushman D. Meta-Learning with Selective Data Augmentation for Medical Entity Recognition. International Journal of Computational Linguistics and Applications (IJCLA) 7(2): 167-182 (2016)
    Abstract | 1_IJCLA.pdf
    AbstractDownload
  • Candemir S, Jaeger S, Antani S, Bagci U, Folio LR, Xu Z, Thoma G. Atlas-based rib-bone detection in chest X-rays. Comput Med Imaging Graph. 2016 Jul;51:32-9. doi: 10.1016/j.compmedimag.2016.04.002. Epub 2016 Apr 13.
    Abstract | PMID:  27156048 | PMCID:  PMC4923658 | URL:  https://www.sciencedirect.com/science/article/pii/S0895611116300337
    AbstractExternal link
  • KC S, Alam M, Roy P, Wendling L, Antani SK, Thoma GR. A simple and efficient arrowhead detection in biomedical images. International J Pattern Recognition and Artificial Intelligence (IJPRAI), 30(5), 1657002, 2016, DOI: 10.1142/S0218001416570020.
    Abstract | pub9469.pdf
    AbstractDownload
  • Kilicoglu H. Software: Bio-SCoRes
    Abstract
    Abstract
  • KC S, Wendling L, Antani SK, Thoma GR. Overlaid arrow detection for labeling biomedical image regions. IEEE Intelligent Systems, Special Issue on Pattern Recognition, 31(3):66-75, May-June 2016.DOI: 10.1109/MIS.2016.24.
    Abstract | pub9470.pdf
    AbstractDownload
  • Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Sortal anaphora resolution to enhance relation extraction from biomedical literature. BMC Bioinformatics. 2016 Apr 14;17:163. doi: 10.1186/s12859-016-1009-6.
    Abstract | PMID:  27080229 | PMCID:  PMC4832532
    Abstract
  • Morid MA, Fiszman M, Raja K, Jonnalagadda SR, Del Fiol G. Classification of clinically useful sentences in clinical evidence resources. J Biomed Inform. 2016 Apr;60:14-22. doi: 10.1016/j.jbi.2016.01.003. Epub 2016 Jan 13.
    Abstract | PMID:  26774763 | PMCID:  PMC4836984
    Abstract

Pages