Data Assistant
Resume:
Benafsh Husain
Biomedical and Data Informatics Scientist
B adbd8w@r.postjobfree.com
bhusain.github.io
Education
April, 2020 Ph.D. candidate in Biomedical Data Science and Informatics, Clemson Uni- versity and Medical University of South Carolina.
2011 M.S in Electrical and Computer Engineering, California Polytechnic, SLO. 2008 B.S in Biomedical Engineering, Mumbai University, India. PhD Dissertation
Title EdgeCrafting:Mining embedded, latent, non-linear patterns to construct Gene Re- lationship Networks.
Description Typical gene correlation networks have been constructed via simple linear metrics that do not explore hidden relationships between genes. In this dissertation, I develop several novel machine learning and deep learning algorithms implemented on Brain tissue and Brian Cancer RNASeq data to detect and construct a network of non-linear gene relationships.
Technical Skills
Programming
Languages
Python, R, C, C++, Matlab
IDE, Libraries,
Frameworks
Visit, VTK, Paraview, QT, OpenGL, DirectX, MPI, OpenMP, OpenCV, NumPy, SciPy, SciKit, Matplotlib, Keras, Processing, Tableau, Cytoscape, MySQL Research Experience
2019 EdgeCrafting:Mining embedded, latent, non-linear patterns to construct Gene Relationship Networks. .
Developing deep learning networks to detect non-linear patterns in RNAseq panCancer and panGtex gene expression matrices.
2018-2019 NetExtractor:Cerebellar Gene Regulatory Network construction based on mutual information.
Building a workflow to detect embedded, non-linear relationships within sample sub- populations for Brain tissues and constructing a cerebellar specific gene regulatory network using gene expression matrix
2017-2018 EdgeScaping:Mapping the spatial distribution of pairwise gene expression intensities.
Using deep learning network to identify latent non-linear patterns to cluster gene-gene edges. 1/5
2016-2017 HeatTree:Exploring calling context trees. Developing techniques to reduce large scale calling context trees using structural similarity and pattern matching. Developing corresponding GUI using QT and OpenGL. 2015–2016 Correlating multivariate scientific application and hardware domains. Developed algorithm and GUI to explore correlation between multivariate scientific data and hardware counters using RANSAC sub-space clustering and mutual information techniques. 2014–2015 Visualizing fine-grained memory accesses using linked software and hardware views.
Developed framework and GUI to link inefficient memory access patterns from the source code to the underlying architecture using functional call graphs. 2014-2015 Relating memory performance data to application domain mesh using an integration API.
Developed an API for Visit (a visualization and graphical analysis tool for viewing scientific data) to integrate an external performance profiler or tool. 2013-2014 Overcoming keyloggers and screendumps.
Creating an application for rendering keyloggers and screendumps ineffective using DirectX and GPUs. In the process of Copyright Licensing in association with Clemson University. 2013-2014 Exascale performance file system with integrated security system . Theoretical and Simulation based analysis of an integrated security system over an Exascale performance File system. Funded by DOE, in association with Los Alamos National Lab, Sandia National Lab, and Argonne National Lab
2009–2011 Face detection and lip localization in moving vehicle.. Developed an algorithm to detect lips (following face detection) on low quality images in a moving car environment. Evaluated Viola-Jones algorithm for test cases on Lips and non-lips images in several color spaces.
Professional Experience
2018 -
Present
PhD Student Researcher and Teaching Assistant, Clemson University and Med- ical University of South Carolina (MUSC).
{ Worked with large scale RNASeq data including panCancer and panGtex to construct, normalize, and analyze gene and transcript expressions.
{ Developed and implemented machine learning algorithms to extract gene correlation networks associated to brain cancer.
{ Constructed one of the first gene regulatory networks associated to cerebellar tissues using machine learning.
{ Developed and taught courses for Database Design and Management, and Introduction to Machine Learning.
2/5
2015-2017 PhD Student Researcher, Lawrence Livermore National Laboratory, Liver- more,CA,
Summer 2015, Summer 2016, Summer 2017.
{ Developed visualization tools to identify performance improvement techniques for scientific application simulations.
{ Identifying and visualizing spatial relationships between application and hardware metrics for multivariate data.
{ Utilized machine learning algorithms to explore correlation between application and hardware domain.
{ Implemented an API for Visit to integrate with external performance tools. 2013 Research Intern, Argonne National Laboratory, Chicago, IL, Summer 2013.
{ Developed a simulation of an integrated security system over a Light Weight File System written in C.
{ Analyzed the effects of authorization and authentication servers on the timing effects to complete operations such as read/write.
2013–2016 Research Assistant, Clemson University, Clemson, SC.
{ Parallelizing and stitching tetrahedral mesh computation.
{ Developing machine learning and visualization techniques to explore multivariate data.
{ Developing visualization techniques and GUI to explore large scale calling context trees. 2011-2012 Technical Editor, CrimsonI, Language Solutions, Mumbai, India. Technical editor pertaining to articles, papers, journal submissions in the field of Computer vision and pattern detection.
2009-2011 Research Assistant, California Polytechnic, San Luis Obispo, CA.
{ Investigating techniques for lip detection in low quality videos with subjects in moving vehicle.
{ In-depth literature review of existing lip detection techniques and their limitations. 2008 Software Engineer, Shailtec Co., Mumbai, India. Designed and implemented the power supply board in the continuous, pulsed and super pulsed mode. Successfully interfaced with a High Tension Transformer, A cooling unit, Control panel for switching mode application and a gassed filled CO2 laser tube. 2007 Biomedical Intern, Sir H.N.Hospital and Research Centre, Mumbai, India, Summer 2009.
Assisted Biomedical engineers in trouble shooting errors, periodic maintenance and installa- tion of various machines and equipment.
Honor, Awards, and Activities
2015 Awarded Best Short Paper award at CISR ’15, Analysis of Botnet Counter-Counter- Measures.
2013-2015 Volunteer as a part of Future Engineering Group to assist elementary and high school students to develop software applications and motivate them to pursue a future in Science/Mathematics
3/5
2013-2014 Active member of the cyber defense and security team in Clemson University, with focus on penetration testing and Linux, and Windows Operating systems 2013-2013 Captained team to 1st position in the PCDC cyber security competition Publications
Accepted
[1] Benafsh Husain, F. Alex Feltus. EdgeScaping: Mapping the spatial distribution of pairwise gene expression intensities. PLoS ONE 14(8): e0220279, Aug 2019.
[2] Allison R. Hickman, Yuqing Hang, Benafsh Husain, and F. Alex Feltus. Identifying Regulatory Biomarkers in Autism Spectrum Disorder. Human Genetics, Poster, May 2019.
[3] Yu Fu, Lu Yu, Benafsh Husain, et.al. Stealthy Domain Generation Algorithms in IEEE Transactions on Information Forensics and Security, vol. 12, no. 6, pp. 1430-1443, June 2017.
[4] Yu Fu, Benafsh Husain, and Richard R. Brooks. 2015. Analysis of Botnet Counter- Counter-Measures. In Proceedings of the 10th Annual Cyber and Information Security Research Conference (CISR ’15). (Best Short Paper).
[5] Benafsh Husain, et. al. 2015. Relating memory performance data to application domain data using an integration API. In Proceedings of the 2nd Workshop on Visual Performance Analysis.
[6] Benafsh Husain, et. al. Visualizing Fine-Grained Memory Accesses using Linked Software and Hardware Views. IEEE Vis 2015, Poster.
[7] Alfredo Gimenez, Benafsh Husain, et. al. Mitos: A simple Interface for Complex Hardware Sampling and Attribution. SC, 2015, Poster
[8] Richard Brooks, Benafsh Husain, SeokBae Yun, and Juan Deng. 2013. Security and performance evaluation of security protocols. In Proceedings of the Eighth Annual Cyber Security and Information Intelligence Research Workshop
[9] Karan Sapra, Benafsh Husain, Richard Brooks, Melissa Smith. Circumventing keyloggers and screendumps", in Proc. MALWARE ’13, 2013, p. 103- 108
[10] Benafsh Husain. Face Detection and Lip Localization. Master’s thesis, Cal Poly, SLO, 2011
[11] Xiaomin Jin, Sean Jobe, Simeon Trieu, Benafsh Husain, Jason Flickinger. Mode pattern analysis of gallium nitride-based laser diodes. Proc. SPIE 7382, International Symposium on Photoelectronic Detection and Imaging 2009: Laser Sensing and Imaging (August 28, 2009).
Submitted
[1] Benafsh Husain, Allison Hickman, Yuqing Hang, Ben Shealy, Karan Sapra, F. Alex Feltus. NetExtractor: Cerebellar Gene Regulatory Network construction based on mutual information. G3Journal, submitted, Dec 2019. 4/5
[2] Yuqing Hang, Mohammed Aburidi, Benafsh Husain, Allison Hickman, and F. Alex Feltus. Tissue Specific Brain Gene Co-expression Networks Reveal Genes That Sub-type Human Tumors. G3Journal, submitted, Oct 2019. 5/5
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