Publications

Journals, Conferences and Workshops

  • Bayesian Clustering For HIV1 Protease Inhibitor Contact Maps

    Sandhya Prabhakaran and Julia E. Vogt.

    Artificial Intelligence in Medicine (AIME), Springer Lecture Notes in Artificial Intelligence (In press), 2019.

  • A Nonparametric Multi-view Model for Estimating Cell Type-Specific Gene Regulatory Networks

    Cassandra Burdziak, Elham Azizi, Sandhya Prabhakaran, Dana Pe'er.

    arXiv:1902.08138 in stat.ML, 2019. view pdf

  • A Bayesian Model for Overlapping Clusters from Distance Data

    Sandhya Prabhakaran, Severin Kasser, Sven Wellmann and Julia E. Vogt.

    Spotlight, ALL OF BAYESIAN NONPARAMETRICS, BNP@Neurips, 2018. view pdf

  • Single-Cell Immune Map of Breast Carcinoma Reveals Diverse Phenotypic States Driven by the Tumor Microenvironment

    Elham Azizi*, Ambrose J. Carr*, George Plitas*, Andrew E. Cornish*, Catherine Konopacki, Sandhya Prabhakaran, Juozas Nainys, Kenmin Wu, Vaidotas Kiseliovas, Manu Setty, Kristy Choi, Phuong Dao, Linas Mazutis, Alexander Y. Rudensky, Dana Pe'er. bioRxiv, 2017.view pdf, Cell 174(5): 1293-1308, 2018. view pdf

    (*Authors contributed equally)

  • Bayesian Inference for Single-cell Clustering and Imputing

    Elham Azizi*, Sandhya Prabhakaran*, Ambrose Carr, Dana Peer. Genomics and Computational Biology, 2017.view pdf

    (*Authors contributed equally)

  • Tensor decomposition for single-cell RNA-seq data

    Kristy Choi*, Ambrose J Carr*, Sandhya Prabhakaran and Dana Pe'er.

    (*Authors contributed equally)

    Practical Bayesian Nonparametrics Workshop, BNP@Neurips, 2016. view pdf

  • Bayesian Nonparametric Extensions to the K-mer Motif Multinomial Mixture Model

    Brian Trippe and Sandhya Prabhakaran. Practical Bayesian Nonparametrics Workshop, BNP@Neurips, 2016. view pdf

  • K-mer Motif Multinomial Mixtures

    Brian L Trippe, Sandhya Prabhakaran, Harmen Bussemaker.

    bioRxiv:096735, 2016.view pdf
  • Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data

    Sandhya Prabhakaran*, Elham Azizi*, Ambrose Carr, Dana Peer. The 33rd International Conference on Machine Learning (ICML’16), pages 1070 --1079, 2016.view pdfview supplementary

    (*Authors contributed equally)

  • Probabilistic Clustering of Time-Evolving Distance Data

    Julia E. Vogt, Marius Kloft, Stefan Stark, Sudhir Raman, Sandhya Prabhakaran, Volker Roth, Gunnar Rätsch. Machine Learning Journal, 2015,view pdf

  • Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

    Francesca Di Giallonardo, Armin Töpfer, Melanie Rey, Sandhya Prabhakaran, Yannick Duport, Christine Leemann, Stefan Schmutz et al. Nucleic Acid Research (NAR) 42, no. 14, 2014. view pdf

  • HIV Haplotype Inference using a propagating Dirichlet Process Mixture Model

    Sandhya Prabhakaran, Melanie Rey, Osvaldo Zagordi, Niko Beerenwinkel and Volker Roth. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), volume 11, no.1, 2014. view pdf -- An extended abstract was presented at the Machine Learning in Computational Biology (MLCB) Workshop, NIPS 2010

  • Recovering networks from distance data

    Sandhya Prabhakaran, David Adametz, Karin J. Metzner, Alexander Boehm and Volker Roth. Machine Learning Journal, volume 92:2-3, pages 251--283, 2013. view pdf -- A conference proceeding has appeared here: Asian Conference of Machine Learning (ACML'12), Journal of Machine Learning Research Workshop and Conference Proceedings, volume 25, pages 349--364, 2012.
    view pdf Best Student Paper award

  • Probabilistic Inference of Viral Quasispecies Subject to Recombination

    Armin Toepfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Roth, Eran Halperin and Niko Beerenwinkel. Journal of Computational Biology (JCB), volume 20:2, pages 113--123, 2013. view pdf -- A conference proceeding has appeared here: The 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB'12), pages 342--354, 2012. view pdf

  • Automatic Model Selection in Archetype Analysis

    Sandhya Prabhakaran, Sudhir Raman, Julia E. Vogt and Volker Roth. 34th German Conference on Pattern Recognition (DAGM/OAGM), volume 7476 of Lecture Notes in Computer Science, page 458--467, 2012.
    view pdf

  • The Translation-invariant Wishart-Dirichlet Process for Clustering Distance Data

    Julia E. Vogt, Sandhya Prabhakaran, Thomas J. Fuchs and Volker Roth. The 27th International Conference on Machine Learning (ICML'10), pages 1111--1118, 2010. view pdf Best Paper award runner-up

  • Converting z/OS assembler code to COBOL

    Sandhya Prabhakaran IBM developerworks, 2007. Visit Site

Book Chapter

  • Structure Preserving Embedding of Dissimilarity Data

    Volker Roth, Thomas J. Fuchs, Julia E. Vogt, Sandhya Prabhakaran and Joachim M. Buhmann. Similarity-Based Pattern Analysis and Recognition, Advances in Computer Vision and Pattern Recognition series, Springer London, pages 157–177, 2013. view pdf

Theses

  • Machine Learning Methods for HIV/AIDS Diagnostics and Therapy Planning, Doctoral Thesis, 2014. view pdf

  • Multi-scale, Reactive Motion Planning with Deformable Linear Objects, Masters Thesis, 2008. view pdf

Intellectual Property (IP) Disclosure

  • Data Transfer from JCL to COBOL

    Padmaraj Meethal and Sandhya Prabhakaran, IBM Software Laboratories.

    Disclosure number: IPCOM000167543D, 2008 Visit Site