Selected Publications
Selected Journal Publications - from 2018:
X. Liu, S. Prasath, I. Siddiqui, T. Walters, L. A Denson, PROTECT consortium, J. Dhaliwal. Machine learning-based prediction of pediatric ulcerative colitis treatment response using diagnostic histopathology. Gastroenterology, 166, May 2024. doi:10.1053/j.gastro.2024.01.033
R. Nakagaki, S. S. Debsarkar, H. Kawanaka, B. Aronow, V. B. S. Prasath. Deep learning-based IDH1 gene mutation prediction using histopathological imaging and clinical data. Computers in Biology and Medicine, 2024. doi:TBA
X. Liu, J. Reigle, V. B. S. Prasath, J. Dhaliwal. Artificial intelligence image-based prediction models in IBD exhibit high risk of bias: A systematic review. Computers in Biology and Medicine, 171, 108093, March 2024. doi:10.1016/j.compbiomed.2024.108093
E. G. Zarajabad, P. D. Grimm, B. Saremi, J. Wang, S. A. Ahmad, S. A. Shah, R. C. Quillin III, S. H. Patel, A. J. Knapp, V. B. S. Prasath, T. D. Mast. Deep learning-enhanced 3D echo decorrelation imaging for monitoring radiofrequency ablation in ex vivo human liver. Proceedings of Meetings on Acoustics (POMA), 51(1), February 2024. doi:10.1121/2.0001821
N. Gaddis, J. Fortriede, M. Guo, E. E. Bardes, M. Kouril, S. Tabar, K. Burns, M. E. Ardini-Poleske, S. Loos, D. Schnell, K. Jin, B. Iyer, Y. Du, B.-X. Huo, A. Bhattacharjee, J. Korte, R. Munshi, V. Smith, A. Herbst, J. A. Kitzmiller, G. C. Clair, J. Carson, J. Adkins, E. E. Morrisey, G. S. Pryhuber, R. Misra, J. A. Whitsett, X. Sun, T. Heathorn, B. Paten, V. B. S. Prasath, Y. Xu, T. Tickle, B. J. Aronow, N. Salomonis. LungMAP portal ecosystem: Systems-level exploration of the lung. American Journal of Respiratory Cell and Molecular Biology, 129-139, 70(2), February 2024. doi:10.1165/rcmb.2022-0165OC
P.-J. Van Camp, V. B. S. Prasath, D. B. Haslam, A. Porallo. MGS2AMR: A gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile. Microbiome, 11, Article number 223, October 2023. doi:10.1186/s40168-023-01674-z (Github)
T. A Cazares, F. W. Rizvi, B. Iyer, X. Chen, M. Kotliar, J. A. Wayman, A. Bejjani, O. Donmez, B. Wronowski, S. Parameswaran, L. C. Kottyan, A. Barski, M. T. Weirauch, V. B. S. Prasath, E. R. Miraldi. maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLOS Computational Biology, 19(1), e1010863, January 2023. doi:10.1371/journal.pcbi.1010863Â
G. Li, B. Song, H. Singh, V. B. S. Prasath, H. L. Grimes, N. Salomonis. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications, 14, 406, January 2023. doi:10.1038/s41467-023-36016-y (Github, PyPI)
M. Shah, D. Jain, V. B. S. Prasath, K. Dufendach. Artificial intelligence in bronchopulmonary dysplasia - Current research and unexplored frontiers. Pediatric Research, 93(2), 287-290, January 2023. doi:10.1038/s41390-022-02387-z
K. Jin, D. Schnell, G. Li, N. Salomonis, S. Prasath, R. Szczesniak, B. J. Aronow. CellDrift: Inferring perturbation responses in temporally sampled single-cell data. Briefings in Bioinformatics, 23(5), September 2022. doi:10.1093/bib/bbac324
(Github)
G. Li, B. Iyer, V. B. S. Prasath, Y. Ni, N. Salomonis. DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Briefings in Bioinformatics, 22(6), 1-16, November 2021. doi:10.1093/bib/bbab160 (ScienceBlog, Featured-Research, Portal, Github)
M. Shah, D. Shu, V. B. S. Prasath, Y. Ni, A. Schapiro, K. Dufendach. Machine learning for detection of correct peripherally inserted central catheter tip position from radiology reports in infants. Applied Clinical Informatics, 12(04), 856-863, August 2021. doi:10.1055/s-0041-1735178
J. Zhang, Q. Wu, C. B. Johnson, G. Pham, J. M. Kinder, A. Olsson, A. Slaughter, M. May, B. Weinhaus, A. D'Alessandro, J. D. Engel, J. X. Jiang, J. M. Kofron, L. F. Huang, V. B. S. Prasath, S. S. Way, N. Salomonis, H. L. Grimes, D. Lucas. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature, 590, 457-462, February 2021. doi:10.1038/s41586-021-03201-2 (Euerkalert, ScienceMag)
T. Hayakawa, V. B. S. Prasath, H. Kawanaka, B. J. Aronow, S. Tsuruoka. Computational nuclei segmentation methods in digital pathology - A survey. Archives of Computational Methods in Engineering, 28(1), 1-13, January 2021. doi:10.1007/s11831-019-09366-4
D. N. H. Thanh, V. B. S. Prasath, L. M. Hieu, N. N. Hien. Melanoma skin cancer detection method based on adaptive principal curvature, colour normalisation and feature extraction with the ABCD rule. Journal of Digital Imaging, 33(3), 574-585, June 2020. doi:10.1007/s10278-019-00316-x
S. Bidani, R. P. Priya, V. Vijayarajan, V. B. S. Prasath. Automatic body mass index detection using correlation of face visual cues. Technology and Health Care, 28(1), 107-112, January 2020. doi:10.3233/THC-191850
H. A. A. Alfeilat, A. B. A. Hassanat, O. Lasassmeh, A. S. Tarawneh, M. B. Alhasanat, H. S. E. Salman, V. B. S. Prasath. Effects of distance measure choice on KNN classifier performance - A review. Big Data, 7(4), 221-248, December 2019. doi:10.1089/big.2018.0175
V. B. S. Prasath, R. Pelapur, G. Seetharaman, K. Palaniappan. Multiscale structure tensor for improved feature extraction and image regularization. IEEE Transactions on Image Processing, 28(12), 6198-6210, December 2019. doi:10.1109/TIP.2019.2924799
A. Yonekura, H. Kawanaka, V. B. S. Prasath, B. J. Aronow, H. Takase. Automatic disease stage classification of glioblastoma multiforme histopathological images using deep convolutional neural network. Biomedical Engineering Letters, 8(3), 321-327, August 2018. doi:10.1007/s13534-018-0077-0
Selected Conference Publications:
G. Sumi, B. Iyer, H. Kawanaka, B. J. Aronow, V. B. S. Prasath. Gait analysis for cerebral palsy using memory-augmented auto-encoder model. 11th International Conference on Informatics, Electronics & Vision (ICIEV), London, UK, October 2023. Proc. IEEE. (Excellent Paper Award)
S. Isaka, H. Kawanaka, B. Aronow, V. B. S. Prasath. Multi-class segmentation of lung immunofluorescence confocal images using deep learning. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), International Workshop on Deep Learning in Bioinformatics, Biomedicine, and Healthcare Informatics (DLB2H), San Diego, CA, USA. Proc. IEEE, 2362-2368, November 2019. doi:10.1109/BIBM47256.2019.8983146
A. Yonekura, H. Kawanaka, V. B. S. Prasath, B. J. Aronow, H. Takase. Improving the generalization of disease stage classification with deep CNN for glioma histopathological images. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), International Workshop on Deep Learning in Bioinformatics, Biomedicine, and Healthcare Informatics (DLB2H), Kansas, MO, USA. Proc. IEEE, pp. 1222-1226, November 2017. doi:10.1109/BIBM.2017.8217831
R. Pelapur, V. B. S. Prasath, J. C. Moreno, M. Heck. 3D Workflow for segmentation and interactive visualization in brain MR images using multiphase active contours. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Kansas, MO, USA. Proc. IEEE, pp. 921-926, November 2017. doi:10.1109/BIBM.2017.8217780
A. Yonekura, H. Kawanaka, V. B. S. Prasath, B. J. Aronow, H. Takase. Glioblastoma multiforme tissue histopathology images based disease stage classification with deep CNN. 6th International Conference on Informatics, Electronics & Vision (ICIEV), Himeji, Hyogo, Japan. Proc. IEEE, September 2017. doi:10.1109/ICIEV.2017.8338558 (Best Paper Award Finalist)
V. B. S. Prasath, Y. M. Kassim, Z. A. Oraibi, J.-B. Guiriec, A. Hafiane, K. Palaniappan. HEp-2 cell classification and segmentation using motif texture patterns and spatial features with random forests. 23rd International Conference on Pattern Recognition (ICPR), International Contest on Pattern Recognition Techniques for Indirect Immunofluorescence Images Analysis, Cancun, Mexico. Proc. IEEE, pp. 90-95, December 2016. doi:10.1109/ICPR.2016.7899614
Y. M. Kassim, V. B. S. Prasath, R. Pelapur, O. Glinskii, R. J. Maude, V. Glinsky, V. Huxley, K. Palaniappan. Random forests for dura mater microvasculature segmentation using epifluorescence images. 38th Annual International Conference of the Engineering in Medicine and Biology Society (IEEE EMBC), Orlando, FL, USA. (EMBS Student Paper Competition Finalist) Proc. IEEE, pp. 2901-2904, August 2016. doi:10.1109/EMBC.2016.7591336
V. B. S. Prasath, K. Fukuma, B. J. Aronow, H. Kawanaka. Cell nuclei segmentation in glioma histopathology images with color decomposition based active contours. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Washington, DC, USA. Proc. IEEE, pp. 1734-1736, November 2015. doi:10.1109/BIBM.2015.7359944 Available at figshare: doi:10.6084/m9.figshare.1588805
V. B. S. Prasath, R. Pelapur, O. Glinskii, V. Glinsky, V. Huxley, K. Palaniappan. Multiscale tensor anisotropic filtering of fluorescence microscopy for denoising microvasculature. IEEE International Symposium on Biomedical Imaging (IEEE ISBI), New York, USA. Proc. IEEE, pp. 540-543, April 2015. doi:10.1109/ISBI.2015.7163930 Available at figshare: doi:10.6084/m9.figshare.1309773
S. Meena, V. B. S. Prasath, K. Palaniappan, G. Seetharaman. Elastic body spline based image segmentation. IEEE International Conference on Image Processing (IEEE ICIP), Paris, France, October 2014. Proc. IEEE, pp. 4378-4382. doi:10.1109/ICIP.2014.7025888 Available at figshare: doi:10.6084/m9.figshare.1203638
R. Pelapur, V. B. S. Prasath, F. Bunyak, O. Glinskii, V. Glinsky, V. Huxley, K. Palaniappan. Multi-focus image fusion using epifluorescence microscopy for robust vascular segmentation. 36th Annual International Conference of the Engineering in Medicine and Biology Society (IEEE EMBC), Chicago, IL, USA. Proc. IEEE, pp. 6055-6058, August 2014. doi:10.1109/EMBC.2014.6944682 Available at figshare: doi:10.6084/m9.figshare.1147490
V. B. S. Prasath, R. Delhibabu. Automatic contrast parameter estimation in anisotropic diffusion for image restoration. Analysis of Images, Social Networks, and Texts (AIST), Yekaterinburg, Russia. Proc. in Springer Communications in Computer and Information Science 436 (Eds.: D. I. Ignatov, M. Khachay, A. Panchenko, N. Konstantinova, R. Yavorsky), pp. 198-206, April 2014. doi:10.1007/978-3-319-12580-0_20 (Best Paper Award)
J. C. Moreno, V. B. S. Prasath, H. Proenca. Robust periocular recognition by fusing local to holistic sparse representations. 6th International Conference on Security of Information and Networks (SIN), Aksaray, Turkey. Proc. ACM Digital Library. pp. 160-164, November, 2013. doi:10.1145/2523514.2523540
V. B. S. Prasath, O. Haddad, F. Bunyak, O. Glinskii, V. Glinsky, V. Huxley, K. Palaniappan. Robust filtering based segmentation of dura mater laminae using fluorescence microscopy. 35th Annual International Conference of the Engineering in Medicine and Biology Society (IEEE EMBC), Osaka, Japan. Proc. IEEE, pp. 6055-6058, July 2013. doi:10.1109/EMBC.2013.6610933
I. N. Figueiredo, J. C. Moreno, V. B. S. Prasath, P. N. Figueiredo. A segmentation model and application to endoscopic images. International Conference on Image Analysis and Recognition (ICIAR), Aveiro, Portugal. Proc. in Springer LNCS 7325 (Eds.: A. Campilho and M. Kamel), Part II, pp. 164-171, June 2012. doi:10.1007/978-3-642-31298-4_20
V. B. S. Prasath, I. N. Figueiredo, P. N. Figueiredo, K. Palaniappan. Mucosal region detection and 3D reconstruction in wireless capsule endoscopy videos using active contours. 34th Annual International Conference of the Engineering in Medicine and Biology Society (IEEE EMBC), San Diego, USA. Proc. IEEE, pp. 4014-4017, August 2012. doi:10.1109/EMBC.2012.6346847
V. B. S. Prasath, A. Singh. Edge detectors based anisotropic diffusion for enhancement of digital images. 6th Indian Conference on Computer Vision, Graphics and Image Processing (ICVGIP), Bhubaneswar, India. Proc. in IEEE Computer Society, pp. 33-38, December 2008. (Best Paper Award) doi:10.1109/ICVGIP.2008.68