Alex Firpi

Johns Hopkins University-Applied Physics Laboratory

***** ***** ******* ****

Mail Stop MP2-N143/Office MP2-N142

Laurel, MD 20723-6009

Cell: 1-317-***-****

accv14@r.postjobfree.com

EDUCATION

Continuing Education

2006

Indiana University-Purdue University, Indianapolis, IN

Courses: Bioinformatics

Ph.D., Electrical Engineering

2001-2005

Michigan State University, East Lansing, MI

Ph.D. Dissertation Title: On Prediction and Detection of Epileptic Seizures by Means of

Genetic Programming Artificial Features

Master of Science, Electrical Engineering

1999–2001

University of Puerto Rico-Mayagüez, Mayagüez, PR

Master Thesis Title: Genetically Found, Neurally Computed Artificial Features with

Applications to Epileptic Seizure Detection and Prediction

Bachelor of Science, Electrical Engineering

1994–1998

Polytechnic University of Puerto Rico, San Juan, PR

Cum Laude Honor

Major: Automatic Controls and Systems

EXPERIENCE

1 Neural & Spectral Signal Processing Engineer

Dec. 2012-Present

Research and Exploratory Development Department (REDD)

Johns Hopkins University Applied Physics Laboratory Laurel, MD

Develop desk-based and portable brain computer interfaces (BCIs) for different

applications, using different devices such as eye-trackers, EEG recorder devices, different

types of evoked potentials: SSVEPs, P300s, and RSVP (i.e., a P300 "train").

Research and development of a head-mounted display powered by augmented reality and

controlled through brain signals and eye tracking (i.e., hand-free interface) commands.

Research, develop, and implement machine learning algorithms to analyze bio-

physiological data modalities (ECG, EEG, GSR, EOG, eye tracking signals) to detect

different types of patterns and physiological events.

Prototype algorithms in MATLAB, Java translation, and software development for hyper-

spectral imaging and spectral signature applications. Develop MATLAB scripts to

communicate with Google Earth, acquisition and processing of images, and automation of

any process that was found to be time-consuming. Implementation of atmosphere and

radiation models (e.g., QUAK, MODTRAN). Development of SQL scripts.

Write proposals, technical reports, scientific publications, and presentations.

2 Brain-Computer Interface Postdoctoral Fellow

Dec. 2010-Dec. 2012

Research and Exploratory Development Department (REDD)

Johns Hopkins University Applied Physics Laboratory Laurel, MD

Developed brain-computer interface (BCI) interfaces where the user selects/executes

commands using eye trackers and evoked potentials patterns.

Development of interface algorithms for eye tracker (ViewPoint, Eyelink) technology.

Development of interface algorithms for EEG recorder (gtec, Biosemi) technology.

Development and implementation of pattern recognition algorithms for detecting EEG

patterns for multiple problems.

Implementing tools and solutions for bio-physiological data (e.g., ECG, GSR, EEG, EOG,

eye positions) analysis.

Developing MATLAB solutions for satellite image analysis.

3 Postdoctoral Fellow

Feb. 2009-Dec. 2010

Tan Laboratory, Department of Internal Medicine

University of Iowa, Iowa City, IA

Understanding of high-throughput technologies such as ChIP-chip and ChIP-Seq for

epigenomic studies (e.g., bed or gff files)

Development of tools for preprocessing, registration, and visualization of histone

modifications/chromatin signals

Research and development of computational tools (e.g., time-delay neural networks) for

prediction of regulatory DNA elements (e.g., enhancers, promoters) using histone

modifications/chromatin data

Preparing proposals for NIH grants/fellowships. Dr. Tan was awarded an NIH

Exploratory/Developmental Research Grant (R21) product of one those proposals.

Developing a structuring-element and filtering image processing tool for Dr. Long-Sheng

Song with the Division of Cardiovascular.

4 Postdoctoral Fellow

Aug 2007–Jan 2009

Center for Neuroimaging, Division of Imaging Sciences

Indiana University School of Medicine, Indianapolis, IN

Bridging structural and functional neuroimaging (MRI, fMRI, Freesurfer) and genetics

Implement computational tools relevant for neuroscience image and pattern analysis.

Collaborate with members of the center, mentor graduate students, and prepare grant

applications.

Evaluate machine learning tools and statistical analysis on different brain disorder datasets

(i.e., Alzheimer, Schizophrenia, Dementia, Chemotherapy).

Configure supercomputer Quarry to run Freesurfer (FS) and develop all the pipelining (i.e.,

algorithms) to ensure/validate output from FS.

5 Postdoctoral Fellow

Aug 2006–Jul 2007

Center for Computational Biology and Bioinformatics (CCBB)

Indiana University School of Medicine, Indianapolis, IN

Applying pattern discovery and creation by means of Particle Swarm-Neural Networks to

predict active catalytic residues in enzymes. Comparisons with other feature

extractions/classifiers were conducted.

Feature extraction programs were coded to create a feature set (e.g., S-Blest, PSI-Blast,

FEATURES) for prediction of protein-protein interaction sites.

Provide machine learning and pattern recognition expertise to the center.

Attending seminars/workshops in bioinformatics.

6 Postdoctoral Fellow

May 2005–Jul 2006

Intelligent Control System Laboratory

Georgia Institute of Technology, Atlanta, GA

Supervising and guiding Ph.D. students in their biomedical research projects

Running experiments on pattern discovery in different research topics: fault detection, rat

epileptic seizures, and human epileptic seizures. Developing algorithms to design

controllers to stimulate (control) epileptic seizures.

Collaborating with neuroscientists at University of Pennsylvania, Dr. Brian Litt and his

group.

Management of the laboratory.

Collaborating with BioQuantix, Inc., a spin-off company developing technology for

epileptic seizure control.

7 Research Assistant

Aug 2001–May 2005

Genetic Algorithms Research and Applications Group (GARAGe)

Michigan State University, East Lansing, MI

Conducting research on genetic programming to find patterns that can help to predict/detect

epileptic seizures with a higher accuracy than other traditional approaches

Instructor Jun–

Jul 2001

Department of Electrical and Computer Engineering

Polytechnic University of Puerto Rico, San Juan, PR

2 Teach, administer, and grade tests for Logic Circuit course

Teach, administer, and grade tests for Circuit Analysis course.

1 Research Assistant

Aug 1999–May 2001

Department of Electrical and Computer Engineering

University of Puerto Rico-Mayagüez Mayagüez, PR

Research and development on the feature extraction methods for pattern recognition.

Teaching Assistant Jan–

May 1999

Department of Electrical and Computer Engineering

University of Puerto Rico-Mayagüez Mayagüez, PR

Prepare, administrate, and correct experiments, and tests for Electronic laboratory course.

3

C Language Tutor

4

Mar–May 1997

Department of Electrical and Computer Engineering

Polytechnic University of Puerto Rico, San Juan, PR

Teach and assist students with the C code, compile, and run programs.

SOFTWARE AND COMPUTING SKILLS

Leadership, Self-Starter, Team-Work Oriented

Computer literacy:

MATLAB and Mex-Function/Simulink/Psychtoolbox

C/C++

Java

SQL

Hadoop/Pig/Hive

Windows OS, MacOS, and Linux/Unix

Freesurfer

Parallel Computing/GPU Computing

Biosemi Active 2, gTech, Eyelink 1000, Arrington's ViewPoint

RESEARCH SKILLS

Machine learning, data mining, pattern recognition, computational intelligence (e.g., fuzzy logic,

neural networks, evolutionary algorithms), support vector machines, image processing, signal

processing, computer vision, and augmented reality. Mathematical modeling, statistics,

estimation, and regression. Nonlinear dynamics, system analysis, chaos theory, and complex

systems. Algorithm development.

Provide solutions for problems such as hyper-dimensional datasets, biomarkers and pattern

discovery, bioinformatics, computational biology, biological signal processing (e.g., EEG, EKG),

neuroscience (e.g., brain disorders such as Alzheimer’s, Dementia), eye-tracking and brain-

computer interfaces, and time-series forecasting (e.g., financial). Remote sensing.

DIVERSION

Reading, drawing, painting, biking and mountain biking, hiking, fitness, geography, and

history.

PUBLICATIONS

Conferences

A. H. Firpi, H. J. Mitchell, J. Oxenrider, N. Tzeng, Vignesh Ramachandran, and B. Rodriguez

“Signature Modeling for LWIR Spectrometer”, IEEE Aerospace Conference, Mar. 1-8, 2014.

Vignesh R. Ramachandran, H. J. Mitchell, S. K. Jacobs, N. Tzeng, A. H. Firpi, and B.

Rodriguez “Spectral Comparison Using K-Means Clustering”, IEEE Aerospace Conference, Mar.

1-8, 2014.

K. Katyal, M. Johannes, T. McGee, A. Harris, R. Armiger, A. H. Firpi, D. McMullen, G. Hotson,

M. Fifer, N. E. Crone, R. J. Vogelstein, and B. Wester "HARMONIE: A Multimodal Control

Framework for Human Assistive Robotics" 6th International IEEE EMBS Conference

on Neural Engineering, Nov. 6th-8th, 2013.

H. A. Firpi and R. Jacob Vogelstein, “Particle swarm optimization-based feature selection for

cognitive state detection” 33rd International Conference of the IEEE Engineering in Medicine

and Biology Society (EMBS), pp. 6556-6559, Aug-Sep. 2011.

A. Firpi, F. Tenore, M. McLoughlin, and J. Vogelstein, “Particle Swarm Optimization-based

Feature Selection for Brain-Computer Interfaces”, HCI International 2011, Orlando, FL, 9-14

July 2011.

L. Shen, H. Firpi, A. Saykin, and J. West, “Parametric surface modeling and registration for

comparison of manual and automated segmentation of the hippocampus,” MICCAI 2008

Workshop on the Computational Anatomy and Physiology of the Hippocampus, NYC, Sep 6,

2008.

H. Firpi, E. Youn, and S. Mooney, “Comparative study of particle swarm approached for the

prediction of functionally important residues in proteins,“ BioCom 2008, Okinawa, JP, pp. 714-

719, Mar. 25-28, 2008.

B. Litt, A. Gardner, O. Smart, G. Georgoulas, G.J. Vachtsevanos, H. Firpi, and J. Echauz

“Monitoring, signal analysis, and control of epileptic seizures: A paradigm in brain research,”

15th Mediterranean Conference on Control and Automation, Athens, Greece, pp. 1-6, 2007.

M. C. Wiggings, H. Firpi, and S. C. Dudley, Jr., “Prediction of atrial fibrillation following

cardiac surgery using rough set derived rules,” 28th International Conference of the IEEE

Engineering in Medicine and Biology Society (EMBS), pp. 4006-4009, New York, 2006.

H. Firpi, “Swarmed neuro-artificial features from vibration data applied to fault detection and

isolation,” IEEE Congress on Computational Intelligence 2006, pp. 3214-3219, Vancouver, BC,

Canada, 2006.

H. Firpi, E. Goodman, and J. Echauz, “Genetic programming artificial features with applications

to epileptic seizure prediction,” 27th International Conference of the IEEE Engineering in

Medicine and Biology Society (EMBS), Shanghai, Sep.1-4, pp. 4510-4513, 2005.

H. Firpi, E. Goodman, and J. Echauz, “Epileptic seizure detection by means of genetically

programmed artificial features,” Proceedings of Genetic and Evolutionary Computation

Conference, pp. 461-467, Washington D.C., Jun. 25-29, 2005.

H. Firpi and E. Goodman, “Designing templates for cellular neural networks using particle

swarm optimization,” 33rd Applied Imagery Pattern Recognition Workshop 2004, pp. 119-123,

Washington DC, Oct. 13-15, 2004.

H. Firpi and E. Goodman, “Swarmed feature selection,” 33rd Applied Imagery Pattern

Recognition Workshop 2004, pp. 112-118, Washington DC, Oct. 13-15, 2004.

H. Firpi and J. Echauz, “Genetically found, neurally computed artificial features applied to

epileptic seizures prediction,” Computing Research Conference 2001, UPR-Mayagüez, PR, pp.

101-105, Mar. 31, 2001.

H. Firpi, “Parameter estimation of Markov random field models using genetic algorithm with

applications to post-classification,” Computing Research Conference 2001, UPR-Mayagüez, PR,

Mar. 31, 2001.

H. Firpi and J. Echauz, “Genetically found, neurally computed artificial features from relevant

and irrelevant data,” Group Technology/Cellular Manufacturing World Symposium - Year 2000,

San Juan, PR, Mar. 27-29, 2000, pp. 327-331.

H. Firpi and J. Echauz, “Genetically found, neurally computed artificial features,” Computing

Research Conference 1999, UPR-Mayagüez, PR, Dec. 4, 1999, pp. 29-32.

Journals

L. Teng, H. Firpi, and K. Tan, “Enhancers in embryonic stem cells are enriched for transposable

elements and genetic variations associated with cancers,” Nucleic Acids Research, vol. 39, no. 17,

7371-7379, 2011.

H. Firpi, D. Ucar, and K. Tan “Discover regulatory DNA elements using chromatin signatures

and artificial neural network,” Bioinformatics, vol. 26, no. 13, 1579-1586, 2010.

L. Shen, A. Saykin, S. Kim, H. Firpi, J. West, S. Risacher, B. McDonald, T. McHugh, H.

Wishart, and L. Flashman, “Comparison of Manual and Automated Determination of

Hippocampal Volumes in MCI and Early AD,” Brain Imaging and Behavior, vol. 4, no. 1, 86-95,

March, 2010.

L. Shen, H. Firpi, A. Saykin, and J. West, “Parametric surface modeling and registration for

comparison of manual and automated segmentation of the hippocampus,” Hippocampus (Special

Issue on Computational Anatomy and Physiology of the Hippocampus), vol. 19, no. 6, pp. 588-

595, 2009.

S. Risacher, A. Saykin, J. West, L. Shen, H. Firpi, B. McDonald, and ADNI, “Baseline MRI

predictors of conversion from MCI to probable AD in the ADNI cohort,” Current Alzheimer

Research, vol. 6, no. 4, pp. 347-361, 2009.

A. A. Cardi, H. Firpi, M. T. Bement, and S. Y. Liang, “Workpiece dynamic analysis and

prediction during chatter of turning process,” Mechanical Systems and Signal Processing vol. 22

no. 6 pp. 1481-1494, 2008.

O. Smart, H. Firpi, and G. Vachtsevanos, “Genetic programming of conventional features to

detect seizure precursors,” Engineering Applications of Artificial Intelligence vol. 20 no. 8 pp.

1070-1085, 2007.

H. Firpi, O. Smart, G. Worrell, E. Marsh, D. Dlugos, and B. Litt, “High frequency oscillations

detected in epileptic networks using swarmed neuro-artificial features,” Annals of Biomedical

Engineering vol. 35, no. 9, pp. 1573-1584, 2007.

H. Firpi and G. Vachtsevanos, “GP-based artificial features from vibration data applied to fault

detection and isolation,” Engineering Applications of Artificial Intelligence, vol. 21 no. 4, pp.

558-568. 2007.

H. Firpi, E. Goodman, and J. Echauz, “Epileptic seizure detection using genetically programmed

artificial features,” IEEE Transactions on Biomedical Engineering, vol. 54, no. 2, pp. 212-224,

2007.

H. Firpi, E. Goodman, and J. Echauz, “On prediction of epileptic seizures by means of genetic

programming artificial features,” Annals of Biomedical Engineering, vol. 34, no. 3, pp. 515-529,

2006.

Abstracts & Posters

D. Ucar, H. Firpi, Q. Hu, K. Tan, “Revealing the Histone Code by the Identification of

Consistent and Combinatorial Patterns in the Human Genome,” Intelligence Systems for

Molecular Biology 2010, Boston, MA, USA.

H. Firpi, D. Ucar, K. Tan, “Predicting enhancers using chromatin modifications and time-delay

neural network”, CHSL Meetings 2010: System Biology: Global Regulation of Gene Expression,

Cold Harbor, NY, USA.

L. Shen, A. Saykin, H. Firpi, J. West, T. McHugh, H. Wishart, L. Flashman, A. Wessels, B.

McDonald, A. Cannon, “Comparison of manual and automated determination of hippocampal

volumes in MCI and older adults with cognitive complaints,” Alzheimer's & Dementia, vol. 4, no.

4, Suppl 2:T29-30, 2008.

H. Firpi, A. J. Saykin, L. Shen, and J. West, “Pattern analysis methods for identifying structural

MRI abnormalities in mild cognitive impairment,” CUE Life and Health Sciences Faculty

Research Showcase, Mar., 2008.

A. J. Saykin, J. West, L. Shen, H. Firpi, A. Wessels, A. Cannon, S. Risacher, B. C. McDonald,

and the Alzheimer's Disease Neuroimaging Initiative “Hippocampal and distributed gray matter

abnormalities in MCI and early AD in the ADNI Baseline 1.5t MRI scans: Cross-sectional

analysis and relation to verbal learning,” AD Imaging Conference 2008, vol. 4, no. 4, Suppl

2:T59, 2008.

L. Shen, A. J. Saykin, H. Firpi, J. D. West, T. L. McHugh, H. A. Wishart, L. A. Flashman, A. M.

Wessels, B. C. McDonald, and A. Cannon “Comparison of manual and automated determination

of hippocampal volumes in MCI and older adults with cognitive complaints,” International

Conference on Alzheimer’s Disease 2008.

L. Shen, A. J. Saykin, H. Firpi, J. West, A. M. Wessels, B. C. McDonald, A. Cannon,

“Computational methods for mapping anatomical and genetic effects on brain,” CUE Life and

Health Sciences Faculty Research Showcase, Mar., 2008.

H. Firpi, E. Youn, and S. Mooney, “Comparative study of particle swarm approaches for the

prediction of functionality important residues in protein structures,” Indy 2007 Bioinformatics

Conference, p. 10, 2007.

J. Fairley, S. Herman, H. Firpi, S. Kuna, G. Vachtsevanos, and B. Litt, “ Automatic removal of

extreme artifact within polysomnographic data ”, American Clinical Neurophysiology Society

60th Anniversary Annual Meeting, Wyndham Chicago Hotel, Chicago, Illinois Nov.2006.

Theses

H. Firpi, On Prediction and Detection of Epileptic Seizures by Means of Genetic Programming

Artificial Features, Ph.D. dissertation, Michigan State University, 2005, ISBN: 0-542-08142-3.

H. Firpi, Genetically Found, Neurally Computed Artificial Features with Applications to

Epileptic Seizure Detection and Prediction, Master’s thesis, University of Puerto Rico-Mayagüez,

2001.

Book Chapters

J. Echauz, H. Firpi, and G. Georgolas, “Intelligent Control Strategies for Neurostimulation,”

Applications of Intelligent Control Strategies to Engineering Systems, K. Valavanis. Springer,

Vol. 39, pp. 247-263, ISBN: 978-90-481-3017-7 (2009).

H. Firpi, E. Goodman, and J. Echauz, “On prediction of epileptic seizures by computing multiple

genetic programming artificial features,” Lecture Notes in Computer Science, M. Keijzer et al.

(Eds.) Springer, Vol. 3447, pp. 321-330, ISBN: 978-3-540-25436-2.

Journal and Book Reviews

Reviewer, Journal: Annals of Biomedical Engineering, 2005–Pres.

Reviewer, Journal: Journal of Neuroscience Methods, 2007–Pres.

Reviewer, Journal: Computer Methods and Programs in Biomedicine, 2007–Pres.

Reviewer, Journal: Epilepsy Research, 2007–Pres.

Reviewer, Journal: IEEE Transactions on Biomedical Engineering, 2011–Pres.

Review: Stephan Olariu and Albert Y. Zomaya, Handbook of Bioinspired Algorithms and

Applications, Briefings in Bioinformatics vol. 8, no. 4, pp. 275-276, 2007.

AFFILIATIONS AND REGISTRATION

Member of Tau Beta Pi Honor Society

Member of Institute of Electrical and Electronics Engineers (IEEE)

Passed Fundamentals of Engineering (FE) examination

HONORS AND AWARDS

Ruth L. Kirschstein National Research Service Award (NRSA) Institutional Research Training

NASA/Harriett G. Jenkins Fellowship Predoctoral Fellowship (2002-2005)

Competitive Doctoral Enrichment Fellowships, Michigan State University

National Action Council for Minorities in Engineering Inc. (NACME)

Program for Research in Computing and Information Sciences and Engineering (NSF EIA-

9977071)

REFERENCES

Indiana University, School of Medicine

Dr. Li Shen

email: accv14@r.postjobfree.com

phone: 317-***-****

Michigan State University

Dr. Erik Goodman

email: accv14@r.postjobfree.com

phone: 517-***-****

JE Research, Inc.

Dr. Javier Echauz

email: accv14@r.postjobfree.com

phone: 404-***-****

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